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Dec 10

The Imaging Database for Epilepsy And Surgery (IDEAS)

Magnetic resonance imaging (MRI) is a crucial tool to identify brain abnormalities in a wide range of neurological disorders. In focal epilepsy MRI is used to identify structural cerebral abnormalities. For covert lesions, machine learning and artificial intelligence algorithms may improve lesion detection if abnormalities are not evident on visual inspection. The success of this approach depends on the volume and quality of training data. Herein, we release an open-source dataset of preprocessed MRI scans from 442 individuals with drug-refractory focal epilepsy who had neurosurgical resections, and detailed demographic information. The MRI scan data includes the preoperative 3D T1 and where available 3D FLAIR, as well as a manually inspected complete surface reconstruction and volumetric parcellations. Demographic information includes age, sex, age of onset of epilepsy, location of surgery, histopathology of resected specimen, occurrence and frequency of focal seizures with and without impairment of awareness, focal to bilateral tonic-clonic seizures, number of anti-seizure medications (ASMs) at time of surgery, and a total of 1764 patient years of post-surgical follow up. Crucially, we also include resection masks delineated from post-surgical imaging. To demonstrate the veracity of our data, we successfully replicated previous studies showing long-term outcomes of seizure freedom in the range of around 50%. Our imaging data replicates findings of group level atrophy in patients compared to controls. Resection locations in the cohort were predominantly in the temporal and frontal lobes. We envisage our dataset, shared openly with the community, will catalyse the development and application of computational methods in clinical neurology.

  • 15 authors
·
Jun 10, 2024

Reasoning with Language Model is Planning with World Model

Large language models (LLMs) have shown remarkable reasoning capabilities, especially when prompted to generate intermediate reasoning steps (e.g., Chain-of-Thought, CoT). However, LLMs can still struggle with problems that are easy for humans, such as generating action plans for executing tasks in a given environment, or performing complex math, logical, and commonsense reasoning. The deficiency stems from the key fact that LLMs lack an internal world model to predict the world state (e.g., environment status, intermediate variable values) and simulate long-term outcomes of actions. This prevents LLMs from performing deliberate planning akin to human brains, which involves exploring alternative reasoning paths, anticipating future states and rewards, and iteratively refining existing reasoning steps. To overcome the limitations, we propose a new LLM reasoning framework, Reasoning via Planning (RAP). RAP repurposes the LLM as both a world model and a reasoning agent, and incorporates a principled planning algorithm (based on Monto Carlo Tree Search) for strategic exploration in the vast reasoning space. During reasoning, the LLM (as agent) incrementally builds a reasoning tree under the guidance of the LLM (as world model) and task-specific rewards, and obtains a high-reward reasoning path efficiently with a proper balance between exploration vs. exploitation. We apply RAP to a variety of challenging reasoning problems including plan generation, math reasoning, and logical inference. Empirical results on these tasks demonstrate the superiority of RAP over various strong baselines, including CoT and least-to-most prompting with self-consistency. RAP on LLAMA-33B surpasses CoT on GPT-4 with 33% relative improvement in a plan generation setting.

  • 7 authors
·
May 24, 2023 2

DVIS: Decoupled Video Instance Segmentation Framework

Video instance segmentation (VIS) is a critical task with diverse applications, including autonomous driving and video editing. Existing methods often underperform on complex and long videos in real world, primarily due to two factors. Firstly, offline methods are limited by the tightly-coupled modeling paradigm, which treats all frames equally and disregards the interdependencies between adjacent frames. Consequently, this leads to the introduction of excessive noise during long-term temporal alignment. Secondly, online methods suffer from inadequate utilization of temporal information. To tackle these challenges, we propose a decoupling strategy for VIS by dividing it into three independent sub-tasks: segmentation, tracking, and refinement. The efficacy of the decoupling strategy relies on two crucial elements: 1) attaining precise long-term alignment outcomes via frame-by-frame association during tracking, and 2) the effective utilization of temporal information predicated on the aforementioned accurate alignment outcomes during refinement. We introduce a novel referring tracker and temporal refiner to construct the Decoupled VIS framework (DVIS). DVIS achieves new SOTA performance in both VIS and VPS, surpassing the current SOTA methods by 7.3 AP and 9.6 VPQ on the OVIS and VIPSeg datasets, which are the most challenging and realistic benchmarks. Moreover, thanks to the decoupling strategy, the referring tracker and temporal refiner are super light-weight (only 1.69\% of the segmenter FLOPs), allowing for efficient training and inference on a single GPU with 11G memory. The code is available at https://github.com/zhang-tao-whu/DVIS{https://github.com/zhang-tao-whu/DVIS}.

  • 7 authors
·
Jun 6, 2023

Model-free Approach to Evaluate a Censored Intermediate Outcome as a Surrogate for Overall Survival

Clinical trials or studies oftentimes require long-term and/or costly follow-up of participants to evaluate a novel treatment/drug/vaccine. There has been increasing interest in the past few decades in using short-term surrogate outcomes as a replacement of the primary outcome i.e., in using the surrogate outcome, which can potentially be observed sooner, to make inference about the treatment effect on the long-term primary outcome. Very few of the available statistical methods to evaluate a surrogate are applicable to settings where both the surrogate and the primary outcome are time-to-event outcomes subject to censoring. Methods that can handle this setting tend to require parametric assumptions or be limited to assessing only the restricted mean survival time. In this paper, we propose a non-parametric approach to evaluate a censored surrogate outcome, such as time to progression, when the primary outcome is also a censored time-to-event outcome, such as time to death, and the treatment effect of interest is the difference in overall survival. Specifically, we define the proportion of the treatment effect on the primary outcome that is explained (PTE) by the censored surrogate outcome in this context, and estimate this proportion by defining and deriving an optimal transformation of the surrogate information. Our approach provides the added advantage of relaxed assumptions to guarantee that the true PTE is within (0,1), along with being model-free. Finite sample performance of our estimators are illustrated via extensive simulation studies and a real data application examining progression-free survival as a surrogate for overall survival for patients with metastatic colorectal cancer.

  • 4 authors
·
Dec 18, 2024

ReSurgSAM2: Referring Segment Anything in Surgical Video via Credible Long-term Tracking

Surgical scene segmentation is critical in computer-assisted surgery and is vital for enhancing surgical quality and patient outcomes. Recently, referring surgical segmentation is emerging, given its advantage of providing surgeons with an interactive experience to segment the target object. However, existing methods are limited by low efficiency and short-term tracking, hindering their applicability in complex real-world surgical scenarios. In this paper, we introduce ReSurgSAM2, a two-stage surgical referring segmentation framework that leverages Segment Anything Model 2 to perform text-referred target detection, followed by tracking with reliable initial frame identification and diversity-driven long-term memory. For the detection stage, we propose a cross-modal spatial-temporal Mamba to generate precise detection and segmentation results. Based on these results, our credible initial frame selection strategy identifies the reliable frame for the subsequent tracking. Upon selecting the initial frame, our method transitions to the tracking stage, where it incorporates a diversity-driven memory mechanism that maintains a credible and diverse memory bank, ensuring consistent long-term tracking. Extensive experiments demonstrate that ReSurgSAM2 achieves substantial improvements in accuracy and efficiency compared to existing methods, operating in real-time at 61.2 FPS. Our code and datasets will be available at https://github.com/jinlab-imvr/ReSurgSAM2.

  • 7 authors
·
May 13 2

Interactive Recommendation Agent with Active User Commands

Traditional recommender systems rely on passive feedback mechanisms that limit users to simple choices such as like and dislike. However, these coarse-grained signals fail to capture users' nuanced behavior motivations and intentions. In turn, current systems cannot also distinguish which specific item attributes drive user satisfaction or dissatisfaction, resulting in inaccurate preference modeling. These fundamental limitations create a persistent gap between user intentions and system interpretations, ultimately undermining user satisfaction and harming system effectiveness. To address these limitations, we introduce the Interactive Recommendation Feed (IRF), a pioneering paradigm that enables natural language commands within mainstream recommendation feeds. Unlike traditional systems that confine users to passive implicit behavioral influence, IRF empowers active explicit control over recommendation policies through real-time linguistic commands. To support this paradigm, we develop RecBot, a dual-agent architecture where a Parser Agent transforms linguistic expressions into structured preferences and a Planner Agent dynamically orchestrates adaptive tool chains for on-the-fly policy adjustment. To enable practical deployment, we employ simulation-augmented knowledge distillation to achieve efficient performance while maintaining strong reasoning capabilities. Through extensive offline and long-term online experiments, RecBot shows significant improvements in both user satisfaction and business outcomes.

  • 15 authors
·
Sep 25 2

Spatial Reasoning and Planning for Deep Embodied Agents

Humans can perform complex tasks with long-term objectives by planning, reasoning, and forecasting outcomes of actions. For embodied agents to achieve similar capabilities, they must gain knowledge of the environment transferable to novel scenarios with a limited budget of additional trial and error. Learning-based approaches, such as deep RL, can discover and take advantage of inherent regularities and characteristics of the application domain from data, and continuously improve their performances, however at a cost of large amounts of training data. This thesis explores the development of data-driven techniques for spatial reasoning and planning tasks, focusing on enhancing learning efficiency, interpretability, and transferability across novel scenarios. Four key contributions are made. 1) CALVIN, a differential planner that learns interpretable models of the world for long-term planning. It successfully navigated partially observable 3D environments, such as mazes and indoor rooms, by learning the rewards and state transitions from expert demonstrations. 2) SOAP, an RL algorithm that discovers options unsupervised for long-horizon tasks. Options segment a task into subtasks and enable consistent execution of the subtask. SOAP showed robust performances on history-conditional corridor tasks as well as classical benchmarks such as Atari. 3) LangProp, a code optimisation framework using LLMs to solve embodied agent problems that require reasoning by treating code as learnable policies. The framework successfully generated interpretable code with comparable or superior performance to human-written experts in the CARLA autonomous driving benchmark. 4) Voggite, an embodied agent with a vision-to-action transformer backend that solves complex tasks in Minecraft. It achieved third place in the MineRL BASALT Competition by identifying action triggers to segment tasks into multiple stages.

  • 1 authors
·
Sep 28, 2024

Stabilizing Long-term Multi-turn Reinforcement Learning with Gated Rewards

Reward sparsity in long-horizon reinforcement learning (RL) tasks remains a significant challenge, while existing outcome-based reward shaping struggles to define meaningful immediate rewards without introducing bias or requiring explicit task decomposition. Alternatively, verification-based reward shaping uses stepwise critics, but misalignment between immediate rewards and long-term objectives can lead to reward hacking and suboptimal policies. In this work, we address this problem in the context of software engineering (SWE) tasks, where multi-turn reasoning and rule-based verification are critical. We introduce the SWE-oriented RL Framework, a unified system supporting multi-turn interaction, docker-based execution, and customizable reward functions. Additionally, we propose Gated Reward Accumulation (G-RA), a novel method that accumulates immediate rewards only when high-level (long-term) rewards meet a predefined threshold, ensuring stable RL optimization. Experiments on SWE-bench Verified and kBench demonstrate that G-RA leads to an increase in completion rates (47.6\% \rightarrow 93.8\% and 22.0\% \rightarrow 86.0\%) and modification rates (19.6\% \rightarrow 23.8\% and 12.0\% \rightarrow 42.0\%), while avoiding policy degradation caused by reward misalignment. Our findings highlight the importance of balanced reward accumulation in long-horizon RL and provide a practical solution.

  • 5 authors
·
Aug 14

VerIPO: Cultivating Long Reasoning in Video-LLMs via Verifier-Gudied Iterative Policy Optimization

Applying Reinforcement Learning (RL) to Video Large Language Models (Video-LLMs) shows significant promise for complex video reasoning. However, popular Reinforcement Fine-Tuning (RFT) methods, such as outcome-based Group Relative Policy Optimization (GRPO), are limited by data preparation bottlenecks (e.g., noise or high cost) and exhibit unstable improvements in the quality of long chain-of-thoughts (CoTs) and downstream performance.To address these limitations, we propose VerIPO, a Verifier-guided Iterative Policy Optimization method designed to gradually improve video LLMs' capacity for generating deep, long-term reasoning chains. The core component is Rollout-Aware Verifier, positioned between the GRPO and Direct Preference Optimization (DPO) training phases to form the GRPO-Verifier-DPO training loop. This verifier leverages small LLMs as a judge to assess the reasoning logic of rollouts, enabling the construction of high-quality contrastive data, including reflective and contextually consistent CoTs. These curated preference samples drive the efficient DPO stage (7x faster than GRPO), leading to marked improvements in reasoning chain quality, especially in terms of length and contextual consistency. This training loop benefits from GRPO's expansive search and DPO's targeted optimization. Experimental results demonstrate: 1) Significantly faster and more effective optimization compared to standard GRPO variants, yielding superior performance; 2) Our trained models exceed the direct inference of large-scale instruction-tuned Video-LLMs, producing long and contextually consistent CoTs on diverse video reasoning tasks; and 3) Our model with one iteration outperforms powerful LMMs (e.g., Kimi-VL) and long reasoning models (e.g., Video-R1), highlighting its effectiveness and stability.

  • 8 authors
·
May 25 6

Enhancing End Stage Renal Disease Outcome Prediction: A Multi-Sourced Data-Driven Approach

Objective: To improve prediction of Chronic Kidney Disease (CKD) progression to End Stage Renal Disease (ESRD) using machine learning (ML) and deep learning (DL) models applied to an integrated clinical and claims dataset of varying observation windows, supported by explainable AI (XAI) to enhance interpretability and reduce bias. Materials and Methods: We utilized data about 10,326 CKD patients, combining their clinical and claims information from 2009 to 2018. Following data preprocessing, cohort identification, and feature engineering, we evaluated multiple statistical, ML and DL models using data extracted from five distinct observation windows. Feature importance and Shapley value analysis were employed to understand key predictors. Models were tested for robustness, clinical relevance, misclassification errors and bias issues. Results: Integrated data models outperformed those using single data sources, with the Long Short-Term Memory (LSTM) model achieving the highest AUC (0.93) and F1 score (0.65). A 24-month observation window was identified as optimal for balancing early detection and prediction accuracy. The 2021 eGFR equation improved prediction accuracy and reduced racial bias, notably for African American patients. Discussion: Improved ESRD prediction accuracy, results interpretability and bias mitigation strategies presented in this study have the potential to significantly enhance CKD and ESRD management, support targeted early interventions and reduce healthcare disparities. Conclusion: This study presents a robust framework for predicting ESRD outcomes in CKD patients, improving clinical decision-making and patient care through multi-sourced, integrated data and AI/ML methods. Future research will expand data integration and explore the application of this framework to other chronic diseases.

  • 2 authors
·
Oct 1, 2024

VeriGUI: Verifiable Long-Chain GUI Dataset

Recent studies have delved into constructing autonomous agents capable of performing complex Graphical User Interface (GUI)-based computer tasks, with the potential to revolutionize human-computer interaction. Despite encouraging results, existing efforts mainly focus on short-term interactions and rely on outcome-only verification, thereby limiting their scalability in real-world GUI applications that demand long-horizon task decomposition and execution. In this work, we introduce VeriGUI, a novel verifiable long-chain GUI dataset designed to facilitate the development and evaluation of generalist GUI agents operating in realistic computer environments. Our dataset emphasizes two critical dimensions: (1) long-chain complexity, with tasks decomposed into a sequence of interdependent subtasks spanning hundreds of steps, explicitly designed to allow any subtask to serve as a valid starting point; and (2) subtask-level verifiability, which enables diverse exploration strategies within each subtask, while ensuring that each subtask-level goal remains verifiable and consistent. The dataset consists of GUI task trajectories across both desktop and web, annotated by human experts. Extensive experiments on VeriGUI using various agents with different foundation models reveal significant performance gaps in handling long-horizon tasks, highlighting the need for more robust planning and decision-making capabilities in GUI agents.