Daily Papers

Money laundering detection faces challenges due to excessive false positives and inadequate adaptation to sophisticated multi-stage schemes that exploit modern financial networks. Graph analytics and AI are promising tools, but they struggle with the fuzziness of laundering patterns, which exhibit structural and temporal variations. Conventional data mining techniques require the detailed enumeration of pattern variants, which not only complicates the analyst's task to specify them, but also leads to large run-time overheads and difficulty training accurate AI models. The paper presents BlazingAML, a scalable AML system design that introduces: 1. A novel multi-stage framework for expressing fuzzy money laundering patterns 2. A domain-specific compiler that transforms high-level pattern descriptions into high-performance code for CPU and GPU back-ends The multi-stage abstraction decomposes complex laundering schemes into logical stages connected by graph operations, enabling diverse patterns to be expressed using unified primitives while capturing structural and temporal fuzziness. The compiler applies sophisticated optimizations, eliminating manual parallel programming requirements for financial analysts. Evaluation on IBM AML datasets shows BlazingAML achieves the same F1 score as state-of-the-art approaches while delivering 210x and 333x higher speedup on CPU and GPU respectively, with superior scalability.

Graph-based malware classifiers can achieve over 94% accuracy on standard Android datasets, yet we find they suffer accuracy drops of up to 45% when evaluated on previously unseen malware variants from the same family - a scenario where strong generalization would typically be expected. This highlights a key limitation in existing approaches: both the model architectures and their structure-only representations often fail to capture deeper semantic patterns. In this work, we propose a robust semantic enrichment framework that enhances function call graphs with contextual features, including function-level metadata and, when available, code embeddings derived from large language models. The framework is designed to operate under real-world constraints where feature availability is inconsistent, and supports flexible integration of semantic signals. To evaluate generalization under realistic domain and temporal shifts, we introduce two new benchmarks: MalNet-Tiny-Common and MalNet-Tiny-Distinct, constructed using malware family partitioning to simulate cross-family generalization and evolving threat behavior. Experiments across multiple graph neural network backbones show that our method improves classification performance by up to 8% under distribution shift and consistently enhances robustness when integrated with adaptation-based methods. These results offer a practical path toward building resilient malware detection systems in evolving threat environments.

Multimodal large language models (MLLMs) have recently achieved significant progress in visual tasks, including semantic scene understanding and text-image alignment, with reasoning variants enhancing performance on complex tasks involving mathematics and logic. However, their capacity for reasoning tasks involving fine-grained visual understanding remains insufficiently evaluated. To address this gap, we introduce ReasonMap, a benchmark designed to assess the fine-grained visual understanding and spatial reasoning abilities of MLLMs. ReasonMap encompasses high-resolution transit maps from 30 cities across 13 countries and includes 1,008 question-answer pairs spanning two question types and three templates. Furthermore, we design a two-level evaluation pipeline that properly assesses answer correctness and quality. Comprehensive evaluations of 15 popular MLLMs, including both base and reasoning variants, reveal a counterintuitive pattern: among open-source models, base models outperform reasoning ones, while the opposite trend is observed in closed-source models. Additionally, performance generally degrades when visual inputs are masked, indicating that while MLLMs can leverage prior knowledge to answer some questions, fine-grained visual reasoning tasks still require genuine visual perception for strong performance. Our benchmark study offers new insights into visual reasoning and contributes to investigating the gap between open-source and closed-source models.

Online alignment (e.g., GRPO) is generally more performant than offline alignment (e.g., DPO) -- but why? Drawing on prospect theory from behavioral economics, we propose a human-centric explanation. We prove that online on-policy sampling better approximates the human-perceived distribution of what the model can produce, and PPO/GRPO-style clipping -- originally introduced to just stabilize training -- recovers a perceptual bias in how humans perceive probability. In this sense, PPO/GRPO act as perceptual losses already. Our theory further suggests that the online/offline dichotomy is itself incidental to maximizing human utility, since we can achieve the same effect by selectively training on any data in a manner that mimics human perception, rather than restricting ourselves to online on-policy data. Doing so would allow us to post-train more quickly, cheaply, and flexibly without sacrificing performance. To this end, we propose a design pattern that explicitly incorporates perceptual distortions of probability into objectives like DPO/KTO/GRPO, creating humanline variants of them. Surprisingly, we find that these humanline variants, even when trained with offline off-policy data, can match the performance of their online counterparts on both verifiable and unverifiable tasks.

LLM-based multi-agent pipelines flip from correct to incorrect answers under simulated peer disagreement at rates we term yield, a vulnerability widely attributed to RLHF-induced sycophancy. We test this attribution across four model families and find it largely wrong: pretrained base models exhibit the same substitution pattern as their Instruct variants, averaging higher yield than Instruct. Using activation patching, we localize the corruption to a narrow mid-layer window where attention carries the causal weight and MLP contribution is negligible; patching above this window restores 96% of the clean-to-pressured P(correct) gap. The attack surface decomposes into two independent factors (channel framing and consensus strength) whose interaction produces a 47.5 percentage-point yield gap at majority consensus, preserved across jury sizes N in {4, 5, 6}. Two converging activation-space interventions show that pressure suppresses clean-reasoning features rather than activating a new sycophancy circuit. A single correctly-arguing dissenter reduces yield by 54-73 percentage points across all framings tested, whereas the strongest prompt-level defense fails on attack variants outside its design surface. Mitigations should target the mechanism, structured dissent at the pipeline level, rather than prompt-level defenses.

Any optimization algorithm programming interface can be seen as a black-box function with additional free parameters. In this spirit, simulated annealing (SA) can be implemented in pseudo-code within the dimensions of a single slide with free parameters relating to the annealing schedule. Such an implementation, however, necessarily neglects much of the structure necessary to take advantage of advances in computing resources and algorithmic breakthroughs. Simulated annealing is often introduced in myriad disciplines, from discrete examples like the Traveling Salesman Problem (TSP) to molecular cluster potential energy exploration or even explorations of a protein's configurational space. Theoretical guarantees also demand a stricter structure in terms of statistical quantities, which cannot simply be left to the user. We will introduce several standard paradigms and demonstrate how these can be "lifted" into a unified framework using object-oriented programming in Python. We demonstrate how clean, interoperable, reproducible programming libraries can be used to access and rapidly iterate on variants of Simulated Annealing in a manner which can be extended to serve as a best practices blueprint or design pattern for a data-driven optimization library.

Time series play a fundamental role in many domains, capturing a plethora of information about the underlying data-generating processes. When a process generates multiple synchronized signals we are faced with multidimensional time series. In this context a fundamental problem is that of motif mining, where we seek patterns repeating twice with minor variations, spanning some of the dimensions. State of the art exact solutions for this problem run in time quadratic in the length of the input time series. We provide a scalable method to find the top-k motifs in multidimensional time series with probabilistic guarantees on the quality of the results. Our algorithm runs in time subquadratic in the length of the input, and returns the exact solution with probability at least 1-δ, where δ is a user-defined parameter. The algorithm is designed to be adaptive to the input distribution, self-tuning its parameters while respecting user-defined limits on the memory to use. Our theoretical analysis is complemented by an extensive experimental evaluation, showing that our algorithm is orders of magnitude faster than the state of the art.

We introduce a pattern mining framework that operates on semi-structured datasets and exploits the dichotomy between outcomes. Our approach takes advantage of constraint reasoning to find sequential patterns that occur frequently and exhibit desired properties. This allows the creation of novel pattern embeddings that are useful for knowledge extraction and predictive modeling. Finally, we present an application on customer intent prediction from digital clickstream data. Overall, we show that pattern embeddings play an integrator role between semi-structured data and machine learning models, improve the performance of the downstream task and retain interpretability.

Previous studies have shown that automated text-mining tools are becoming increasingly important for successfully unlocking variant information in scientific literature at large scale. Despite multiple attempts in the past, existing tools are still of limited recognition scope and precision. We propose tmVar 3.0: an improved variant recognition and normalization tool. Compared to its predecessors, tmVar 3.0 is able to recognize a wide spectrum of variant related entities (e.g., allele and copy number variants), and to group different variant mentions belonging to the same concept in an article for improved accuracy. Moreover, tmVar3 provides additional variant normalization options such as allele-specific identifiers from the ClinGen Allele Registry. tmVar3 exhibits a state-of-the-art performance with over 90% accuracy in F-measure in variant recognition and normalization, when evaluated on three independent benchmarking datasets. tmVar3 is freely available for download. We have also processed the entire PubMed and PMC with tmVar3 and released its annotations on our FTP. Availability: ftp://ftp.ncbi.nlm.nih.gov/pub/lu/tmVar3

We introduce a framework for automatically defining and learning deep generative models with problem-specific structure. We tackle problem domains that are more traditionally solved by algorithms such as sorting, constraint satisfaction for Sudoku, and matrix factorization. Concretely, we train diffusion models with an architecture tailored to the problem specification. This problem specification should contain a graphical model describing relationships between variables, and often benefits from explicit representation of subcomputations. Permutation invariances can also be exploited. Across a diverse set of experiments we improve the scaling relationship between problem dimension and our model's performance, in terms of both training time and final accuracy. Our code can be found at https://github.com/plai-group/gsdm.

It is well known that anti-malware scanners depend on malware signatures to identify malware. However, even minor modifications to malware code structure results in a change in the malware signature thus enabling the variant to evade detection by scanners. Therefore, there exists the need for a proactively generated malware variant dataset to aid detection of such diverse variants by automated antivirus scanners. This paper proposes and demonstrates a generic assembly source code based framework that facilitates any evolutionary algorithm to generate diverse and potential variants of an input malware, while retaining its maliciousness, yet capable of evading antivirus scanners. Generic code transformation functions and a novelty search supported quality metric have been proposed as components of the framework to be used respectively as variation operators and fitness function, for evolutionary algorithms. The results demonstrate the effectiveness of the framework in generating diverse variants and the generated variants have been shown to evade over 98% of popular antivirus scanners. The malware variants evolved by the framework can serve as antigens to assist malware analysis engines to improve their malware detection algorithms.

Context. Behaviour-Driven Development (BDD) software test suites accumulate duplicated step subsequences. Three published refactoring patterns are available (within-file Background, within-repo reusable-scenario invocation, cross-organisational shared higher-level step), but no prior work automates which recurring subsequences are worth extracting or which mechanism applies. Objective. Rank recurring step subsequences ("slices") by refactoring suitability (extraction-worthy), pre-map each to one of the three patterns, and quantify prevalence across the public BDD ecosystem. Method. Every contiguous L-step window (L in [2, 18]) in a 339-repository / 276-upstream-owner Gherkin corpus is keyed by paraphrase-robust cluster identifiers and counted under three scopes. Sentence-BERT (SBERT) / Uniform Manifold Approximation and Projection (UMAP) / Hierarchical Density-Based Clustering (HDBSCAN) recovers paraphrase-equivalent slices. Three authors label a stratified 200-slice pool against a written rubric. An eXtreme Gradient Boosting (XGBoost) extraction-worthy classifier trained under 5-fold cross-validation is compared with a tuned rule baseline and two open-weight Large Language Model (LLM) judges. Results. The miner produces 5,382,249 slices collapsing to 692,020 recurring patterns. Three-author Fleiss' kappa = 0.56 (extraction-worthy) and 0.79 (mechanism). The classifier reaches out-of-fold F1 = 0.891 (95% CI [0.852, 0.927]), outperforming both the rule baseline (F1 = 0.836, p = 0.017) and the better LLM judge (F1 = 0.728, p < 1e-4). 75.0%, 59.5%, and 11.7% of scenarios carry a within-file Background, within-repo reusable-scenario, or cross-organisational shared-step candidate. Conclusion. Paraphrase-robust subscenario discovery yields a corpus-wide census of BDD refactoring opportunities; pipeline, classifier predictions, labelled pool, and rubric are released under Apache-2.0.

Network Architecture Search and specifically Regularized Evolution is a common way to refine the structure of a deep learning model.However, little is known about how models empirically evolve over time which has design implications for designing caching policies, refining the search algorithm for particular applications, and other important use cases.In this work, we algorithmically analyze and quantitatively characterize the patterns of model evolution for a set of models from the Candle project and the Nasbench-201 search space.We show how the evolution of the model structure is influenced by the regularized evolution algorithm. We describe how evolutionary patterns appear in distributed settings and opportunities for caching and improved scheduling. Lastly, we describe the conditions that affect when particular model architectures rise and fall in popularity based on their frequency of acting as a donor in a sliding window.

Frequent itemset mining is a popular data mining technique. Apriori, Eclat, and FP-Growth are among the most common algorithms for frequent itemset mining. Considerable research has been performed to compare the relative performance between these three algorithms, by evaluating the scalability of each algorithm as the dataset size increases. While scalability as data size increases is important, previous papers have not examined the performance impact of similarly sized datasets that contain different itemset characteristics. This paper explores the effects that two dataset characteristics can have on the performance of these three frequent itemset algorithms. To perform this empirical analysis, a dataset generator is created to measure the effects of frequent item density and the maximum transaction size on performance. The generated datasets contain the same number of rows. This provides some insight into dataset characteristics that are conducive to each algorithm. The results of this paper's research demonstrate Eclat and FP-Growth both handle increases in maximum transaction size and frequent itemset density considerably better than the Apriori algorithm. This paper explores the effects that two dataset characteristics can have on the performance of these three frequent itemset algorithms. To perform this empirical analysis, a dataset generator is created to measure the effects of frequent item density and the maximum transaction size on performance. The generated datasets contain the same number of rows. This provides some insight into dataset characteristics that are conducive to each algorithm. The results of this paper's research demonstrate Eclat and FP-Growth both handle increases in maximum transaction size and frequent itemset density considerably better than the Apriori algorithm.

We present a new method for constructing Hadamard matrices that combines transformer neural networks with local search in the PatternBoost framework. Our approach is designed for extremely sparse combinatorial search problems and is particularly effective for Hadamard matrices of Goethals--Seidel type, where Fourier methods permit fast scoring and optimisation. For orders between 100 and 200, it produces large numbers of inequivalent Hadamard matrices, and for larger orders, it succeeds where local search from random initialisation fails. The largest example found by our method has order 252. In addition to these new constructions, our experiments reveal that the transformer can discover and exploit useful hidden symmetry in the search space.

Data profiling is an essential process in modern data-driven industries. One of its critical components is the discovery and validation of complex statistics, including functional dependencies, data constraints, association rules, and others. However, most existing data profiling systems that focus on complex statistics do not provide proper integration with the tools used by contemporary data scientists. This creates a significant barrier to the adoption of these tools in the industry. Moreover, existing systems were not created with industrial-grade workloads in mind. Finally, they do not aim to provide descriptive explanations, i.e. why a given pattern is not found. It is a significant issue as it is essential to understand the underlying reasons for a specific pattern's absence to make informed decisions based on the data. Because of that, these patterns are effectively rest in thin air: their application scope is rather limited, they are rarely used by the broader public. At the same time, as we are going to demonstrate in this presentation, complex statistics can be efficiently used to solve many classic data quality problems. Desbordante is an open-source data profiler that aims to close this gap. It is built with emphasis on industrial application: it is efficient, scalable, resilient to crashes, and provides explanations. Furthermore, it provides seamless Python integration by offloading various costly operations to the C++ core, not only mining. In this demonstration, we show several scenarios that allow end users to solve different data quality problems. Namely, we showcase typo detection, data deduplication, and data anomaly detection scenarios.

With the advent of neural language models, the performance of code generation has been significantly boosted. However, the problem of repetitions during the generation process continues to linger. Previous work has primarily focused on content repetition, which is merely a fraction of the broader repetition problem in code generation. A more prevalent and challenging problem is structural repetition. In structural repetition, the repeated code appears in various patterns but possesses a fixed structure, which can be inherently reflected in grammar. In this paper, we formally define structural repetition and propose an efficient decoding approach called RPG, which stands for Repetition Penalization based on Grammar, to alleviate the repetition problems in code generation for LLMs. Specifically, RPG first leverages grammar rules to identify repetition problems during code generation, and then strategically decays the likelihood of critical tokens that contribute to repetitions, thereby mitigating them in code generation. To facilitate this study, we construct a new dataset CodeRepetEval to comprehensively evaluate approaches for mitigating the repetition problems in code generation. Extensive experimental results demonstrate that RPG substantially outperforms the best-performing baselines on CodeRepetEval dataset as well as HumanEval and MBPP benchmarks, effectively reducing repetitions and enhancing the quality of generated code.

Measuring the full abilities of large language models (LLMs) requires benchmarks representing multiple tasks. We aim to create large, high-quality datasets for comparison of logical reasoning skills across several languages and of suitable difficulty for LLMs of various reasoning ability. We explore multiple ways of increasing difficulty. We generate zebra puzzles in multiple languages, themes, sizes and including 14 different clue types and 8 red herring types (uninformative clues). We find puzzle sizes 2x3 and 4x5 are sufficiently challenging for GPT-4o mini (a non-reasoning model) and o3-mini (a reasoning model), respectively. Including 5 red herrings decreases o3-mini puzzle-level accuracy on 4x5 puzzles by 15pm7 %. Scores of o3-mini on 4x5 puzzles are not significantly affected by use of English vs. Danish or the common houses theme vs. the country-specific smoerrebroed theme. We find no correlation between difficulty and the selected clue types. Datasets of 128+1024 puzzles are published as MultiZebraLogic in each of nine Germanic languages for sizes 2x3 and 4x5. We publish code for puzzle generation, designed for adaptablity into more languages and themes.

Recent work pairs LLMs with evolutionary search to iteratively generate, modify, and select code using task-specific feedback. These systems have produced strong results in mathematical discovery and algorithm design, yet a fundamental question remains: what do they actually evolve? Progress is typically summarized by the best score a run reaches under a task-specific evaluator, but that score can reflect several different mechanisms: new algorithmic structure, re-tuning an existing strategy, recombining ideas already in the model's internal knowledge, or overfitting to the evaluator. Distinguishing these mechanisms requires inspecting the search process itself, not only its final outcome. We introduce EvoTrace, a dataset of evolutionary coding traces spanning four evolutionary frameworks, reasoning and non-reasoning models, and 16 tasks across mathematics and algorithm design. To analyze these traces, we develop EvoReplay, a replay-based methodology that reconstructs the local search states behind high-scoring solutions and tests controlled interventions, including adjusting constants, removing program components and substituting models or prompting contexts. We annotate every code edit in EvoTrace with one of nine recurring edit types using an LLM-as-judge pipeline validated against blind human re-annotation. Across EvoTrace, most score gains come from a small subset of these edit types. We further find a deterministic cycling pattern: about 30% of code lines added during search are byte-identical re-introductions of previously-deleted lines, present throughout nearly every run. These results show that benchmark gains in evolutionary coding agents can arise from qualitatively different mechanisms, only some of which correspond to new algorithmic structure. EvoTrace enables more diagnostic evaluation of evolutionary coding agents beyond final benchmark scores.

Seminal research in the field of graph neural networks (GNNs) has revealed a direct correspondence between the expressive capabilities of GNNs and the k-dimensional Weisfeiler-Leman (kWL) test, a widely-recognized method for verifying graph isomorphism. This connection has reignited interest in comprehending the specific graph properties effectively distinguishable by the kWL test. A central focus of research in this field revolves around determining the least dimensionality k, for which kWL can discern graphs with different number of occurrences of a pattern graph P. We refer to such a least k as the WL-dimension of this pattern counting problem. This inquiry traditionally delves into two distinct counting problems related to patterns: subgraph counting and induced subgraph counting. Intriguingly, despite their initial appearance as separate challenges with seemingly divergent approaches, both of these problems are interconnected components of a more comprehensive problem: "graph motif parameters". In this paper, we provide a precise characterization of the WL-dimension of labeled graph motif parameters. As specific instances of this result, we obtain characterizations of the WL-dimension of the subgraph counting and induced subgraph counting problem for every labeled pattern P. We additionally demonstrate that in cases where the kWL test distinguishes between graphs with varying occurrences of a pattern P, the exact number of occurrences of P can be computed uniformly using only local information of the last layer of a corresponding GNN. We finally delve into the challenge of recognizing the WL-dimension of various graph parameters. We give a polynomial time algorithm for determining the WL-dimension of the subgraph counting problem for given pattern P, answering an open question from previous work.

In this paper we look at the ability of recent large language models (LLMs) at solving mathematical problems in combinatorics. We compare models LLaMA-2, LLaMA-3.1, GPT-4, and Mixtral against each other and against human pupils and undergraduates with prior experience in mathematical olympiads. To facilitate these comparisons we introduce the Combi-Puzzles dataset, which contains 125 problem variants based on 25 combinatorial reasoning problems. Each problem is presented in one of five distinct forms, created by systematically manipulating the problem statements through adversarial additions, numeric parameter changes, and linguistic obfuscation. Our variations preserve the mathematical core and are designed to measure the generalisability of LLM problem-solving abilities, while also increasing confidence that problems are submitted to LLMs in forms that have not been seen as training instances. We found that a model based on GPT-4 outperformed all other models in producing correct responses, and performed significantly better in the mathematical variation of the problems than humans. We also found that modifications to problem statements significantly impact the LLM's performance, while human performance remains unaffected.

In this work, we unveil a novel tool for generating Italian crossword puzzles from text, utilizing advanced language models such as GPT-4o, Mistral-7B-Instruct-v0.3, and Llama3-8b-Instruct. Crafted specifically for educational applications, this cutting-edge generator makes use of the comprehensive Italian-Clue-Instruct dataset, which comprises over 30,000 entries including diverse text, solutions, and types of clues. This carefully assembled dataset is designed to facilitate the creation of contextually relevant clues in various styles associated with specific texts and keywords. The study delves into four distinctive styles of crossword clues: those without format constraints, those formed as definite determiner phrases, copular sentences, and bare noun phrases. Each style introduces unique linguistic structures to diversify clue presentation. Given the lack of sophisticated educational tools tailored to the Italian language, this project seeks to enhance learning experiences and cognitive development through an engaging, interactive platform. By meshing state-of-the-art AI with contemporary educational strategies, our tool can dynamically generate crossword puzzles from Italian educational materials, thereby providing an enjoyable and interactive learning environment. This technological advancement not only redefines educational paradigms but also sets a new benchmark for interactive and cognitive language learning solutions.

Many have observed that the development and deployment of generative machine learning (ML) and artificial intelligence (AI) models follow a distinctive pattern in which pre-trained models are adapted and fine-tuned for specific downstream tasks. However, there is limited empirical work that examines the structure of these interactions. This paper analyzes 1.86 million models on Hugging Face, a leading peer production platform for model development. Our study of model family trees -- networks that connect fine-tuned models to their base or parent -- reveals sprawling fine-tuning lineages that vary widely in size and structure. Using an evolutionary biology lens to study ML models, we use model metadata and model cards to measure the genetic similarity and mutation of traits over model families. We find that models tend to exhibit a family resemblance, meaning their genetic markers and traits exhibit more overlap when they belong to the same model family. However, these similarities depart in certain ways from standard models of asexual reproduction, because mutations are fast and directed, such that two `sibling' models tend to exhibit more similarity than parent/child pairs. Further analysis of the directional drifts of these mutations reveals qualitative insights about the open machine learning ecosystem: Licenses counter-intuitively drift from restrictive, commercial licenses towards permissive or copyleft licenses, often in violation of upstream license's terms; models evolve from multi-lingual compatibility towards english-only compatibility; and model cards reduce in length and standardize by turning, more often, to templates and automatically generated text. Overall, this work takes a step toward an empirically grounded understanding of model fine-tuning and suggests that ecological models and methods can yield novel scientific insights.

Many events occur in the world. Some event types are stochastically excited or inhibited---in the sense of having their probabilities elevated or decreased---by patterns in the sequence of previous events. Discovering such patterns can help us predict which type of event will happen next and when. We model streams of discrete events in continuous time, by constructing a neurally self-modulating multivariate point process in which the intensities of multiple event types evolve according to a novel continuous-time LSTM. This generative model allows past events to influence the future in complex and realistic ways, by conditioning future event intensities on the hidden state of a recurrent neural network that has consumed the stream of past events. Our model has desirable qualitative properties. It achieves competitive likelihood and predictive accuracy on real and synthetic datasets, including under missing-data conditions.

Elucidating the functional effect of missense variants is of crucial importance, yet challenging. To understand the impact of such variants, we fine-tuned the ESM2 protein language model to classify 20 protein features at amino acid resolution. We used the resulting models to: 1) identify protein features that are enriched in either pathogenic or benign missense variants, 2) compare the characteristics of proteins with reference or alternate alleles to understand how missense variants affect protein functionality. We show that our model can be used to reclassify some variants of unknown significance. We also demonstrate the usage of our models for understanding the potential effect of variants on protein features.

Generative protein language models are a natural way to design new proteins with desired functions. However, current models are either difficult to direct to produce a protein from a specific family of interest, or must be trained on a large multiple sequence alignment (MSA) from the specific family of interest, making them unable to benefit from transfer learning across families. To address this, we propose Protein Evolutionary Transformer (PoET), an autoregressive generative model of whole protein families that learns to generate sets of related proteins as sequences-of-sequences across tens of millions of natural protein sequence clusters. PoET can be used as a retrieval-augmented language model to generate and score arbitrary modifications conditioned on any protein family of interest, and can extrapolate from short context lengths to generalize well even for small families. This is enabled by a unique Transformer layer; we model tokens sequentially within sequences while attending between sequences order invariantly, allowing PoET to scale to context lengths beyond those used during training. In extensive experiments on deep mutational scanning datasets, we show that PoET outperforms existing protein language models and evolutionary sequence models for variant function prediction across proteins of all MSA depths. We also demonstrate PoET's ability to controllably generate new protein sequences.

We present new methods and results for constructing optimal Kobon triangle arrangements. First, we introduce a compact table notation for describing arrangements of pseudolines, enabling the representation and analysis of complex cases, including symmetrical arrangements, arrangements with parallel lines, and arrangements with multiple-line intersection points. Building on this, we provide a simple heuristic method and tools for recovering straight-line arrangements from a given table, with the ability to enforce additional properties such as symmetries. The tool successfully recovers arrangements for many previously known optimal solutions. Additionally, we develop a tool that transforms the search for optimal Kobon arrangement tables into a SAT problem, allowing us to leverage modern SAT solvers (specifically Kissat) to efficiently find new solutions or to show that no other solutions exist (for example, confirming that no optimal solution exists in the 11-line case). Using these techniques, we find new optimal Kobon arrangements for 23 and 27 lines, along with several other new results.

Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to reduce pesticide use, adaptation to climate change, resistance to heat and drought stresses, or low gluten content of grains. Wheat breeding experiments are documented by a large body of scientific literature and observational data obtained in-field and under controlled conditions. The cross-referencing of complementary information from the literature and observational data is essential to the study of the genotype-phenotype relationship and to the improvement of wheat selection. The scientific literature on genetic marker-assisted selection describes much information about the genotype-phenotype relationship. However, the variety of expressions used to refer to traits and phenotype values in scientific articles is a hinder to finding information and cross-referencing it. When trained adequately by annotated examples, recent text mining methods perform highly in named entity recognition and linking in the scientific domain. While several corpora contain annotations of human and animal phenotypes, currently, no corpus is available for training and evaluating named entity recognition and entity-linking methods in plant phenotype literature. The Triticum aestivum trait Corpus is a new gold standard for traits and phenotypes of wheat. It consists of 540 PubMed references fully annotated for trait, phenotype, and species named entities using the Wheat Trait and Phenotype Ontology and the species taxonomy of the National Center for Biotechnology Information. A study of the performance of tools trained on the Triticum aestivum trait Corpus shows that the corpus is suitable for the training and evaluation of named entity recognition and linking.

Data of sequential nature arise in many application domains in forms of, e.g. textual data, DNA sequences, and software execution traces. Different research disciplines have developed methods to learn sequence models from such datasets: (i) in the machine learning field methods such as (hidden) Markov models and recurrent neural networks have been developed and successfully applied to a wide-range of tasks, (ii) in process mining process discovery techniques aim to generate human-interpretable descriptive models, and (iii) in the grammar inference field the focus is on finding descriptive models in the form of formal grammars. Despite their different focuses, these fields share a common goal - learning a model that accurately describes the behavior in the underlying data. Those sequence models are generative, i.e, they can predict what elements are likely to occur after a given unfinished sequence. So far, these fields have developed mainly in isolation from each other and no comparison exists. This paper presents an interdisciplinary experimental evaluation that compares sequence modeling techniques on the task of next-element prediction on four real-life sequence datasets. The results indicate that machine learning techniques that generally have no aim at interpretability in terms of accuracy outperform techniques from the process mining and grammar inference fields that aim to yield interpretable models.

Large language models (LLMs) trained on text demonstrated remarkable results on natural language processing (NLP) tasks. These models have been adapted to decipher the language of DNA, where sequences of nucleotides act as "words" that encode genomic functions. However, the genome differs fundamentally from natural language, as it lacks clearly defined words or a consistent grammar. Although DNA language models (DNALMs) such as DNABERT, GENA-LM have achieved high level of performance on genome-related biological tasks, these models do not encode biological functions in the presence of sequence variations. To address this problem, we pre-train foundation models that effectively integrate sequence variations, in particular Single Nucleotide Polymorphisms (SNPs), as they underlie important biological functions. Specifically, we use ModernBERT to pre-train two different Biomedical Foundation Models (BMFM), namely, BMFM-DNA-REF in which the model is trained with sequences of varying lengths along with their reverse complements derived from the reference genome and BMFM-DNA-SNP in which the model is trained with sequences created using a novel representation scheme that encodes sequence variations. Our findings indicate that integrating sequence variations into DNALMs helps capture the biological functions as seen in improvements on all fine-tuning tasks. To explore the model's practical utility, we experimented with various strategies for SNP imputation on promoter detection task introduced in DNABERT-2. However, we acknowledge that the current benchmarks are limited in their ability to fully evaluate these models. To enable more comprehensive assessment in the future and encourage community contributions, we release our models through HuggingFace and the code to reproduce the results at https://github.com/BiomedSciAI/biomed-multi-omic

Instance-specific algorithm configuration and algorithm portfolios have been shown to offer significant improvements over single algorithm approaches in a variety of application domains. In the SAT and CSP domains algorithm portfolios have consistently dominated the main competitions in these fields for the past five years. For a portfolio approach to be effective there are two crucial conditions that must be met. First, there needs to be a collection of complementary solvers with which to make a portfolio. Second, there must be a collection of problem features that can accurately identify structural differences between instances. This paper focuses on the latter issue: feature representation, because, unlike SAT, not every problem has well-studied features. We employ the well-known SATzilla feature set, but compute alternative sets on different SAT encodings of CSPs. We show that regardless of what encoding is used to convert the instances, adequate structural information is maintained to differentiate between problem instances, and that this can be exploited to make an effective portfolio-based CSP solver.

We investigate the generalization capabilities of small language models under two popular adaptation paradigms: few-shot prompting and supervised fine-tuning. While prompting is often favored for its parameter efficiency and flexibility, it remains unclear how robust this approach is in low-resource settings and under distributional shifts. This paper presents a comparative study of prompting and fine-tuning across task formats, prompt styles, and model scales, with a focus on their behavior in both in-distribution and out-of-distribution (OOD) settings. Beyond accuracy, we analyze the internal representations learned by each approach to assess the stability and abstraction of task-specific features. Our findings highlight critical differences in how small models internalize and generalize knowledge under different adaptation strategies. This work offers practical guidance for model selection in low-data regimes and contributes empirical insight into the ongoing debate over prompting versus fine-tuning. Code for the experiments is available at the following

Protein Language Models (PLMs) have emerged as performant and scalable tools for predicting the functional impact and clinical significance of protein-coding variants, but they still lag experimental accuracy. Here, we present a novel fine-tuning approach to improve the performance of PLMs with experimental maps of variant effects from Deep Mutational Scanning (DMS) assays using a Normalised Log-odds Ratio (NLR) head. We find consistent improvements in a held-out protein test set, and on independent DMS and clinical variant annotation benchmarks from ProteinGym and ClinVar. These findings demonstrate that DMS is a promising source of sequence diversity and supervised training data for improving the performance of PLMs for variant effect prediction.

Code generation with large language models has shown significant promise, especially when employing retrieval-augmented generation (RAG) with few-shot examples. However, selecting effective examples that enhance generation quality remains a challenging task, particularly when the target programming language (PL) is underrepresented. In this study, we present two key findings: (1) retrieving examples whose presented algorithmic plans can be referenced for generating the desired behavior significantly improves generation accuracy, and (2) converting code into pseudocode effectively captures such algorithmic plans, enhancing retrieval quality even when the source and the target PLs are different. Based on these findings, we propose Plan-as-query Example Retrieval for few-shot prompting in Code generation (PERC), a novel framework that utilizes algorithmic plans to identify and retrieve effective examples. We validate the effectiveness of PERC through extensive experiments on the CodeContests, HumanEval and MultiPL-E benchmarks: PERC consistently outperforms the state-of-the-art RAG methods in code generation, both when the source and target programming languages match or differ, highlighting its adaptability and robustness in diverse coding environments.

Recent advances in large language model (LLM) embeddings have enabled powerful representations for biological data, but most applications to date focus only on gene-level information. We present one of the first systematic frameworks to generate variant-level embeddings across the entire human genome. Using curated annotations from FAVOR, ClinVar, and the GWAS Catalog, we constructed semantic text descriptions for 8.9 billion possible variants and generated embeddings at three scales: 1.5 million HapMap3+MEGA variants, ~90 million imputed UK Biobank variants, and ~9 billion all possible variants. Embeddings were produced with both OpenAI's text-embedding-3-large and the open-source Qwen3-Embedding-0.6B models. Baseline experiments demonstrate high predictive accuracy for variant properties, validating the embeddings as structured representations of genomic variation. We outline two downstream applications: embedding-informed hypothesis testing by extending the Frequentist And Bayesian framework to genome-wide association studies, and embedding-augmented genetic risk prediction that enhances standard polygenic risk scores. These resources, publicly available on Hugging Face, provide a foundation for advancing large-scale genomic discovery and precision medicine.

A primary concern regarding training large language models (LLMs) is whether they abuse copyrighted online text. With the increasing training data scale and the prevalence of LLMs in daily lives, two problems arise: 1) false positive membership inference results misled by similar examples; 2) membership inference methods are usually too complex for end users to understand and use. To address these issues, we propose an alternative insert-and-detect methodology, advocating that web users and content platforms employ \textit{unique identifiers} for reliable and independent membership inference. Users and platforms can create their identifiers, embed them in copyrighted text, and independently detect them in future LLMs. As an initial demonstration, we introduce \textbf{ghost sentences} and a user-friendly last-k words test, allowing end users to chat with LLMs for membership inference. Ghost sentences consist primarily of unique passphrases of random natural words, which can come with customized elements to bypass possible filter rules. The last-k words test requires a significant repetition time of ghost sentences~(ge10). For cases with fewer repetitions, we designed an extra perplexity test, as LLMs exhibit high perplexity when encountering unnatural passphrases. We also conduct a comprehensive study on the memorization and membership inference of ghost sentences, examining factors such as training data scales, model sizes, repetition times, insertion positions, wordlist of passphrases, alignment, etc. Our study shows the possibility of applying ghost sentences in real scenarios and provides instructions for the potential application.

The democratization of machine learning systems has made the process of fine-tuning accessible to practitioners, leading to a wide range of open-source models fine-tuned on specialized tasks and datasets. Recent work has proposed to merge such models to combine their functionalities. However, prior approaches are usually restricted to models that are fine-tuned from the same base model. Furthermore, the final merged model is typically required to be of the same size as the original models. In this work, we propose a new two-step algorithm to merge models -- termed PLeaS -- which relaxes these constraints. First, leveraging the Permutation symmetries inherent in the two models, PLeaS partially matches nodes in each layer by maximizing alignment. Next, PLeaS computes the weights of the merged model as a layer-wise Least Squares solution to minimize the approximation error between the features of the merged model and the permuted features of the original models. PLeaS allows a practitioner to merge two models sharing the same architecture into a single performant model of a desired size, even when the two original models are fine-tuned from different base models. We also demonstrate how our method can be extended to address a challenging scenario where no data is available from the fine-tuning domains. We demonstrate our method to merge ResNet and ViT models trained with shared and different label spaces, and show improvement over the state-of-the-art merging methods of up to 15 percentage points for the same target compute while merging models trained on DomainNet and fine-grained classification tasks. Our code is open-sourced at https://github.com/SewoongLab/PLeaS-Merging .

Fine-tuning is widely used to adapt language models for specific goals, often leveraging real-world data such as patient records, customer-service interactions, or web content in languages not covered in pre-training. These datasets are typically massive, noisy, and often confidential, making their direct inspection challenging. However, understanding them is essential for guiding model deployment and informing decisions about data cleaning or suppressing any harmful behaviors learned during fine-tuning. In this study, we introduce the task of novelty discovery through generation, which aims to identify novel properties of a fine-tuning dataset by generating examples that illustrate these properties. Our approach, Contrastive Generative Exploration (CGE), assumes no direct access to the data but instead relies on a pre-trained model and the same model after fine-tuning. By contrasting the predictions of these two models, CGE can generate examples that highlight novel characteristics of the fine-tuning data. However, this simple approach may produce examples that are too similar to one another, failing to capture the full range of novel phenomena present in the dataset. We address this by introducing an iterative version of CGE, where the previously generated examples are used to update the pre-trained model, and this updated model is then contrasted with the fully fine-tuned model to generate the next example, promoting diversity in the generated outputs. Our experiments demonstrate the effectiveness of CGE in detecting novel content, such as toxic language, as well as new natural and programming languages. Furthermore, we show that CGE remains effective even when models are fine-tuned using differential privacy techniques.

We study the classic Text-to-Pattern Hamming Distances problem: given a pattern P of length m and a text T of length n, both over a polynomial-size alphabet, compute the Hamming distance between P and T[i, ., . , i+m-1] for every shift i, under the standard Word-RAM model with Theta(log n)-bit words. - We provide an O(nm) time Las Vegas randomized algorithm for this problem, beating the decades-old O(n m log m) running time [Abrahamson, SICOMP 1987]. We also obtain a deterministic algorithm, with a slightly higher O(nm(log mloglog m)^{1/4}) running time. Our randomized algorithm extends to the k-bounded setting, with running time Obig(n+nk{m}big), removing all the extra logarithmic factors from earlier algorithms [Gawrychowski and Uzna\'{n}ski, ICALP 2018; Chan, Golan, Kociumaka, Kopelowitz and Porat, STOC 2020]. - For the (1+epsilon)-approximate version of Text-to-Pattern Hamming Distances, we give an O(epsilon^{-0.93}n) time Monte Carlo randomized algorithm, beating the previous O(epsilon^{-1}n) running time [Kopelowitz and Porat, FOCS 2015; Kopelowitz and Porat, SOSA 2018]. Our approximation algorithm exploits a connection with 3SUM, and uses a combination of Fredman's trick, equality matrix product, and random sampling; in particular, we obtain new results on approximate counting versions of 3SUM and Exact Triangle, which may be of independent interest. Our exact algorithms use a novel combination of hashing, bit-packed FFT, and recursion; in particular, we obtain a faster algorithm for computing the sumset of two integer sets, in the regime when the universe size is close to quadratic in the number of elements. We also prove a fine-grained equivalence between the exact Text-to-Pattern Hamming Distances problem and a range-restricted, counting version of 3SUM.

Pre-trained large language models demonstrate potential in extracting information from DNA sequences, yet adapting to a variety of tasks and data modalities remains a challenge. To address this, we propose DNAGPT, a generalized DNA pre-training model trained on over 200 billion base pairs from all mammals. By enhancing the classic GPT model with a binary classification task (DNA sequence order), a numerical regression task (guanine-cytosine content prediction), and a comprehensive token language, DNAGPT can handle versatile DNA analysis tasks while processing both sequence and numerical data. Our evaluation of genomic signal and region recognition, mRNA abundance regression, and artificial genomes generation tasks demonstrates DNAGPT's superior performance compared to existing models designed for specific downstream tasks, benefiting from pre-training using the newly designed model structure.

In this paper, we propose a multi-modal search engine for interior design that combines visual and textual queries. The goal of our engine is to retrieve interior objects, e.g. furniture or wall clocks, that share visual and aesthetic similarities with the query. Our search engine allows the user to take a photo of a room and retrieve with a high recall a list of items identical or visually similar to those present in the photo. Additionally, it allows to return other items that aesthetically and stylistically fit well together. To achieve this goal, our system blends the results obtained using textual and visual modalities. Thanks to this blending strategy, we increase the average style similarity score of the retrieved items by 11%. Our work is implemented as a Web-based application and it is planned to be opened to the public.

Tabular data in knowledge-rich domains often carries a latent prior in the form of Boolean implication relationships (BIRs) between pairs of features. We mine such relationships with a sparse-exception binomial test. The mined implications form a typed directed graph, equivalent to a propositional rule base of 2-literal clauses. We encode this graph as the connectivity of a layered neural network, called BIRDNet, in which each hidden unit corresponds to one mined rule and binds only to its two features. We show two consequences of this design: First, the architecture is sparse by construction: at most 2/d of the weights in each BIR layer are active, where d is the input dimension. Second, the model is interpretable: every trained unit keeps a stable symbolic identity, so rules can be read off the network without surrogate models. Unlike most neurosymbolic models, BIRDNet does not consume an external rule base; its structural prior is mined from the data. We evaluate BIRDNet on six transcriptomic and proteomic benchmarks. Our results show that BIRDNet stays within 0.02 AUROC of the strongest dense baseline, at a small accuracy cost, while using up to 96times fewer active parameters than an architecture-matched dense MLP. First-layer rules recover known biological signatures across multiple cancer subtypes and tissue types, including canonical amplicons, lineage-defining co-expression modules, and immune-infiltration markers. Data and code are available at: https://github.com/MAHI-Group/BIRDNet.

Programming-by-Examples (PBE) aims to generate an algorithm from input-output examples. Such systems are practically and theoretically important: from an end-user perspective, they are deployed to millions of people, and from an AI perspective, PBE corresponds to a very general form of few-shot inductive inference. Given the success of Large Language Models (LLMs) in code-generation tasks, we investigate here the extent to which LLMs can be said to have `solved' PBE. We experiment on classic domains such as lists and strings, and an uncommon graphics programming domain not well represented in typical pretraining data. We find that pretrained models are not effective at PBE, but that they can be fine-tuned for much higher performance, provided the test problems are in-distribution. We analyze empirically what causes these models to succeed and fail, and take steps toward understanding how to achieve better out-of-distribution generalization. Collectively these results suggest that LLMs make strong progress toward solving the typical suite of PBE tasks, potentially increasing the flexibility and applicability of PBE systems, while also identifying ways in which LLMs still fall short.

A subgraph is constructed by using a subset of vertices and edges of a given graph. There exist many graph properties that are hereditary for subgraphs. Hence, researchers from different communities have paid a great deal of attention in studying numerous subgraph problems, on top of the ordinary graph problems. Many algorithms are proposed in studying subgraph problems, where one common approach is by extracting the patterns and structures of a given graph. Due to the complex structures of certain types of graphs and to improve overall performances of the existing frameworks, machine learning techniques have recently been employed in dealing with various subgraph problems. In this article, we present a comprehensive review on five well known subgraph problems that have been tackled by using machine learning methods. They are subgraph isomorphism (both counting and matching), maximum common subgraph, community detection and community search problems. We provide an outline of each proposed method, and examine its designs and performances. We also explore non-learning-based algorithms for each problem and a brief discussion is given. We then suggest some promising research directions in this area, hoping that relevant subgraph problems can be tackled by using a similar strategy. Since there is a huge growth in employing machine learning techniques in recent years, we believe that this survey will serve as a good reference point to relevant research communities.

We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can traverse any series of modules in any order. DNAs are a natural generalization of the sparse methods such as Mixture-of-Experts, Mixture-of-Depths, parameter sharing, etc. Computation and communication patterns of DNA modules are learnt end-to-end during training and depend on the content and context of each token (or patch). These patterns can be shaped by further requirements added to the optimization objective such as compute/memory efficiency or load balancing. We empirically show that (i) trained DNAs are competitive with the dense baselines in both domains and (ii) compute efficiency/parameter sharing can be learnt from data. Next, we analyze the emergent connectivity and computation patterns in the trained DNAs. We find that the paths that tokens take through the models are themselves distributed according to a power-law. We show that some paths (or, equivalently, groups of modules) show emergent specialization. Finally, we demonstrate that models learn to allocate compute and active parameters in an interpretable way.

Large language models must satisfy hard orthographic constraints during controlled text generation, yet systematic cross-architecture evaluation remains limited. We evaluate 28 configurations spanning three model families (Qwen3, Claude Haiku-4.5, GPT-5-mini) on 58 word puzzles requiring character-level constraint satisfaction. Architectural differences produce substantially larger performance gaps (2.0-2.2x, F1=0.761 vs. 0.343) than parameter scaling within families (83% gain from eightfold scaling), suggesting that constraint satisfaction may require specialized architectural features or training objectives beyond standard language model scaling. Thinking budget sensitivity proves heterogeneous: high-capacity models show strong returns (+0.102 to +0.136 F1), while mid-sized variants saturate or degrade. These patterns are inconsistent with uniform compute benefits. Using difficulty ratings from 10,000 human solvers per puzzle, we establish modest but consistent calibration (r=0.24-0.38) across all families, yet identify systematic failures on common words with unusual orthography ("data", "poop", "loll": 86-95% human success, 89-96% model miss rate). These failures reveal over-reliance on distributional plausibility that penalizes orthographically atypical but constraint-valid patterns, suggesting architectural innovations may be required beyond simply scaling parameters or computational budgets.

We consider the Similarity Sketching problem: Given a universe [u] = {0,ldots, u-1} we want a random function S mapping subsets Asubseteq [u] into vectors S(A) of size t, such that the Jaccard similarity J(A,B) = |Acap B|/|Acup B| between sets A and B is preserved. More precisely, define X_i = [S(A)[i] = S(B)[i]] and X = sum_{iin [t]} X_i. We want E[X_i]=J(A,B), and we want X to be strongly concentrated around E[X] = t cdot J(A,B) (i.e. Chernoff-style bounds). This is a fundamental problem which has found numerous applications in data mining, large-scale classification, computer vision, similarity search, etc. via the classic MinHash algorithm. The vectors S(A) are also called sketches. Strong concentration is critical, for often we want to sketch many sets B_1,ldots,B_n so that we later, for a query set A, can find (one of) the most similar B_i. It is then critical that no B_i looks much more similar to A due to errors in the sketch. The seminal ttimesMinHash algorithm uses t random hash functions h_1,ldots, h_t, and stores left ( min_{ain A} h_1(A),ldots, min_{ain A} h_t(A) right ) as the sketch of A. The main drawback of MinHash is, however, its O(tcdot |A|) running time, and finding a sketch with similar properties and faster running time has been the subject of several papers. (continued...)

A challenging problem in many modern machine learning tasks is to process weight-space features, i.e., to transform or extract information from the weights and gradients of a neural network. Recent works have developed promising weight-space models that are equivariant to the permutation symmetries of simple feedforward networks. However, they are not applicable to general architectures, since the permutation symmetries of a weight space can be complicated by recurrence or residual connections. This work proposes an algorithm that automatically constructs permutation equivariant models, which we refer to as universal neural functionals (UNFs), for any weight space. Among other applications, we demonstrate how UNFs can be substituted into existing learned optimizer designs, and find promising improvements over prior methods when optimizing small image classifiers and language models. Our results suggest that learned optimizers can benefit from considering the (symmetry) structure of the weight space they optimize. We open-source our library for constructing UNFs at https://github.com/AllanYangZhou/universal_neural_functional.

Generalization is arguably the most important goal of statistical language modeling research. Publicly available benchmarks and papers published with an open-source code have been critical to advancing the field. However, it is often very difficult, and sometimes even impossible, to reproduce the results fully as reported in publications. In this paper, we propose a simple framework that should help advance the state of the art in language modeling in terms of generalization. We propose to publish not just the code, but also probabilities on dev and test sets with future publications so that one can easily add the new model into an ensemble. This has crucial advantages: it is much easier to determine whether a newly proposed model is actually complementary to the current baseline. Therefore, instead of inventing new names for the old tricks, the scientific community can advance faster. Finally, this approach promotes diversity of ideas: one does not need to create an individual model that is the new state of the art to attract attention; it will be sufficient to develop a new model that learns patterns which other models do not. Thus, even a suboptimal model can be found to have value. Remarkably, our approach has yielded new state-of-the-art results across various language modeling benchmarks up to 10%.

As opposed to scaling-up protein language models (PLMs), we seek improving performance via protein-specific optimization. Although the proportionality between the language model size and the richness of its learned representations is validated, we prioritize accessibility and pursue a path of data-efficient, cost-reduced, and knowledge-guided optimization. Through over twenty experiments ranging from masking, architecture, and pre-training data, we derive insights from protein-specific experimentation into building a model that interprets the language of life, optimally. We present Ankh, the first general-purpose PLM trained on Google's TPU-v4 surpassing the state-of-the-art performance with fewer parameters (<10% for pre-training, <7% for inference, and <30% for the embedding dimension). We provide a representative range of structure and function benchmarks where Ankh excels. We further provide a protein variant generation analysis on High-N and One-N input data scales where Ankh succeeds in learning protein evolutionary conservation-mutation trends and introducing functional diversity while retaining key structural-functional characteristics. We dedicate our work to promoting accessibility to research innovation via attainable resources.

We study the problem of designing models for machine learning tasks defined on sets. In contrast to traditional approach of operating on fixed dimensional vectors, we consider objective functions defined on sets that are invariant to permutations. Such problems are widespread, ranging from estimation of population statistics poczos13aistats, to anomaly detection in piezometer data of embankment dams Jung15Exploration, to cosmology Ntampaka16Dynamical,Ravanbakhsh16ICML1. Our main theorem characterizes the permutation invariant functions and provides a family of functions to which any permutation invariant objective function must belong. This family of functions has a special structure which enables us to design a deep network architecture that can operate on sets and which can be deployed on a variety of scenarios including both unsupervised and supervised learning tasks. We also derive the necessary and sufficient conditions for permutation equivariance in deep models. We demonstrate the applicability of our method on population statistic estimation, point cloud classification, set expansion, and outlier detection.

Discrete event sequences are ubiquitous, such as an ordered event series of process interactions in Information and Communication Technology systems. Recent years have witnessed increasing efforts in detecting anomalies with discrete-event sequences. However, it still remains an extremely difficult task due to several intrinsic challenges including data imbalance issues, the discrete property of the events, and sequential nature of the data. To address these challenges, in this paper, we propose OC4Seq, a multi-scale one-class recurrent neural network for detecting anomalies in discrete event sequences. Specifically, OC4Seq integrates the anomaly detection objective with recurrent neural networks (RNNs) to embed the discrete event sequences into latent spaces, where anomalies can be easily detected. In addition, given that an anomalous sequence could be caused by either individual events, subsequences of events, or the whole sequence, we design a multi-scale RNN framework to capture different levels of sequential patterns simultaneously. Experimental results on three benchmark datasets show that OC4Seq consistently outperforms various representative baselines by a large margin. Moreover, through both quantitative and qualitative analysis, the importance of capturing multi-scale sequential patterns for event anomaly detection is verified.

The ability to accurately model the fitness landscape of protein sequences is critical to a wide range of applications, from quantifying the effects of human variants on disease likelihood, to predicting immune-escape mutations in viruses and designing novel biotherapeutic proteins. Deep generative models of protein sequences trained on multiple sequence alignments have been the most successful approaches so far to address these tasks. The performance of these methods is however contingent on the availability of sufficiently deep and diverse alignments for reliable training. Their potential scope is thus limited by the fact many protein families are hard, if not impossible, to align. Large language models trained on massive quantities of non-aligned protein sequences from diverse families address these problems and show potential to eventually bridge the performance gap. We introduce Tranception, a novel transformer architecture leveraging autoregressive predictions and retrieval of homologous sequences at inference to achieve state-of-the-art fitness prediction performance. Given its markedly higher performance on multiple mutants, robustness to shallow alignments and ability to score indels, our approach offers significant gain of scope over existing approaches. To enable more rigorous model testing across a broader range of protein families, we develop ProteinGym -- an extensive set of multiplexed assays of variant effects, substantially increasing both the number and diversity of assays compared to existing benchmarks.

Time series have numerous applications in finance, healthcare, IoT, and smart city. In many of these applications, time series typically contain personal data, so privacy infringement may occur if they are released directly to the public. Recently, local differential privacy (LDP) has emerged as the state-of-the-art approach to protecting data privacy. However, existing works on LDP-based collections cannot preserve the shape of time series. A recent work, PatternLDP, attempts to address this problem, but it can only protect a finite group of elements in a time series due to {\omega}-event level privacy guarantee. In this paper, we propose PrivShape, a trie-based mechanism under user-level LDP to protect all elements. PrivShape first transforms a time series to reduce its length, and then adopts trie-expansion and two-level refinement to improve utility. By extensive experiments on real-world datasets, we demonstrate that PrivShape outperforms PatternLDP when adapted for offline use, and can effectively extract frequent shapes.

This paper proposes a novel column generation framework for combinatorial software testing. In particular, it combines Mathematical Programming and Constraint Programming in a hybrid decomposition to generate covering arrays. The approach allows generating parameterized test cases with coverage guarantees between parameter interactions of a given application. Compared to exhaustive testing, combinatorial test case generation reduces the number of tests to run significantly. Our column generation algorithm is generic and can accommodate mixed coverage arrays over heterogeneous alphabets. The algorithm is realized in practice as a cloud service and recognized as one of the five winners of the company-wide cloud application challenge at Oracle. The service is currently helping software developers from a range of different product teams in their testing efforts while exposing declarative constraint models and hybrid optimization techniques to a broader audience.

Despite being self-supervised, protein language models have shown remarkable performance in fundamental biological tasks such as predicting impact of genetic variation on protein structure and function. The effectiveness of these models on diverse set of tasks suggests that they learn meaningful representations of fitness landscape that can be useful for downstream clinical applications. Here, we interrogate the use of these language models in characterizing known pathogenic mutations in curated, medically actionable genes through an exhaustive search of putative compensatory mutations on each variant's genetic background. Systematic analysis of the predicted effects of these compensatory mutations reveal unappreciated structural features of proteins that are missed by other structure predictors like AlphaFold. While deep mutational scan experiments provide an unbiased estimate of the mutational landscape, we encourage the community to generate and curate rescue mutation experiments to inform the design of more sophisticated co-masking strategies and leverage large language models more effectively for downstream clinical prediction tasks.

Anomaly detection in multivariate time series is challenging as heterogeneous subsequence anomalies may occur. Reconstruction-based methods, which focus on learning normal patterns in the frequency domain to detect diverse abnormal subsequences, achieve promising results, while still falling short on capturing fine-grained frequency characteristics and channel correlations. To contend with the limitations, we introduce CATCH, a framework based on frequency patching. We propose to patchify the frequency domain into frequency bands, which enhances its ability to capture fine-grained frequency characteristics. To perceive appropriate channel correlations, we propose a Channel Fusion Module (CFM), which features a patch-wise mask generator and a masked-attention mechanism. Driven by a bi-level multi-objective optimization algorithm, the CFM is encouraged to iteratively discover appropriate patch-wise channel correlations, and to cluster relevant channels while isolating adverse effects from irrelevant channels. Extensive experiments on 10 real-world datasets and 12 synthetic datasets demonstrate that CATCH achieves state-of-the-art performance. We make our code and datasets available at https://github.com/decisionintelligence/CATCH.

In this note we establish a 1-to-1 correspondence between the class of generalized quadrangles with ovoids and the class of balanced incomplete block designs that posses a non-triangular local resolution system and have the appropriate parameters. We present a non-triangular local resolution system for a difference family BIBD construction of Sprott.

In this paper, we describe and present the first dataset of source code plagiarism specifically aimed at contest plagiarism. The dataset contains 251 pairs of plagiarized solutions of competitive programming tasks in Java, as well as 660 non-plagiarized ones, however, the described approach can be used to extend the dataset in the future. Importantly, each pair comes in two versions: (a) "raw" and (b) with participants' repeated template code removed, allowing for evaluating tools in different settings. We used the collected dataset to compare the available source code plagiarism detection tools, including state-of-the-art ones, specifically in their ability to detect contest plagiarism. Our results indicate that the tools show significantly worse performance on the contest plagiarism because of the template code and the presence of other misleadingly similar code. Of the tested tools, token-based ones demonstrated the best performance in both variants of the dataset.

The field of Automatic Machine Learning (AutoML) has recently attained impressive results, including the discovery of state-of-the-art machine learning solutions, such as neural image classifiers. This is often done by applying an evolutionary search method, which samples multiple candidate solutions from a large space and evaluates the quality of each candidate through a long training process. As a result, the search tends to be slow. In this paper, we show that large efficiency gains can be obtained by employing a fast unified functional hash, especially through the functional equivalence caching technique, which we also present. The central idea is to detect by hashing when the search method produces equivalent candidates, which occurs very frequently, and this way avoid their costly re-evaluation. Our hash is "functional" in that it identifies equivalent candidates even if they were represented or coded differently, and it is "unified" in that the same algorithm can hash arbitrary representations; e.g. compute graphs, imperative code, or lambda functions. As evidence, we show dramatic improvements on multiple AutoML domains, including neural architecture search and algorithm discovery. Finally, we consider the effect of hash collisions, evaluation noise, and search distribution through empirical analysis. Altogether, we hope this paper may serve as a guide to hashing techniques in AutoML.

Machine learning research has advanced in multiple aspects, including model structures and learning methods. The effort to automate such research, known as AutoML, has also made significant progress. However, this progress has largely focused on the architecture of neural networks, where it has relied on sophisticated expert-designed layers as building blocks---or similarly restrictive search spaces. Our goal is to show that AutoML can go further: it is possible today to automatically discover complete machine learning algorithms just using basic mathematical operations as building blocks. We demonstrate this by introducing a novel framework that significantly reduces human bias through a generic search space. Despite the vastness of this space, evolutionary search can still discover two-layer neural networks trained by backpropagation. These simple neural networks can then be surpassed by evolving directly on tasks of interest, e.g. CIFAR-10 variants, where modern techniques emerge in the top algorithms, such as bilinear interactions, normalized gradients, and weight averaging. Moreover, evolution adapts algorithms to different task types: e.g., dropout-like techniques appear when little data is available. We believe these preliminary successes in discovering machine learning algorithms from scratch indicate a promising new direction for the field.

Recently, deep learning techniques have shown great success in automatic code generation. Inspired by the code reuse, some researchers propose copy-based approaches that can copy the content from similar code snippets to obtain better performance. Practically, human developers recognize the content in the similar code that is relevant to their needs, which can be viewed as a code sketch. The sketch is further edited to the desired code. However, existing copy-based approaches ignore the code sketches and tend to repeat the similar code without necessary modifications, which leads to generating wrong results. In this paper, we propose a sketch-based code generation approach named SkCoder to mimic developers' code reuse behavior. Given a natural language requirement, SkCoder retrieves a similar code snippet, extracts relevant parts as a code sketch, and edits the sketch into the desired code. Our motivations are that the extracted sketch provides a well-formed pattern for telling models "how to write". The post-editing further adds requirement-specific details to the sketch and outputs the complete code. We conduct experiments on two public datasets and a new dataset collected by this work. We compare our approach to 20 baselines using 5 widely used metrics. Experimental results show that (1) SkCoder can generate more correct programs, and outperforms the state-of-the-art - CodeT5-base by 30.30%, 35.39%, and 29.62% on three datasets. (2) Our approach is effective to multiple code generation models and improves them by up to 120.1% in Pass@1. (3) We investigate three plausible code sketches and discuss the importance of sketches. (4) We manually evaluate the generated code and prove the superiority of our SkCoder in three aspects.

In the past few years, Differentiable Neural Architecture Search (DNAS) rapidly imposed itself as the trending approach to automate the discovery of deep neural network architectures. This rise is mainly due to the popularity of DARTS, one of the first major DNAS methods. In contrast with previous works based on Reinforcement Learning or Evolutionary Algorithms, DNAS is faster by several orders of magnitude and uses fewer computational resources. In this comprehensive survey, we focus specifically on DNAS and review recent approaches in this field. Furthermore, we propose a novel challenge-based taxonomy to classify DNAS methods. We also discuss the contributions brought to DNAS in the past few years and its impact on the global NAS field. Finally, we conclude by giving some insights into future research directions for the DNAS field.

We present a new implementation of the LLM-driven genetic algorithm {\it funsearch}, whose aim is to generate examples of interest to mathematicians and which has already had some success in problems in extremal combinatorics. Our implementation is designed to be useful in practice for working mathematicians; it does not require expertise in machine learning or access to high-performance computing resources. Applying {\it funsearch} to a new problem involves modifying a small segment of Python code and selecting a large language model (LLM) from one of many third-party providers. We benchmarked our implementation on three different problems, obtaining metrics that may inform applications of {\it funsearch} to new problems. Our results demonstrate that {\it funsearch} successfully learns in a variety of combinatorial and number-theoretic settings, and in some contexts learns principles that generalize beyond the problem originally trained on.

Recently, Stitchable Neural Networks (SN-Net) is proposed to stitch some pre-trained networks for quickly building numerous networks with different complexity and performance trade-offs. In this way, the burdens of designing or training the variable-sized networks, which can be used in application scenarios with diverse resource constraints, are alleviated. However, SN-Net still faces a few challenges. 1) Stitching from multiple independently pre-trained anchors introduces high storage resource consumption. 2) SN-Net faces challenges to build smaller models for low resource constraints. 3). SN-Net uses an unlearned initialization method for stitch layers, limiting the final performance. To overcome these challenges, motivated by the recently proposed Learngene framework, we propose a novel method called Learngene Pool. Briefly, Learngene distills the critical knowledge from a large pre-trained model into a small part (termed as learngene) and then expands this small part into a few variable-sized models. In our proposed method, we distill one pretrained large model into multiple small models whose network blocks are used as learngene instances to construct the learngene pool. Since only one large model is used, we do not need to store more large models as SN-Net and after distilling, smaller learngene instances can be created to build small models to satisfy low resource constraints. We also insert learnable transformation matrices between the instances to stitch them into variable-sized models to improve the performance of these models. Exhaustive experiments have been implemented and the results validate the effectiveness of the proposed Learngene Pool compared with SN-Net.

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

We present POTATO, a task- and languageindependent framework for human-in-the-loop (HITL) learning of rule-based text classifiers using graph-based features. POTATO handles any type of directed graph and supports parsing text into Abstract Meaning Representations (AMR), Universal Dependencies (UD), and 4lang semantic graphs. A streamlit-based user interface allows users to build rule systems from graph patterns, provides real-time evaluation based on ground truth data, and suggests rules by ranking graph features using interpretable machine learning models. Users can also provide patterns over graphs using regular expressions, and POTATO can recommend refinements of such rules. POTATO is applied in projects across domains and languages, including classification tasks on German legal text and English social media data. All components of our system are written in Python, can be installed via pip, and are released under an MIT License on GitHub.

Language models (LMs), like other neural networks, often favor shortcut heuristics based on surface-level patterns. Although LMs behave like n-gram models early in training, they must eventually learn hierarchical syntactic representations to correctly apply grammatical rules out-of-distribution (OOD). In this work, we use case studies of English grammar to explore how complex, diverse training data drives models to generalize OOD. We construct a framework that unifies our understanding of random variation with training dynamics, rule selection with memorization, and data diversity with complexity. We show that these factors are nuanced, and that intermediate levels of diversity and complexity lead to inconsistent behavior across random seeds and to unstable training dynamics. Our findings emphasize the critical role of training data in shaping generalization patterns and illuminate how competing model strategies lead to inconsistent generalization outcomes across random seeds. Code is available at https://github.com/sunnytqin/concept_comp.git.

Iterative improvement of model architectures is fundamental to deep learning: Transformers first enabled scaling, and recent advances in model hybridization have pushed the quality-efficiency frontier. However, optimizing architectures remains challenging and expensive. Current automated or manual approaches fall short, largely due to limited progress in the design of search spaces and due to the simplicity of resulting patterns and heuristics. In this work, we propose a new approach for the synthesis of tailored architectures (STAR). Our approach combines a novel search space based on the theory of linear input-varying systems, supporting a hierarchical numerical encoding into architecture genomes. STAR genomes are automatically refined and recombined with gradient-free, evolutionary algorithms to optimize for multiple model quality and efficiency metrics. Using STAR, we optimize large populations of new architectures, leveraging diverse computational units and interconnection patterns, improving over highly-optimized Transformers and striped hybrid models on the frontier of quality, parameter size, and inference cache for autoregressive language modeling.

Generative modeling of discrete variables is challenging yet crucial for applications in natural language processing and biological sequence design. We introduce the Shortlisting Model (SLM), a novel simplex-based diffusion model inspired by progressive candidate pruning. SLM operates on simplex centroids, reducing generation complexity and enhancing scalability. Additionally, SLM incorporates a flexible implementation of classifier-free guidance, enhancing unconditional generation performance. Extensive experiments on DNA promoter and enhancer design, protein design, character-level and large-vocabulary language modeling demonstrate the competitive performance and strong potential of SLM. Our code can be found at https://github.com/GenSI-THUAIR/SLM

This work introduces a general code generation framework that incorporates infilling operations into auto-regressive decoding. Our approach capitalizes on the observation that recent code language models with infilling capabilities can perform self-infilling: whereas infilling operations aim to fill in the middle based on a predefined prefix and suffix, self-infilling sequentially generates both such surrounding context and the infilled content. We utilize this feature to develop an infilling-augmented decoding process that facilitates non-monotonic generation. This approach allows for postponing the generation of uncertain code snippets until a definitive suffix is established, leading to improved control over the generation sequence. In addition, it facilitates a looping mechanism, which can iteratively update and synchronize each piece of generation in a cyclic manner. Extensive experiments are conducted to demonstrate that our proposed decoding process is effective in enhancing regularity and quality across several code generation benchmarks.

Large language models (LLMs) fine-tuned with reinforcement learning from human feedback (RLHF) have been used in some of the most widely deployed AI models to date, such as OpenAI's ChatGPT, Anthropic's Claude, or Meta's LLaMA-2. While there has been significant work developing these methods, our understanding of the benefits and downsides of each stage in RLHF is still limited. To fill this gap, we present an extensive analysis of how each stage of the process (i.e. supervised fine-tuning (SFT), reward modelling, and RLHF) affects two key properties: out-of-distribution (OOD) generalisation and output diversity. OOD generalisation is crucial given the wide range of real-world scenarios in which these models are being used, while output diversity refers to the model's ability to generate varied outputs and is important for a variety of use cases. We perform our analysis across two base models on both summarisation and instruction following tasks, the latter being highly relevant for current LLM use cases. We find that RLHF generalises better than SFT to new inputs, particularly as the distribution shift between train and test becomes larger. However, RLHF significantly reduces output diversity compared to SFT across a variety of measures, implying a tradeoff in current LLM fine-tuning methods between generalisation and diversity. Our results provide guidance on which fine-tuning method should be used depending on the application, and show that more research is needed to improve the trade-off between generalisation and diversity.

We present the Chinese Elementary School Math Word Problems (CMATH) dataset, comprising 1.7k elementary school-level math word problems with detailed annotations, source from actual Chinese workbooks and exams. This dataset aims to provide a benchmark tool for assessing the following question: to what grade level of elementary school math do the abilities of popular large language models (LLMs) correspond? We evaluate a variety of popular LLMs, including both commercial and open-source options, and discover that only GPT-4 achieves success (accuracy geq 60\%) across all six elementary school grades, while other models falter at different grade levels. Furthermore, we assess the robustness of several top-performing LLMs by augmenting the original problems in the CMATH dataset with distracting information. Our findings reveal that GPT-4 is able to maintains robustness, while other model fail. We anticipate that our study will expose limitations in LLMs' arithmetic and reasoning capabilities, and promote their ongoing development and advancement.

Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the sequence-to-sequence (seq2seq) framework which employs the chain rule to efficiently represent the joint probability of sequences. In many cases, however, variable sized inputs and/or outputs might not be naturally expressed as sequences. For instance, it is not clear how to input a set of numbers into a model where the task is to sort them; similarly, we do not know how to organize outputs when they correspond to random variables and the task is to model their unknown joint probability. In this paper, we first show using various examples that the order in which we organize input and/or output data matters significantly when learning an underlying model. We then discuss an extension of the seq2seq framework that goes beyond sequences and handles input sets in a principled way. In addition, we propose a loss which, by searching over possible orders during training, deals with the lack of structure of output sets. We show empirical evidence of our claims regarding ordering, and on the modifications to the seq2seq framework on benchmark language modeling and parsing tasks, as well as two artificial tasks -- sorting numbers and estimating the joint probability of unknown graphical models.

We investigate the problem of producing structured graph representations of visual scenes. Our work analyzes the role of motifs: regularly appearing substructures in scene graphs. We present new quantitative insights on such repeated structures in the Visual Genome dataset. Our analysis shows that object labels are highly predictive of relation labels but not vice-versa. We also find that there are recurring patterns even in larger subgraphs: more than 50% of graphs contain motifs involving at least two relations. Our analysis motivates a new baseline: given object detections, predict the most frequent relation between object pairs with the given labels, as seen in the training set. This baseline improves on the previous state-of-the-art by an average of 3.6% relative improvement across evaluation settings. We then introduce Stacked Motif Networks, a new architecture designed to capture higher order motifs in scene graphs that further improves over our strong baseline by an average 7.1% relative gain. Our code is available at github.com/rowanz/neural-motifs.

The lottery ticket hypothesis (LTH) has increased attention to pruning neural networks at initialization. We study this problem in the linear setting. We show that finding a sparse mask at initialization is equivalent to the sketching problem introduced for efficient matrix multiplication. This gives us tools to analyze the LTH problem and gain insights into it. Specifically, using the mask found at initialization, we bound the approximation error of the pruned linear model at the end of training. We theoretically justify previous empirical evidence that the search for sparse networks may be data independent. By using the sketching perspective, we suggest a generic improvement to existing algorithms for pruning at initialization, which we show to be beneficial in the data-independent case.

We introduce a new neural architecture to learn the conditional probability of an output sequence with elements that are discrete tokens corresponding to positions in an input sequence. Such problems cannot be trivially addressed by existent approaches such as sequence-to-sequence and Neural Turing Machines, because the number of target classes in each step of the output depends on the length of the input, which is variable. Problems such as sorting variable sized sequences, and various combinatorial optimization problems belong to this class. Our model solves the problem of variable size output dictionaries using a recently proposed mechanism of neural attention. It differs from the previous attention attempts in that, instead of using attention to blend hidden units of an encoder to a context vector at each decoder step, it uses attention as a pointer to select a member of the input sequence as the output. We call this architecture a Pointer Net (Ptr-Net). We show Ptr-Nets can be used to learn approximate solutions to three challenging geometric problems -- finding planar convex hulls, computing Delaunay triangulations, and the planar Travelling Salesman Problem -- using training examples alone. Ptr-Nets not only improve over sequence-to-sequence with input attention, but also allow us to generalize to variable size output dictionaries. We show that the learnt models generalize beyond the maximum lengths they were trained on. We hope our results on these tasks will encourage a broader exploration of neural learning for discrete problems.

We explore the relations between the zeta distribution and algorithmic information theory via a new model of the transfer learning problem. The program distribution is approximated by a zeta distribution with parameter near 1. We model the training sequence as a stochastic process. We analyze the upper temporal bound for learning a training sequence and its entropy rates, assuming an oracle for the transfer learning problem. We argue from empirical evidence that power-law models are suitable for natural processes. Four sequence models are proposed. Random typing model is like no-free lunch where transfer learning does not work. Zeta process independently samples programs from the zeta distribution. A model of common sub-programs inspired by genetics uses a database of sub-programs. An evolutionary zeta process samples mutations from Zeta distribution. The analysis of stochastic processes inspired by evolution suggest that AI may be feasible in nature, countering no-free lunch sort of arguments.

We report a peculiar observation that LLMs can assign hidden meanings to sequences that seem visually incomprehensible to humans: for example, a nonsensical phrase consisting of Byzantine musical symbols is recognized by gpt-4o as "say abracadabra". Moreover, some models can communicate using these sequences. Some of these meanings are hypothesized to partly originate in the massive spurious correlations due to BPE tokenization. We systematically evaluate the presence of such abilities in a wide range of models: Claude-3.5 Haiku, Claude-3.5 Sonnet (New and Old), Claude-3.7 Sonnet, gpt-4o mini, gpt-4o, o1-mini, Llama-3.3 70B, DeepSeek-R1-Distill-Lllama 70B, Qwen2.5 1.5B, Qwen2.5 32B, Phi-3.5 mini, GigaChat-Max, Vikhr-Llama-3.2 1B. We argue that this observation might have far-reaching consequences for both safety and security of the modern and future LLMs and systems that employ them. As an illustration, we show that applying this method in combination with simple templates is sufficient to jailbreak previous generation models, with ASR = 0.4 on gpt-4o mini. Our code and data artifacts are available at https://github.com/L3G5/llm-hidden-meanings

We discover that DALLE-2 seems to have a hidden vocabulary that can be used to generate images with absurd prompts. For example, it seems that Apoploe vesrreaitais means birds and Contarra ccetnxniams luryca tanniounons (sometimes) means bugs or pests. We find that these prompts are often consistent in isolation but also sometimes in combinations. We present our black-box method to discover words that seem random but have some correspondence to visual concepts. This creates important security and interpretability challenges.

Event sequences (ESs) arise in many practical domains including finance, retail, social networks, and healthcare. In the context of machine learning, event sequences can be seen as a special type of tabular data with annotated timestamps. Despite the importance of ESs modeling and analysis, little effort was made in adapting large language models (LLMs) to the ESs domain. In this paper, we highlight the common difficulties of ESs processing and propose a novel solution capable of solving multiple downstream tasks with little or no finetuning. In particular, we solve the problem of working with long sequences and improve time and numeric features processing. The resulting method, called ESQA, effectively utilizes the power of LLMs and, according to extensive experiments, achieves state-of-the-art results in the ESs domain.

While scaling training compute has led to remarkable improvements in large language models (LLMs), scaling inference compute has not yet yielded analogous gains. We hypothesize that a core missing component is a lack of diverse LLM outputs, leading to inefficient search due to models repeatedly sampling highly similar, yet incorrect generations. We empirically demonstrate that this lack of diversity can be mitigated by searching over candidate plans for solving a problem in natural language. Based on this insight, we propose PLANSEARCH, a novel search algorithm which shows strong results across HumanEval+, MBPP+, and LiveCodeBench (a contamination-free benchmark for competitive coding). PLANSEARCH generates a diverse set of observations about the problem and then uses these observations to construct plans for solving the problem. By searching over plans in natural language rather than directly over code solutions, PLANSEARCH explores a significantly more diverse range of potential solutions compared to baseline search methods. Using PLANSEARCH on top of Claude 3.5 Sonnet achieves a state-of-the-art pass@200 of 77.0% on LiveCodeBench, outperforming both the best score achieved without search (pass@1 = 41.4%) and using standard repeated sampling (pass@200 = 60.6%). Finally, we show that, across all models, search algorithms, and benchmarks analyzed, we can accurately predict performance gains due to search as a direct function of the diversity over generated ideas.

Commit messages are a valuable resource in comprehension of software evolution, since they provide a record of changes such as feature additions and bug repairs. Unfortunately, programmers often neglect to write good commit messages. Different techniques have been proposed to help programmers by automatically writing these messages. These techniques are effective at describing what changed, but are often verbose and lack context for understanding the rationale behind a change. In contrast, humans write messages that are short and summarize the high level rationale. In this paper, we adapt Neural Machine Translation (NMT) to automatically "translate" diffs into commit messages. We trained an NMT algorithm using a corpus of diffs and human-written commit messages from the top 1k Github projects. We designed a filter to help ensure that we only trained the algorithm on higher-quality commit messages. Our evaluation uncovered a pattern in which the messages we generate tend to be either very high or very low quality. Therefore, we created a quality-assurance filter to detect cases in which we are unable to produce good messages, and return a warning instead.

Many fields use search algorithms, which automatically explore a search space to find high-performing solutions: chemists search through the space of molecules to discover new drugs; engineers search for stronger, cheaper, safer designs, scientists search for models that best explain data, etc. The goal of search algorithms has traditionally been to return the single highest-performing solution in a search space. Here we describe a new, fundamentally different type of algorithm that is more useful because it provides a holistic view of how high-performing solutions are distributed throughout a search space. It creates a map of high-performing solutions at each point in a space defined by dimensions of variation that a user gets to choose. This Multi-dimensional Archive of Phenotypic Elites (MAP-Elites) algorithm illuminates search spaces, allowing researchers to understand how interesting attributes of solutions combine to affect performance, either positively or, equally of interest, negatively. For example, a drug company may wish to understand how performance changes as the size of molecules and their cost-to-produce vary. MAP-Elites produces a large diversity of high-performing, yet qualitatively different solutions, which can be more helpful than a single, high-performing solution. Interestingly, because MAP-Elites explores more of the search space, it also tends to find a better overall solution than state-of-the-art search algorithms. We demonstrate the benefits of this new algorithm in three different problem domains ranging from producing modular neural networks to designing simulated and real soft robots. Because MAP- Elites (1) illuminates the relationship between performance and dimensions of interest in solutions, (2) returns a set of high-performing, yet diverse solutions, and (3) improves finding a single, best solution, it will advance science and engineering.

The problem of designing NLP solvers for math word problems (MWP) has seen sustained research activity and steady gains in the test accuracy. Since existing solvers achieve high performance on the benchmark datasets for elementary level MWPs containing one-unknown arithmetic word problems, such problems are often considered "solved" with the bulk of research attention moving to more complex MWPs. In this paper, we restrict our attention to English MWPs taught in grades four and lower. We provide strong evidence that the existing MWP solvers rely on shallow heuristics to achieve high performance on the benchmark datasets. To this end, we show that MWP solvers that do not have access to the question asked in the MWP can still solve a large fraction of MWPs. Similarly, models that treat MWPs as bag-of-words can also achieve surprisingly high accuracy. Further, we introduce a challenge dataset, SVAMP, created by applying carefully chosen variations over examples sampled from existing datasets. The best accuracy achieved by state-of-the-art models is substantially lower on SVAMP, thus showing that much remains to be done even for the simplest of the MWPs.

Earthquakes are evaluated among the most destructive disasters for human beings, as also experienced for Turkiye region. Data science has the property of discovering hidden patterns in case a sufficient volume of data is supplied. Time dependency of events, specifically being defined by co-occurrence in a specific time window, may be handled as an associate rule mining task such as a market-basket analysis application. In this regard, we assumed each day's seismic activity as a single basket of events, leading to discovering the association patterns between these events. Consequently, this study presents the most prominent association rules for the earthquakes recorded in Turkiye region in the last 5 years, each year presented separately. Results indicate statistical inference with events recorded from regions of various distances, which could be further verified with geologic evidence from the field. As a result, we believe that the current study may form a statistical basis for the future works with the aid of machine learning algorithm performed for associate rule mining.

Large Reasoning Models (LRMs) have demonstrated impressive performance on complex tasks, including logical puzzle games that require deriving solutions satisfying all constraints. However, whether they can flexibly apply appropriate rules to varying conditions, particularly when faced with non-canonical game variants, remains an open question. Existing corpora focus on popular puzzles like 9x9 Sudoku, risking overfitting to canonical formats and memorization of solution patterns, which can mask deficiencies in understanding novel rules or adapting strategies to new variants. To address this, we introduce HardcoreLogic, a challenging benchmark of over 5,000 puzzles across 10 games, designed to test the robustness of LRMs on the "long-tail" of logical games. HardcoreLogic systematically transforms canonical puzzles through three dimensions: Increased Complexity (IC), Uncommon Elements (UE), and Unsolvable Puzzles (UP), reducing reliance on shortcut memorization. Evaluations on a diverse set of LRMs reveal significant performance drops, even for models achieving top scores on existing benchmarks, indicating heavy reliance on memorized stereotypes. While increased complexity is the dominant source of difficulty, models also struggle with subtle rule variations that do not necessarily increase puzzle difficulty. Our systematic error analysis on solvable and unsolvable puzzles further highlights gaps in genuine reasoning. Overall, HardcoreLogic exposes the limitations of current LRMs and establishes a benchmark for advancing high-level logical reasoning.

Pretrained language models have shown superior performance on many natural language processing tasks, yet they still struggle at multi-step formal reasoning tasks like grade school math problems. One key challenge of finetuning them to solve such math reasoning problems is that many existing datasets only contain one reference solution for each problem, despite the fact that there are often alternative solutions resembling different reasoning paths to the final answer. This way, the finetuned models are biased towards the limited reference solutions, which limits their generalization to unseen examples. To mitigate this issue, we propose to let the model perform sampling during training and learn from both self-sampled fully-correct solutions, which yield the correct answer upon execution, and partially-correct solutions, whose intermediate state matches an intermediate state of a known correct solution. We show that our use of self-sampled correct and partially-correct solutions can benefit learning and help guide the sampling process, leading to more efficient exploration of the solution space. Additionally, we explore various training objectives to support learning from multiple solutions per example and find they greatly affect the performance. Experiments on two math reasoning datasets show the effectiveness of our method compared to learning from a single reference solution with MLE, where we improve PASS@100 from 35.5% to 44.5% for GSM8K, and 27.6% to 36.2% PASS@80 for MathQA. Such improvements are also consistent across different model sizes. Our code is available at https://github.com/microsoft/TraceCodegen.

Recent work such as AlphaEvolve has shown that combining LLM-driven optimization with evolutionary search can effectively improve programs, prompts, and algorithms across domains. In this paradigm, previously evaluated solutions are reused to guide the model toward new candidate solutions. Crucially, the effectiveness of this evolution process depends on the search strategy: how prior solutions are selected and varied to generate new candidates. However, most existing methods rely on fixed search strategies with predefined knobs (e.g., explore-exploit ratios) that remain static throughout execution. While effective in some settings, these approaches often fail to adapt across tasks, or even within the same task as the search space changes over time. We introduce EvoX, an adaptive evolution method that optimizes its own evolution process. EvoX jointly evolves candidate solutions and the search strategies used to generate them, continuously updating how prior solutions are selected and varied based on progress. This enables the system to dynamically shift between different search strategies during the optimization process. Across nearly 200 real-world optimization tasks, EvoX outperforms existing AI-driven evolutionary methods including AlphaEvolve, OpenEvolve, GEPA, and ShinkaEvolve on the majority of tasks.

Automated Machine Learning (AutoML) systems have been shown to efficiently build good models for new datasets. However, it is often not clear how well they can adapt when the data evolves over time. The main goal of this study is to understand the effect of data stream challenges such as concept drift on the performance of AutoML methods, and which adaptation strategies can be employed to make them more robust. To that end, we propose 6 concept drift adaptation strategies and evaluate their effectiveness on different AutoML approaches. We do this for a variety of AutoML approaches for building machine learning pipelines, including those that leverage Bayesian optimization, genetic programming, and random search with automated stacking. These are evaluated empirically on real-world and synthetic data streams with different types of concept drift. Based on this analysis, we propose ways to develop more sophisticated and robust AutoML techniques.

ClueWeb22, the newest iteration of the ClueWeb line of datasets, provides 10 billion web pages affiliated with rich information. Its design was influenced by the need for a high quality, large scale web corpus to support a range of academic and industry research, for example, in information systems, retrieval-augmented AI systems, and model pretraining. Compared with earlier ClueWeb corpora, the ClueWeb22 corpus is larger, more varied, of higher-quality, and aligned with the document distributions in commercial web search. Besides raw HTML, ClueWeb22 includes rich information about the web pages provided by industry-standard document understanding systems, including the visual representation of pages rendered by a web browser, parsed HTML structure information from a neural network parser, and pre-processed cleaned document text to lower the barrier to entry. Many of these signals have been widely used in industry but are available to the research community for the first time at this scale.

Retrieval algorithms like BM25 and query likelihood with Dirichlet smoothing remain strong and efficient first-stage rankers, yet improvements have mostly relied on parameter tuning and human intuition. We investigate whether a large language model, guided by an evaluator and evolutionary search, can automatically discover improved lexical retrieval algorithms. We introduce RankEvolve, a program evolution setup based on AlphaEvolve, in which candidate ranking algorithms are represented as executable code and iteratively mutated, recombined, and selected based on retrieval performance across 12 IR datasets from BEIR and BRIGHT. RankEvolve starts from two seed programs: BM25 and query likelihood with Dirichlet smoothing. The evolved algorithms are novel, effective, and show promising transfer to the full BEIR and BRIGHT benchmarks as well as TREC DL 19 and 20. Our results suggest that evaluator-guided LLM program evolution is a practical path towards automatic discovery of novel ranking algorithms.

Large Language Models (LLMs) can comply with harmful instructions, raising serious safety concerns despite their impressive capabilities. Recent work has leveraged probing-based approaches to study the separability of malicious and benign inputs in LLMs' internal representations, and researchers have proposed using such probing methods for safety detection. We systematically re-examine this paradigm. Motivated by poor out-of-distribution performance, we hypothesize that probes learn superficial patterns rather than semantic harmfulness. Through controlled experiments, we confirm this hypothesis and identify the specific patterns learned: instructional patterns and trigger words. Our investigation follows a systematic approach, progressing from demonstrating comparable performance of simple n-gram methods, to controlled experiments with semantically cleaned datasets, to detailed analysis of pattern dependencies. These results reveal a false sense of security around current probing-based approaches and highlight the need to redesign both models and evaluation protocols, for which we provide further discussions in the hope of suggesting responsible further research in this direction. We have open-sourced the project at https://github.com/WangCheng0116/Why-Probe-Fails.

Large language models have achieved substantial progress in mathematical reasoning, yet their advancement is limited by the scarcity of high-quality, high-difficulty training data. Existing synthesis methods largely rely on transforming human-written templates, limiting both diversity and scalability. We propose MathSmith, a novel framework for synthesizing challenging mathematical problems to enhance LLM reasoning. Rather than modifying existing problems, MathSmith constructs new ones from scratch by randomly sampling concept-explanation pairs from PlanetMath, ensuring data independence and avoiding contamination. To increase difficulty, we design nine predefined strategies as soft constraints during rationales. We further adopts reinforcement learning to jointly optimize structural validity, reasoning complexity, and answer consistency. The length of the reasoning trace generated under autoregressive prompting is used to reflect cognitive complexity, encouraging the creation of more demanding problems aligned with long-chain-of-thought reasoning. Experiments across five benchmarks, categorized as easy & medium (GSM8K, MATH-500) and hard (AIME2024, AIME2025, OlympiadBench), show that MathSmith consistently outperforms existing baselines under both short and long CoT settings. Additionally, a weakness-focused variant generation module enables targeted improvement on specific concepts. Overall, MathSmith exhibits strong scalability, generalization, and transferability, highlighting the promise of high-difficulty synthetic data in advancing LLM reasoning capabilities.

Diverse outputs in text generation are necessary for effective exploration in complex reasoning tasks, such as code generation and mathematical problem solving. Such Pass@k problems benefit from distinct candidates covering the solution space. However, traditional sampling approaches often waste computational resources on repetitive failure modes. While Diffusion Language Models have emerged as a competitive alternative to the prevailing Autoregressive paradigm, they remain susceptible to this redundancy, with independent samples frequently collapsing into similar modes. To address this, we propose a training free, low cost intervention to enhance generative diversity in Diffusion Language Models. Our approach modifies intermediate samples in a batch sequentially, where each sample is repelled from the feature space of previous samples, actively penalising redundancy. Unlike prior methods that require retraining or beam search, our strategy incurs negligible computational overhead, while ensuring that each sample contributes a unique perspective to the batch. We evaluate our method on the HumanEval and GSM8K benchmarks using the LLaDA-8B-Instruct model. Our results demonstrate significantly improved diversity and Pass@k performance across various temperature settings. As a simple modification to the sampling process, our method offers an immediate, low-cost improvement for current and future Diffusion Language Models in tasks that benefit from diverse solution search. We make our code available at https://github.com/sean-lamont/odd.

In recent years, large language models (LLMs) have achieved state-of-the-art results in various biological sequence analysis tasks, such as sequence classification, structure prediction, and function prediction. Similar to advancements in AI for other scientific fields, deeper research into biological LLMs has begun to focus on using these models to rediscover important existing biological laws or uncover entirely new patterns in biological sequences.This study leverages GPT-like LLMs to utilize language transfer capabilities to rediscover the genetic code rules of the central dogma. In our experimental design, we transformed the central dogma into a binary classification problem of aligning DNA sequences with protein sequences, where positive examples are matching DNA and protein sequences, and negative examples are non-matching pairs.We first trained a GPT-2 model from scratch using a dataset comprising protein sequences, DNA sequences, and sequences from languages such as English and Chinese. Subsequently, we fine-tuned the model using the English similarity judgment dataset from PAWS-X. When tested on a dataset for DNA and protein sequence alignment judgment, the fine-tuned model achieved a classification accuracy of 76%. The study also analyzed factors contributing to this zero-shot capability, including model training stability and types of training data.This research demonstrates that LLMs can, through the transfer of natural language capabilities and solely relying on the analysis of sequences themselves, rediscover the central dogma without prior knowledge of it. This study opens a new door for AI-driven biological research.

During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns within the genome or a specific gene. In this project, we harnessed the power of Large Language Models(LLMs) to predict the evolution of SARS-CoV-2. By treating the mutation process from one generation to the next as a translation task, we trained a transformer model, called VirusT5, to capture the mutation patterns underlying SARS-CoV-2 evolution. We evaluated the VirusT5's ability to detect these mutation patterns including its ability to identify mutation hotspots and explored the potential of using VirusT5 to predict future virus variants. Our findings demonstrate the feasibility of using a large language model to model viral evolution as a translation process. This study establishes the groundbreaking concept of "mutation-as-translation," paving the way for new methodologies and tools for combating virus threats