Daily Papers

Electrocardiography plays a central role in cardiovascular diagnostics, yet existing automated approaches often struggle to generalize across clinical tasks and offer limited support for open-ended reasoning. We present DiagECG, a novel framework that integrates time-series and language modeling by enabling large language models to process 12-lead ECG signals for clinical text generation tasks. Our approach discretizes continuous ECG embeddings into symbolic tokens using a lead-independent encoder and quantization module. These tokens are then used to extend the vocabulary of LLM, allowing the model to handle both ECG and natural language inputs in a unified manner. To bridge the modality gap, we pretrain the model on an autoregressive ECG forecasting task, enabling the LLM to model temporal dynamics using its native language modeling capabilities. Finally, we perform instruction tuning on both ECG question answering and diagnostic report generation. Without modifying the core model, DiagECG achieves strong performance across tasks while maintaining generalization to out-of-distribution settings. Extensive experiments demonstrate the effectiveness of each component and highlight the potential of integrating symbolic ECG representations into LLMs for medical reasoning.

Accurate and interpretable multi-disease diagnosis remains a critical challenge in medical research, particularly when leveraging heterogeneous multimodal medical data. Current approaches often rely on single-modal data, limiting their ability to comprehensively understand complex diseases. To address this, we propose MedTVT-R1, a novel Multimodal Large Language Model (MLLM) framework designed to integrate clinical multimodal data for reasoning and diagnosing multiple diseases. We construct MedTVT-QA, a curated instruction dataset that provides question-answer pairs for physiological-level interpretations and disease-level diagnoses with a Chain of Evidence approach. MedTVT-R1 incorporates a modality perception layer to capture inter-modal dependencies and adaptively weight modality contributions. Additionally, we employ Group Relative Policy Optimization (GRPO)-based Reinforcement Fine-Tuning with a Jaccard Reward function to enhance diagnostic reasoning. Experimental results demonstrate MedTVT-R1's superiority in multimodal feature utilization and multi-disease diagnosis, offering significant potential for clinical applications such as diagnostic report generation and comorbidity reasoning. The dataset and code are available at https://github.com/keke-nice/MedTVT-R1.

Breast ultrasound (BUS) is a critical diagnostic tool in the field of breast imaging, aiding in the early detection and characterization of breast abnormalities. Interpreting breast ultrasound images commonly involves creating comprehensive medical reports, containing vital information to promptly assess the patient's condition. However, the ultrasound imaging system necessitates capturing multiple images of various parts to compile a single report, presenting a time-consuming challenge. To address this problem, we propose the integration of multiple image analysis tools through a LangChain using Large Language Models (LLM), into the breast reporting process. Through a combination of designated tools and text generation through LangChain, our method can accurately extract relevant features from ultrasound images, interpret them in a clinical context, and produce comprehensive and standardized reports. This approach not only reduces the burden on radiologists and healthcare professionals but also enhances the consistency and quality of reports. The extensive experiments shows that each tools involved in the proposed method can offer qualitatively and quantitatively significant results. Furthermore, clinical evaluation on the generated reports demonstrates that the proposed method can make report in clinically meaningful way.

Radiology reporting generative AI holds significant potential to alleviate clinical workloads and streamline medical care. However, achieving high clinical accuracy is challenging, as radiological images often feature subtle lesions and intricate structures. Existing systems often fall short, largely due to their reliance on fixed size, patch-level image features and insufficient incorporation of pathological information. This can result in the neglect of such subtle patterns and inconsistent descriptions of crucial pathologies. To address these challenges, we propose an innovative approach that leverages pathology-aware regional prompts to explicitly integrate anatomical and pathological information of various scales, significantly enhancing the precision and clinical relevance of generated reports. We develop an anatomical region detector that extracts features from distinct anatomical areas, coupled with a novel multi-label lesion detector that identifies global pathologies. Our approach emulates the diagnostic process of radiologists, producing clinically accurate reports with comprehensive diagnostic capabilities. Experimental results show that our model outperforms previous state-of-the-art methods on most natural language generation and clinical efficacy metrics, with formal expert evaluations affirming its potential to enhance radiology practice.

This paper introduces a novel, entity-aware metric, termed as Radiological Report (Text) Evaluation (RaTEScore), to assess the quality of medical reports generated by AI models. RaTEScore emphasizes crucial medical entities such as diagnostic outcomes and anatomical details, and is robust against complex medical synonyms and sensitive to negation expressions. Technically, we developed a comprehensive medical NER dataset, RaTE-NER, and trained an NER model specifically for this purpose. This model enables the decomposition of complex radiological reports into constituent medical entities. The metric itself is derived by comparing the similarity of entity embeddings, obtained from a language model, based on their types and relevance to clinical significance. Our evaluations demonstrate that RaTEScore aligns more closely with human preference than existing metrics, validated both on established public benchmarks and our newly proposed RaTE-Eval benchmark.

Chest Xray imaging is a widely used diagnostic tool in modern medicine, and its high utilization creates substantial workloads for radiologists. To alleviate this burden, vision language models are increasingly applied to automate Chest Xray radiology report generation (CXRRRG), aiming for clinically accurate descriptions while reducing manual effort. Conventional approaches, however, typically rely on single images, failing to capture the longitudinal context necessary for producing clinically faithful comparison statements. Recently, growing attention has been directed toward incorporating longitudinal data into CXR RRG, enabling models to leverage historical studies in ways that mirror radiologists diagnostic workflows. Nevertheless, existing surveys primarily address single image CXRRRG and offer limited guidance for longitudinal settings, leaving researchers without a systematic framework for model design. To address this gap, this survey provides the first comprehensive review of longitudinal radiology report generation (LRRG). Specifically, we examine dataset construction strategies, report generation architectures alongside longitudinally tailored designs, and evaluation protocols encompassing both longitudinal specific measures and widely used benchmarks. We further summarize LRRG methods performance, alongside analyses of different ablation studies, which collectively highlight the critical role of longitudinal information and architectural design choices in improving model performance. Finally, we summarize five major limitations of current research and outline promising directions for future development, aiming to lay a foundation for advancing this emerging field.

Automated structured radiology report generation (SRRG) from chest X-ray images offers significant potential to reduce workload of radiologists by generating reports in structured formats that ensure clarity, consistency, and adherence to clinical reporting standards. While radiologists effectively utilize available clinical contexts in their diagnostic reasoning, existing SRRG systems overlook these essential elements. This fundamental gap leads to critical problems including temporal hallucinations when referencing non-existent clinical contexts. To address these limitations, we propose contextualized SRRG (C-SRRG) that comprehensively incorporates rich clinical context for SRRG. We curate C-SRRG dataset by integrating comprehensive clinical context encompassing 1) multi-view X-ray images, 2) clinical indication, 3) imaging techniques, and 4) prior studies with corresponding comparisons based on patient histories. Through extensive benchmarking with state-of-the-art multimodal large language models, we demonstrate that incorporating clinical context with the proposed C-SRRG significantly improves report generation quality. We publicly release dataset, code, and checkpoints to facilitate future research for clinically-aligned automated RRG at https://github.com/vuno/contextualized-srrg.

Electrocardiogram (ECG) serves as the primary non-invasive diagnostic tool for cardiac conditions monitoring, are crucial in assisting clinicians. Recent studies have concentrated on classifying cardiac conditions using ECG data but have overlooked ECG report generation, which is not only time-consuming but also requires clinical expertise. To automate ECG report generation and ensure its versatility, we propose the Multimodal ECG Instruction Tuning (MEIT) framework, the first attempt to tackle ECG report generation with LLMs and multimodal instructions. To facilitate future research, we establish a benchmark to evaluate MEIT with various LLMs backbones across two large-scale ECG datasets. Our approach uniquely aligns the representations of the ECG signal and the report, and we conduct extensive experiments to benchmark MEIT with nine open source LLMs, using more than 800,000 ECG reports. MEIT's results underscore the superior performance of instruction-tuned LLMs, showcasing their proficiency in quality report generation, zero-shot capabilities, and resilience to signal perturbation. These findings emphasize the efficacy of our MEIT framework and its potential for real-world clinical application.

Automatic medical report generation (MRG) is of great research value as it has the potential to relieve radiologists from the heavy burden of report writing. Despite recent advancements, accurate MRG remains challenging due to the need for precise clinical understanding and the identification of clinical findings. Moreover, the imbalanced distribution of diseases makes the challenge even more pronounced, as rare diseases are underrepresented in training data, making their diagnostic performance unreliable. To address these challenges, we propose diagnosis-driven prompts for medical report generation (PromptMRG), a novel framework that aims to improve the diagnostic accuracy of MRG with the guidance of diagnosis-aware prompts. Specifically, PromptMRG is based on encoder-decoder architecture with an extra disease classification branch. When generating reports, the diagnostic results from the classification branch are converted into token prompts to explicitly guide the generation process. To further improve the diagnostic accuracy, we design cross-modal feature enhancement, which retrieves similar reports from the database to assist the diagnosis of a query image by leveraging the knowledge from a pre-trained CLIP. Moreover, the disease imbalanced issue is addressed by applying an adaptive logit-adjusted loss to the classification branch based on the individual learning status of each disease, which overcomes the barrier of text decoder's inability to manipulate disease distributions. Experiments on two MRG benchmarks show the effectiveness of the proposed method, where it obtains state-of-the-art clinical efficacy performance on both datasets.

Chest X-Ray (CXR) report generation is a promising approach to improving the efficiency of CXR interpretation. However, a significant increase in diagnostic accuracy is required before that can be realised. Motivated by this, we propose a framework that is more inline with a radiologist's workflow by considering longitudinal data. Here, the decoder is additionally conditioned on the report from the subject's previous imaging study via a prompt. We also propose a new reward for reinforcement learning based on CXR-BERT, which computes the similarity between reports. We conduct experiments on the MIMIC-CXR dataset. The results indicate that longitudinal data improves CXR report generation. CXR-BERT is also shown to be a promising alternative to the current state-of-the-art reward based on RadGraph. This investigation indicates that longitudinal CXR report generation can offer a substantial increase in diagnostic accuracy. Our Hugging Face model is available at: https://huggingface.co/aehrc/cxrmate and code is available at: https://github.com/aehrc/cxrmate.

Radiology reports are crucial for planning treatment strategies and enhancing doctor-patient communication, yet manually writing these reports is burdensome for radiologists. While automatic report generation offers a solution, existing methods often rely on single-view radiographs, limiting diagnostic accuracy. To address this problem, we propose MCL, a Multi-view enhanced Contrastive Learning method for chest X-ray report generation. Specifically, we first introduce multi-view enhanced contrastive learning for visual representation by maximizing agreements between multi-view radiographs and their corresponding report. Subsequently, to fully exploit patient-specific indications (e.g., patient's symptoms) for report generation, we add a transitional ``bridge" for missing indications to reduce embedding space discrepancies caused by their presence or absence. Additionally, we construct Multi-view CXR and Two-view CXR datasets from public sources to support research on multi-view report generation. Our proposed MCL surpasses recent state-of-the-art methods across multiple datasets, achieving a 5.0% F1 RadGraph improvement on MIMIC-CXR, a 7.3% BLEU-1 improvement on MIMIC-ABN, a 3.1% BLEU-4 improvement on Multi-view CXR, and an 8.2% F1 CheXbert improvement on Two-view CXR.

Conversational AI tools that can generate and discuss clinically correct radiology reports for a given medical image have the potential to transform radiology. Such a human-in-the-loop radiology assistant could facilitate a collaborative diagnostic process, thus saving time and improving the quality of reports. Towards this goal, we introduce RaDialog, the first thoroughly evaluated and publicly available large vision-language model for radiology report generation and interactive dialog. RaDialog effectively integrates visual image features and structured pathology findings with a large language model (LLM) while simultaneously adapting it to a specialized domain using parameter-efficient fine-tuning. To keep the conversational abilities of the underlying LLM, we propose a comprehensive, semi-automatically labeled, image-grounded instruct dataset for chest X-ray radiology tasks. By training with this dataset, our method achieves state-of-the-art clinical correctness in report generation and shows impressive abilities in interactive tasks such as correcting reports and answering questions, serving as a foundational step toward clinical dialog systems. Our code is available on github: https://github.com/ChantalMP/RaDialog.

This study investigates the integration of diverse patient data sources into multimodal language models for automated chest X-ray (CXR) report generation. Traditionally, CXR report generation relies solely on CXR images and limited radiology data, overlooking valuable information from patient health records, particularly from emergency departments. Utilising the MIMIC-CXR and MIMIC-IV-ED datasets, we incorporate detailed patient information such as aperiodic vital signs, medications, and clinical history to enhance diagnostic accuracy. We introduce a novel approach to transform these heterogeneous data sources into embeddings that prompt a multimodal language model, significantly enhancing the diagnostic accuracy of generated radiology reports. Our comprehensive evaluation demonstrates the benefits of using a broader set of patient data, underscoring the potential for enhanced diagnostic capabilities and better patient outcomes through the integration of multimodal data in CXR report generation.

Automated radiology report generation offers an effective solution to alleviate radiologists' workload. However, most existing methods focus primarily on single or fixed-view images to model current disease conditions, which limits diagnostic accuracy and overlooks disease progression. Although some approaches utilize longitudinal data to track disease progression, they still rely on single images to analyze current visits. To address these issues, we propose enhanced contrastive learning with Multi-view Longitudinal data to facilitate chest X-ray Report Generation, named MLRG. Specifically, we introduce a multi-view longitudinal contrastive learning method that integrates spatial information from current multi-view images and temporal information from longitudinal data. This method also utilizes the inherent spatiotemporal information of radiology reports to supervise the pre-training of visual and textual representations. Subsequently, we present a tokenized absence encoding technique to flexibly handle missing patient-specific prior knowledge, allowing the model to produce more accurate radiology reports based on available prior knowledge. Extensive experiments on MIMIC-CXR, MIMIC-ABN, and Two-view CXR datasets demonstrate that our MLRG outperforms recent state-of-the-art methods, achieving a 2.3% BLEU-4 improvement on MIMIC-CXR, a 5.5% F1 score improvement on MIMIC-ABN, and a 2.7% F1 RadGraph improvement on Two-view CXR.

Automatic medical report generation (MRG), which possesses significant research value as it can aid radiologists in clinical diagnosis and report composition, has garnered increasing attention. Despite recent progress, generating accurate reports remains arduous due to the requirement for precise clinical comprehension and disease diagnosis inference. Furthermore, owing to the limited accessibility of medical data and the imbalanced distribution of diseases, the underrepresentation of rare diseases in training data makes large-scale medical visual language models (LVLMs) prone to hallucinations, such as omissions or fabrications, severely undermining diagnostic performance and further intensifying the challenges for MRG in practice. In this study, to effectively mitigate hallucinations in medical report generation, we propose a chain-of-medical-thought approach (CoMT), which intends to imitate the cognitive process of human doctors by decomposing diagnostic procedures. The radiological features with different importance are structured into fine-grained medical thought chains to enhance the inferential ability during diagnosis, thereby alleviating hallucination problems and enhancing the diagnostic accuracy of MRG. The code and dataset have been released at https://github.com/FRENKIE-CHIANG/CoMT.

The automated generation of imaging reports proves invaluable in alleviating the workload of radiologists. A clinically applicable reports generation algorithm should demonstrate its effectiveness in producing reports that accurately describe radiology findings and attend to patient-specific indications. In this paper, we introduce a novel method, Structural Entities extraction and patient indications Incorporation (SEI) for chest X-ray report generation. Specifically, we employ a structural entities extraction (SEE) approach to eliminate presentation-style vocabulary in reports and improve the quality of factual entity sequences. This reduces the noise in the following cross-modal alignment module by aligning X-ray images with factual entity sequences in reports, thereby enhancing the precision of cross-modal alignment and further aiding the model in gradient-free retrieval of similar historical cases. Subsequently, we propose a cross-modal fusion network to integrate information from X-ray images, similar historical cases, and patient-specific indications. This process allows the text decoder to attend to discriminative features of X-ray images, assimilate historical diagnostic information from similar cases, and understand the examination intention of patients. This, in turn, assists in triggering the text decoder to produce high-quality reports. Experiments conducted on MIMIC-CXR validate the superiority of SEI over state-of-the-art approaches on both natural language generation and clinical efficacy metrics.

Recent progress in Large Vision-Language Models (LVLMs) has enabled promising applications in medical tasks, such as report generation and visual question answering. However, existing benchmarks focus mainly on the final diagnostic answer, offering limited insight into whether models engage in clinically meaningful reasoning. To address this, we present CheXStruct and CXReasonBench, a structured pipeline and benchmark built on the publicly available MIMIC-CXR-JPG dataset. CheXStruct automatically derives a sequence of intermediate reasoning steps directly from chest X-rays, such as segmenting anatomical regions, deriving anatomical landmarks and diagnostic measurements, computing diagnostic indices, and applying clinical thresholds. CXReasonBench leverages this pipeline to evaluate whether models can perform clinically valid reasoning steps and to what extent they can learn from structured guidance, enabling fine-grained and transparent assessment of diagnostic reasoning. The benchmark comprises 18,988 QA pairs across 12 diagnostic tasks and 1,200 cases, each paired with up to 4 visual inputs, and supports multi-path, multi-stage evaluation including visual grounding via anatomical region selection and diagnostic measurements. Even the strongest of 10 evaluated LVLMs struggle with structured reasoning and generalization, often failing to link abstract knowledge with anatomically grounded visual interpretation. The code is available at https://github.com/ttumyche/CXReasonBench

The widespread use of chest X-rays (CXRs), coupled with a shortage of radiologists, has driven growing interest in automated CXR analysis and AI-assisted reporting. While existing vision-language models (VLMs) show promise in specific tasks such as report generation or abnormality detection, they often lack support for interactive diagnostic capabilities. In this work we present RadVLM, a compact, multitask conversational foundation model designed for CXR interpretation. To this end, we curate a large-scale instruction dataset comprising over 1 million image-instruction pairs containing both single-turn tasks -- such as report generation, abnormality classification, and visual grounding -- and multi-turn, multi-task conversational interactions. After fine-tuning RadVLM on this instruction dataset, we evaluate it across different tasks along with re-implemented baseline VLMs. Our results show that RadVLM achieves state-of-the-art performance in conversational capabilities and visual grounding while remaining competitive in other radiology tasks. Ablation studies further highlight the benefit of joint training across multiple tasks, particularly for scenarios with limited annotated data. Together, these findings highlight the potential of RadVLM as a clinically relevant AI assistant, providing structured CXR interpretation and conversational capabilities to support more effective and accessible diagnostic workflows.

Recent research on large language models (LLMs) has primarily focused on their adaptation and application in specialized domains. The application of LLMs in the medical field is mainly concentrated on tasks such as the automation of medical report generation, summarization, diagnostic reasoning, and question-and-answer interactions between doctors and patients. The challenge of becoming a good teacher is more formidable than that of becoming a good student, and this study pioneers the application of LLMs in the field of medical education. In this work, we investigate the extent to which LLMs can generate medical qualification exam questions and corresponding answers based on few-shot prompts. Utilizing a real-world Chinese dataset of elderly chronic diseases, we tasked the LLMs with generating open-ended questions and answers based on a subset of sampled admission reports across eight widely used LLMs, including ERNIE 4, ChatGLM 4, Doubao, Hunyuan, Spark 4, Qwen, Llama 3, and Mistral. Furthermore, we engaged medical experts to manually evaluate these open-ended questions and answers across multiple dimensions. The study found that LLMs, after using few-shot prompts, can effectively mimic real-world medical qualification exam questions, whereas there is room for improvement in the correctness, evidence-based statements, and professionalism of the generated answers. Moreover, LLMs also demonstrate a decent level of ability to correct and rectify reference answers. Given the immense potential of artificial intelligence in the medical field, the task of generating questions and answers for medical qualification exams aimed at medical students, interns and residents can be a significant focus of future research.

Medical imaging provides critical evidence for clinical diagnosis, treatment planning, and surgical decisions, yet most existing imaging models are narrowly focused and require multiple specialized networks, limiting their generalization. Although large-scale language and multimodal models exhibit strong reasoning and multi-task capabilities, real-world clinical applications demand precise visual grounding, multimodal integration, and chain-of-thought reasoning. We introduce Citrus-V, a multimodal medical foundation model that combines image analysis with textual reasoning. The model integrates detection, segmentation, and multimodal chain-of-thought reasoning, enabling pixel-level lesion localization, structured report generation, and physician-like diagnostic inference in a single framework. We propose a novel multimodal training approach and release a curated open-source data suite covering reasoning, detection, segmentation, and document understanding tasks. Evaluations demonstrate that Citrus-V outperforms existing open-source medical models and expert-level imaging systems across multiple benchmarks, delivering a unified pipeline from visual grounding to clinical reasoning and supporting precise lesion quantification, automated reporting, and reliable second opinions.

Artificial intelligence (AI) that can effectively learn ultrasound representations by integrating multi-source data holds significant promise for advancing clinical care. However, the scarcity of large labeled datasets in real-world clinical environments and the limited generalizability of task-specific models have hindered the development of generalizable clinical AI models for ultrasound applications. In this study, we present EchoCare, a novel ultrasound foundation model for generalist clinical use, developed via self-supervised learning on our curated, publicly available, large-scale dataset EchoCareData. EchoCareData comprises 4.5 million ultrasound images, sourced from over 23 countries across 5 continents and acquired via a diverse range of distinct imaging devices, thus encompassing global cohorts that are multi-center, multi-device, and multi-ethnic. Unlike prior studies that adopt off-the-shelf vision foundation model architectures, we introduce a hierarchical classifier into EchoCare to enable joint learning of pixel-level and representation-level features, capturing both global anatomical contexts and local ultrasound characteristics. With minimal training, EchoCare outperforms state-of-the-art comparison models across 10 representative ultrasound benchmarks of varying diagnostic difficulties, spanning disease diagnosis, lesion segmentation, organ detection, landmark prediction, quantitative regression, imaging enhancement and report generation. The code and pretrained model are publicly released, rendering EchoCare accessible for fine-tuning and local adaptation, supporting extensibility to additional applications. EchoCare provides a fully open and generalizable foundation model to boost the development of AI technologies for diverse clinical ultrasound applications.

Automatically evaluating the quality of language generation is critical. Although recent learned metrics show high correlation with human judgement, these metrics can not explain their verdict or associate the scores with defects in generated text. To address this limitation, we present InstructScore, an explainable evaluation metric for text generation. By harnessing both explicit human instruction and the implicit knowledge of GPT-4, we fine-tune a text evaluation metric based on LLaMA, producing both a score for generated text and a human readable diagnostic report. We evaluate InstructScore on a variety of generation tasks, including translation, captioning, data-to-text and commonsense generation. Experiments show that our 7B model surpasses all other unsupervised metrics, including those based on 175B GPT-3 and GPT-4. Surprisingly, our InstructScore, even without direct supervision from human-rated data, achieves performance levels on par with state-of-the-art metrics like COMET22, which were fine-tuned on human ratings.

Multimodal large language models (MLLMs) have achieved significant success in the general field of image processing. Their emerging task generalization and freeform conversational capabilities can greatly facilitate medical diagnostic assistance, helping patients better understand their conditions and enhancing doctor-patient trust. Computed Tomography (CT) is a non-invasive imaging technique used to capture the internal mechanisms of a patient's condition and is widely utilized. However, in past research, the complex textural features of this imaging data have made accurate interpretation by algorithms challenging, impeding the performance of general LLMs in diagnostic assistance. To address this, we developed OrthoDoc, a MLLM designed for CT diagnostics. OrthoDoc is trained on 120,000 CT images and diagnostic reports and includes a Retrieval-Augmented Generation (RAG) module capable of effectively mitigating model hallucinations. This module is informed by extensive medical literature, textbooks, and explanatory data. Thus, OrthoDoc not only processes complex CT images but also stores, understands, and reasons over medical knowledge and language. In extensive experiments, OrthoDoc outperforms commercial models led by GPT-4, demonstrating superior diagnostic capabilities and accuracy. Specifically, OrthoDoc significantly surpasses existing models in the diagnosis of common orthopedic conditions such as fractures, arthritis, and tumors. Additionally, OrthoDoc exhibits robust generalization and stability when handling rare and complex cases.

The rapid increase of computed tomography (CT) scans and their time-consuming manual analysis have created an urgent need for robust automated analysis techniques in clinical settings. These aim to assist radiologists and help them managing their growing workload. Existing methods typically generate entire reports directly from 3D CT images, without explicitly focusing on observed abnormalities. This unguided approach often results in repetitive content or incomplete reports, failing to prioritize anomaly-specific descriptions. We propose a new anomaly-guided report generation model, which first predicts abnormalities and then generates targeted descriptions for each. Evaluation on a public dataset demonstrates significant improvements in report quality and clinical relevance. We extend our work by conducting an ablation study to demonstrate its effectiveness.

This paper explores the task of radiology report generation, which aims at generating free-text descriptions for a set of radiographs. One significant challenge of this task is how to correctly maintain the consistency between the images and the lengthy report. Previous research explored solving this issue through planning-based methods, which generate reports only based on high-level plans. However, these plans usually only contain the major observations from the radiographs (e.g., lung opacity), lacking much necessary information, such as the observation characteristics and preliminary clinical diagnoses. To address this problem, the system should also take the image information into account together with the textual plan and perform stronger reasoning during the generation process. In this paper, we propose an observation-guided radiology report generation framework (ORGAN). It first produces an observation plan and then feeds both the plan and radiographs for report generation, where an observation graph and a tree reasoning mechanism are adopted to precisely enrich the plan information by capturing the multi-formats of each observation. Experimental results demonstrate that our framework outperforms previous state-of-the-art methods regarding text quality and clinical efficacy

Heart disease remains a significant threat to human health. As a non-invasive diagnostic tool, the electrocardiogram (ECG) is one of the most widely used methods for cardiac screening. However, the scarcity of high-quality ECG data, driven by privacy concerns and limited medical resources, creates a pressing need for effective ECG signal generation. Existing approaches for generating ECG signals typically rely on small training datasets, lack comprehensive evaluation frameworks, and overlook potential applications beyond data augmentation. To address these challenges, we propose DiffuSETS, a novel framework capable of generating ECG signals with high semantic alignment and fidelity. DiffuSETS accepts various modalities of clinical text reports and patient-specific information as inputs, enabling the creation of clinically meaningful ECG signals. Additionally, to address the lack of standardized evaluation in ECG generation, we introduce a comprehensive benchmarking methodology to assess the effectiveness of generative models in this domain. Our model achieve excellent results in tests, proving its superiority in the task of ECG generation. Furthermore, we showcase its potential to mitigate data scarcity while exploring novel applications in cardiology education and medical knowledge discovery, highlighting the broader impact of our work.

Medical imaging plays a crucial role in diagnosis, with radiology reports serving as vital documentation. Automating report generation has emerged as a critical need to alleviate the workload of radiologists. While machine learning has facilitated report generation for 2D medical imaging, extending this to 3D has been unexplored due to computational complexity and data scarcity. We introduce the first method to generate radiology reports for 3D medical imaging, specifically targeting chest CT volumes. Given the absence of comparable methods, we establish a baseline using an advanced 3D vision encoder in medical imaging to demonstrate our method's effectiveness, which leverages a novel auto-regressive causal transformer. Furthermore, recognizing the benefits of leveraging information from previous visits, we augment CT2Rep with a cross-attention-based multi-modal fusion module and hierarchical memory, enabling the incorporation of longitudinal multimodal data. Access our code at https://github.com/ibrahimethemhamamci/CT2Rep

Generating clinical reports from raw recordings such as X-rays and electroencephalogram (EEG) is an essential and routine task for doctors. However, it is often time-consuming to write accurate and detailed reports. Most existing methods try to generate the whole reports from the raw input with limited success because 1) generated reports often contain errors that need manual review and correction, 2) it does not save time when doctors want to write additional information into the report, and 3) the generated reports are not customized based on individual doctors' preference. We propose {\it CL}inic{\it A}l {\it R}eport {\it A}uto-completion (CLARA), an interactive method that generates reports in a sentence by sentence fashion based on doctors' anchor words and partially completed sentences. CLARA searches for most relevant sentences from existing reports as the template for the current report. The retrieved sentences are sequentially modified by combining with the input feature representations to create the final report. In our experimental evaluation, CLARA achieved 0.393 CIDEr and 0.248 BLEU-4 on X-ray reports and 0.482 CIDEr and 0.491 BLEU-4 for EEG reports for sentence-level generation, which is up to 35% improvement over the best baseline. Also via our qualitative evaluation, CLARA is shown to produce reports which have a significantly higher level of approval by doctors in a user study (3.74 out of 5 for CLARA vs 2.52 out of 5 for the baseline).

Medical diagnostic applications require models that can process multimodal medical inputs (images, patient histories, lab results) and generate diverse outputs including both textual reports and visual content (annotations, segmentation masks, and images). Despite this need, existing medical AI systems disrupt this unified process: medical image understanding models interpret images but cannot generate visual outputs, while medical image generation models synthesize images but cannot provide textual explanations. This leads to gaps in data representation, feature integration, and task-level multimodal capabilities. To this end, we propose a multi-level framework that draws inspiration from diagnostic workflows through the Observation-Knowledge-Analysis (OKA) paradigm. Specifically, at the observation level, we construct UniMed-5M, a dataset comprising over 5.6M samples that reformat diverse unimodal data into multimodal pairs for foundational observation. At the knowledge level, we propose Progressive Curriculum Learning that systematically introduces medical multimodal knowledge. At the analysis level, we introduce UniMedVL, the first medical unified multimodal model for the simultaneous analysis of image understanding and generation tasks within a single architecture. UniMedVL achieves superior performance on five medical image understanding benchmarks, while matching specialized models in generation quality across eight medical imaging modalities. Crucially, our unified architecture enables bidirectional knowledge sharing: generation tasks enhance visual understanding features, demonstrating that integrating traditionally separate capabilities within a single medical framework unlocks improvements across diverse medical vision-language tasks. Code is available at https://github.com/uni-medical/UniMedVL.

A radiology report comprises several sections, including the Findings and Impression of the diagnosis. Automatically generating the Impression from the Findings is crucial for reducing radiologists' workload and improving diagnostic accuracy. Pretrained models that excel in common abstractive summarization problems encounter challenges when applied to specialized medical domains largely due to the complex terminology and the necessity for accurate clinical context. Such tasks in medical domains demand extracting core information, avoiding context shifts, and maintaining proper flow. Misuse of medical terms can lead to drastic clinical errors. To address these issues, we introduce a sequential transfer learning that ensures key content extraction and coherent summarization. Sequential transfer learning often faces challenges like initial parameter decay and knowledge loss, which we resolve with the Fisher matrix regularization. Using MIMIC-CXR and Open-I datasets, our model, CSTRL - Context-driven Sequential TRansfer Learning - achieved state-of-the-art performance, showing 56.2% improvement in BLEU-1, 40.5% in BLEU-2, 84.3% in BLEU-3, 28.9% in ROUGE-1, 41.0% in ROUGE-2 and 26.5% in ROGUE-3 score over benchmark studies. We also analyze factual consistency scores while preserving the medical context. Our code is publicly available at https://github.com/fahmidahossain/Report_Summarization.

Automating radiology report generation can significantly alleviate radiologists' workloads. Previous research has primarily focused on realizing highly concise observations while neglecting the precise attributes that determine the severity of diseases (e.g., small pleural effusion). Since incorrect attributes will lead to imprecise radiology reports, strengthening the generation process with precise attribute modeling becomes necessary. Additionally, the temporal information contained in the historical records, which is crucial in evaluating a patient's current condition (e.g., heart size is unchanged), has also been largely disregarded. To address these issues, we propose RECAP, which generates precise and accurate radiology reports via dynamic disease progression reasoning. Specifically, RECAP first predicts the observations and progressions (i.e., spatiotemporal information) given two consecutive radiographs. It then combines the historical records, spatiotemporal information, and radiographs for report generation, where a disease progression graph and dynamic progression reasoning mechanism are devised to accurately select the attributes of each observation and progression. Extensive experiments on two publicly available datasets demonstrate the effectiveness of our model.

Radiology report generation (RRG) aims to automatically generate free-text descriptions from clinical radiographs, e.g., chest X-Ray images. RRG plays an essential role in promoting clinical automation and presents significant help to provide practical assistance for inexperienced doctors and alleviate radiologists' workloads. Therefore, consider these meaningful potentials, research on RRG is experiencing explosive growth in the past half-decade, especially with the rapid development of deep learning approaches. Existing studies perform RRG from the perspective of enhancing different modalities, provide insights on optimizing the report generation process with elaborated features from both visual and textual information, and further facilitate RRG with the cross-modal interactions among them. In this paper, we present a comprehensive review of deep learning-based RRG from various perspectives. Specifically, we firstly cover pivotal RRG approaches based on the task-specific features of radiographs, reports, and the cross-modal relations between them, and then illustrate the benchmark datasets conventionally used for this task with evaluation metrics, subsequently analyze the performance of different approaches and finally offer our summary on the challenges and the trends in future directions. Overall, the goal of this paper is to serve as a tool for understanding existing literature and inspiring potential valuable research in the field of RRG.

Radiology reporting is a complex task that requires detailed image understanding, integration of multiple inputs, including comparison with prior imaging, and precise language generation. This makes it ideal for the development and use of generative multimodal models. Here, we extend report generation to include the localisation of individual findings on the image - a task we call grounded report generation. Prior work indicates that grounding is important for clarifying image understanding and interpreting AI-generated text. Therefore, grounded reporting stands to improve the utility and transparency of automated report drafting. To enable evaluation of grounded reporting, we propose a novel evaluation framework - RadFact - leveraging the reasoning capabilities of large language models (LLMs). RadFact assesses the factuality of individual generated sentences, as well as correctness of generated spatial localisations when present. We introduce MAIRA-2, a large multimodal model combining a radiology-specific image encoder with a LLM, and trained for the new task of grounded report generation on chest X-rays. MAIRA-2 uses more comprehensive inputs than explored previously: the current frontal image, the current lateral image, the prior frontal image and prior report, as well as the Indication, Technique and Comparison sections of the current report. We demonstrate that these additions significantly improve report quality and reduce hallucinations, establishing a new state of the art on findings generation (without grounding) on MIMIC-CXR while demonstrating the feasibility of grounded reporting as a novel and richer task.

Medical report generation from X-ray images is a challenging task, particularly in an unpaired setting where paired image-report data is unavailable for training. To address this challenge, we propose a novel model that leverages the available information in two distinct datasets, one comprising reports and the other consisting of images. The core idea of our model revolves around the notion that combining auto-encoding report generation with multi-modal (report-image) alignment can offer a solution. However, the challenge persists regarding how to achieve this alignment when pair correspondence is absent. Our proposed solution involves the use of auxiliary tasks, particularly contrastive learning and classification, to position related images and reports in close proximity to each other. This approach differs from previous methods that rely on pre-processing steps, such as using external information stored in a knowledge graph. Our model, named MedRAT, surpasses previous state-of-the-art methods, demonstrating the feasibility of generating comprehensive medical reports without the need for paired data or external tools.

Automated radiology report generation (RRG) aims to produce detailed textual reports from clinical imaging, such as computed tomography (CT) scans, to improve the accuracy and efficiency of diagnosis and provision of management advice. RRG is complicated by two key challenges: (1) inherent complexity in extracting relevant information from imaging data under resource constraints, and (2) difficulty in objectively evaluating discrepancies between model-generated and expert-written reports. To address these challenges, we propose mu^2LLM, a textbf{mu}ltiscale textbf{mu}ltimodal large language models for RRG tasks. The novel {mu}^2Tokenizer, as an intermediate layer, integrates multi-modal features from the multiscale visual tokenizer and the text tokenizer, then enhances report generation quality through direct preference optimization (DPO), guided by GREEN-RedLlama. Experimental results on four large CT image-report medical datasetdemonstrate that our method outperforms existing approaches, highlighting the potential of our fine-tuned mu^2LLMs on limited data for RRG tasks.

Recent advancements in Large Language Models (LLMs) have drawn increasing attention since the learned embeddings pretrained on large-scale datasets have shown powerful ability in various downstream applications. However, whether the learned knowledge by LLMs can be transferred to clinical cardiology remains unknown. In this work, we aim to bridge this gap by transferring the knowledge of LLMs to clinical Electrocardiography (ECG). We propose an approach for cardiovascular disease diagnosis and automatic ECG diagnosis report generation. We also introduce an additional loss function by Optimal Transport (OT) to align the distribution between ECG and language embedding. The learned embeddings are evaluated on two downstream tasks: (1) automatic ECG diagnosis report generation, and (2) zero-shot cardiovascular disease detection. Our approach is able to generate high-quality cardiac diagnosis reports and also achieves competitive zero-shot classification performance even compared with supervised baselines, which proves the feasibility of transferring knowledge from LLMs to the cardiac domain.

Medical imaging plays a pivotal role in modern healthcare, with computed tomography pulmonary angiography (CTPA) being a critical tool for diagnosing pulmonary embolism and other thoracic conditions. However, the complexity of interpreting CTPA scans and generating accurate radiology reports remains a significant challenge. This paper introduces Abn-BLIP (Abnormality-aligned Bootstrapping Language-Image Pretraining), an advanced diagnosis model designed to align abnormal findings to generate the accuracy and comprehensiveness of radiology reports. By leveraging learnable queries and cross-modal attention mechanisms, our model demonstrates superior performance in detecting abnormalities, reducing missed findings, and generating structured reports compared to existing methods. Our experiments show that Abn-BLIP outperforms state-of-the-art medical vision-language models and 3D report generation methods in both accuracy and clinical relevance. These results highlight the potential of integrating multimodal learning strategies for improving radiology reporting. The source code is available at https://github.com/zzs95/abn-blip.

Radiology plays a pivotal role in modern medicine due to its non-invasive diagnostic capabilities. However, the manual generation of unstructured medical reports is time consuming and prone to errors. It creates a significant bottleneck in clinical workflows. Despite advancements in AI-generated radiology reports, challenges remain in achieving detailed and accurate report generation. In this study we have evaluated different combinations of multimodal models that integrate Computer Vision and Natural Language Processing to generate comprehensive radiology reports. We employed a pretrained Vision Transformer (ViT-B16) and a SWIN Transformer as the image encoders. The BART and GPT-2 models serve as the textual decoders. We used Chest X-ray images and reports from the IU-Xray dataset to evaluate the usability of the SWIN Transformer-BART, SWIN Transformer-GPT-2, ViT-B16-BART and ViT-B16-GPT-2 models for report generation. We aimed at finding the best combination among the models. The SWIN-BART model performs as the best-performing model among the four models achieving remarkable results in almost all the evaluation metrics like ROUGE, BLEU and BERTScore.

In recent years, automated radiology report generation has experienced significant growth. This paper introduces MRScore, an automatic evaluation metric tailored for radiology report generation by leveraging Large Language Models (LLMs). Conventional NLG (natural language generation) metrics like BLEU are inadequate for accurately assessing the generated radiology reports, as systematically demonstrated by our observations within this paper. To address this challenge, we collaborated with radiologists to develop a framework that guides LLMs for radiology report evaluation, ensuring alignment with human analysis. Our framework includes two key components: i) utilizing GPT to generate large amounts of training data, i.e., reports with different qualities, and ii) pairing GPT-generated reports as accepted and rejected samples and training LLMs to produce MRScore as the model reward. Our experiments demonstrate MRScore's higher correlation with human judgments and superior performance in model selection compared to traditional metrics. Our code and datasets will be available on GitHub.

Radiology report generation (RRG) has attracted significant attention due to its potential to reduce the workload of radiologists. Current RRG approaches are still unsatisfactory against clinical standards. This paper introduces a novel RRG method, LM-RRG, that integrates large models (LMs) with clinical quality reinforcement learning to generate accurate and comprehensive chest X-ray radiology reports. Our method first designs a large language model driven feature extractor to analyze and interpret different regions of the chest X-ray image, emphasizing specific regions with medical significance. Next, based on the large model's decoder, we develop a multimodal report generator that leverages multimodal prompts from visual features and textual instruction to produce the radiology report in an auto-regressive way. Finally, to better reflect the clinical significant and insignificant errors that radiologists would normally assign in the report, we introduce a novel clinical quality reinforcement learning strategy. It utilizes the radiology report clinical quality (RadCliQ) metric as a reward function in the learning process. Extensive experiments on the MIMIC-CXR and IU-Xray datasets demonstrate the superiority of our method over the state of the art.

Developing an interpretable system for generating reports in chest X-ray (CXR) analysis is becoming increasingly crucial in Computer-aided Diagnosis (CAD) systems, enabling radiologists to comprehend the decisions made by these systems. Despite the growth of diverse datasets and methods focusing on report generation, there remains a notable gap in how closely these models' generated reports align with the interpretations of real radiologists. In this study, we tackle this challenge by initially introducing Fine-Grained CXR (FG-CXR) dataset, which provides fine-grained paired information between the captions generated by radiologists and the corresponding gaze attention heatmaps for each anatomy. Unlike existing datasets that include a raw sequence of gaze alongside a report, with significant misalignment between gaze location and report content, our FG-CXR dataset offers a more grained alignment between gaze attention and diagnosis transcript. Furthermore, our analysis reveals that simply applying black-box image captioning methods to generate reports cannot adequately explain which information in CXR is utilized and how long needs to attend to accurately generate reports. Consequently, we propose a novel explainable radiologist's attention generator network (Gen-XAI) that mimics the diagnosis process of radiologists, explicitly constraining its output to closely align with both radiologist's gaze attention and transcript. Finally, we perform extensive experiments to illustrate the effectiveness of our method. Our datasets and checkpoint is available at https://github.com/UARK-AICV/FG-CXR.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

The objective of Radiology Report Generation (RRG) is to automatically generate coherent textual analyses of diseases based on radiological images, thereby alleviating the workload of radiologists. Current AI-based methods for RRG primarily focus on modifications to the encoder-decoder model architecture. To advance these approaches, this paper introduces an Organ-Regional Information Driven (ORID) framework which can effectively integrate multi-modal information and reduce the influence of noise from unrelated organs. Specifically, based on the LLaVA-Med, we first construct an RRG-related instruction dataset to improve organ-regional diagnosis description ability and get the LLaVA-Med-RRG. After that, we propose an organ-based cross-modal fusion module to effectively combine the information from the organ-regional diagnosis description and radiology image. To further reduce the influence of noise from unrelated organs on the radiology report generation, we introduce an organ importance coefficient analysis module, which leverages Graph Neural Network (GNN) to examine the interconnections of the cross-modal information of each organ region. Extensive experiments an1d comparisons with state-of-the-art methods across various evaluation metrics demonstrate the superior performance of our proposed method.

Automatic radiology report generation is booming due to its huge application potential for the healthcare industry. However, existing computer vision and natural language processing approaches to tackle this problem are limited in two aspects. First, when extracting image features, most of them neglect multi-view reasoning in vision and model single-view structure of medical images, such as space-view or channel-view. However, clinicians rely on multi-view imaging information for comprehensive judgment in daily clinical diagnosis. Second, when generating reports, they overlook context reasoning with multi-modal information and focus on pure textual optimization utilizing retrieval-based methods. We aim to address these two issues by proposing a model that better simulates clinicians' perspectives and generates more accurate reports. Given the above limitation in feature extraction, we propose a Globally-intensive Attention (GIA) module in the medical image encoder to simulate and integrate multi-view vision perception. GIA aims to learn three types of vision perception: depth view, space view, and pixel view. On the other hand, to address the above problem in report generation, we explore how to involve multi-modal signals to generate precisely matched reports, i.e., how to integrate previously predicted words with region-aware visual content in next word prediction. Specifically, we design a Visual Knowledge-guided Decoder (VKGD), which can adaptively consider how much the model needs to rely on visual information and previously predicted text to assist next word prediction. Hence, our final Intensive Vision-guided Network (IVGN) framework includes a GIA-guided Visual Encoder and the VKGD. Experiments on two commonly-used datasets IU X-Ray and MIMIC-CXR demonstrate the superior ability of our method compared with other state-of-the-art approaches.

In this paper, we present a framework for training large language models (LLMs) as diagnostic agents with reinforcement learning, enabling them to manage multi-turn diagnostic processes, adaptively select examinations, and commit to final diagnoses. Unlike instruction-tuned models trained on static case summaries, our method acquires diagnostic strategies through interactive exploration and outcome-based feedback. Our contributions are fourfold: (i) We present DiagGym, a diagnostics world model trained with electronic health records that emits examination outcomes conditioned on patient history and recommended examination, serving as a virtual clinical environment for realistic diagnosis training and evaluation; (ii) We train DiagAgent via end-to-end, multi-turn reinforcement learning to learn diagnostic policies that optimize both information yield and diagnostic accuracy; (iii) We introduce DiagBench, a diagnostic benchmark comprising 750 cases with physician-validated examination recommendations and 99 cases annotated with 973 physician-written rubrics on diagnosis process; (iv) we demonstrate superior performance across diverse diagnostic settings. DiagAgent significantly outperforms 10 state-of-the-art LLMs, including DeepSeek-v3 and GPT-4o, as well as two prompt-engineered agents. In single-turn settings, DiagAgent achieves 9.34% higher diagnostic accuracy and 44.03% improvement in examination recommendation hit ratio. In end-to-end settings, it delivers 15.12% increase in diagnostic accuracy and 23.09% boost in examination recommendation F1 score. In rubric-based evaluation, it surpasses the next-best model, Claude-sonnet-4, by 7.1% in weighted rubric score. These findings indicate that learning policies in interactive clinical environments confers dynamic and clinically meaningful diagnostic management abilities unattainable through passive training alone.

Evaluating radiology reports is a challenging problem as factual correctness is extremely important due to the need for accurate medical communication about medical images. Existing automatic evaluation metrics either suffer from failing to consider factual correctness (e.g., BLEU and ROUGE) or are limited in their interpretability (e.g., F1CheXpert and F1RadGraph). In this paper, we introduce GREEN (Generative Radiology Report Evaluation and Error Notation), a radiology report generation metric that leverages the natural language understanding of language models to identify and explain clinically significant errors in candidate reports, both quantitatively and qualitatively. Compared to current metrics, GREEN offers: 1) a score aligned with expert preferences, 2) human interpretable explanations of clinically significant errors, enabling feedback loops with end-users, and 3) a lightweight open-source method that reaches the performance of commercial counterparts. We validate our GREEN metric by comparing it to GPT-4, as well as to error counts of 6 experts and preferences of 2 experts. Our method demonstrates not only higher correlation with expert error counts, but simultaneously higher alignment with expert preferences when compared to previous approaches."

Automatic medical report generation supports clinical diagnosis, reduces the workload of radiologists, and holds the promise of improving diagnosis consistency. However, existing evaluation metrics primarily assess the accuracy of key medical information coverage in generated reports compared to human-written reports, while overlooking crucial details such as the location and certainty of reported abnormalities. These limitations hinder the comprehensive assessment of the reliability of generated reports and pose risks in their selection for clinical use. Therefore, we propose a Granular Explainable Multi-Agent Score (GEMA-Score) in this paper, which conducts both objective quantification and subjective evaluation through a large language model-based multi-agent workflow. Our GEMA-Score parses structured reports and employs NER-F1 calculations through interactive exchanges of information among agents to assess disease diagnosis, location, severity, and uncertainty. Additionally, an LLM-based scoring agent evaluates completeness, readability, and clinical terminology while providing explanatory feedback. Extensive experiments validate that GEMA-Score achieves the highest correlation with human expert evaluations on a public dataset, demonstrating its effectiveness in clinical scoring (Kendall coefficient = 0.70 for Rexval dataset and Kendall coefficient = 0.54 for RadEvalX dataset). The anonymous project demo is available at: https://github.com/Zhenxuan-Zhang/GEMA_score.

Previous research on radiology report generation has made significant progress in terms of increasing the clinical accuracy of generated reports. In this paper, we emphasize another crucial quality that it should possess, i.e., inter-report consistency, which refers to the capability of generating consistent reports for semantically equivalent radiographs. This quality is even of greater significance than the overall report accuracy in terms of ensuring the system's credibility, as a system prone to providing conflicting results would severely erode users' trust. Regrettably, existing approaches struggle to maintain inter-report consistency, exhibiting biases towards common patterns and susceptibility to lesion variants. To address this issue, we propose ICON, which improves the inter-report consistency of radiology report generation. Aiming at enhancing the system's ability to capture the similarities in semantically equivalent lesions, our approach involves first extracting lesions from input images and examining their characteristics. Then, we introduce a lesion-aware mix-up augmentation technique to ensure that the representations of the semantically equivalent lesions align with the same attributes, by linearly interpolating them during the training phase. Extensive experiments on three publicly available chest X-ray datasets verify the effectiveness of our approach, both in terms of improving the consistency and accuracy of the generated reports.

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

Large language models (LLMs) have demonstrated remarkable capabilities in various domains, including radiology report generation. Previous approaches have attempted to utilize multimodal LLMs for this task, enhancing their performance through the integration of domain-specific knowledge retrieval. However, these approaches often overlook the knowledge already embedded within the LLMs, leading to redundant information integration and inefficient utilization of learned representations. To address this limitation, we propose RADAR, a framework for enhancing radiology report generation with supplementary knowledge injection. RADAR improves report generation by systematically leveraging both the internal knowledge of an LLM and externally retrieved information. Specifically, it first extracts the model's acquired knowledge that aligns with expert image-based classification outputs. It then retrieves relevant supplementary knowledge to further enrich this information. Finally, by aggregating both sources, RADAR generates more accurate and informative radiology reports. Extensive experiments on MIMIC-CXR, CheXpert-Plus, and IU X-ray demonstrate that our model outperforms state-of-the-art LLMs in both language quality and clinical accuracy

Clinical diagnosis is critical in medical practice, typically requiring a continuous and evolving process that includes primary diagnosis, differential diagnosis, and final diagnosis. However, most existing clinical diagnostic tasks are single-step processes, which does not align with the complex multi-step diagnostic procedures found in real-world clinical settings. In this paper, we propose a multi-step diagnostic task and annotate a clinical diagnostic dataset (MSDiagnosis). This dataset includes primary diagnosis, differential diagnosis, and final diagnosis questions. Additionally, we propose a novel and effective framework. This framework combines forward inference, backward inference, reflection, and refinement, enabling the LLM to self-evaluate and adjust its diagnostic results. To assess the effectiveness of our proposed method, we design and conduct extensive experiments. The experimental results demonstrate the effectiveness of the proposed method. We also provide a comprehensive experimental analysis and suggest future research directions for this task.

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficiency metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

Reading and interpreting chest X-ray images is one of the most radiologist's routines. However, it still can be challenging, even for the most experienced ones. Therefore, we proposed a multi-model deep learning-based automated chest X-ray report generator system designed to assist radiologists in their work. The basic idea of the proposed system is by utilizing multi binary-classification models for detecting multi abnormalities, with each model responsible for detecting one abnormality, in a single image. In this study, we limited the radiology abnormalities detection to only cardiomegaly, lung effusion, and consolidation. The system generates a radiology report by performing the following three steps: image pre-processing, utilizing deep learning models to detect abnormalities, and producing a report. The aim of the image pre-processing step is to standardize the input by scaling it to 128x128 pixels and slicing it into three segments, which covers the upper, lower, and middle parts of the lung. After pre-processing, each corresponding model classifies the image, resulting in a 0 (zero) for no abnormality detected and a 1 (one) for the presence of an abnormality. The prediction outputs of each model are then concatenated to form a 'result code'. The 'result code' is used to construct a report by selecting the appropriate pre-determined sentence for each detected abnormality in the report generation step. The proposed system is expected to reduce the workload of radiologists and increase the accuracy of chest X-ray diagnosis.

Medical imaging plays a significant role in clinical practice of medical diagnosis, where the text reports of the images are essential in understanding them and facilitating later treatments. By generating the reports automatically, it is beneficial to help lighten the burden of radiologists and significantly promote clinical automation, which already attracts much attention in applying artificial intelligence to medical domain. Previous studies mainly follow the encoder-decoder paradigm and focus on the aspect of text generation, with few studies considering the importance of cross-modal mappings and explicitly exploit such mappings to facilitate radiology report generation. In this paper, we propose a cross-modal memory networks (CMN) to enhance the encoder-decoder framework for radiology report generation, where a shared memory is designed to record the alignment between images and texts so as to facilitate the interaction and generation across modalities. Experimental results illustrate the effectiveness of our proposed model, where state-of-the-art performance is achieved on two widely used benchmark datasets, i.e., IU X-Ray and MIMIC-CXR. Further analyses also prove that our model is able to better align information from radiology images and texts so as to help generating more accurate reports in terms of clinical indicators.

Chest X-ray imaging is crucial for diagnosing pulmonary and cardiac diseases, yet its interpretation demands extensive clinical experience and suffers from inter-observer variability. While deep learning models offer high diagnostic accuracy, their black-box nature hinders clinical adoption in high-stakes medical settings. To address this, we propose X-Ray-CoT (Chest X-Ray Chain-of-Thought), a novel framework leveraging Vision-Language Large Models (LVLMs) for intelligent chest X-ray diagnosis and interpretable report generation. X-Ray-CoT simulates human radiologists' "chain-of-thought" by first extracting multi-modal features and visual concepts, then employing an LLM-based component with a structured Chain-of-Thought prompting strategy to reason and produce detailed natural language diagnostic reports. Evaluated on the CORDA dataset, X-Ray-CoT achieves competitive quantitative performance, with a Balanced Accuracy of 80.52% and F1 score of 78.65% for disease diagnosis, slightly surpassing existing black-box models. Crucially, it uniquely generates high-quality, explainable reports, as validated by preliminary human evaluations. Our ablation studies confirm the integral role of each proposed component, highlighting the necessity of multi-modal fusion and CoT reasoning for robust and transparent medical AI. This work represents a significant step towards trustworthy and clinically actionable AI systems in medical imaging.

Radiology reports convey detailed clinical observations and capture diagnostic reasoning that evolves over time. However, existing evaluation methods are limited to single-report settings and rely on coarse metrics that fail to capture fine-grained clinical semantics and temporal dependencies. We introduce LUNGUAGE,a benchmark dataset for structured radiology report generation that supports both single-report evaluation and longitudinal patient-level assessment across multiple studies. It contains 1,473 annotated chest X-ray reports, each reviewed by experts, and 80 of them contain longitudinal annotations to capture disease progression and inter-study intervals, also reviewed by experts. Using this benchmark, we develop a two-stage framework that transforms generated reports into fine-grained, schema-aligned structured representations, enabling longitudinal interpretation. We also propose LUNGUAGESCORE, an interpretable metric that compares structured outputs at the entity, relation, and attribute level while modeling temporal consistency across patient timelines. These contributions establish the first benchmark dataset, structuring framework, and evaluation metric for sequential radiology reporting, with empirical results demonstrating that LUNGUAGESCORE effectively supports structured report evaluation. The code is available at: https://github.com/SuperSupermoon/Lunguage

Radiological imaging is central to diagnosis, treatment planning, and clinical decision-making. Vision-language foundation models have spurred interest in automated radiology report generation (RRG), but safe deployment requires reliable clinical evaluation of generated reports. Existing metrics often rely on surface-level similarity or behave as black boxes, lacking interpretability. We introduce ICARE (Interpretable and Clinically-grounded Agent-based Report Evaluation), an interpretable evaluation framework leveraging large language model agents and dynamic multiple-choice question answering (MCQA). Two agents, each with either the ground-truth or generated report, generate clinically meaningful questions and quiz each other. Agreement on answers captures preservation and consistency of findings, serving as interpretable proxies for clinical precision and recall. By linking scores to question-answer pairs, ICARE enables transparent, and interpretable assessment. Clinician studies show ICARE aligns significantly more with expert judgment than prior metrics. Perturbation analyses confirm sensitivity to clinical content and reproducibility, while model comparisons reveal interpretable error patterns.

Millions of melanocytic skin lesions are examined by pathologists each year, the majority of which concern common nevi (i.e., ordinary moles). While most of these lesions can be diagnosed in seconds, writing the corresponding pathology report is much more time-consuming. Automating part of the report writing could, therefore, alleviate the increasing workload of pathologists. In this work, we develop a vision-language model specifically for the pathology domain of cutaneous melanocytic lesions. The model follows the Contrastive Captioner framework and was trained and evaluated using a melanocytic lesion dataset of 42,512 H&E-stained whole slide images and 19,645 corresponding pathology reports. Our results show that the quality scores of model-generated reports were on par with pathologist-written reports for common nevi, assessed by an expert pathologist in a reader study. While report generation revealed to be more difficult for rare melanocytic lesion subtypes, the cross-modal retrieval performance for these cases was considerably better.

BACKGROUND: Radiology reports are typically written in a free-text format, making clinical information difficult to extract and use. Recently the adoption of structured reporting (SR) has been recommended by various medical societies thanks to the advantages it offers, e.g. standardization, completeness and information retrieval. We propose a pipeline to extract information from free-text radiology reports, that fits with the items of the reference SR registry proposed by a national society of interventional and medical radiology, focusing on CT staging of patients with lymphoma. METHODS: Our work aims to leverage the potential of Natural Language Processing (NLP) and Transformer-based models to deal with automatic SR registry filling. With the availability of 174 radiology reports, we investigate a rule-free generative Question Answering approach based on a domain-specific version of T5 (IT5). Two strategies (batch-truncation and ex-post combination) are implemented to comply with the model's context length limitations. Performance is evaluated in terms of strict accuracy, F1, and format accuracy, and compared with the widely used GPT-3.5 Large Language Model. A 5-point Likert scale questionnaire is used to collect human-expert feedback on the similarity between medical annotations and generated answers. RESULTS: The combination of fine-tuning and batch splitting allows IT5 to achieve notable results; it performs on par with GPT-3.5 albeit its size being a thousand times smaller in terms of parameters. Human-based assessment scores show a high correlation (Spearman's correlation coefficients>0.88, p-values<0.001) with AI performance metrics (F1) and confirm the superior ability of LLMs (i.e., GPT-3.5, 175B of parameters) in generating plausible human-like statements.

Rare diseases, including Inborn Errors of Metabolism (IEM), pose significant diagnostic challenges. Case reports serve as key but computationally underutilized resources to inform diagnosis. Clinical dense information extraction refers to organizing medical information into structured predefined categories. Large Language Models (LLMs) may enable scalable information extraction from case reports but are rarely evaluated for this task. We introduce CaseReportBench, an expert-annotated dataset for dense information extraction of case reports, focusing on IEMs. Using this dataset, we assess various models and prompting strategies, introducing novel approaches such as category-specific prompting and subheading-filtered data integration. Zero-shot chain-of-thought prompting offers little advantage over standard zero-shot prompting. Category-specific prompting improves alignment with the benchmark. The open-source model Qwen2.5-7B outperforms GPT-4o for this task. Our clinician evaluations show that LLMs can extract clinically relevant details from case reports, supporting rare disease diagnosis and management. We also highlight areas for improvement, such as LLMs' limitations in recognizing negative findings important for differential diagnosis. This work advances LLM-driven clinical natural language processing and paves the way for scalable medical AI applications.

Vision-language models in pathology enable multimodal case retrieval and automated report generation. Many of the models developed so far, however, have been trained on pathology reports that include information which cannot be inferred from paired whole slide images (e.g., patient history), potentially leading to hallucinated sentences in generated reports. To this end, we investigate how the selection of information from pathology reports for vision-language modeling affects the quality of the multimodal representations and generated reports. More concretely, we compare a model trained on full reports against a model trained on preprocessed reports that only include sentences describing the cell and tissue appearances based on the H&E-stained slides. For the experiments, we built upon the BLIP-2 framework and used a cutaneous melanocytic lesion dataset of 42,433 H&E-stained whole slide images and 19,636 corresponding pathology reports. Model performance was assessed using image-to-text and text-to-image retrieval, as well as qualitative evaluation of the generated reports by an expert pathologist. Our results demonstrate that text preprocessing prevents hallucination in report generation. Despite the improvement in the quality of the generated reports, training the vision-language model on full reports showed better cross-modal retrieval performance.

Medical phrase grounding is crucial for identifying relevant regions in medical images based on phrase queries, facilitating accurate image analysis and diagnosis. However, current methods rely on manual extraction of key phrases from medical reports, reducing efficiency and increasing the workload for clinicians. Additionally, the lack of model confidence estimation limits clinical trust and usability. In this paper, we introduce a novel task called Medical Report Grounding (MRG), which aims to directly identify diagnostic phrases and their corresponding grounding boxes from medical reports in an end-to-end manner. To address this challenge, we propose uMedGround, a robust and reliable framework that leverages a multimodal large language model to predict diagnostic phrases by embedding a unique token, <BOX>, into the vocabulary to enhance detection capabilities. A vision encoder-decoder processes the embedded token and input image to generate grounding boxes. Critically, uMedGround incorporates an uncertainty-aware prediction model, significantly improving the robustness and reliability of grounding predictions. Experimental results demonstrate that uMedGround outperforms state-of-the-art medical phrase grounding methods and fine-tuned large visual-language models, validating its effectiveness and reliability. This study represents a pioneering exploration of the MRG task, marking the first-ever endeavor in this domain. Additionally, we demonstrate the applicability of uMedGround in medical visual question answering and class-based localization tasks, where it highlights visual evidence aligned with key diagnostic phrases, supporting clinicians in interpreting various types of textual inputs, including free-text reports, visual question answering queries, and class labels.

Recent advancements in artificial intelligence (AI) have precipitated significant breakthroughs in healthcare, particularly in refining diagnostic procedures. However, previous studies have often been constrained to limited functionalities. This study introduces MiniGPT-Med, a vision-language model derived from large-scale language models and tailored for medical applications. MiniGPT-Med demonstrates remarkable versatility across various imaging modalities, including X-rays, CT scans, and MRIs, enhancing its utility. The model is capable of performing tasks such as medical report generation, visual question answering (VQA), and disease identification within medical imagery. Its integrated processing of both image and textual clinical data markedly improves diagnostic accuracy. Our empirical assessments confirm MiniGPT-Med's superior performance in disease grounding, medical report generation, and VQA benchmarks, representing a significant step towards reducing the gap in assisting radiology practice. Furthermore, it achieves state-of-the-art performance on medical report generation, higher than the previous best model by 19\% accuracy. MiniGPT-Med promises to become a general interface for radiology diagnoses, enhancing diagnostic efficiency across a wide range of medical imaging applications.

Vision-grounded medical report generation aims to produce clinically accurate descriptions of medical images, anchored in explicit visual evidence to improve interpretability and facilitate integration into clinical workflows. However, existing methods often rely on separately trained detection modules that require extensive expert annotations, introducing high labeling costs and limiting generalizability due to pathology distribution bias across datasets. To address these challenges, we propose Self-Supervised Anatomical Consistency Learning (SS-ACL) -- a novel and annotation-free framework that aligns generated reports with corresponding anatomical regions using simple textual prompts. SS-ACL constructs a hierarchical anatomical graph inspired by the invariant top-down inclusion structure of human anatomy, organizing entities by spatial location. It recursively reconstructs fine-grained anatomical regions to enforce intra-sample spatial alignment, inherently guiding attention maps toward visually relevant areas prompted by text. To further enhance inter-sample semantic alignment for abnormality recognition, SS-ACL introduces a region-level contrastive learning based on anatomical consistency. These aligned embeddings serve as priors for report generation, enabling attention maps to provide interpretable visual evidence. Extensive experiments demonstrate that SS-ACL, without relying on expert annotations, (i) generates accurate and visually grounded reports -- outperforming state-of-the-art methods by 10\% in lexical accuracy and 25\% in clinical efficacy, and (ii) achieves competitive performance on various downstream visual tasks, surpassing current leading visual foundation models by 8\% in zero-shot visual grounding.

Radiology report generation (RRG) is a challenging task, as it requires a thorough understanding of medical images, integration of multiple temporal inputs, and accurate report generation. Effective interpretation of medical images, such as chest X-rays (CXRs), demands sophisticated visual-language reasoning to map visual findings to structured reports. Recent studies have shown that multimodal large language models (MLLMs) can acquire multimodal capabilities by aligning with pre-trained vision encoders. However, current approaches predominantly focus on single-image analysis or utilise rule-based symbolic processing to handle multiple images, thereby overlooking the essential temporal information derived from comparing current images with prior ones. To overcome this critical limitation, we introduce Libra, a temporal-aware MLLM tailored for CXR report generation using temporal images. Libra integrates a radiology-specific image encoder with a MLLM and utilises a novel Temporal Alignment Connector to capture and synthesise temporal information of images across different time points with unprecedented precision. Extensive experiments show that Libra achieves new state-of-the-art performance among the same parameter scale MLLMs for RRG tasks on the MIMIC-CXR. Specifically, Libra improves the RadCliQ metric by 12.9% and makes substantial gains across all lexical metrics compared to previous models.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

As the field of artificial intelligence progresses, assistive technologies are becoming more widely used across all industries. The healthcare industry is no different, with numerous studies being done to develop assistive tools for healthcare professionals. Automatic diagnostic systems are one such beneficial tool that can assist with a variety of tasks, including collecting patient information, analyzing test results, and diagnosing patients. However, the idea of developing systems that can provide a differential diagnosis has been largely overlooked in most of these research studies. In this study, we propose a transformer-based approach for providing differential diagnoses based on a patient's age, sex, medical history, and symptoms. We use the DDXPlus dataset, which provides differential diagnosis information for patients based on 49 disease types. Firstly, we propose a method to process the tabular patient data from the dataset and engineer them into patient reports to make them suitable for our research. In addition, we introduce two data modification modules to diversify the training data and consequently improve the robustness of the models. We approach the task as a multi-label classification problem and conduct extensive experiments using four transformer models. All the models displayed promising results by achieving over 97% F1 score on the held-out test set. Moreover, we design additional behavioral tests to get a broader understanding of the models. In particular, for one of our test cases, we prepared a custom test set of 100 samples with the assistance of a doctor. The results on the custom set showed that our proposed data modification modules improved the model's generalization capabilities. We hope our findings will provide future researchers with valuable insights and inspire them to develop reliable systems for automatic differential diagnosis.

We consider the problem of automatically generating a narrative biomedical evidence summary from multiple trial reports. We evaluate modern neural models for abstractive summarization of relevant article abstracts from systematic reviews previously conducted by members of the Cochrane collaboration, using the authors conclusions section of the review abstract as our target. We enlist medical professionals to evaluate generated summaries, and we find that modern summarization systems yield consistently fluent and relevant synopses, but that they are not always factual. We propose new approaches that capitalize on domain-specific models to inform summarization, e.g., by explicitly demarcating snippets of inputs that convey key findings, and emphasizing the reports of large and high-quality trials. We find that these strategies modestly improve the factual accuracy of generated summaries. Finally, we propose a new method for automatically evaluating the factuality of generated narrative evidence syntheses using models that infer the directionality of reported findings.

We present a radiology-specific multimodal model for the task for generating radiological reports from chest X-rays (CXRs). Our work builds on the idea that large language model(s) can be equipped with multimodal capabilities through alignment with pre-trained vision encoders. On natural images, this has been shown to allow multimodal models to gain image understanding and description capabilities. Our proposed model (MAIRA-1) leverages a CXR-specific image encoder in conjunction with a fine-tuned large language model based on Vicuna-7B, and text-based data augmentation, to produce reports with state-of-the-art quality. In particular, MAIRA-1 significantly improves on the radiologist-aligned RadCliQ metric and across all lexical metrics considered. Manual review of model outputs demonstrates promising fluency and accuracy of generated reports while uncovering failure modes not captured by existing evaluation practices. More information and resources can be found on the project website: https://aka.ms/maira.

Many clinical tasks require an understanding of specialized data, such as medical images and genomics, which is not typically found in general-purpose large multimodal models. Building upon Gemini's multimodal models, we develop several models within the new Med-Gemini family that inherit core capabilities of Gemini and are optimized for medical use via fine-tuning with 2D and 3D radiology, histopathology, ophthalmology, dermatology and genomic data. Med-Gemini-2D sets a new standard for AI-based chest X-ray (CXR) report generation based on expert evaluation, exceeding previous best results across two separate datasets by an absolute margin of 1% and 12%, where 57% and 96% of AI reports on normal cases, and 43% and 65% on abnormal cases, are evaluated as "equivalent or better" than the original radiologists' reports. We demonstrate the first ever large multimodal model-based report generation for 3D computed tomography (CT) volumes using Med-Gemini-3D, with 53% of AI reports considered clinically acceptable, although additional research is needed to meet expert radiologist reporting quality. Beyond report generation, Med-Gemini-2D surpasses the previous best performance in CXR visual question answering (VQA) and performs well in CXR classification and radiology VQA, exceeding SoTA or baselines on 17 of 20 tasks. In histopathology, ophthalmology, and dermatology image classification, Med-Gemini-2D surpasses baselines across 18 out of 20 tasks and approaches task-specific model performance. Beyond imaging, Med-Gemini-Polygenic outperforms the standard linear polygenic risk score-based approach for disease risk prediction and generalizes to genetically correlated diseases for which it has never been trained. Although further development and evaluation are necessary in the safety-critical medical domain, our results highlight the potential of Med-Gemini across a wide range of medical tasks.

The field of medical diagnosis has undergone a significant transformation with the advent of large language models (LLMs), yet the challenges of interpretability within these models remain largely unaddressed. This study introduces Chain-of-Diagnosis (CoD) to enhance the interpretability of LLM-based medical diagnostics. CoD transforms the diagnostic process into a diagnostic chain that mirrors a physician's thought process, providing a transparent reasoning pathway. Additionally, CoD outputs the disease confidence distribution to ensure transparency in decision-making. This interpretability makes model diagnostics controllable and aids in identifying critical symptoms for inquiry through the entropy reduction of confidences. With CoD, we developed DiagnosisGPT, capable of diagnosing 9604 diseases. Experimental results demonstrate that DiagnosisGPT outperforms other LLMs on diagnostic benchmarks. Moreover, DiagnosisGPT provides interpretability while ensuring controllability in diagnostic rigor.

Accurate diagnostic coding of medical notes is crucial for enhancing patient care, medical research, and error-free billing in healthcare organizations. Manual coding is a time-consuming task for providers, and diagnostic codes often exhibit low sensitivity and specificity, whereas the free text in medical notes can be a more precise description of a patients status. Thus, accurate automated diagnostic coding of medical notes has become critical for a learning healthcare system. Recent developments in long-document transformer architectures have enabled attention-based deep-learning models to adjudicate medical notes. In addition, contrastive loss functions have been used to jointly pre-train large language and image models with noisy labels. To further improve the automated adjudication of medical notes, we developed an approach based on i) models for ICD-10 diagnostic code sequences using a large real-world data set, ii) large language models for medical notes, and iii) contrastive pre-training to build an integrated model of both ICD-10 diagnostic codes and corresponding medical text. We demonstrate that a contrastive approach for pre-training improves performance over prior state-of-the-art models for the MIMIC-III-50, MIMIC-III-rare50, and MIMIC-III-full diagnostic coding tasks.

Multimodal large language models (MLLMs) demonstrate significant potential in the field of medical diagnosis. However, they face critical challenges in specialized domains such as ophthalmology, particularly the fragmentation of annotation granularity and inconsistencies in clinical reasoning logic, which hinder precise cross-modal understanding. This paper introduces FundusExpert, an ophthalmology-specific MLLM with integrated positioning-diagnosis reasoning capabilities, along with FundusGen, a dataset constructed through the intelligent Fundus-Engine system. Fundus-Engine automates localization and leverages MLLM-based semantic expansion to integrate global disease classification, local object detection, and fine-grained feature analysis within a single fundus image. Additionally, by constructing a clinically aligned cognitive chain, it guides the model to generate interpretable reasoning paths. FundusExpert, fine-tuned with instruction data from FundusGen, achieves the best performance in ophthalmic question-answering tasks, surpassing the average accuracy of the 40B MedRegA by 26.6%. It also excels in zero-shot report generation tasks, achieving a clinical consistency of 77.0%, significantly outperforming GPT-4o's 47.6%. Furthermore, we reveal a scaling law between data quality and model capability (L propto N^{0.068}), demonstrating that the cognitive alignment annotations in FundusGen enhance data utilization efficiency. By integrating region-level localization with diagnostic reasoning chains, our work develops a scalable, clinically-aligned MLLM and explores a pathway toward bridging the visual-language gap in specific MLLMs. Our project can be found at https://github.com/MeteorElf/FundusExpert.

Experts in various fields routinely perform methodical writing tasks to plan, organize, and report their work. From a clinician writing a differential diagnosis for a patient, to a teacher writing a lesson plan for students, these tasks are pervasive, requiring to methodically generate structured long-form output for a given input. We develop a typology of methodical tasks structured in the form of a task objective, procedure, input, and output, and introduce DoLoMiTes, a novel benchmark with specifications for 519 such tasks elicited from hundreds of experts from across 25 fields. Our benchmark further contains specific instantiations of methodical tasks with concrete input and output examples (1,857 in total) which we obtain by collecting expert revisions of up to 10 model-generated examples of each task. We use these examples to evaluate contemporary language models highlighting that automating methodical tasks is a challenging long-form generation problem, as it requires performing complex inferences, while drawing upon the given context as well as domain knowledge.

With the emergence of large-scale vision language models (VLM), it is now possible to produce realistic-looking radiology reports for chest X-ray images. However, their clinical translation has been hampered by the factual errors and hallucinations in the produced descriptions during inference. In this paper, we present a novel phrase-grounded fact-checking model (FC model) that detects errors in findings and their indicated locations in automatically generated chest radiology reports. Specifically, we simulate the errors in reports through a large synthetic dataset derived by perturbing findings and their locations in ground truth reports to form real and fake findings-location pairs with images. A new multi-label cross-modal contrastive regression network is then trained on this dataset. We present results demonstrating the robustness of our method in terms of accuracy of finding veracity prediction and localization on multiple X-ray datasets. We also show its effectiveness for error detection in reports of SOTA report generators on multiple datasets achieving a concordance correlation coefficient of 0.997 with ground truth-based verification, thus pointing to its utility during clinical inference in radiology workflows.

The rapid advancement of large-scale vision-language models has showcased remarkable capabilities across various tasks. However, the lack of extensive and high-quality image-text data in medicine has greatly hindered the development of large-scale medical vision-language models. In this work, we present a diagnosis-guided bootstrapping strategy that exploits both image and label information to construct vision-language datasets. Based on the constructed dataset, we developed MedDr, a generalist foundation model for healthcare capable of handling diverse medical data modalities, including radiology, pathology, dermatology, retinography, and endoscopy. Moreover, during inference, we propose a simple but effective retrieval-augmented medical diagnosis strategy, which enhances the model's generalization ability. Extensive experiments on visual question answering, medical report generation, and medical image diagnosis demonstrate the superiority of our method.

Synthetic medical data generation has opened up new possibilities in the healthcare domain, offering a powerful tool for simulating clinical scenarios, enhancing diagnostic and treatment quality, gaining granular medical knowledge, and accelerating the development of unbiased algorithms. In this context, we present a novel approach called ViewXGen, designed to overcome the limitations of existing methods that rely on general domain pipelines using only radiology reports to generate frontal-view chest X-rays. Our approach takes into consideration the diverse view positions found in the dataset, enabling the generation of chest X-rays with specific views, which marks a significant advancement in the field. To achieve this, we introduce a set of specially designed tokens for each view position, tailoring the generation process to the user's preferences. Furthermore, we leverage multi-view chest X-rays as input, incorporating valuable information from different views within the same study. This integration rectifies potential errors and contributes to faithfully capturing abnormal findings in chest X-ray generation. To validate the effectiveness of our approach, we conducted statistical analyses, evaluating its performance in a clinical efficacy metric on the MIMIC-CXR dataset. Also, human evaluation demonstrates the remarkable capabilities of ViewXGen, particularly in producing realistic view-specific X-rays that closely resemble the original images.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

Recently a number of studies demonstrated impressive performance on diverse vision-language multi-modal tasks such as image captioning and visual question answering by extending the BERT architecture with multi-modal pre-training objectives. In this work we explore a broad set of multi-modal representation learning tasks in the medical domain, specifically using radiology images and the unstructured report. We propose Medical Vision Language Learner (MedViLL), which adopts a BERT-based architecture combined with a novel multi-modal attention masking scheme to maximize generalization performance for both vision-language understanding tasks (diagnosis classification, medical image-report retrieval, medical visual question answering) and vision-language generation task (radiology report generation). By statistically and rigorously evaluating the proposed model on four downstream tasks with three radiographic image-report datasets (MIMIC-CXR, Open-I, and VQA-RAD), we empirically demonstrate the superior downstream task performance of MedViLL against various baselines, including task-specific architectures. The source code is publicly available at: https://github.com/SuperSupermoon/MedViLL

Surgical site infection (SSI) is one of the most common and costly healthcare-associated infections and and surgical wound care remains a significant clinical challenge in preventing SSIs and improving patient outcomes. While recent studies have explored the use of deep learning for preliminary surgical wound screening, progress has been hindered by concerns over data privacy and the high costs associated with expert annotation. Currently, no publicly available dataset or benchmark encompasses various types of surgical wounds, resulting in the absence of an open-source Surgical-Wound screening tool. To address this gap: (1) we present SurgWound, the first open-source dataset featuring a diverse array of surgical wound types. It contains 697 surgical wound images annotated by 3 professional surgeons with eight fine-grained clinical attributes. (2) Based on SurgWound, we introduce the first benchmark for surgical wound diagnosis, which includes visual question answering (VQA) and report generation tasks to comprehensively evaluate model performance. (3) Furthermore, we propose a three-stage learning framework, WoundQwen, for surgical wound diagnosis. In the first stage, we employ five independent MLLMs to accurately predict specific surgical wound characteristics. In the second stage, these predictions serve as additional knowledge inputs to two MLLMs responsible for diagnosing outcomes, which assess infection risk and guide subsequent interventions. In the third stage, we train a MLLM that integrates the diagnostic results from the previous two stages to produce a comprehensive report. This three-stage framework can analyze detailed surgical wound characteristics and provide subsequent instructions to patients based on surgical images, paving the way for personalized wound care, timely intervention, and improved patient outcomes.

Radiology reports contain rich clinical information that can be used to train imaging models without relying on costly manual annotation. However, existing approaches face critical limitations: rule-based methods struggle with linguistic variability, supervised models require large annotated datasets, and recent LLM-based systems depend on closed-source or resource-intensive models that are unsuitable for clinical use. Moreover, current solutions are largely restricted to English and single-modality, single-taxonomy datasets. We introduce MOSAIC, a multilingual, taxonomy-agnostic, and computationally efficient approach for radiological report classification. Built on a compact open-access language model (MedGemma-4B), MOSAIC supports both zero-/few-shot prompting and lightweight fine-tuning, enabling deployment on consumer-grade GPUs. We evaluate MOSAIC across seven datasets in English, Spanish, French, and Danish, spanning multiple imaging modalities and label taxonomies. The model achieves a mean macro F1 score of 88 across five chest X-ray datasets, approaching or exceeding expert-level performance, while requiring only 24 GB of GPU memory. With data augmentation, as few as 80 annotated samples are sufficient to reach a weighted F1 score of 82 on Danish reports, compared to 86 with the full 1600-sample training set. MOSAIC offers a practical alternative to large or proprietary LLMs in clinical settings. Code and models are open-source. We invite the community to evaluate and extend MOSAIC on new languages, taxonomies, and modalities.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

LLMs for clinical decision support often fail under small but clinically meaningful input shifts such as masking a symptom or negating a finding, despite high performance on static benchmarks. These reasoning failures frequently go undetected by standard NLP metrics, which are insensitive to latent representation shifts that drive diagnosis instability. We propose a geometry-aware evaluation framework, LAPD (Latent Agentic Perturbation Diagnostics), which systematically probes the latent robustness of clinical LLMs under structured adversarial edits. Within this framework, we introduce Latent Diagnosis Flip Rate (LDFR), a model-agnostic diagnostic signal that captures representational instability when embeddings cross decision boundaries in PCA-reduced latent space. Clinical notes are generated using a structured prompting pipeline grounded in diagnostic reasoning, then perturbed along four axes: masking, negation, synonym replacement, and numeric variation to simulate common ambiguities and omissions. We compute LDFR across both foundation and clinical LLMs, finding that latent fragility emerges even under minimal surface-level changes. Finally, we validate our findings on 90 real clinical notes from the DiReCT benchmark (MIMIC-IV), confirming the generalizability of LDFR beyond synthetic settings. Our results reveal a persistent gap between surface robustness and semantic stability, underscoring the importance of geometry-aware auditing in safety-critical clinical AI.

The emergence of groundbreaking large language models capable of performing complex reasoning tasks holds significant promise for addressing various scientific challenges, including those arising in complex clinical scenarios. To enable their safe and effective deployment in real-world healthcare settings, it is urgently necessary to benchmark the diagnostic capabilities of current models systematically. Given the limitations of existing medical benchmarks in evaluating advanced diagnostic reasoning, we present DiagnosisArena, a comprehensive and challenging benchmark designed to rigorously assess professional-level diagnostic competence. DiagnosisArena consists of 1,113 pairs of segmented patient cases and corresponding diagnoses, spanning 28 medical specialties, deriving from clinical case reports published in 10 top-tier medical journals. The benchmark is developed through a meticulous construction pipeline, involving multiple rounds of screening and review by both AI systems and human experts, with thorough checks conducted to prevent data leakage. Our study reveals that even the most advanced reasoning models, o3-mini, o1, and DeepSeek-R1, achieve only 45.82%, 31.09%, and 17.79% accuracy, respectively. This finding highlights a significant generalization bottleneck in current large language models when faced with clinical diagnostic reasoning challenges. Through DiagnosisArena, we aim to drive further advancements in AIs diagnostic reasoning capabilities, enabling more effective solutions for real-world clinical diagnostic challenges. We provide the benchmark and evaluation tools for further research and development https://github.com/SPIRAL-MED/DiagnosisArena.

There has been a rapidly growing interest in Automatic Symptom Detection (ASD) and Automatic Diagnosis (AD) systems in the machine learning research literature, aiming to assist doctors in telemedicine services. These systems are designed to interact with patients, collect evidence about their symptoms and relevant antecedents, and possibly make predictions about the underlying diseases. Doctors would review the interactions, including the evidence and the predictions, collect if necessary additional information from patients, before deciding on next steps. Despite recent progress in this area, an important piece of doctors' interactions with patients is missing in the design of these systems, namely the differential diagnosis. Its absence is largely due to the lack of datasets that include such information for models to train on. In this work, we present a large-scale synthetic dataset of roughly 1.3 million patients that includes a differential diagnosis, along with the ground truth pathology, symptoms and antecedents for each patient. Unlike existing datasets which only contain binary symptoms and antecedents, this dataset also contains categorical and multi-choice symptoms and antecedents useful for efficient data collection. Moreover, some symptoms are organized in a hierarchy, making it possible to design systems able to interact with patients in a logical way. As a proof-of-concept, we extend two existing AD and ASD systems to incorporate the differential diagnosis, and provide empirical evidence that using differentials as training signals is essential for the efficiency of such systems or for helping doctors better understand the reasoning of those systems.

Counterfactual medical image generation enables clinicians to explore clinical hypotheses, such as predicting disease progression, facilitating their decision-making. While existing methods can generate visually plausible images from disease progression prompts, they produce silent predictions that lack interpretation to verify how the generation reflects the hypothesized progression -- a critical gap for medical applications that require traceable reasoning. In this paper, we propose Interpretable Counterfactual Generation (ICG), a novel task requiring the joint generation of counterfactual images that reflect the clinical hypothesis and interpretation texts that outline the visual changes induced by the hypothesis. To enable ICG, we present ICG-CXR, the first dataset pairing longitudinal medical images with hypothetical progression prompts and textual interpretations. We further introduce ProgEmu, an autoregressive model that unifies the generation of counterfactual images and textual interpretations. We demonstrate the superiority of ProgEmu in generating progression-aligned counterfactuals and interpretations, showing significant potential in enhancing clinical decision support and medical education. Project page: https://progemu.github.io.

With Artificial Intelligence (AI) increasingly permeating various aspects of society, including healthcare, the adoption of the Transformers neural network architecture is rapidly changing many applications. Transformer is a type of deep learning architecture initially developed to solve general-purpose Natural Language Processing (NLP) tasks and has subsequently been adapted in many fields, including healthcare. In this survey paper, we provide an overview of how this architecture has been adopted to analyze various forms of data, including medical imaging, structured and unstructured Electronic Health Records (EHR), social media, physiological signals, and biomolecular sequences. Those models could help in clinical diagnosis, report generation, data reconstruction, and drug/protein synthesis. We identified relevant studies using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We also discuss the benefits and limitations of using transformers in healthcare and examine issues such as computational cost, model interpretability, fairness, alignment with human values, ethical implications, and environmental impact.

Medical vision-and-language models (MVLMs) have attracted substantial interest due to their capability to offer a natural language interface for interpreting complex medical data. Their applications are versatile and have the potential to improve diagnostic accuracy and decision-making for individual patients while also contributing to enhanced public health monitoring, disease surveillance, and policy-making through more efficient analysis of large data sets. MVLMS integrate natural language processing with medical images to enable a more comprehensive and contextual understanding of medical images alongside their corresponding textual information. Unlike general vision-and-language models trained on diverse, non-specialized datasets, MVLMs are purpose-built for the medical domain, automatically extracting and interpreting critical information from medical images and textual reports to support clinical decision-making. Popular clinical applications of MVLMs include automated medical report generation, medical visual question answering, medical multimodal segmentation, diagnosis and prognosis and medical image-text retrieval. Here, we provide a comprehensive overview of MVLMs and the various medical tasks to which they have been applied. We conduct a detailed analysis of various vision-and-language model architectures, focusing on their distinct strategies for cross-modal integration/exploitation of medical visual and textual features. We also examine the datasets used for these tasks and compare the performance of different models based on standardized evaluation metrics. Furthermore, we highlight potential challenges and summarize future research trends and directions. The full collection of papers and codes is available at: https://github.com/YtongXie/Medical-Vision-and-Language-Tasks-and-Methodologies-A-Survey.

The non-invasive assessment of increasingly incidentally discovered renal masses is a critical challenge in urologic oncology, where diagnostic uncertainty frequently leads to the overtreatment of benign or indolent tumors. In this study, we developed and validated RenalCLIP using a dataset of 27,866 CT scans from 8,809 patients across nine Chinese medical centers and the public TCIA cohort, a visual-language foundation model for characterization, diagnosis and prognosis of renal mass. The model was developed via a two-stage pre-training strategy that first enhances the image and text encoders with domain-specific knowledge before aligning them through a contrastive learning objective, to create robust representations for superior generalization and diagnostic precision. RenalCLIP achieved better performance and superior generalizability across 10 core tasks spanning the full clinical workflow of kidney cancer, including anatomical assessment, diagnostic classification, and survival prediction, compared with other state-of-the-art general-purpose CT foundation models. Especially, for complicated task like recurrence-free survival prediction in the TCIA cohort, RenalCLIP achieved a C-index of 0.726, representing a substantial improvement of approximately 20% over the leading baselines. Furthermore, RenalCLIP's pre-training imparted remarkable data efficiency; in the diagnostic classification task, it only needs 20% training data to achieve the peak performance of all baseline models even after they were fully fine-tuned on 100% of the data. Additionally, it achieved superior performance in report generation, image-text retrieval and zero-shot diagnosis tasks. Our findings establish that RenalCLIP provides a robust tool with the potential to enhance diagnostic accuracy, refine prognostic stratification, and personalize the management of patients with kidney cancer.

Ultrasound imaging has become the preferred imaging modality for early cancer screening due to its advantages of non-ionizing radiation, low cost, and real-time imaging capabilities. However, conventional ultrasound diagnosis heavily relies on physician expertise, presenting challenges of high subjectivity and low diagnostic efficiency. Vision-language models (VLMs) offer promising solutions for this issue, but existing general-purpose models demonstrate limited knowledge in ultrasound medical tasks, with poor generalization in multi-organ lesion recognition and low efficiency across multi-task diagnostics. To address these limitations, we propose EchoVLM, a vision-language model specifically designed for ultrasound medical imaging. The model employs a Mixture of Experts (MoE) architecture trained on data spanning seven anatomical regions. This design enables the model to perform multiple tasks, including ultrasound report generation, diagnosis and visual question-answering (VQA). The experimental results demonstrated that EchoVLM achieved significant improvements of 10.15 and 4.77 points in BLEU-1 scores and ROUGE-1 scores respectively compared to Qwen2-VL on the ultrasound report generation task. These findings suggest that EchoVLM has substantial potential to enhance diagnostic accuracy in ultrasound imaging, thereby providing a viable technical solution for future clinical applications. Source code and model weights are available at https://github.com/Asunatan/EchoVLM.

Clinical Question Answering (QA) systems enable doctors to quickly access patient information from electronic health records (EHRs). However, training these systems requires significant annotated data, which is limited due to the expertise needed and the privacy concerns associated with clinical data. This paper explores generating Clinical QA data using large language models (LLMs) in a zero-shot setting. We find that naive prompting often results in easy questions that do not reflect the complexity of clinical scenarios. To address this, we propose two prompting strategies: 1) instructing the model to generate questions that do not overlap with the input context, and 2) summarizing the input record using a predefined schema to scaffold question generation. Experiments on two Clinical QA datasets demonstrate that our method generates more challenging questions, significantly improving fine-tuning performance over baselines. We compare synthetic and gold data and find a gap between their training efficacy resulting from the quality of synthetically generated answers.

Recent medical vision-language models have shown promise on tasks such as VQA, report generation, and anomaly detection. However, most are adapted to structured adult imaging and underperform in fetal ultrasound, which poses challenges of multi-view image reasoning, numerous diseases, and image diversity. To bridge this gap, we introduce FetalMind, a medical AI system tailored to fetal ultrasound for both report generation and diagnosis. Guided by clinical workflow, we propose Salient Epistemic Disentanglement (SED), which injects an expert-curated bipartite graph into the model to decouple view-disease associations and to steer preference selection along clinically faithful steps via reinforcement learning. This design mitigates variability across diseases and heterogeneity across views, reducing learning bottlenecks while aligning the model's inference with obstetric practice. To train FetalMind at scale, we curate FetalSigma-1M dataset, the first large-scale fetal ultrasound report corpus, comprising 20K reports from twelve medical centers, addressing the scarcity of domain data. Extensive experiments show that FetalMind outperforms open- and closed-source baselines across all gestational stages, achieving +14% average gains and +61.2% higher accuracy on critical conditions while remaining efficient, stable, and scalable. Project Page: https://hexiao0275.github.io/FetalMind.

Medical image grounding aims to align natural language phrases with specific regions in medical images, serving as a foundational task for intelligent diagnosis, visual question answering (VQA), and automated report generation (MRG). However, existing research is constrained by limited modality coverage, coarse-grained annotations, and the absence of a unified, generalizable grounding framework. To address these challenges, we construct a large-scale medical grounding dataset Med-GLIP-5M comprising over 5.3 million region-level annotations across seven imaging modalities, covering diverse anatomical structures and pathological findings. The dataset supports both segmentation and grounding tasks with hierarchical region labels, ranging from organ-level boundaries to fine-grained lesions. Based on this foundation, we propose Med-GLIP, a modality-aware grounding framework trained on Med-GLIP-5M. Rather than relying on explicitly designed expert modules, Med-GLIP implicitly acquires hierarchical semantic understanding from diverse training data -- enabling it to recognize multi-granularity structures, such as distinguishing lungs from pneumonia lesions. Extensive experiments demonstrate that Med-GLIP consistently outperforms state-of-the-art baselines across multiple grounding benchmarks. Furthermore, integrating its spatial outputs into downstream tasks, including medical VQA and report generation, leads to substantial performance gains. Our dataset will be released soon.

Multi-modal interpretation of biomedical images opens up novel opportunities in biomedical image analysis. Conventional AI approaches typically rely on disjointed training, i.e., Large Language Models (LLMs) for clinical text generation and segmentation models for target extraction, which results in inflexible real-world deployment and a failure to leverage holistic biomedical information. To this end, we introduce UniBiomed, the first universal foundation model for grounded biomedical image interpretation. UniBiomed is based on a novel integration of Multi-modal Large Language Model (MLLM) and Segment Anything Model (SAM), which effectively unifies the generation of clinical texts and the segmentation of corresponding biomedical objects for grounded interpretation. In this way, UniBiomed is capable of tackling a wide range of biomedical tasks across ten diverse biomedical imaging modalities. To develop UniBiomed, we curate a large-scale dataset comprising over 27 million triplets of images, annotations, and text descriptions across ten imaging modalities. Extensive validation on 84 internal and external datasets demonstrated that UniBiomed achieves state-of-the-art performance in segmentation, disease recognition, region-aware diagnosis, visual question answering, and report generation. Moreover, unlike previous models that rely on clinical experts to pre-diagnose images and manually craft precise textual or visual prompts, UniBiomed can provide automated and end-to-end grounded interpretation for biomedical image analysis. This represents a novel paradigm shift in clinical workflows, which will significantly improve diagnostic efficiency. In summary, UniBiomed represents a novel breakthrough in biomedical AI, unlocking powerful grounded interpretation capabilities for more accurate and efficient biomedical image analysis.

Recent advances in generative models, including large language models (LLMs), vision language models (VLMs), and diffusion models, have accelerated the field of natural language and image processing in medicine and marked a significant paradigm shift in how biomedical models can be developed and deployed. While these models are highly adaptable to new tasks, scaling and evaluating their usage presents new challenges not addressed in previous frameworks. In particular, the ability of these models to produce useful outputs with little to no specialized training data ("zero-" or "few-shot" approaches), as well as the open-ended nature of their outputs, necessitate the development of new guidelines for robust reporting of clinical generative model research. In response to gaps in standards and best practices for the development of clinical AI tools identified by US Executive Order 141103 and several emerging national networks for clinical AI evaluation, we begin to formalize some of these guidelines by building on the original MI-CLAIM checklist. The new checklist, MI-CLAIM-GEN (Table 1), aims to address differences in training, evaluation, interpretability, and reproducibility of new generative models compared to non-generative ("predictive") AI models. This MI-CLAIM-GEN checklist also seeks to clarify cohort selection reporting with unstructured clinical data and adds additional items on alignment with ethical standards for clinical AI research.

The goal of automated summarization techniques (Paice, 1990; Kupiec et al, 1995) is to condense text by focusing on the most critical information. Generative large language models (LLMs) have shown to be robust summarizers, yet traditional metrics struggle to capture resulting performance (Goyal et al, 2022) in more powerful LLMs. In safety-critical domains such as medicine, more rigorous evaluation is required, especially given the potential for LLMs to omit important information in the resulting summary. We propose MED-OMIT, a new omission benchmark for medical summarization. Given a doctor-patient conversation and a generated summary, MED-OMIT categorizes the chat into a set of facts and identifies which are omitted from the summary. We further propose to determine fact importance by simulating the impact of each fact on a downstream clinical task: differential diagnosis (DDx) generation. MED-OMIT leverages LLM prompt-based approaches which categorize the importance of facts and cluster them as supporting or negating evidence to the diagnosis. We evaluate MED-OMIT on a publicly-released dataset of patient-doctor conversations and find that MED-OMIT captures omissions better than alternative metrics.

We present a labeled large-scale, high resolution chest x-ray dataset for the automated exploration of medical images along with their associated reports. This dataset includes more than 160,000 images obtained from 67,000 patients that were interpreted and reported by radiologists at Hospital San Juan Hospital (Spain) from 2009 to 2017, covering six different position views and additional information on image acquisition and patient demography. The reports were labeled with 174 different radiographic findings, 19 differential diagnoses and 104 anatomic locations organized as a hierarchical taxonomy and mapped onto standard Unified Medical Language System (UMLS) terminology. Of these reports, 27% were manually annotated by trained physicians and the remaining set was labeled using a supervised method based on a recurrent neural network with attention mechanisms. The labels generated were then validated in an independent test set achieving a 0.93 Micro-F1 score. To the best of our knowledge, this is one of the largest public chest x-ray database suitable for training supervised models concerning radiographs, and the first to contain radiographic reports in Spanish. The PadChest dataset can be downloaded from http://bimcv.cipf.es/bimcv-projects/padchest/.

Doctors and patients alike increasingly use Large Language Models (LLMs) to diagnose clinical cases. However, unlike domains such as math or coding, where correctness can be objectively defined by the final answer, medical diagnosis requires both the outcome and the reasoning process to be accurate. Currently, widely used medical benchmarks like MedQA and MMLU assess only accuracy in the final answer, overlooking the quality and faithfulness of the clinical reasoning process. To address this limitation, we introduce MedCaseReasoning, the first open-access dataset for evaluating LLMs on their ability to align with clinician-authored diagnostic reasoning. The dataset includes 14,489 diagnostic question-and-answer cases, each paired with detailed reasoning statements derived from open-access medical case reports. We evaluate state-of-the-art reasoning LLMs on MedCaseReasoning and find significant shortcomings in their diagnoses and reasoning: for instance, the top-performing open-source model, DeepSeek-R1, achieves only 48% 10-shot diagnostic accuracy and mentions only 64% of the clinician reasoning statements (recall). However, we demonstrate that fine-tuning LLMs on the reasoning traces derived from MedCaseReasoning significantly improves diagnostic accuracy and clinical reasoning recall by an average relative gain of 29% and 41%, respectively. The open-source dataset, code, and models are available at https://github.com/kevinwu23/Stanford-MedCaseReasoning.

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

We introduce RadEval, a unified, open-source framework for evaluating radiology texts. RadEval consolidates a diverse range of metrics, from classic n-gram overlap (BLEU, ROUGE) and contextual measures (BERTScore) to clinical concept-based scores (F1CheXbert, F1RadGraph, RaTEScore, SRR-BERT, TemporalEntityF1) and advanced LLM-based evaluators (GREEN). We refine and standardize implementations, extend GREEN to support multiple imaging modalities with a more lightweight model, and pretrain a domain-specific radiology encoder, demonstrating strong zero-shot retrieval performance. We also release a richly annotated expert dataset with over 450 clinically significant error labels and show how different metrics correlate with radiologist judgment. Finally, RadEval provides statistical testing tools and baseline model evaluations across multiple publicly available datasets, facilitating reproducibility and robust benchmarking in radiology report generation.

Generative modeling has experienced substantial progress in recent years, particularly in text-to-image and text-to-video synthesis. However, the medical field has not yet fully exploited the potential of large-scale foundational models for synthetic data generation. In this paper, we introduce GenerateCT, the first method for text-conditional computed tomography (CT) generation, addressing the limitations in 3D medical imaging research and making our entire framework open-source. GenerateCT consists of a pre-trained large language model, a transformer-based text-conditional 3D chest CT generation architecture, and a text-conditional spatial super-resolution diffusion model. We also propose CT-ViT, which efficiently compresses CT volumes while preserving auto-regressiveness in-depth, enabling the generation of 3D CT volumes with variable numbers of axial slices. Our experiments demonstrate that GenerateCT can produce realistic, high-resolution, and high-fidelity 3D chest CT volumes consistent with medical language text prompts. We further investigate the potential of GenerateCT by training a model using generated CT volumes for multi-abnormality classification of chest CT volumes. Our contributions provide a valuable foundation for future research in text-conditional 3D medical image generation and have the potential to accelerate advancements in medical imaging research. Our code, pre-trained models, and generated data are available at https://github.com/ibrahimethemhamamci/GenerateCT.

In this paper we present a hybrid method for the automatic detection of dermatological pathologies in medical reports. We use a large language model combined with medical ontologies to predict, given a first appointment or follow-up medical report, the pathology a person may suffer from. The results show that teaching the model to learn the type, severity and location on the body of a dermatological pathology, as well as in which order it has to learn these three features, significantly increases its accuracy. The article presents the demonstration of state-of-the-art results for classification of medical texts with a precision of 0.84, micro and macro F1-score of 0.82 and 0.75, and makes both the method and the data set used available to the community.

Daily progress notes are common types in the electronic health record (EHR) where healthcare providers document the patient's daily progress and treatment plans. The EHR is designed to document all the care provided to patients, but it also enables note bloat with extraneous information that distracts from the diagnoses and treatment plans. Applications of natural language processing (NLP) in the EHR is a growing field with the majority of methods in information extraction. Few tasks use NLP methods for downstream diagnostic decision support. We introduced the 2022 National NLP Clinical Challenge (N2C2) Track 3: Progress Note Understanding - Assessment and Plan Reasoning as one step towards a new suite of tasks. The Assessment and Plan Reasoning task focuses on the most critical components of progress notes, Assessment and Plan subsections where health problems and diagnoses are contained. The goal of the task was to develop and evaluate NLP systems that automatically predict causal relations between the overall status of the patient contained in the Assessment section and its relation to each component of the Plan section which contains the diagnoses and treatment plans. The goal of the task was to identify and prioritize diagnoses as the first steps in diagnostic decision support to find the most relevant information in long documents like daily progress notes. We present the results of 2022 n2c2 Track 3 and provide a description of the data, evaluation, participation and system performance.

With over 85 million CT scans performed annually in the United States, creating tumor-related reports is a challenging and time-consuming task for radiologists. To address this need, we present RadGPT, an Anatomy-Aware Vision-Language AI Agent for generating detailed reports from CT scans. RadGPT first segments tumors, including benign cysts and malignant tumors, and their surrounding anatomical structures, then transforms this information into both structured reports and narrative reports. These reports provide tumor size, shape, location, attenuation, volume, and interactions with surrounding blood vessels and organs. Extensive evaluation on unseen hospitals shows that RadGPT can produce accurate reports, with high sensitivity/specificity for small tumor (<2 cm) detection: 80/73% for liver tumors, 92/78% for kidney tumors, and 77/77% for pancreatic tumors. For large tumors, sensitivity ranges from 89% to 97%. The results significantly surpass the state-of-the-art in abdominal CT report generation. RadGPT generated reports for 17 public datasets. Through radiologist review and refinement, we have ensured the reports' accuracy, and created the first publicly available image-text 3D medical dataset, comprising over 1.8 million text tokens and 2.7 million images from 9,262 CT scans, including 2,947 tumor scans/reports of 8,562 tumor instances. Our reports can: (1) localize tumors in eight liver sub-segments and three pancreatic sub-segments annotated per-voxel; (2) determine pancreatic tumor stage (T1-T4) in 260 reports; and (3) present individual analyses of multiple tumors--rare in human-made reports. Importantly, 948 of the reports are for early-stage tumors.

An accurate differential diagnosis (DDx) is a cornerstone of medical care, often reached through an iterative process of interpretation that combines clinical history, physical examination, investigations and procedures. Interactive interfaces powered by Large Language Models (LLMs) present new opportunities to both assist and automate aspects of this process. In this study, we introduce an LLM optimized for diagnostic reasoning, and evaluate its ability to generate a DDx alone or as an aid to clinicians. 20 clinicians evaluated 302 challenging, real-world medical cases sourced from the New England Journal of Medicine (NEJM) case reports. Each case report was read by two clinicians, who were randomized to one of two assistive conditions: either assistance from search engines and standard medical resources, or LLM assistance in addition to these tools. All clinicians provided a baseline, unassisted DDx prior to using the respective assistive tools. Our LLM for DDx exhibited standalone performance that exceeded that of unassisted clinicians (top-10 accuracy 59.1% vs 33.6%, [p = 0.04]). Comparing the two assisted study arms, the DDx quality score was higher for clinicians assisted by our LLM (top-10 accuracy 51.7%) compared to clinicians without its assistance (36.1%) (McNemar's Test: 45.7, p < 0.01) and clinicians with search (44.4%) (4.75, p = 0.03). Further, clinicians assisted by our LLM arrived at more comprehensive differential lists than those without its assistance. Our study suggests that our LLM for DDx has potential to improve clinicians' diagnostic reasoning and accuracy in challenging cases, meriting further real-world evaluation for its ability to empower physicians and widen patients' access to specialist-level expertise.

Current medical retrieval benchmarks primarily emphasize lexical or shallow semantic similarity, overlooking the reasoning-intensive demands that are central to clinical decision-making. In practice, physicians often retrieve authoritative medical evidence to support diagnostic hypotheses. Such evidence typically aligns with an inferred diagnosis rather than the surface form of a patient's symptoms, leading to low lexical or semantic overlap between queries and relevant documents. To address this gap, we introduce R2MED, the first benchmark explicitly designed for reasoning-driven medical retrieval. It comprises 876 queries spanning three tasks: Q&A reference retrieval, clinical evidence retrieval, and clinical case retrieval. These tasks are drawn from five representative medical scenarios and twelve body systems, capturing the complexity and diversity of real-world medical information needs. We evaluate 15 widely-used retrieval systems on R2MED and find that even the best model achieves only 31.4 nDCG@10, demonstrating the benchmark's difficulty. Classical re-ranking and generation-augmented retrieval methods offer only modest improvements. Although large reasoning models improve performance via intermediate inference generation, the best results still peak at 41.4 nDCG@10. These findings underscore a substantial gap between current retrieval techniques and the reasoning demands of real clinical tasks. We release R2MED as a challenging benchmark to foster the development of next-generation medical retrieval systems with enhanced reasoning capabilities. Data and code are available at https://github.com/R2MED/R2MED

Radiology reports are critical for clinical decision-making but often lack a standardized format, limiting both human interpretability and machine learning (ML) applications. While large language models (LLMs) have shown strong capabilities in reformatting clinical text, their high computational requirements, lack of transparency, and data privacy concerns hinder practical deployment. To address these challenges, we explore lightweight encoder-decoder models (<300M parameters)-specifically T5 and BERT2BERT-for structuring radiology reports from the MIMIC-CXR and CheXpert Plus datasets. We benchmark these models against eight open-source LLMs (1B-70B), adapted using prefix prompting, in-context learning (ICL), and low-rank adaptation (LoRA) finetuning. Our best-performing lightweight model outperforms all LLMs adapted using prompt-based techniques on a human-annotated test set. While some LoRA-finetuned LLMs achieve modest gains over the lightweight model on the Findings section (BLEU 6.4%, ROUGE-L 4.8%, BERTScore 3.6%, F1-RadGraph 1.1%, GREEN 3.6%, and F1-SRR-BERT 4.3%), these improvements come at the cost of substantially greater computational resources. For example, LLaMA-3-70B incurred more than 400 times the inference time, cost, and carbon emissions compared to the lightweight model. These results underscore the potential of lightweight, task-specific models as sustainable and privacy-preserving solutions for structuring clinical text in resource-constrained healthcare settings.

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. We will publish our code and all the generated data in https://github.com/ritaranx/ClinGen.

Depression poses significant challenges to patients and healthcare organizations, necessitating efficient assessment methods. Existing paradigms typically focus on a patient-doctor way that overlooks multi-role interactions, such as family involvement in the evaluation and caregiving process. Moreover, current automatic depression detection (ADD) methods usually model depression detection as a classification or regression task, lacking interpretability for the decision-making process. To address these issues, we developed InterMind, a doctor-patient-family interactive depression assessment system empowered by large language models (LLMs). Our system enables patients and families to contribute descriptions, generates assistive diagnostic reports for doctors, and provides actionable insights, improving diagnostic precision and efficiency. To enhance LLMs' performance in psychological counseling and diagnostic interpretability, we integrate retrieval-augmented generation (RAG) and chain-of-thoughts (CoT) techniques for data augmentation, which mitigates the hallucination issue of LLMs in specific scenarios after instruction fine-tuning. Quantitative experiments and professional assessments by clinicians validate the effectiveness of our system.

Fact-checking requires retrieving evidence related to a claim under investigation. The task can be formulated as question generation based on a claim, followed by question answering. However, recent question generation approaches assume that the answer is known and typically contained in a passage given as input, whereas such passages are what is being sought when verifying a claim. In this paper, we present {\it Varifocal}, a method that generates questions based on different focal points within a given claim, i.e.\ different spans of the claim and its metadata, such as its source and date. Our method outperforms previous work on a fact-checking question generation dataset on a wide range of automatic evaluation metrics. These results are corroborated by our manual evaluation, which indicates that our method generates more relevant and informative questions. We further demonstrate the potential of focal points in generating sets of clarification questions for product descriptions.

Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.

Hypothesis generation is a fundamental step in scientific discovery, yet it is increasingly challenged by information overload and disciplinary fragmentation. Recent advances in Large Language Models (LLMs) have sparked growing interest in their potential to enhance and automate this process. This paper presents a comprehensive survey of hypothesis generation with LLMs by (i) reviewing existing methods, from simple prompting techniques to more complex frameworks, and proposing a taxonomy that categorizes these approaches; (ii) analyzing techniques for improving hypothesis quality, such as novelty boosting and structured reasoning; (iii) providing an overview of evaluation strategies; and (iv) discussing key challenges and future directions, including multimodal integration and human-AI collaboration. Our survey aims to serve as a reference for researchers exploring LLMs for hypothesis generation.

Retrieval-augmented generation (RAG) is a well-suited technique for retrieving privacy-sensitive Electronic Health Records (EHR). It can serve as a key module of the healthcare copilot, helping reduce misdiagnosis for healthcare practitioners and patients. However, the diagnostic accuracy and specificity of existing heuristic-based RAG models used in the medical domain are inadequate, particularly for diseases with similar manifestations. This paper proposes MedRAG, a RAG model enhanced by knowledge graph (KG)-elicited reasoning for the medical domain that retrieves diagnosis and treatment recommendations based on manifestations. MedRAG systematically constructs a comprehensive four-tier hierarchical diagnostic KG encompassing critical diagnostic differences of various diseases. These differences are dynamically integrated with similar EHRs retrieved from an EHR database, and reasoned within a large language model. This process enables more accurate and specific decision support, while also proactively providing follow-up questions to enhance personalized medical decision-making. MedRAG is evaluated on both a public dataset DDXPlus and a private chronic pain diagnostic dataset (CPDD) collected from Tan Tock Seng Hospital, and its performance is compared against various existing RAG methods. Experimental results show that, leveraging the information integration and relational abilities of the KG, our MedRAG provides more specific diagnostic insights and outperforms state-of-the-art models in reducing misdiagnosis rates. Our code will be available at https://github.com/SNOWTEAM2023/MedRAG

Safe and trustworthy use of Large Language Models (LLM) in the processing of healthcare documents and scientific papers could substantially help clinicians, scientists and policymakers in overcoming information overload and focusing on the most relevant information at a given moment. Retrieval Augmented Generation (RAG) is a promising method to leverage the potential of LLMs while enhancing the accuracy of their outcomes. This report assesses the potentials and shortcomings of such approaches in the automatic knowledge synthesis of different types of documents in the health domain. To this end, it describes: (1) an internally developed proof of concept pipeline that employs state-of-the-art practices to deliver safe and trustable analysis for healthcare documents and scientific papers called RAGEv (Retrieval Augmented Generation Evaluation); (2) a set of evaluation tools for LLM-based document retrieval and generation; (3) a benchmark dataset to verify the accuracy and veracity of the results called RAGEv-Bench. It concludes that careful implementations of RAG techniques could minimize most of the common problems in the use of LLMs for document processing in the health domain, obtaining very high scores both on short yes/no answers and long answers. There is a high potential for incorporating it into the day-to-day work of policy support tasks, but additional efforts are required to obtain a consistent and trustworthy tool.

Recent advances in generative medical models are constrained by modality-specific scenarios that hinder the integration of complementary evidence from imaging, pathology, and clinical notes. This fragmentation limits their evolution into foundation models that can learn and reason across the full spectrum of biomedical data. We propose MeDiM, the first medical discrete diffusion model that learns shared distributions across modalities without modality-specific components. MeDiM unifies multiple generative tasks: translating between images and text, and jointly producing image-report pairs across domains in response to prompts. Built on a discrete diffusion framework, MeDiM bridges vision and language representations through a shared probabilistic space. To enable unified and flexible medical generation, we employ a multimodal large language model (MLLM) as the diffusion backbone, leveraging its prior knowledge and cross-modal reasoning. Two key designs are introduced: (1) removing the causal attention mask for bidirectional context, and (2) injecting continuous timestep embeddings for diffusion awareness. Experiments demonstrate high-fidelity medical generation (FID 16.60 on MIMIC-CXR and FID 24.19 on PathGen) and accurate report generation (METEOR 0.2650 and 0.2580). Jointly generated image-report pairs further enhance downstream performance (plus6.43 percent BLEU-1, plus18.57 percent BLEU-2, plus31.58 percent BLEU-3, plus4.80 percent METEOR), showing that MeDiM supports coherent and clinically grounded multimodal outputs.

Current medical language models, adapted from large language models (LLMs), typically predict ICD code-based diagnosis from electronic health records (EHRs) because these labels are readily available. However, ICD codes do not capture the nuanced, context-rich reasoning clinicians use for diagnosis. Clinicians synthesize diverse patient data and reference clinical practice guidelines (CPGs) to make evidence-based decisions. This misalignment limits the clinical utility of existing models. We introduce GARMLE-G, a Generation-Augmented Retrieval framework that grounds medical language model outputs in authoritative CPGs. Unlike conventional Retrieval-Augmented Generation based approaches, GARMLE-G enables hallucination-free outputs by directly retrieving authoritative guideline content without relying on model-generated text. It (1) integrates LLM predictions with EHR data to create semantically rich queries, (2) retrieves relevant CPG knowledge snippets via embedding similarity, and (3) fuses guideline content with model output to generate clinically aligned recommendations. A prototype system for hypertension diagnosis was developed and evaluated on multiple metrics, demonstrating superior retrieval precision, semantic relevance, and clinical guideline adherence compared to RAG-based baselines, while maintaining a lightweight architecture suitable for localized healthcare deployment. This work provides a scalable, low-cost, and hallucination-free method for grounding medical language models in evidence-based clinical practice, with strong potential for broader clinical deployment.

Artificial intelligence holds great promise for expanding access to expert medical knowledge and reasoning. However, most evaluations of language models rely on static vignettes and multiple-choice questions that fail to reflect the complexity and nuance of evidence-based medicine in real-world settings. In clinical practice, physicians iteratively formulate and revise diagnostic hypotheses, adapting each subsequent question and test to what they've just learned, and weigh the evolving evidence before committing to a final diagnosis. To emulate this iterative process, we introduce the Sequential Diagnosis Benchmark, which transforms 304 diagnostically challenging New England Journal of Medicine clinicopathological conference (NEJM-CPC) cases into stepwise diagnostic encounters. A physician or AI begins with a short case abstract and must iteratively request additional details from a gatekeeper model that reveals findings only when explicitly queried. Performance is assessed not just by diagnostic accuracy but also by the cost of physician visits and tests performed. We also present the MAI Diagnostic Orchestrator (MAI-DxO), a model-agnostic orchestrator that simulates a panel of physicians, proposes likely differential diagnoses and strategically selects high-value, cost-effective tests. When paired with OpenAI's o3 model, MAI-DxO achieves 80% diagnostic accuracy--four times higher than the 20% average of generalist physicians. MAI-DxO also reduces diagnostic costs by 20% compared to physicians, and 70% compared to off-the-shelf o3. When configured for maximum accuracy, MAI-DxO achieves 85.5% accuracy. These performance gains with MAI-DxO generalize across models from the OpenAI, Gemini, Claude, Grok, DeepSeek, and Llama families. We highlight how AI systems, when guided to think iteratively and act judiciously, can advance diagnostic precision and cost-effectiveness in clinical care.

Automated diagnostic systems (ADS) have shown significant potential in the early detection of polyps during endoscopic examinations, thereby reducing the incidence of colorectal cancer. However, due to high annotation costs and strict privacy concerns, acquiring high-quality endoscopic images poses a considerable challenge in the development of ADS. Despite recent advancements in generating synthetic images for dataset expansion, existing endoscopic image generation algorithms failed to accurately generate the details of polyp boundary regions and typically required medical priors to specify plausible locations and shapes of polyps, which limited the realism and diversity of the generated images. To address these limitations, we present Polyp-Gen, the first full-automatic diffusion-based endoscopic image generation framework. Specifically, we devise a spatial-aware diffusion training scheme with a lesion-guided loss to enhance the structural context of polyp boundary regions. Moreover, to capture medical priors for the localization of potential polyp areas, we introduce a hierarchical retrieval-based sampling strategy to match similar fine-grained spatial features. In this way, our Polyp-Gen can generate realistic and diverse endoscopic images for building reliable ADS. Extensive experiments demonstrate the state-of-the-art generation quality, and the synthetic images can improve the downstream polyp detection task. Additionally, our Polyp-Gen has shown remarkable zero-shot generalizability on other datasets. The source code is available at https://github.com/CUHK-AIM-Group/Polyp-Gen.

Large Language Models (LLMs) have revolutionized natural language processing through their state of art reasoning capabilities. This paper explores the convergence of LLM reasoning techniques and feature generation for machine learning tasks. We examine four key reasoning approaches: Chain of Thought, Tree of Thoughts, Retrieval-Augmented Generation, and Thought Space Exploration. Our analysis reveals how these approaches can be used to identify effective feature generation rules without having to manually specify search spaces. The paper categorizes LLM-based feature generation methods across various domains including finance, healthcare, and text analytics. LLMs can extract key information from clinical notes and radiology reports in healthcare, by enabling more efficient data utilization. In finance, LLMs facilitate text generation, summarization, and entity extraction from complex documents. We analyze evaluation methodologies for assessing feature quality and downstream performance, with particular attention to OCTree's decision tree reasoning approach that provides language-based feedback for iterative improvements. Current challenges include hallucination, computational efficiency, and domain adaptation. As of March 2025, emerging approaches include inference-time compute scaling, reinforcement learning, and supervised fine-tuning with model distillation. Future directions point toward multimodal feature generation, self-improving systems, and neuro-symbolic approaches. This paper provides a detailed overview of an emerging field that promises to automate and enhance feature engineering through language model reasoning.

AI holds promise for transforming scientific processes, including hypothesis generation. Prior work on hypothesis generation can be broadly categorized into theory-driven and data-driven approaches. While both have proven effective in generating novel and plausible hypotheses, it remains an open question whether they can complement each other. To address this, we develop the first method that combines literature-based insights with data to perform LLM-powered hypothesis generation. We apply our method on five different datasets and demonstrate that integrating literature and data outperforms other baselines (8.97\% over few-shot, 15.75\% over literature-based alone, and 3.37\% over data-driven alone). Additionally, we conduct the first human evaluation to assess the utility of LLM-generated hypotheses in assisting human decision-making on two challenging tasks: deception detection and AI generated content detection. Our results show that human accuracy improves significantly by 7.44\% and 14.19\% on these tasks, respectively. These findings suggest that integrating literature-based and data-driven approaches provides a comprehensive and nuanced framework for hypothesis generation and could open new avenues for scientific inquiry.

Tumor documentation in Germany is largely done manually, requiring reading patient records and entering data into structured databases. Large language models (LLMs) could potentially enhance this process by improving efficiency and reliability. This evaluation tests eleven different open source LLMs with sizes ranging from 1-70 billion model parameters on three basic tasks of the tumor documentation process: identifying tumor diagnoses, assigning ICD-10 codes, and extracting the date of first diagnosis. For evaluating the LLMs on these tasks, a dataset of annotated text snippets based on anonymized doctors' notes from urology was prepared. Different prompting strategies were used to investigate the effect of the number of examples in few-shot prompting and to explore the capabilities of the LLMs in general. The models Llama 3.1 8B, Mistral 7B, and Mistral NeMo 12 B performed comparably well in the tasks. Models with less extensive training data or having fewer than 7 billion parameters showed notably lower performance, while larger models did not display performance gains. Examples from a different medical domain than urology could also improve the outcome in few-shot prompting, which demonstrates the ability of LLMs to handle tasks needed for tumor documentation. Open source LLMs show a strong potential for automating tumor documentation. Models from 7-12 billion parameters could offer an optimal balance between performance and resource efficiency. With tailored fine-tuning and well-designed prompting, these models might become important tools for clinical documentation in the future. The code for the evaluation is available from https://github.com/stefan-m-lenz/UroLlmEval. We also release the dataset as a new valuable resource that addresses the shortage of authentic and easily accessible benchmarks in German-language medical NLP.

Online medical consultation (OMC) restricts doctors to gathering patient information solely through inquiries, making the already complex sequential decision-making process of diagnosis even more challenging. Recently, the rapid advancement of large language models has demonstrated a significant potential to transform OMC. However, most studies have primarily focused on improving diagnostic accuracy under conditions of relatively sufficient information, while paying limited attention to the "inquiry" phase of the consultation process. This lack of focus has left the relationship between "inquiry" and "diagnosis" insufficiently explored. In this paper, we first extract real patient interaction strategies from authentic doctor-patient conversations and use these strategies to guide the training of a patient simulator that closely mirrors real-world behavior. By inputting medical records into our patient simulator to simulate patient responses, we conduct extensive experiments to explore the relationship between "inquiry" and "diagnosis" in the consultation process. Experimental results demonstrate that inquiry and diagnosis adhere to the Liebig's law: poor inquiry quality limits the effectiveness of diagnosis, regardless of diagnostic capability, and vice versa. Furthermore, the experiments reveal significant differences in the inquiry performance of various models. To investigate this phenomenon, we categorize the inquiry process into four types: (1) chief complaint inquiry; (2) specification of known symptoms; (3) inquiry about accompanying symptoms; and (4) gathering family or medical history. We analyze the distribution of inquiries across the four types for different models to explore the reasons behind their significant performance differences. We plan to open-source the weights and related code of our patient simulator at https://github.com/LIO-H-ZEN/PatientSimulator.

Visualizations play a crucial part in effective communication of concepts and information. Recent advances in reasoning and retrieval augmented generation have enabled Large Language Models (LLMs) to perform deep research and generate comprehensive reports. Despite its progress, existing deep research frameworks primarily focus on generating text-only content, leaving the automated generation of interleaved texts and visualizations underexplored. This novel task poses key challenges in designing informative visualizations and effectively integrating them with text reports. To address these challenges, we propose Formal Description of Visualization (FDV), a structured textual representation of charts that enables LLMs to learn from and generate diverse, high-quality visualizations. Building on this representation, we introduce Multimodal DeepResearcher, an agentic framework that decomposes the task into four stages: (1) researching, (2) exemplar report textualization, (3) planning, and (4) multimodal report generation. For the evaluation of generated multimodal reports, we develop MultimodalReportBench, which contains 100 diverse topics served as inputs along with 5 dedicated metrics. Extensive experiments across models and evaluation methods demonstrate the effectiveness of Multimodal DeepResearcher. Notably, utilizing the same Claude 3.7 Sonnet model, Multimodal DeepResearcher achieves an 82\% overall win rate over the baseline method.

Generating synthetic text addresses the challenge of data availability in privacy-sensitive domains such as healthcare. This study explores the applicability of synthetic data in real-world medical settings. We introduce MedSyn, a novel medical text generation framework that integrates large language models with a Medical Knowledge Graph (MKG). We use MKG to sample prior medical information for the prompt and generate synthetic clinical notes with GPT-4 and fine-tuned LLaMA models. We assess the benefit of synthetic data through application in the ICD code prediction task. Our research indicates that synthetic data can increase the classification accuracy of vital and challenging codes by up to 17.8% compared to settings without synthetic data. Furthermore, to provide new data for further research in the healthcare domain, we present the largest open-source synthetic dataset of clinical notes for the Russian language, comprising over 41k samples covering 219 ICD-10 codes.

Extracting structured clinical information from free-text radiology reports can enable the use of radiology report information for a variety of critical healthcare applications. In our work, we present RadGraph, a dataset of entities and relations in full-text chest X-ray radiology reports based on a novel information extraction schema we designed to structure radiology reports. We release a development dataset, which contains board-certified radiologist annotations for 500 radiology reports from the MIMIC-CXR dataset (14,579 entities and 10,889 relations), and a test dataset, which contains two independent sets of board-certified radiologist annotations for 100 radiology reports split equally across the MIMIC-CXR and CheXpert datasets. Using these datasets, we train and test a deep learning model, RadGraph Benchmark, that achieves a micro F1 of 0.82 and 0.73 on relation extraction on the MIMIC-CXR and CheXpert test sets respectively. Additionally, we release an inference dataset, which contains annotations automatically generated by RadGraph Benchmark across 220,763 MIMIC-CXR reports (around 6 million entities and 4 million relations) and 500 CheXpert reports (13,783 entities and 9,908 relations) with mappings to associated chest radiographs. Our freely available dataset can facilitate a wide range of research in medical natural language processing, as well as computer vision and multi-modal learning when linked to chest radiographs.

Counterfactual medical image generation effectively addresses data scarcity and enhances the interpretability of medical images. However, due to the complex and diverse pathological features of medical images and the imbalanced class distribution in medical data, generating high-quality and diverse medical images from limited data is significantly challenging. Additionally, to fully leverage the information in limited data, such as anatomical structure information and generate more structurally stable medical images while avoiding distortion or inconsistency. In this paper, in order to enhance the clinical relevance of generated data and improve the interpretability of the model, we propose a novel medical image generation framework, which generates independent pathological and structural features based on causal disentanglement and utilizes text-guided modeling of pathological features to regulate the generation of counterfactual images. First, we achieve feature separation through causal disentanglement and analyze the interactions between features. Here, we introduce group supervision to ensure the independence of pathological and identity features. Second, we leverage a diffusion model guided by pathological findings to model pathological features, enabling the generation of diverse counterfactual images. Meanwhile, we enhance accuracy by leveraging a large language model to extract lesion severity and location from medical reports. Additionally, we improve the performance of the latent diffusion model on long-tailed categories through initial noise optimization.

Interpreting electrocardiograms (ECGs) and generating comprehensive reports remain challenging tasks in cardiology, often requiring specialized expertise and significant time investment. To address these critical issues, we propose ECG-ReGen, a retrieval-based approach for ECG-to-text report generation and question answering. Our method leverages a self-supervised learning for the ECG encoder, enabling efficient similarity searches and report retrieval. By combining pre-training with dynamic retrieval and Large Language Model (LLM)-based refinement, ECG-ReGen effectively analyzes ECG data and answers related queries, with the potential of improving patient care. Experiments conducted on the PTB-XL and MIMIC-IV-ECG datasets demonstrate superior performance in both in-domain and cross-domain scenarios for report generation. Furthermore, our approach exhibits competitive performance on ECG-QA dataset compared to fully supervised methods when utilizing off-the-shelf LLMs for zero-shot question answering. This approach, effectively combining self-supervised encoder and LLMs, offers a scalable and efficient solution for accurate ECG interpretation, holding significant potential to enhance clinical decision-making.

Automated diagnosis prediction from medical images is a valuable resource to support clinical decision-making. However, such systems usually need to be trained on large amounts of annotated data, which often is scarce in the medical domain. Zero-shot methods address this challenge by allowing a flexible adaption to new settings with different clinical findings without relying on labeled data. Further, to integrate automated diagnosis in the clinical workflow, methods should be transparent and explainable, increasing medical professionals' trust and facilitating correctness verification. In this work, we introduce Xplainer, a novel framework for explainable zero-shot diagnosis in the clinical setting. Xplainer adapts the classification-by-description approach of contrastive vision-language models to the multi-label medical diagnosis task. Specifically, instead of directly predicting a diagnosis, we prompt the model to classify the existence of descriptive observations, which a radiologist would look for on an X-Ray scan, and use the descriptor probabilities to estimate the likelihood of a diagnosis. Our model is explainable by design, as the final diagnosis prediction is directly based on the prediction of the underlying descriptors. We evaluate Xplainer on two chest X-ray datasets, CheXpert and ChestX-ray14, and demonstrate its effectiveness in improving the performance and explainability of zero-shot diagnosis. Our results suggest that Xplainer provides a more detailed understanding of the decision-making process and can be a valuable tool for clinical diagnosis.

This paper explores the use of Large Language Models (LLMs) in the generation and evaluation of analytical reports derived from Earnings Calls (ECs). Addressing a current gap in research, we explore the generation of analytical reports with LLMs in a multi-agent framework, designing specialized agents that introduce diverse viewpoints and desirable topics of analysis into the report generation process. Through multiple analyses, we examine the alignment between generated and human-written reports and the impact of both individual and collective agents. Our findings suggest that the introduction of additional agents results in more insightful reports, although reports generated by human experts remain preferred in the majority of cases. Finally, we address the challenging issue of report evaluation, we examine the limitations and strengths of LLMs in assessing the quality of generated reports in different settings, revealing a significant correlation with human experts across multiple dimensions.

AI-driven models have demonstrated significant potential in automating radiology report generation for chest X-rays. However, there is no standardized benchmark for objectively evaluating their performance. To address this, we present ReXrank, https://rexrank.ai, a public leaderboard and challenge for assessing AI-powered radiology report generation. Our framework incorporates ReXGradient, the largest test dataset consisting of 10,000 studies, and three public datasets (MIMIC-CXR, IU-Xray, CheXpert Plus) for report generation assessment. ReXrank employs 8 evaluation metrics and separately assesses models capable of generating only findings sections and those providing both findings and impressions sections. By providing this standardized evaluation framework, ReXrank enables meaningful comparisons of model performance and offers crucial insights into their robustness across diverse clinical settings. Beyond its current focus on chest X-rays, ReXrank's framework sets the stage for comprehensive evaluation of automated reporting across the full spectrum of medical imaging.

Retrieval-augmented learning based on radiology reports has emerged as a promising direction to improve performance on long-tail medical imaging tasks, such as rare disease detection in chest X-rays. Most existing methods rely on comparing high-dimensional text embeddings from models like CLIP or CXR-BERT, which are often difficult to interpret, computationally expensive, and not well-aligned with the structured nature of medical knowledge. We propose a novel, ontology-driven alternative for comparing radiology report texts based on clinically grounded concepts from the Unified Medical Language System (UMLS). Our method extracts standardised medical entities from free-text reports using an enhanced pipeline built on RadGraph-XL and SapBERT. These entities are linked to UMLS concepts (CUIs), enabling a transparent, interpretable set-based representation of each report. We then define a task-adaptive similarity measure based on a modified and weighted version of the Tversky Index that accounts for synonymy, negation, and hierarchical relationships between medical entities. This allows efficient and semantically meaningful similarity comparisons between reports. We demonstrate that our approach outperforms state-of-the-art embedding-based retrieval methods in a radiograph classification task on MIMIC-CXR, particularly in long-tail settings. Additionally, we use our pipeline to generate ontology-backed disease labels for MIMIC-CXR, offering a valuable new resource for downstream learning tasks. Our work provides more explainable, reliable, and task-specific retrieval strategies in clinical AI systems, especially when interpretability and domain knowledge integration are essential. Our code is available at https://github.com/Felix-012/ontology-concept-distillation

This research introduces ScoreRAG, an approach to enhance the quality of automated news generation. Despite advancements in Natural Language Processing and large language models, current news generation methods often struggle with hallucinations, factual inconsistencies, and lack of domain-specific expertise when producing news articles. ScoreRAG addresses these challenges through a multi-stage framework combining retrieval-augmented generation, consistency relevance evaluation, and structured summarization. The system first retrieves relevant news documents from a vector database, maps them to complete news items, and assigns consistency relevance scores based on large language model evaluations. These documents are then reranked according to relevance, with low-quality items filtered out. The framework proceeds to generate graded summaries based on relevance scores, which guide the large language model in producing complete news articles following professional journalistic standards. Through this methodical approach, ScoreRAG aims to significantly improve the accuracy, coherence, informativeness, and professionalism of generated news articles while maintaining stability and consistency throughout the generation process. The code and demo are available at: https://github.com/peiyun2260/ScoreRAG.

In this study, we aimed to determine if fine-tuned large language models (LLMs) can generate accurate, personalized impressions for whole-body PET reports. Twelve language models were trained on a corpus of PET reports using the teacher-forcing algorithm, with the report findings as input and the clinical impressions as reference. An extra input token encodes the reading physician's identity, allowing models to learn physician-specific reporting styles. Our corpus comprised 37,370 retrospective PET reports collected from our institution between 2010 and 2022. To identify the best LLM, 30 evaluation metrics were benchmarked against quality scores from two nuclear medicine (NM) physicians, with the most aligned metrics selecting the model for expert evaluation. In a subset of data, model-generated impressions and original clinical impressions were assessed by three NM physicians according to 6 quality dimensions (3-point scale) and an overall utility score (5-point scale). Each physician reviewed 12 of their own reports and 12 reports from other physicians. Bootstrap resampling was used for statistical analysis. Of all evaluation metrics, domain-adapted BARTScore and PEGASUSScore showed the highest Spearman's rank correlations (0.568 and 0.563) with physician preferences. Based on these metrics, the fine-tuned PEGASUS model was selected as the top LLM. When physicians reviewed PEGASUS-generated impressions in their own style, 89% were considered clinically acceptable, with a mean utility score of 4.08 out of 5. Physicians rated these personalized impressions as comparable in overall utility to the impressions dictated by other physicians (4.03, P=0.41). In conclusion, personalized impressions generated by PEGASUS were clinically useful, highlighting its potential to expedite PET reporting.

Medical coding is essential for standardizing clinical data and communication but is often time-consuming and prone to errors. Traditional Natural Language Processing (NLP) methods struggle with automating coding due to the large label space, lengthy text inputs, and the absence of supporting evidence annotations that justify code selection. Recent advancements in Generative Artificial Intelligence (AI) offer promising solutions to these challenges. In this work, we introduce MedCodER, a Generative AI framework for automatic medical coding that leverages extraction, retrieval, and re-ranking techniques as core components. MedCodER achieves a micro-F1 score of 0.60 on International Classification of Diseases (ICD) code prediction, significantly outperforming state-of-the-art methods. Additionally, we present a new dataset containing medical records annotated with disease diagnoses, ICD codes, and supporting evidence texts (https://doi.org/10.5281/zenodo.13308316). Ablation tests confirm that MedCodER's performance depends on the integration of each of its aforementioned components, as performance declines when these components are evaluated in isolation.

Large language models, particularly GPT-3, are able to produce high quality summaries of general domain news articles in few- and zero-shot settings. However, it is unclear if such models are similarly capable in more specialized, high-stakes domains such as biomedicine. In this paper, we enlist domain experts (individuals with medical training) to evaluate summaries of biomedical articles generated by GPT-3, given zero supervision. We consider both single- and multi-document settings. In the former, GPT-3 is tasked with generating regular and plain-language summaries of articles describing randomized controlled trials; in the latter, we assess the degree to which GPT-3 is able to synthesize evidence reported across a collection of articles. We design an annotation scheme for evaluating model outputs, with an emphasis on assessing the factual accuracy of generated summaries. We find that while GPT-3 is able to summarize and simplify single biomedical articles faithfully, it struggles to provide accurate aggregations of findings over multiple documents. We release all data and annotations used in this work.

Tumor synthesis can generate examples that AI often misses or over-detects, improving AI performance by training on these challenging cases. However, existing synthesis methods, which are typically unconditional -- generating images from random variables -- or conditioned only by tumor shapes, lack controllability over specific tumor characteristics such as texture, heterogeneity, boundaries, and pathology type. As a result, the generated tumors may be overly similar or duplicates of existing training data, failing to effectively address AI's weaknesses. We propose a new text-driven tumor synthesis approach, termed TextoMorph, that provides textual control over tumor characteristics. This is particularly beneficial for examples that confuse the AI the most, such as early tumor detection (increasing Sensitivity by +8.5%), tumor segmentation for precise radiotherapy (increasing DSC by +6.3%), and classification between benign and malignant tumors (improving Sensitivity by +8.2%). By incorporating text mined from radiology reports into the synthesis process, we increase the variability and controllability of the synthetic tumors to target AI's failure cases more precisely. Moreover, TextoMorph uses contrastive learning across different texts and CT scans, significantly reducing dependence on scarce image-report pairs (only 141 pairs used in this study) by leveraging a large corpus of 34,035 radiology reports. Finally, we have developed rigorous tests to evaluate synthetic tumors, including Text-Driven Visual Turing Test and Radiomics Pattern Analysis, showing that our synthetic tumors is realistic and diverse in texture, heterogeneity, boundaries, and pathology.

Extraction of relevant pathological terms from radiology reports is important for correct image label generation and disease population studies. In this letter, we compare the performance of some known application program interface (APIs) for the task of thoracic abnormality extraction from radiology reports. We explored several medical domain specific annotation tools like Medical Text Indexer(MTI) with Non-MEDLINE and Mesh On Demand(MOD) options and generic Natural Language Understanding (NLU) API provided by the IBM cloud. Our results show that although MTI and MOD are intended for extracting medical terms, their performance is worst compared to generic extraction API like IBM NLU. Finally, we trained a DNN-based Named Entity Recognition (NER) model to extract the key concept words from radiology reports. Our model outperforms the medical specific and generic API performance by a large margin. Our results demonstrate the inadequacy of generic APIs for pathology extraction task and establish the importance of domain specific model training for improved results. We hope that these results motivate the research community to release larger de-identified radiology reports corpus for building high accuracy machine learning models for the important task of pathology extraction.

Background: Electronic Health Records hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Existing approaches focus mostly on structured data and a subset of single-domain outcomes. We explore how temporal modelling of patients from free text and structured data, using deep generative transformers can be used to forecast a wide range of future disorders, substances, procedures or findings. Methods: We present Foresight, a novel transformer-based pipeline that uses named entity recognition and linking tools to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, substances, procedures and findings. We processed the entire free-text portion from three different hospital datasets totalling 811336 patients covering both physical and mental health. Findings: On tests in two UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 0.68, 0.76 and 0.88 was achieved for forecasting the next disorder in a patient timeline, while precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by five clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. As a generative model, it can forecast follow-on biomedical concepts for as many steps as required. Interpretation: Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials and clinical research to study the progression of disorders, simulate interventions and counterfactuals, and educational purposes.

Clinical diagnosis is a highly specialized discipline requiring both domain expertise and strict adherence to rigorous guidelines. While current AI-driven medical research predominantly focuses on knowledge graphs or natural text pretraining paradigms to incorporate medical knowledge, these approaches primarily rely on implicitly encoded knowledge within model parameters, neglecting task-specific knowledge required by diverse downstream tasks. To address this limitation, we propose Retrieval-Augmented Diagnosis (RAD), a novel framework that explicitly injects external knowledge into multimodal models directly on downstream tasks. Specifically, RAD operates through three key mechanisms: retrieval and refinement of disease-centered knowledge from multiple medical sources, a guideline-enhanced contrastive loss that constrains the latent distance between multi-modal features and guideline knowledge, and the dual transformer decoder that employs guidelines as queries to steer cross-modal fusion, aligning the models with clinical diagnostic workflows from guideline acquisition to feature extraction and decision-making. Moreover, recognizing the lack of quantitative evaluation of interpretability for multimodal diagnostic models, we introduce a set of criteria to assess the interpretability from both image and text perspectives. Extensive evaluations across four datasets with different anatomies demonstrate RAD's generalizability, achieving state-of-the-art performance. Furthermore, RAD enables the model to concentrate more precisely on abnormal regions and critical indicators, ensuring evidence-based, trustworthy diagnosis. Our code is available at https://github.com/tdlhl/RAD.

Vision-language pre-training for chest X-rays has made significant strides, primarily by utilizing paired radiographs and radiology reports. However, existing approaches often face challenges in encoding medical knowledge effectively. While radiology reports provide insights into the current disease manifestation, medical definitions (as used by contemporary methods) tend to be overly abstract, creating a gap in knowledge. To address this, we propose DeViDe, a novel transformer-based method that leverages radiographic descriptions from the open web. These descriptions outline general visual characteristics of diseases in radiographs, and when combined with abstract definitions and radiology reports, provide a holistic snapshot of knowledge. DeViDe incorporates three key features for knowledge-augmented vision language alignment: First, a large-language model-based augmentation is employed to homogenise medical knowledge from diverse sources. Second, this knowledge is aligned with image information at various levels of granularity. Third, a novel projection layer is proposed to handle the complexity of aligning each image with multiple descriptions arising in a multi-label setting. In zero-shot settings, DeViDe performs comparably to fully supervised models on external datasets and achieves state-of-the-art results on three large-scale datasets. Additionally, fine-tuning DeViDe on four downstream tasks and six segmentation tasks showcases its superior performance across data from diverse distributions.

Electronic health records contain an enormous amount of valuable information, but many are recorded in free text. Information extraction is the strategy to transform the sequence of characters into structured data, which can be employed for secondary analysis. However, the traditional information extraction components, such as named entity recognition and relation extraction, require annotated data to optimize the model parameters, which has become one of the major bottlenecks in building information extraction systems. With the large language models achieving good performances on various downstream NLP tasks without parameter tuning, it becomes possible to use large language models for zero-shot information extraction. In this study, we aim to explore whether the most popular large language model, ChatGPT, can extract useful information from the radiological reports. We first design the prompt template for the interested information in the CT reports. Then, we generate the prompts by combining the prompt template with the CT reports as the inputs of ChatGPT to obtain the responses. A post-processing module is developed to transform the responses into structured extraction results. We conducted the experiments with 847 CT reports collected from Peking University Cancer Hospital. The experimental results indicate that ChatGPT can achieve competitive performances for some extraction tasks compared with the baseline information extraction system, but some limitations need to be further improved.

The differential diagnosis of neurodegenerative dementias is a challenging clinical task, mainly because of the overlap in symptom presentation and the similarity of patterns observed in structural neuroimaging. To improve diagnostic efficiency and accuracy, deep learning-based methods such as Convolutional Neural Networks and Vision Transformers have been proposed for the automatic classification of brain MRIs. However, despite their strong predictive performance, these models find limited clinical utility due to their opaque decision making. In this work, we propose a framework that integrates two core components to enhance diagnostic transparency. First, we introduce a modular pipeline for converting 3D T1-weighted brain MRIs into textual radiology reports. Second, we explore the potential of modern Large Language Models (LLMs) to assist clinicians in the differential diagnosis between Frontotemporal dementia subtypes, Alzheimer's disease, and normal aging based on the generated reports. To bridge the gap between predictive accuracy and explainability, we employ reinforcement learning to incentivize diagnostic reasoning in LLMs. Without requiring supervised reasoning traces or distillation from larger models, our approach enables the emergence of structured diagnostic rationales grounded in neuroimaging findings. Unlike post-hoc explainability methods that retrospectively justify model decisions, our framework generates diagnostic rationales as part of the inference process-producing causally grounded explanations that inform and guide the model's decision-making process. In doing so, our framework matches the diagnostic performance of existing deep learning methods while offering rationales that support its diagnostic conclusions.

Scientific news reports serve as a bridge, adeptly translating complex research articles into reports that resonate with the broader public. The automated generation of such narratives enhances the accessibility of scholarly insights. In this paper, we present a new corpus to facilitate this paradigm development. Our corpus comprises a parallel compilation of academic publications and their corresponding scientific news reports across nine disciplines. To demonstrate the utility and reliability of our dataset, we conduct an extensive analysis, highlighting the divergences in readability and brevity between scientific news narratives and academic manuscripts. We benchmark our dataset employing state-of-the-art text generation models. The evaluation process involves both automatic and human evaluation, which lays the groundwork for future explorations into the automated generation of scientific news reports. The dataset and code related to this work are available at https://dongqi.me/projects/SciNews.

Conditional story generation is significant in human-machine interaction, particularly in producing stories with complex plots. While Large language models (LLMs) perform well on multiple NLP tasks, including story generation, it is challenging to generate stories with both complex and creative plots. Existing methods often rely on detailed prompts to guide LLMs to meet target conditions, which inadvertently restrict the creative potential of the generated stories. We argue that leveraging information from exemplary human-written stories facilitates generating more diverse plotlines. Delving deeper into story details helps build complex and credible plots. In this paper, we propose a retrieval-auGmented stoRy generation framework with a fOrest of eVidEnce (GROVE) to enhance stories' complexity. We build a retrieval repository for target conditions to produce few-shot examples to prompt LLMs. Additionally, we design an ``asking-why'' prompting scheme that extracts a forest of evidence, providing compensation for the ambiguities that may occur in the generated story. This iterative process uncovers underlying story backgrounds. Finally, we select the most fitting chains of evidence from the evidence forest and integrate them into the generated story, thereby enhancing the narrative's complexity and credibility. Experimental results and numerous examples verify the effectiveness of our method.

We introduce a radiology-focused visual language model designed to generate radiology reports from chest X-rays. Building on previous findings that large language models (LLMs) can acquire multimodal capabilities when aligned with pretrained vision encoders, we demonstrate similar potential with chest X-ray images. This integration enhances the ability of model to understand and describe chest X-ray images. Our model combines an image encoder with a fine-tuned LLM based on the Vicuna-7B architecture, enabling it to generate different sections of a radiology report with notable accuracy. The training process involves a two-stage approach: (i) initial alignment of chest X-ray features with the LLM (ii) followed by fine-tuning for radiology report generation.

To assess the effectiveness of any medical intervention, researchers must conduct a time-intensive and highly manual literature review. NLP systems can help to automate or assist in parts of this expensive process. In support of this goal, we release MS^2 (Multi-Document Summarization of Medical Studies), a dataset of over 470k documents and 20k summaries derived from the scientific literature. This dataset facilitates the development of systems that can assess and aggregate contradictory evidence across multiple studies, and is the first large-scale, publicly available multi-document summarization dataset in the biomedical domain. We experiment with a summarization system based on BART, with promising early results. We formulate our summarization inputs and targets in both free text and structured forms and modify a recently proposed metric to assess the quality of our system's generated summaries. Data and models are available at https://github.com/allenai/ms2

The discharge summary is a one of critical documents in the patient journey, encompassing all events experienced during hospitalization, including multiple visits, medications, tests, surgery/procedures, and admissions/discharge. Providing a summary of the patient's progress is crucial, as it significantly influences future care and planning. Consequently, clinicians face the laborious and resource-intensive task of manually collecting, organizing, and combining all the necessary data for a discharge summary. Therefore, we propose "NOTE", which stands for "Notable generation Of patient Text summaries through an Efficient approach based on direct preference optimization". NOTE is based on Medical Information Mart for Intensive Care- III dataset and summarizes a single hospitalization of a patient. Patient events are sequentially combined and used to generate a discharge summary for each hospitalization. In the present circumstances, large language models' application programming interfaces (LLMs' APIs) are widely available, but importing and exporting medical data presents significant challenges due to privacy protection policies in healthcare institutions. Moreover, to ensure optimal performance, it is essential to implement a lightweight model for internal server or program within the hospital. Therefore, we utilized DPO and parameter efficient fine tuning (PEFT) techniques to apply a fine-tuning method that guarantees superior performance. To demonstrate the practical application of the developed NOTE, we provide a webpage-based demonstration software. In the future, we will aim to deploy the software available for actual use by clinicians in hospital. NOTE can be utilized to generate various summaries not only discharge summaries but also throughout a patient's journey, thereby alleviating the labor-intensive workload of clinicians and aiming for increased efficiency.