Daily Papers

Person re-identification (re-id) remains challenging due to significant intra-class variations across different cameras. Recently, there has been a growing interest in using generative models to augment training data and enhance the invariance to input changes. The generative pipelines in existing methods, however, stay relatively separate from the discriminative re-id learning stages. Accordingly, re-id models are often trained in a straightforward manner on the generated data. In this paper, we seek to improve learned re-id embeddings by better leveraging the generated data. To this end, we propose a joint learning framework that couples re-id learning and data generation end-to-end. Our model involves a generative module that separately encodes each person into an appearance code and a structure code, and a discriminative module that shares the appearance encoder with the generative module. By switching the appearance or structure codes, the generative module is able to generate high-quality cross-id composed images, which are online fed back to the appearance encoder and used to improve the discriminative module. The proposed joint learning framework renders significant improvement over the baseline without using generated data, leading to the state-of-the-art performance on several benchmark datasets.

Continual learning, the ability of AI systems to improve through sequential experience, has attracted substantial interest, but no high-quality benchmark exists to evaluate it. We introduce Continual Learning Bench (CL-Bench), the first difficult, expert-validated benchmark designed to measure whether LLM-based systems genuinely improve with experience. CL-Bench spans six diverse domains (software engineering, signal processing, disease outbreak forecasting, database querying, strategic game-playing, and demand forecasting), each validated by domain experts and designed so that tasks share a learnable latent structure (codebase layout, disease outbreak dynamics, opponent strategies) that a stateful system can discover online but a stateless one cannot. We evaluate frontier models across several agent architectures, from naive in-context learning (ICL) to dedicated memory systems, introducing a gain metric to isolate learning from prior capabilities. We find that these systems leave headroom for improved continual learning: agents frequently overfit to immediate observations or fail to reuse knowledge across instances, and dedicated memory systems do not fix this -- in fact, naive ICL outperforms systems dedicated to memory management. CL-Bench is the first benchmark to evaluate continual learning across diverse real-world domains with expert-validated tasks and isolate online learning from underlying model capability, showing a need for better continual learning systems.

Different from the flow semantics of natural languages, programming languages are inherently rigid in structure and grammar. Existing fine-tuning methodologies for code vulnerability detection generally treat code as long text sequences, stripping away structural elements such as newlines ('/n') and whitespace. However, this approach inadvertently results in the loss of crucial structural information, diminishing the distinct characteristics of code and impairing the accuracy of vulnerability detection. To address these challenges, we propose a novel network architecture method based on pre-trained code models, which incorporates structural information awareness. We propose an enhanced code text processing workflow that retains structural elements prior to modeling. This refinement allows the model to retain and exploit line-level structural information and semantic information during the modeling process. Furthermore, we introduce a new network architecture, the Code Structure-Aware Network through Line-level Semantic Learning (CSLS), which integrates three key components: global vulnerability awareness, line-structural awareness, and sensitive-line awareness. We have conducted comprehensive experiments using vulnerability detection datasets from real-world projects. Extensive experiments were conducted on vulnerability detection datasets derived from real-world projects. The results demonstrate that our new code pre-processing flow significantly improves existing baselines (e.g., a 3\% accuracy improvement on the Devign dataset when applied to popular models such as CoderBert and UniXcoder). The proposed network architecture also demonstrates superior accuracy in detecting vulnerabilities, surpassing newly established benchmarks. These findings underscore the importance of structural information in enhancing the efficacy of code vulnerability detection models.

LLM-based code agents navigate repositories through keyword search but miss the structural relationships, such as call graphs, inheritance hierarchies, and configuration dependencies, that define how software actually works. This makes agent navigation stochastic and difficult to reproduce across runs. We investigate whether lightweight static analysis can provide deterministic anchors for these agents: stable structural facts injected as plain-text comments that constrain probabilistic exploration and make navigation more predictable. Starting from a strong baseline, Codex from OpenAI, we systematically inject varying granularities of structural annotations and measure their effects on localization, trajectory behavior, and run-to-run stability. Our study identifies what we call the deterministic anchoring effect: static structure helps less by making agents "smarter" and more by making their navigation disciplined and reproducible. Three observations support this finding: (1) Anchoring works: lightweight call/inheritance topology improves function-level localization (+2.2pp Func@5) and shortens trajectories (-1.6 interaction rounds); (2) Anchoring is scale-sensitive: the optimal granularity and directionality depend on repository characteristics, where denser semantics show diminishing returns and hub-heavy projects benefit from inverse-only links that expose "who-calls-me" without forward edges; (3) Anchoring stabilizes: tags raise link-following rate from 0.15-0.18 to 0.21-0.24, roughly halve run-to-run variance, and improve single-run reliability (Pass@1 +3.4 pp) on medium-scale repositories, at the cost of roughly 10% more input tokens. These observations suggest practical guidelines: default to lightweight topology on medium projects, prune forward edges in large repositories, and reserve dense tags for implicit-dependency cases.

Large language models (LLMs) have made significant advancements in code-related tasks, yet many LLMs treat code as simple sequences, neglecting its structured nature. We introduce AST-T5, a novel pretraining paradigm that leverages the Abstract Syntax Tree (AST) for enhanced code generation, transpilation, and understanding. Using dynamic programming, our AST-Aware Segmentation retains code structure, while our AST-Aware Span Corruption objective equips the model to reconstruct various code structures. Unlike other models, AST-T5 avoids intricate program analyses or architectural changes, so it integrates seamlessly with any encoder-decoder Transformer. Evaluations show that AST-T5 consistently outperforms similar-sized LMs across various code-related tasks. Structure-awareness makes AST-T5 particularly powerful in code-to-code tasks, surpassing CodeT5 by 2 points in exact match score for the Bugs2Fix task and by 3 points in exact match score for Java-C# Transpilation in CodeXGLUE. Our code and model are publicly available at https://github.com/gonglinyuan/ast_t5.

Code pre-trained models (CodePTMs) have recently demonstrated significant success in code intelligence. To interpret these models, some probing methods have been applied. However, these methods fail to consider the inherent characteristics of codes. In this paper, to address the problem, we propose a novel probing method CAT-probing to quantitatively interpret how CodePTMs attend code structure. We first denoise the input code sequences based on the token types pre-defined by the compilers to filter those tokens whose attention scores are too small. After that, we define a new metric CAT-score to measure the commonality between the token-level attention scores generated in CodePTMs and the pair-wise distances between corresponding AST nodes. The higher the CAT-score, the stronger the ability of CodePTMs to capture code structure. We conduct extensive experiments to integrate CAT-probing with representative CodePTMs for different programming languages. Experimental results show the effectiveness of CAT-probing in CodePTM interpretation. Our codes and data are publicly available at https://github.com/nchen909/CodeAttention.

Pre-trained models for programming language have achieved dramatic empirical improvements on a variety of code-related tasks such as code search, code completion, code summarization, etc. However, existing pre-trained models regard a code snippet as a sequence of tokens, while ignoring the inherent structure of code, which provides crucial code semantics and would enhance the code understanding process. We present GraphCodeBERT, a pre-trained model for programming language that considers the inherent structure of code. Instead of taking syntactic-level structure of code like abstract syntax tree (AST), we use data flow in the pre-training stage, which is a semantic-level structure of code that encodes the relation of "where-the-value-comes-from" between variables. Such a semantic-level structure is neat and does not bring an unnecessarily deep hierarchy of AST, the property of which makes the model more efficient. We develop GraphCodeBERT based on Transformer. In addition to using the task of masked language modeling, we introduce two structure-aware pre-training tasks. One is to predict code structure edges, and the other is to align representations between source code and code structure. We implement the model in an efficient way with a graph-guided masked attention function to incorporate the code structure. We evaluate our model on four tasks, including code search, clone detection, code translation, and code refinement. Results show that code structure and newly introduced pre-training tasks can improve GraphCodeBERT and achieves state-of-the-art performance on the four downstream tasks. We further show that the model prefers structure-level attentions over token-level attentions in the task of code search.

Code generation is a core application of large language models (LLMs), yet LLMs still frequently fail on complex programming tasks. Given its success in mathematical reasoning, test-time scaling approaches such as Process Reward Model (PRM)-based Best-of-N selection offer a promising way to improve performance. However, existing PRMs remain ineffective for code generation due to the lack of meaningful step decomposition in code and the noise of Monte Carlo-estimated partial-solution correctness scores (rewards). To address these challenges, we propose FunPRM. FunPRM prompts LLMs to encourage modular code generation organized into functions, with functions treated as PRM reasoning steps. Furthermore, FunPRM introduces a novel meta-learning-based reward correction mechanism that leverages clean final-solution rewards obtained via a unit-test-based evaluation system to purify noisy partial-solution rewards. Experiments on LiveCodeBench and BigCodeBench demonstrate that FunPRM consistently outperforms existing test-time scaling methods across five base LLMs, notably achieving state-of-the-art performance on LiveCodeBench when combined with O4-mini. Furthermore, FunPRM produces code that is more readable and reusable for developers.

Pre-trained programming language (PL) models (such as CodeT5, CodeBERT, GraphCodeBERT, etc.,) have the potential to automate software engineering tasks involving code understanding and code generation. However, these models operate in the natural channel of code, i.e., they are primarily concerned with the human understanding of the code. They are not robust to changes in the input and thus, are potentially susceptible to adversarial attacks in the natural channel. We propose, CodeAttack, a simple yet effective black-box attack model that uses code structure to generate effective, efficient, and imperceptible adversarial code samples and demonstrates the vulnerabilities of the state-of-the-art PL models to code-specific adversarial attacks. We evaluate the transferability of CodeAttack on several code-code (translation and repair) and code-NL (summarization) tasks across different programming languages. CodeAttack outperforms state-of-the-art adversarial NLP attack models to achieve the best overall drop in performance while being more efficient, imperceptible, consistent, and fluent. The code can be found at https://github.com/reddy-lab-code-research/CodeAttack.

Adapting Deep Learning (DL) techniques to automate non-trivial coding activities, such as code documentation and defect detection, has been intensively studied recently. Learning to predict code changes is one of the popular and essential investigations. Prior studies have shown that DL techniques such as Neural Machine Translation (NMT) can benefit meaningful code changes, including bug fixing and code refactoring. However, NMT models may encounter bottleneck when modeling long sequences, thus are limited in accurately predicting code changes. In this work, we design a Transformer-based approach, considering that Transformer has proven effective in capturing long-term dependencies. Specifically, we propose a novel model named DTrans. For better incorporating the local structure of code, i.e., statement-level information in this paper, DTrans is designed with dynamically relative position encoding in the multi-head attention of Transformer. Experiments on benchmark datasets demonstrate that DTrans can more accurately generate patches than the state-of-the-art methods, increasing the performance by at least 5.45\%-46.57\% in terms of the exact match metric on different datasets. Moreover, DTrans can locate the lines to change with 1.75\%-24.21\% higher accuracy than the existing methods.

Supervised fine-tuning of code LLMs typically applies uniform cross-entropy loss to all response tokens, implicitly assuming that every token provides equally useful learning signal. Recent token-level selection methods challenge this assumption in natural-language SFT by supervising only high-value tokens. However, directly transferring token-level masking to code can break syntactically and semantically coherent program units, because code depends on structural completeness and definition-use relations. We therefore propose CodeBlock, a structure-aware sparse supervision framework that selects structure-complete code evidence rather than isolated tokens. CodeBlock first selects high-quality instruction-response pairs, then partitions code responses into syntactically coherent coding items, estimates their utility by aggregating generalized cross-entropy over core logic tokens, and reranks them with data-flow reach and bridge signals to prioritize blocks that propagate or connect important program dependencies. During training, the full response remains available as context, while loss is applied only to selected code items and informative natural-language tokens. Experiments on six code-generation benchmarks show that CodeBlock achieves stronger average pass@1 than full-token SFT and competitive selection baselines, while using only 1.9% of supervised response tokens.

Large language models (LLMs) have achieved strong performance on code completion tasks in general-purpose programming languages. However, existing repository-level code completion benchmarks focus almost exclusively on software code and largely overlook hardware description languages. In this work, we present MHRC-Bench, consisting of MHRC-Bench-Train and MHRC-Bench-Eval, the first benchmark designed for multilingual hardware code completion at the repository level. Our benchmark targets completion tasks and covers three major hardware design coding styles. Each completion target is annotated with code-structure-level and hardware-oriented semantic labels derived from concrete syntax tree analysis. We conduct a comprehensive evaluation of models on MHRC-Bench-Eval. Comprehensive evaluation results and analysis demonstrate the effectiveness of MHRC-Bench.

As researchers and practitioners apply Machine Learning to increasingly more software engineering problems, the approaches they use become more sophisticated. A lot of modern approaches utilize internal code structure in the form of an abstract syntax tree (AST) or its extensions: path-based representation, complex graph combining AST with additional edges. Even though the process of extracting ASTs from code can be done with different parsers, the impact of choosing a parser on the final model quality remains unstudied. Moreover, researchers often omit the exact details of extracting particular code representations. In this work, we evaluate two models, namely Code2Seq and TreeLSTM, in the method name prediction task backed by eight different parsers for the Java language. To unify the process of data preparation with different parsers, we develop SuperParser, a multi-language parser-agnostic library based on PathMiner. SuperParser facilitates the end-to-end creation of datasets suitable for training and evaluation of ML models that work with structural information from source code. Our results demonstrate that trees built by different parsers vary in their structure and content. We then analyze how this diversity affects the models' quality and show that the quality gap between the most and least suitable parsers for both models turns out to be significant. Finally, we discuss other features of the parsers that researchers and practitioners should take into account when selecting a parser along with the impact on the models' quality. The code of SuperParser is publicly available at https://doi.org/10.5281/zenodo.6366591. We also publish Java-norm, the dataset we use to evaluate the models: https://doi.org/10.5281/zenodo.6366599.

Pre-trained language models have demonstrated impressive performance in both natural language processing and program understanding, which represent the input as a token sequence without explicitly modeling its structure. Some prior works show that pre-trained language models can capture the syntactic rules of natural languages without finetuning on syntax understanding tasks. However, there is limited understanding of how well pre-trained models understand the code structure so far. In this work, we perform the first thorough benchmarking of the state-of-the-art pre-trained models for identifying the syntactic structures of programs. Specifically, we introduce CodeSyntax, a large-scale dataset of programs annotated with the syntactic relationships in their corresponding abstract syntax trees. Our key observation is that existing language models pretrained on code still lack the understanding of code syntax. In fact, these pre-trained programming language models fail to match the performance of simple baselines based on positional offsets and keywords. We also present a natural language benchmark to highlight the differences between natural languages and programming languages in terms of syntactic structure understanding. Our findings point out key limitations of existing pre-training methods for programming languages, and suggest the importance of modeling code syntactic structures.

Code retrieval is a crucial component in modern software development, particularly in large-scale projects. However, existing approaches relying on sequence-based models often fail to fully exploit the structural dependencies inherent in code, leading to suboptimal retrieval performance, particularly with structurally complex code fragments. In this paper, we introduce GNN-Coder, a novel framework based on Graph Neural Network (GNN) to utilize Abstract Syntax Tree (AST). We make the first attempt to study how GNN-integrated Transformer can promote the development of semantic retrieval tasks by capturing the structural and semantic features of code. We further propose an innovative graph pooling method tailored for AST, utilizing the number of child nodes as a key feature to highlight the intrinsic topological relationships within the AST. This design effectively integrates both sequential and hierarchical representations, enhancing the model's ability to capture code structure and semantics. Additionally, we introduce the Mean Angular Margin (MAM), a novel metric for quantifying the uniformity of code embedding distributions, providing a standardized measure of feature separability. The proposed method achieves a lower MAM, indicating a more discriminative feature representation. This underscores GNN-Coder's superior ability to distinguish between code snippets, thereby enhancing retrieval accuracy. Experimental results show that GNN-Coder significantly boosts retrieval performance, with a 1\%-10\% improvement in MRR on the CSN dataset, and a notable 20\% gain in zero-shot performance on the CosQA dataset.

A typical approach to programming is to first code the main execution scenario, and then focus on filling out alternative behaviors and corner cases. But, almost always, there exist unusual conditions that trigger atypical behaviors, which are hard to predict in program specifications, and are thus often not coded. In this paper, we consider the problem of detecting and recommending such missing behaviors, a task that we call code sophistication. Previous research on coding assistants usually focuses on recommending code fragments based on specifications of the intended behavior. In contrast, code sophistication happens in the absence of a specification, aiming to help developers complete the logic of their programs with missing and unspecified behaviors. We outline the research challenges to this problem and present early results showing how program logic can be completed by leveraging code structure and information about the usage of input parameters.

Effective instruction tuning is indispensable for optimizing code LLMs, aligning model behavior with user expectations and enhancing model performance in real-world applications. However, most existing methods focus on code snippets, which are limited to specific functionalities and rigid structures, restricting the complexity and diversity of the synthesized data. To address these limitations, we introduce a novel feature tree-based synthesis framework inspired by Abstract Syntax Trees (AST). Unlike AST, which captures syntactic structure of code, our framework models semantic relationships between code elements, enabling the generation of more nuanced and diverse data. The feature tree is constructed from raw data and refined iteratively to increase the quantity and diversity of the extracted features. This process enables the identification of more complex patterns and relationships within the code. By sampling subtrees with controlled depth and breadth, our framework allows precise adjustments to the complexity of the generated code, supporting a wide range of tasks from simple function-level operations to intricate multi-file scenarios. We fine-tuned widely-used base models to create the EpiCoder series, achieving state-of-the-art performance at both the function and file levels across multiple benchmarks. Notably, empirical evidence indicates that our approach shows significant potential in synthesizing highly complex repository-level code data. Further analysis elucidates the merits of this approach by rigorously assessing data complexity and diversity through software engineering principles and LLM-as-a-judge method.

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

Pre-trained Code Language Models (Code-PLMs) have shown many advancements and achieved state-of-the-art results for many software engineering tasks in the past few years. These models are mainly targeted for popular programming languages such as Java and Python, leaving out many other ones like R. Though R has a wide community of developers and users, there is little known about the applicability of Code-PLMs for R. In this preliminary study, we aim to investigate the vulnerability of Code-PLMs for code entities in R. For this purpose, we use an R dataset of code and comment pairs and then apply CodeAttack, a black-box attack model that uses the structure of code to generate adversarial code samples. We investigate how the model can attack different entities in R. This is the first step towards understanding the importance of R token types, compared to popular programming languages (e.g., Java). We limit our study to code summarization. Our results show that the most vulnerable code entity is the identifier, followed by some syntax tokens specific to R. The results can shed light on the importance of token types and help in developing models for code summarization and method name prediction for the R language.

Crafting effective prompts for code generation or editing with Large Language Models (LLMs) is not an easy task. Particularly, the absence of immediate, stable feedback during prompt crafting hinders effective interaction, as users are left to mentally imagine possible outcomes until the code is generated. In response, we introduce Language-Oriented Code Sketching, an interactive approach that provides instant, incremental feedback in the form of code sketches (i.e., incomplete code outlines) during prompt crafting. This approach converts a prompt into a code sketch by leveraging the inherent linguistic structures within the prompt and applying classic natural language processing techniques. The sketch then serves as an intermediate placeholder that not only previews the intended code structure but also guides the LLM towards the desired code, thereby enhancing human-LLM interaction. We conclude by discussing the approach's applicability and future plans.

We propose and release a new vulnerable source code dataset. We curate the dataset by crawling security issue websites, extracting vulnerability-fixing commits and source codes from the corresponding projects. Our new dataset contains 18,945 vulnerable functions spanning 150 CWEs and 330,492 non-vulnerable functions extracted from 7,514 commits. Our dataset covers 295 more projects than all previous datasets combined. Combining our new dataset with previous datasets, we present an analysis of the challenges and promising research directions of using deep learning for detecting software vulnerabilities. We study 11 model architectures belonging to 4 families. Our results show that deep learning is still not ready for vulnerability detection, due to high false positive rate, low F1 score, and difficulty of detecting hard CWEs. In particular, we demonstrate an important generalization challenge for the deployment of deep learning-based models. We show that increasing the volume of training data may not further improve the performance of deep learning models for vulnerability detection, but might be useful to improve the generalization ability to unseen projects. We also identify hopeful future research directions. We demonstrate that large language models (LLMs) are a promising research direction for ML-based vulnerability detection, outperforming Graph Neural Networks (GNNs) with code-structure features in our experiments. Moreover, developing source code specific pre-training objectives is a promising research direction to improve the vulnerability detection performance.

We examine in detail the accuracy, efficiency and implementation issues that arise when a simplified code structure is employed to evaluate the partition function of the two-dimensional square Ising model on periodic lattices though repeated tensor contractions.

Contemporary LLMs pretrained on code are capable of succeeding at a wide variety of programming tasks. However, their performance is very sensitive to syntactic features, such as the names of variables and types, the structure of code, and presence of type hints. We contribute an inference-time technique to make CodeLLMs more robust to syntactic distractors that are semantically irrelevant. Our methodology relies on activation steering, which involves editing internal model activations to steer the model towards the correct prediction. We contribute a novel way to construct steering vectors by taking inspiration from mutation testing, which constructs minimal semantics-breaking code edits. In contrast, we construct steering vectors from semantics-preserving code edits. We apply our approach to the task of type prediction for the gradually typed languages Python and TypeScript. This approach corrects up to 90% of type mispredictions. Finally, we show that steering vectors calculated from Python activations reliably correct type mispredictions in TypeScript, and vice versa. This result suggests that LLMs may be learning to transfer knowledge of types across programming languages.

With easier access to powerful compute resources, there is a growing trend in the field of AI for software development to develop larger and larger language models (LLMs) to address a variety of programming tasks. Even LLMs applied to tasks from the high-performance computing (HPC) domain are huge in size (e.g., billions of parameters) and demand expensive compute resources for training. We found this design choice confusing - why do we need large LLMs trained on natural languages and programming languages unrelated to HPC for HPC-specific tasks? In this line of work, we aim to question design choices made by existing LLMs by developing smaller LLMs for specific domains - we call them domain-specific LLMs. Specifically, we start off with HPC as a domain and propose a novel tokenizer named Tokompiler, designed specifically for preprocessing code in HPC and compilation-centric tasks. Tokompiler leverages knowledge of language primitives to generate language-oriented tokens, providing a context-aware understanding of code structure while avoiding human semantics attributed to code structures completely. We applied Tokompiler to pre-train two state-of-the-art models, SPT-Code and Polycoder, for a Fortran code corpus mined from GitHub. We evaluate the performance of these models against the conventional LLMs. Results demonstrate that Tokompiler significantly enhances code completion accuracy and semantic understanding compared to traditional tokenizers in normalized-perplexity tests, down to ~1 perplexity score. This research opens avenues for further advancements in domain-specific LLMs, catering to the unique demands of HPC and compilation tasks.

AI coding agents are reshaping software development through both autonomous and human-mediated pull requests (PRs). When developers use AI agents to generate code under their own accounts, code authorship attribution becomes critical for repository governance, research validity, and understanding modern development practices. We present the first study on fingerprinting AI coding agents, analyzing 33,580 PRs from five major agents (OpenAI Codex, GitHub Copilot, Devin, Cursor, Claude Code) to identify behavioral signatures. With 41 features spanning commit messages, PR structure, and code characteristics, we achieve 97.2% F1-score in multi-class agent identification. We uncover distinct fingerprints: Codex shows unique multiline commit patterns (67.5% feature importance), and Claude Code exhibits distinctive code structure (27.2% importance of conditional statements). These signatures reveal that AI coding tools produce detectable behavioral patterns, suggesting potential for identifying AI contributions in software repositories.

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.

Large Language Models (LLMs) have shown strong promise for mining Electronic Health Records (EHRs) by reasoning over longitudinal clinical information to capture context-rich patient trajectories. However, leveraging LLMs for structured EHRs (e.g., standardized diagnosis and medication codes) presents two key challenges. First, translating time-stamped EHR sequences into plain text can obscure both temporal structure and code identities, weakening the ability to capture code co-occurrence and longitudinal regularities. Second, unlike cohort-trained predictive models that learn a shared, task-aligned representation space across patients, LLMs are often applied in a case-isolated inference setting where each patient is processed independently without leveraging population-level patterns. To address these challenges, we introduce RePrompT, a time-aware LLM framework that integrates structured EHR encoders through prompt tuning, without modifying underlying architectures. Specifically, RePrompT recurrently incorporates latent states from prior visits to preserve longitudinal information, and injects population-level information through trainable prompt tokens derived from a cohort-trained, task-aligned EHR encoder. Experiments on MIMIC-III and MIMIC-IV demonstrate that RePrompT consistently outperforms both EHR-based and LLM-based baselines across multiple clinical prediction tasks.

The scaling of Large Language Models (LLMs) is increasingly limited by data quality. Most methods handle data mixing and sample selection separately, which can break the structure in code corpora. We introduce UniGeM, a framework that unifies mixing and selection by treating data curation as a manifold approximation problem without training proxy models or relying on external reference datasets. UniGeM operates hierarchically: Macro-Exploration learns mixing weights with stability-based clustering; Micro-Mining filters high-quality instances by their geometric distribution to ensure logical consistency. Validated by training 8B and 16B MoE models on 100B tokens, UniGeM achieves 2.0times data efficiency over a random baseline and further improves overall performance compared to SOTA methods in reasoning-heavy evaluations and multilingual generalization.

Recent advancements in large multimodal models (LMMs) have showcased impressive code generation capabilities, primarily evaluated through image-to-code benchmarks. However, these benchmarks are limited to specific visual programming scenarios where the logic reasoning and the multimodal understanding capacities are split apart. To fill this gap, we propose ScratchEval, a novel benchmark designed to evaluate the visual programming reasoning ability of LMMs. ScratchEval is based on Scratch, a block-based visual programming language widely used in children's programming education. By integrating visual elements and embedded programming logic, ScratchEval requires the model to process both visual information and code structure, thereby comprehensively evaluating its programming intent understanding ability. Our evaluation approach goes beyond the traditional image-to-code mapping and focuses on unified logical thinking and problem-solving abilities, providing a more comprehensive and challenging framework for evaluating the visual programming ability of LMMs. ScratchEval not only fills the gap in existing evaluation methods, but also provides new insights for the future development of LMMs in the field of visual programming. Our benchmark can be accessed at https://github.com/HKBUNLP/ScratchEval .

Agents based on large language models (LLMs) for machine learning engineering (MLE) can automatically implement ML models via code generation. However, existing approaches to build such agents often rely heavily on inherent LLM knowledge and employ coarse exploration strategies that modify the entire code structure at once. This limits their ability to select effective task-specific models and perform deep exploration within specific components, such as experimenting extensively with feature engineering options. To overcome these, we propose MLE-STAR, a novel approach to build MLE agents. MLE-STAR first leverages external knowledge by using a search engine to retrieve effective models from the web, forming an initial solution, then iteratively refines it by exploring various strategies targeting specific ML components. This exploration is guided by ablation studies analyzing the impact of individual code blocks. Furthermore, we introduce a novel ensembling method using an effective strategy suggested by MLE-STAR. Our experimental results show that MLE-STAR achieves medals in 64% of the Kaggle competitions on the MLE-bench Lite, significantly outperforming the best alternative.

Scientific diagrams are vital tools for communicating structured knowledge across disciplines. However, they are often published as static raster images, losing symbolic semantics and limiting reuse. While Multimodal Large Language Models (MLLMs) offer a pathway to bridging vision and structure, existing methods lack semantic control and structural interpretability, especially on complex diagrams. We propose Draw with Thought (DwT), a training-free framework that guides MLLMs to reconstruct diagrams into editable mxGraph XML code through cognitively-grounded Chain-of-Thought reasoning. DwT enables interpretable and controllable outputs without model fine-tuning by dividing the task into two stages: Coarse-to-Fine Planning, which handles perceptual structuring and semantic specification, and Structure-Aware Code Generation, enhanced by format-guided refinement. To support evaluation, we release Plot2XML, a benchmark of 247 real-world scientific diagrams with gold-standard XML annotations. Extensive experiments across eight MLLMs show that our approach yields high-fidelity, semantically aligned, and structurally valid reconstructions, with human evaluations confirming strong alignment in both accuracy and visual aesthetics, offering a scalable solution for converting static visuals into executable representations and advancing machine understanding of scientific graphics.

Large Language Models (LLMs) fine-tuned via Reinforcement Learning from Human Feedback (RLHF) and Reinforcement Learning with Verifiable Rewards (RLVR) significantly improve the alignment of human-AI values and further raise the upper bound of AI capabilities, particularly in reasoning-intensive, long-context Chain-of-Thought (long-CoT) tasks. However, existing RLHF (or RLVR) frameworks commonly face challenges such as inference bottlenecks and complexity barriers, restricting their accessibility for newcomers. To bridge this gap, we introduce OpenRLHF, a user-friendly, scalable, and easy-to-learn open-source RLHF framework built upon Ray, vLLM, DeepSpeed, and HuggingFace Transformers, featuring a simplified design, clear code structure, and comprehensive documentation to facilitate entry for researchers and practitioners. Experimental results show that OpenRLHF achieves superior training efficiency with speedups ranging from 1.22x to 1.68x across different model sizes compared to state-of-the-art frameworks, while requiring significantly fewer lines of code for implementation. OpenRLHF is publicly available at https://github.com/OpenRLHF/OpenRLHF, and has already been adopted by leading institutions to accelerate RLHF research and learning.

HEPfit is a flexible open-source tool which, given the Standard Model or any of its extensions, allows to i) fit the model parameters to a given set of experimental observables; ii) obtain predictions for observables. HEPfit can be used either in Monte Carlo mode, to perform a Bayesian Markov Chain Monte Carlo analysis of a given model, or as a library, to obtain predictions of observables for a given point in the parameter space of the model, allowing HEPfit to be used in any statistical framework. In the present version, around a thousand observables have been implemented in the Standard Model and in several new physics scenarios. In this paper, we describe the general structure of the code as well as models and observables implemented in the current release.

Addressing the limitation of context length in large language models for code-related tasks is the primary focus of this paper. Existing LLMs are constrained by their pre-trained context lengths, leading to performance issues in handling long complex code sequences. Inspired by how human programmers navigate code, we introduce Hierarchical Rotary Position Embedding (HiRoPE), a novel approach that enhances the traditional rotary position embedding into a hierarchical format based on the hierarchical structure of source code. HiRoPE offers easy integration into existing LLMs without extra training costs. Our method is extensively evaluated with various LLMs, demonstrating stable performance in tasks such as language modeling and long code completion. We also introduce a new long code understanding task with real-world code projects, in hopes of promoting further development in this code-related field. Theoretically and experimentally, we find that HiRoPE also addresses the out-of-distribution issue in position encoding. Our HiRoPE significantly expands the context length capabilities of LLMs, enabling inference at lengths exponentially greater than the training length.

Software security vulnerabilities allow attackers to perform malicious activities to disrupt software operations. Recent Transformer-based language models have significantly advanced vulnerability detection, surpassing the capabilities of static analysis based deep learning models. However, language models trained solely on code tokens do not capture either the explanation of vulnerability type or the data flow structure information of code, both of which are crucial for vulnerability detection. We propose a novel technique that integrates a multitask sequence-to-sequence LLM with pro-gram control flow graphs encoded as a graph neural network to achieve sequence-to-classification vulnerability detection. We introduce MSIVD, multitask self-instructed fine-tuning for vulnerability detection, inspired by chain-of-thought prompting and LLM self-instruction. Our experiments demonstrate that MSIVD achieves superior performance, outperforming the highest LLM-based vulnerability detector baseline (LineVul), with a F1 score of 0.92 on the BigVul dataset, and 0.48 on the PreciseBugs dataset. By training LLMs and GNNs simultaneously using a combination of code and explanatory metrics of a vulnerable program, MSIVD represents a promising direction for advancing LLM-based vulnerability detection that generalizes to unseen data. Based on our findings, we further discuss the necessity for new labelled security vulnerability datasets, as recent LLMs have seen or memorized prior datasets' held-out evaluation data.

Recent years have witnessed rapid advances in graph representation learning, with the continuous embedding approach emerging as the dominant paradigm. However, such methods encounter issues regarding parameter efficiency, interpretability, and robustness. Thus, Quantized Graph Representation (QGR) learning has recently gained increasing interest, which represents the graph structure with discrete codes instead of conventional continuous embeddings. Given its analogous representation form to natural language, QGR also possesses the capability to seamlessly integrate graph structures with large language models (LLMs). As this emerging paradigm is still in its infancy yet holds significant promise, we undertake this thorough survey to promote its rapid future prosperity. We first present the background of the general quantization methods and their merits. Moreover, we provide an in-depth demonstration of current QGR studies from the perspectives of quantized strategies, training objectives, distinctive designs, knowledge graph quantization, and applications. We further explore the strategies for code dependence learning and integration with LLMs. At last, we give discussions and conclude future directions, aiming to provide a comprehensive picture of QGR and inspire future research.

Fill-in-the-Middle (FIM) is a common pretraining method for code LLMs, where models complete code segments given surrounding context. However, existing LLMs treat code as plain text and mask random character spans. We propose and evaluate AST-FIM, a pretraining strategy that leverages Abstract Syntax Trees (ASTs) to mask complete syntactic structures at scale, ensuring coherent training examples better aligned with universal code structures and common code editing patterns such as blocks, expressions, or functions. To evaluate real-world fill-in-the-middle (FIM) programming tasks, we introduce Real-FIM-Eval, a benchmark derived from 30,000+ GitHub commits across 12 languages. On infilling tasks, experiments on 1B and 8B parameter models show that AST-FIM is particularly beneficial for real-world code editing as it outperforms standard random-character FIM by up to 5 pts on standard FIM benchmarks. Our code is publicly available at https://github.com/gonglinyuan/ast_fim.

There has been a recent surge of interest in automating software engineering tasks using deep learning. This paper addresses the problem of code generation, where the goal is to generate target code given source code in a different language or a natural language description. Most state-of-the-art deep learning models for code generation use training strategies primarily designed for natural language. However, understanding and generating code requires a more rigorous comprehension of the code syntax and semantics. With this motivation, we develop an encoder-decoder Transformer model where both the encoder and decoder are explicitly trained to recognize the syntax and data flow in the source and target codes, respectively. We not only make the encoder structure-aware by leveraging the source code's syntax tree and data flow graph, but we also support the decoder in preserving the syntax and data flow of the target code by introducing two novel auxiliary tasks: AST (Abstract Syntax Tree) paths prediction and data flow prediction. To the best of our knowledge, this is the first work to introduce a structure-aware Transformer decoder that models both syntax and data flow to enhance the quality of generated code. The proposed StructCoder model achieves state-of-the-art performance on code translation and text-to-code generation tasks in the CodeXGLUE benchmark, and improves over baselines of similar size on the APPS code generation benchmark. Our code is publicly available at https://github.com/reddy-lab-code-research/StructCoder/.

Large Language Models (LLMs) are transforming software engineering tasks, including code vulnerability detection-a critical area of software security. However, existing methods often rely on resource-intensive models or graph-based techniques, limiting their accessibility and practicality. This paper introduces K-ASTRO, a lightweight Transformer model that combines semantic embeddings from LLMs with structural features of Abstract Syntax Trees (ASTs) to improve both efficiency and accuracy in code vulnerability detection. Our approach introduces an AST-based augmentation technique inspired by mutation testing, a structure-aware attention mechanism that incorporates augmented AST features, and a joint adaptation pipeline to unify code semantics and syntax. Experimental results on three large-scale datasets, including BigVul, DiverseVul, and PrimeVul-demonstrate state-of-the-art performance while enabling rapid inference on CPUs with minimal training time. By offering a scalable, interpretable, and efficient solution, K-ASTRO bridges the gap between LLM advancements and practical software vulnerability detection, providing open-sourced tools to foster further research.

Code completion is an essential feature of IDEs, yet current autocompleters are restricted to either grammar-based or NLP-based single token completions. Both approaches have significant drawbacks: grammar-based autocompletion is restricted in dynamically-typed language environments, whereas NLP-based autocompleters struggle to understand the semantics of the programming language and the developer's code context. In this work, we present CodeFill, a language model for autocompletion that combines learned structure and naming information. Using a parallel Transformer architecture and multi-task learning, CodeFill consumes sequences of source code token names and their equivalent AST token types. Uniquely, CodeFill is trained both for single-token and multi-token (statement) prediction, which enables it to learn long-range dependencies among grammatical and naming elements. We train CodeFill on two datasets, consisting of 29M and 425M lines of code, respectively. To make the evaluation more realistic, we develop a method to automatically infer points in the source code at which completion matters. We compare CodeFill against four baselines and two state-of-the-art models, GPT-C and TravTrans+.CodeFill surpasses all baselines in single token prediction (MRR: 70.9% vs. 66.2% and 67.8%) and outperforms the state of the art for multi-token prediction (ROUGE-L: 63.7% vs. 52.4% and 59.2%, for n=4 tokens). We publicly release our source code and datasets.

Large-scale vision-language pre-training has achieved significant performance in multi-modal understanding and generation tasks. However, existing methods often perform poorly on image-text matching tasks that require structured representations, i.e., representations of objects, attributes, and relations. As illustrated in Fig.~reffig:case (a), the models cannot make a distinction between ``An astronaut rides a horse" and ``A horse rides an astronaut". This is because they fail to fully leverage structured knowledge when learning representations in multi-modal scenarios. In this paper, we present an end-to-end framework Structure-CLIP, which integrates Scene Graph Knowledge (SGK) to enhance multi-modal structured representations. Firstly, we use scene graphs to guide the construction of semantic negative examples, which results in an increased emphasis on learning structured representations. Moreover, a Knowledge-Enhance Encoder (KEE) is proposed to leverage SGK as input to further enhance structured representations. To verify the effectiveness of the proposed framework, we pre-train our model with the aforementioned approaches and conduct experiments on downstream tasks. Experimental results demonstrate that Structure-CLIP achieves state-of-the-art (SOTA) performance on VG-Attribution and VG-Relation datasets, with 12.5% and 4.1% ahead of the multi-modal SOTA model respectively. Meanwhile, the results on MSCOCO indicate that Structure-CLIP significantly enhances the structured representations while maintaining the ability of general representations. Our code is available at https://github.com/zjukg/Structure-CLIP.

Multimodal molecular models often suffer from 3D conformer unreliability and modality collapse, limiting their robustness and generalization. We propose MuMo, a structured multimodal fusion framework that addresses these challenges in molecular representation through two key strategies. To reduce the instability of conformer-dependent fusion, we design a Structured Fusion Pipeline (SFP) that combines 2D topology and 3D geometry into a unified and stable structural prior. To mitigate modality collapse caused by naive fusion, we introduce a Progressive Injection (PI) mechanism that asymmetrically integrates this prior into the sequence stream, preserving modality-specific modeling while enabling cross-modal enrichment. Built on a state space backbone, MuMo supports long-range dependency modeling and robust information propagation. Across 29 benchmark tasks from Therapeutics Data Commons (TDC) and MoleculeNet, MuMo achieves an average improvement of 2.7% over the best-performing baseline on each task, ranking first on 22 of them, including a 27% improvement on the LD50 task. These results validate its robustness to 3D conformer noise and the effectiveness of multimodal fusion in molecular representation. The code is available at: github.com/selmiss/MuMo.

Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language models lack explicit structural supervision, despite its relevance to protein function. To address this issue, we introduce the integration of remote homology detection to distill structural information into protein language models without requiring explicit protein structures as input. We evaluate the impact of this structure-informed training on downstream protein function prediction tasks. Experimental results reveal consistent improvements in function annotation accuracy for EC number and GO term prediction. Performance on mutant datasets, however, varies based on the relationship between targeted properties and protein structures. This underscores the importance of considering this relationship when applying structure-aware training to protein function prediction tasks. Code and model weights are available at https://github.com/DeepGraphLearning/esm-s.

Code analysis is fundamental in Software Engineering, supporting debugging, optimization, and security assessment. Human developers approach it through syntax parsing, static semantics inference, and dynamic reasoning. Traditional tools are effective but limited by language specificity and weak cross-language generalization. Large language models (LLMs) are promising for code tasks, yet their capabilities for fundamental code analysis remain underexplored. We structure our study around three aspects aligned with human practices: syntax parsing, static semantics inference, and dynamic reasoning. We evaluate 21 state-of-the-art LLMs across nine tasks in four languages (C, Java, Python, Solidity), including AST generation, CFG construction, data dependency, taint analysis, and flaky test reasoning. We apply a three-layer evaluation protocol (automated metrics, expert adjudication, consistency validation) to 3,124 code samples, achieving high inter-rater reliability (Cohen's kappa = 0.844-0.936) and strong human-machine agreement (Gwet's AC1 = 0.500-0.727, F1 = 0.791-0.882). While the best LLMs excel in syntax parsing (AST 90%+, expression matching 84-100%) and show promise in static analysis, their dynamic reasoning remains limited (<70%) with high data-shift sensitivity (per-project F1 varying 0-1.0). This hierarchy holds across model families and scales, suggesting fundamental rather than transient limitations. These findings show how LLMs complement traditional analyzers: they offer cross-language generalization but non-deterministic outputs needing validation, while traditional tools give deterministic guarantees but need language-specific configuration. We contribute a validated evaluation framework with comparison against traditional analyzers (Tree-sitter, Soot, Joern) and task-specific applicability tiers. Benchmark: https://github.com/mathieu0905/llm_code_analysis.git

Retrieval-Augmented Generation (RAG) has become essential for large-scale code generation, grounding predictions in external code corpora to improve actuality. However, a critical yet underexplored aspect of RAG pipelines is chunking -- the process of dividing documents into retrievable units. Existing line-based chunking heuristics often break semantic structures, splitting functions or merging unrelated code, which can degrade generation quality. We propose chunking via Abstract Syntax Trees (\ourwork), a structure-aware method that recursively breaks large AST nodes into smaller chunks and merges sibling nodes while respecting size limits. This approach generates self-contained, semantically coherent units across programming languages and tasks, improving performance on diverse code generation tasks, e.g., boosting Recall@5 by 4.3 points on RepoEval retrieval and Pass@1 by 2.67 points on SWE-bench generation. Our work highlights the importance of structure-aware chunking for scaling retrieval-enhanced code intelligence.

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce StructTokenBench, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop AminoAseed, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83% and 124.03%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench

With the rapid advancement of tool-use capabilities in Large Language Models (LLMs), Retrieval-Augmented Generation (RAG) is shifting from static, one-shot retrieval toward autonomous, multi-turn evidence acquisition. However, existing agentic search frameworks typically treat long documents as flat collections of unstructured chunks, disregarding the native hierarchical organization and sequential logic essential for human comprehension. To bridge this gap, we introduce DeepRead, a structure-aware document reasoning agent designed to operationalize document-native structural priors into actionable reasoning capabilities. Leveraging the structural fidelity of modern OCR, DeepRead constructs a paragraph-level, coordinate-based navigation system and equips the LLM with two synergistic tools: Retrieve for scanning-aware localization, and ReadSection for contiguous, order-preserving reading within specific hierarchical scopes. This design elicits a human-like ``locate-then-read'' reasoning paradigm, effectively mitigating the context fragmentation inherent in traditional retrieval methods. Extensive evaluations across four benchmarks spanning diverse document types demonstrate that DeepRead outperforms Search-o1-style agentic search baselines by an average of 10.3\%. Fine-grained behavioral analysis further confirms that DeepRead autonomously adopts human-aligned reading strategies, validating the critical role of structural awareness in achieving precise document reasoning. Our code is available at https://github.com/Zhanli-Li/DeepRead.

Cross-modal ship re-identification (ReID) between optical and synthetic aperture radar (SAR) imagery is fundamentally challenged by the severe radiometric discrepancy between passive optical imaging and coherent active radar sensing. While existing approaches primarily rely on statistical distribution alignment or semantic matching, they often overlook a critical physical prior: ships are rigid objects whose geometric structures remain stable across sensing modalities, whereas texture appearance is highly modality-dependent. In this work, we propose SDF-Net, a Structure-Aware Disentangled Feature Learning Network that systematically incorporates geometric consistency into optical--SAR ship ReID. Built upon a ViT backbone, SDF-Net introduces a structure consistency constraint that extracts scale-invariant gradient energy statistics from intermediate layers to robustly anchor representations against radiometric variations. At the terminal stage, SDF-Net disentangles the learned representations into modality-invariant identity features and modality-specific characteristics. These decoupled cues are then integrated through a parameter-free additive residual fusion, effectively enhancing discriminative power. Extensive experiments on the HOSS-ReID dataset demonstrate that SDF-Net consistently outperforms existing state-of-the-art methods. The code and trained models are publicly available at https://github.com/cfrfree/SDF-Net.

Autonomous driving requires understanding infrastructure elements, such as lanes and crosswalks. To navigate safely, this understanding must be derived from sensor data in real-time and needs to be represented in vectorized form. Learned Bird's-Eye View (BEV) encoders are commonly used to combine a set of camera images from multiple views into one joint latent BEV grid. Traditionally, from this latent space, an intermediate raster map is predicted, providing dense spatial supervision but requiring post-processing into the desired vectorized form. More recent models directly derive infrastructure elements as polylines using vectorized map decoders, providing instance-level information. Our approach, Augmentation Map Network (AugMapNet), proposes latent BEV feature grid augmentation, a novel technique that significantly enhances the latent BEV representation. AugMapNet combines vector decoding and dense spatial supervision more effectively than existing architectures while remaining easy to integrate compared to other hybrid approaches. It additionally benefits from extra processing on its latent BEV features. Experiments on nuScenes and Argoverse2 datasets demonstrate significant improvements on vectorized map prediction of up to 13.3% over the StreamMapNet baseline on 60 m range and greater improvements on larger ranges. We confirm transferability by applying our method to another baseline, SQD-MapNet, and find similar improvements. A detailed analysis of the latent BEV grid confirms a more structured latent space of AugMapNet and shows the value of our novel concept beyond pure performance improvement. The code can be found at https://github.com/tmonnin/augmapnet

Personalized vaccines and T-cell immunotherapies depend critically on identifying peptide-MHC class I (pMHC-I) interactions capable of eliciting potent immune responses. However, current benchmarks and models inherit biases present in mass-spectrometry and binding-assay datasets, limiting discovery of novel peptide ligands. To address this issue, we introduce a structure-guided benchmark of pMHC-I peptides designed using diffusion models conditioned on crystal structure interaction distances. Spanning twenty high-priority HLA alleles, this benchmark is independent of previously characterized peptides yet reproduces canonical anchor residue preferences, indicating structural generalization without experimental dataset bias. Using this resource, we demonstrate that state-of-the-art sequence-based predictors perform poorly at recognizing the binding potential of these structurally stable designs, indicating allele-specific limitations invisible in conventional evaluations. Our geometry-aware design pipeline yields peptides with high predicted structural integrity and higher residue diversity than existing datasets, representing a key resource for unbiased model training and evaluation. Our code, and data are available at: https://github.com/sermare/struct-mhc-dev.

Diffusion-based super-resolution (SR) models have recently garnered significant attention due to their potent restoration capabilities. But conventional diffusion models perform noise sampling from a single distribution, constraining their ability to handle real-world scenes and complex textures across semantic regions. With the success of segment anything model (SAM), generating sufficiently fine-grained region masks can enhance the detail recovery of diffusion-based SR model. However, directly integrating SAM into SR models will result in much higher computational cost. In this paper, we propose the SAM-DiffSR model, which can utilize the fine-grained structure information from SAM in the process of sampling noise to improve the image quality without additional computational cost during inference. In the process of training, we encode structural position information into the segmentation mask from SAM. Then the encoded mask is integrated into the forward diffusion process by modulating it to the sampled noise. This adjustment allows us to independently adapt the noise mean within each corresponding segmentation area. The diffusion model is trained to estimate this modulated noise. Crucially, our proposed framework does NOT change the reverse diffusion process and does NOT require SAM at inference. Experimental results demonstrate the effectiveness of our proposed method, showcasing superior performance in suppressing artifacts, and surpassing existing diffusion-based methods by 0.74 dB at the maximum in terms of PSNR on DIV2K dataset. The code and dataset are available at https://github.com/lose4578/SAM-DiffSR.

Recent advances in large language models for test case generation have improved branch coverage via prompt-engineered mutations. However, they still lack principled mechanisms for steering models toward specific high-risk execution branches, limiting their effectiveness for discovering subtle bugs and security vulnerabilities. We propose GLMTest, the first program structure-aware LLM framework for targeted test case generation that seamlessly integrates code property graphs and code semantics using a graph neural network and a language model to condition test case generation on execution branches. This structured conditioning enables controllable and branch-targeted test case generation, thereby potentially enhancing bug and security risk discovery. Experiments on real-world projects show that GLMTest built on a Qwen2.5-Coder-7B-Instruct model improves branch accuracy from 27.4% to 50.2% on TestGenEval benchmark compared with state-of-the-art LLMs, i.e., Claude-Sonnet-4.5 and GPT-4o-mini.

LLM-based code agents treat repositories as unstructured text, applying edits through brittle string matching that frequently fails due to formatting drift or ambiguous patterns. We propose reframing the codebase as a structured action space where agents operate on named AST entities rather than text spans. Our framework, CODESTRUCT, provides readCode for retrieving complete syntactic units and editCode for applying syntax-validated transformations to semantic program elements. Evaluated on SWE-Bench Verified across six LLMs, CODESTRUCT improves Pass@1 accuracy by 1.2-5.0% while reducing token consumption by 12-38% for most models. Models that frequently fail to produce valid patches under text-based interfaces benefit most: GPT-5-nano improves by 20.8% as empty-patch failures drop from 46.6% to 7.2%. On CodeAssistBench, we observe consistent accuracy gains (+0.8-4.4%) with cost reductions up to 33%. Our results show that structure-aware interfaces offer a more reliable foundation for code agents.

Faithful text image super-resolution (SR) is challenging because each character has a unique structure and usually exhibits diverse font styles and layouts. While existing methods primarily focus on English text, less attention has been paid to more complex scripts like Chinese. In this paper, we introduce a high-quality text image SR framework designed to restore the precise strokes of low-resolution (LR) Chinese characters. Unlike methods that rely on character recognition priors to regularize the SR task, we propose a novel structure prior that offers structure-level guidance to enhance visual quality. Our framework incorporates this structure prior within a StyleGAN model, leveraging its generative capabilities for restoration. To maintain the integrity of character structures while accommodating various font styles and layouts, we implement a codebook-based mechanism that restricts the generative space of StyleGAN. Each code in the codebook represents the structure of a specific character, while the vector w in StyleGAN controls the character's style, including typeface, orientation, and location. Through the collaborative interaction between the codebook and style, we generate a high-resolution structure prior that aligns with LR characters both spatially and structurally. Experiments demonstrate that this structure prior provides robust, character-specific guidance, enabling the accurate restoration of clear strokes in degraded characters, even for real-world LR Chinese text with irregular layouts. Our code and pre-trained models will be available at https://github.com/csxmli2016/MARCONetPlusPlus

Impressive results on real-world image super-resolution (Real-ISR) have been achieved by employing pre-trained stable diffusion (SD) models. However, one critical issue of such methods lies in their poor reconstruction of image fine structures, such as small characters and textures, due to the aggressive resolution reduction of the VAE (eg., 8times downsampling) in the SD model. One solution is to employ a VAE with a lower downsampling rate for diffusion; however, adapting its latent features with the pre-trained UNet while mitigating the increased computational cost poses new challenges. To address these issues, we propose a Transfer VAE Training (TVT) strategy to transfer the 8times downsampled VAE into a 4times one while adapting to the pre-trained UNet. Specifically, we first train a 4times decoder based on the output features of the original VAE encoder, then train a 4times encoder while keeping the newly trained decoder fixed. Such a TVT strategy aligns the new encoder-decoder pair with the original VAE latent space while enhancing image fine details. Additionally, we introduce a compact VAE and compute-efficient UNet by optimizing their network architectures, reducing the computational cost while capturing high-resolution fine-scale features. Experimental results demonstrate that our TVT method significantly improves fine-structure preservation, which is often compromised by other SD-based methods, while requiring fewer FLOPs than state-of-the-art one-step diffusion models. The official code can be found at https://github.com/Joyies/TVT.

Molecular structure elucidation involves deducing a molecule's structure from various types of spectral data, which is crucial in chemical experimental analysis. While large language models (LLMs) have shown remarkable proficiency in analyzing and reasoning through complex tasks, they still encounter substantial challenges in molecular structure elucidation. We identify that these challenges largely stem from LLMs' limited grasp of specialized chemical knowledge. In this work, we introduce a Knowledge-enhanced reasoning framework for Molecular Structure Elucidation (K-MSE), leveraging Monte Carlo Tree Search for test-time scaling as a plugin. Specifically, we construct an external molecular substructure knowledge base to extend the LLMs' coverage of the chemical structure space. Furthermore, we design a specialized molecule-spectrum scorer to act as a reward model for the reasoning process, addressing the issue of inaccurate solution evaluation in LLMs. Experimental results show that our approach significantly boosts performance, particularly gaining more than 20% improvement on both GPT-4o-mini and GPT-4o. Our code is available at https://github.com/HICAI-ZJU/K-MSE.

Structure-Based Drug Design (SBDD) is crucial for identifying bioactive molecules. Recent deep generative models are faced with challenges in geometric structure modeling. A major bottleneck lies in the twisted probability path of multi-modalities -- continuous 3D positions and discrete 2D topologies -- which jointly determine molecular geometries. By establishing the fact that noise schedules decide the Variational Lower Bound (VLB) for the twisted probability path, we propose VLB-Optimal Scheduling (VOS) strategy in this under-explored area, which optimizes VLB as a path integral for SBDD. Our model effectively enhances molecular geometries and interaction modeling, achieving state-of-the-art PoseBusters passing rate of 95.9% on CrossDock, more than 10% improvement upon strong baselines, while maintaining high affinities and robust intramolecular validity evaluated on held-out test set. Code is available at https://github.com/AlgoMole/MolCRAFT.

Multimodal Aspect-Based Sentiment Analysis (MABSA) seeks to extract fine-grained information from image-text pairs to identify aspect terms and determine their sentiment polarity. However, existing approaches often fall short in simultaneously addressing three core challenges: Sentiment Cue Perception (SCP), Multimodal Information Misalignment (MIM), and Semantic Noise Elimination (SNE). To overcome these limitations, we propose DASCO (Dependency Structure Augmented Scoping Framework), a fine-grained scope-oriented framework that enhances aspect-level sentiment reasoning by leveraging dependency parsing trees. First, we designed a multi-task pretraining strategy for MABSA on our base model, combining aspect-oriented enhancement, image-text matching, and aspect-level sentiment-sensitive cognition. This improved the model's perception of aspect terms and sentiment cues while achieving effective image-text alignment, addressing key challenges like SCP and MIM. Furthermore, we incorporate dependency trees as syntactic branch combining with semantic branch, guiding the model to selectively attend to critical contextual elements within a target-specific scope while effectively filtering out irrelevant noise for addressing SNE problem. Extensive experiments on two benchmark datasets across three subtasks demonstrate that DASCO achieves state-of-the-art performance in MABSA, with notable gains in JMASA (+2.3\% F1 and +3.5\% precision on Twitter2015). The source code is available at https://github.com/LHaoooo/DASCO .

Reliable high-definition (HD) map construction is crucial for the driving safety of autonomous vehicles. Although recent studies demonstrate improved performance, their generalization capability across unfamiliar driving scenes remains unexplored. To tackle this issue, we propose UIGenMap, an uncertainty-instructed structure injection approach for generalizable HD map vectorization, which concerns the uncertainty resampling in statistical distribution and employs explicit instance features to reduce excessive reliance on training data. Specifically, we introduce the perspective-view (PV) detection branch to obtain explicit structural features, in which the uncertainty-aware decoder is designed to dynamically sample probability distributions considering the difference in scenes. With probabilistic embedding and selection, UI2DPrompt is proposed to construct PV-learnable prompts. These PV prompts are integrated into the map decoder by designed hybrid injection to compensate for neglected instance structures. To ensure real-time inference, a lightweight Mimic Query Distillation is designed to learn from PV prompts, which can serve as an efficient alternative to the flow of PV branches. Extensive experiments on challenging geographically disjoint (geo-based) data splits demonstrate that our UIGenMap achieves superior performance, with +5.7 mAP improvement on the nuScenes dataset. Source code will be available at https://github.com/xiaolul2/UIGenMap.

Pixel-level segmentation of structural cracks across various scenarios remains a considerable challenge. Current methods encounter challenges in effectively modeling crack morphology and texture, facing challenges in balancing segmentation quality with low computational resource usage. To overcome these limitations, we propose a lightweight Structure-Aware Vision Mamba Network (SCSegamba), capable of generating high-quality pixel-level segmentation maps by leveraging both the morphological information and texture cues of crack pixels with minimal computational cost. Specifically, we developed a Structure-Aware Visual State Space module (SAVSS), which incorporates a lightweight Gated Bottleneck Convolution (GBC) and a Structure-Aware Scanning Strategy (SASS). The key insight of GBC lies in its effectiveness in modeling the morphological information of cracks, while the SASS enhances the perception of crack topology and texture by strengthening the continuity of semantic information between crack pixels. Experiments on crack benchmark datasets demonstrate that our method outperforms other state-of-the-art (SOTA) methods, achieving the highest performance with only 2.8M parameters. On the multi-scenario dataset, our method reached 0.8390 in F1 score and 0.8479 in mIoU. The code is available at https://github.com/Karl1109/SCSegamba.

Recently, state-of-the-art approaches for pruning large pre-trained models (LPMs) have demonstrated that the training-free removal of non-critical residual blocks in Transformers is viable for reducing model size, achieving results that outperform previous training-free pruning approaches. Motivated by these findings, we extend BlockPruner (Zhong et al., 2024) and propose MultiPruner, a pruning approach that surpasses recent training-free pruning methods by adopting a multidimensional, iterative, fine-grained pruning strategy. In MultiPruner, multidimensional pruning reinstates the structural balance in block-pruned models by sequentially compressing along three dimensions: i) residual blocks, ii) channels of multilayer perceptrons (MLP), and iii) attention heads. This solution enhances zero-shot accuracy on downstream tasks compared to other techniques while improving model compression ratios, producing compressed models with fewer computing and memory requirements. Extensive experiments demonstrate the advantages of the proposed method across various large pre-trained models. The code and pruning configurations are available at https://github.com/IntelLabs/Hardware-Aware-Automated-Machine-Learning.

Structure-Based molecule optimization (SBMO) aims to optimize molecules with both continuous coordinates and discrete types against protein targets. A promising direction is to exert gradient guidance on generative models given its remarkable success in images, but it is challenging to guide discrete data and risks inconsistencies between modalities. To this end, we leverage a continuous and differentiable space derived through Bayesian inference, presenting Molecule Joint Optimization (MolJO), the gradient-based SBMO framework that facilitates joint guidance signals across different modalities while preserving SE(3)-equivariance. We introduce a novel backward correction strategy that optimizes within a sliding window of the past histories, allowing for a seamless trade-off between explore-and-exploit during optimization. MolJO achieves state-of-the-art performance on CrossDocked2020 benchmark (Success Rate 51.3%, Vina Dock -9.05 and SA 0.78), more than 4x improvement in Success Rate compared to the gradient-based counterpart, and 2x "Me-Better" Ratio as much as 3D baselines. Furthermore, we extend MolJO to a wide range of optimization settings, including multi-objective optimization and challenging tasks in drug design such as R-group optimization and scaffold hopping, further underscoring its versatility. Code is available at https://github.com/AlgoMole/MolCRAFT.

Generative models for structure-based drug design (SBDD) have shown promising results in recent years. Existing works mainly focus on how to generate molecules with higher binding affinity, ignoring the feasibility prerequisites for generated 3D poses and resulting in false positives. We conduct thorough studies on key factors of ill-conformational problems when applying autoregressive methods and diffusion to SBDD, including mode collapse and hybrid continuous-discrete space. In this paper, we introduce MolCRAFT, the first SBDD model that operates in the continuous parameter space, together with a novel noise reduced sampling strategy. Empirical results show that our model consistently achieves superior performance in binding affinity with more stable 3D structure, demonstrating our ability to accurately model interatomic interactions. To our best knowledge, MolCRAFT is the first to achieve reference-level Vina Scores (-6.59 kcal/mol) with comparable molecular size, outperforming other strong baselines by a wide margin (-0.84 kcal/mol). Code is available at https://github.com/AlgoMole/MolCRAFT.

Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure prediction~(MSP) can be well handled in a step-wise assembly fashion using provided dimer structures and predicted protein-protein interactions~(PPIs). However, due to the biological gap in the formation of dimers and larger multimers, directly applying PPI prediction techniques can often cause a poor generalization to the MSP task. To address this challenge, we aim to extend the PPI knowledge to multimers of different scales~(i.e., chain numbers). Specifically, we propose \textsc{PromptMSP}, a pre-training and Prompt tuning framework for Multimer Structure Prediction. First, we tailor the source and target tasks for effective PPI knowledge learning and efficient inference, respectively. We design PPI-inspired prompt learning to narrow the gaps of two task formats and generalize the PPI knowledge to multimers of different scales. We provide a meta-learning strategy to learn a reliable initialization of the prompt model, enabling our prompting framework to effectively adapt to limited data for large-scale multimers. Empirically, we achieve both significant accuracy (RMSD and TM-Score) and efficiency improvements compared to advanced MSP models. The code, data and checkpoints are released at https://github.com/zqgao22/PromptMSP.

Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation graph structure simultaneously. Despite the proliferation of GSL methods developed in recent years, there is no standard experimental setting or fair comparison for performance evaluation, which creates a great obstacle to understanding the progress in this field. To fill this gap, we systematically analyze the performance of GSL in different scenarios and develop a comprehensive Graph Structure Learning Benchmark (GSLB) curated from 20 diverse graph datasets and 16 distinct GSL algorithms. Specifically, GSLB systematically investigates the characteristics of GSL in terms of three dimensions: effectiveness, robustness, and complexity. We comprehensively evaluate state-of-the-art GSL algorithms in node- and graph-level tasks, and analyze their performance in robust learning and model complexity. Further, to facilitate reproducible research, we have developed an easy-to-use library for training, evaluating, and visualizing different GSL methods. Empirical results of our extensive experiments demonstrate the ability of GSL and reveal its potential benefits on various downstream tasks, offering insights and opportunities for future research. The code of GSLB is available at: https://github.com/GSL-Benchmark/GSLB.

Domain adaptation (DA) aims to transfer knowledge from a fully labeled source to a scarcely labeled or totally unlabeled target under domain shift. Recently, semi-supervised learning-based (SSL) techniques that leverage pseudo labeling have been increasingly used in DA. Despite the competitive performance, these pseudo labeling methods rely heavily on the source domain to generate pseudo labels for the target domain and therefore still suffer considerably from source data bias. Moreover, class distribution bias in the target domain is also often ignored in the pseudo label generation and thus leading to further deterioration of performance. In this paper, we propose GeT that learns a non-bias target embedding distribution with high quality pseudo labels. Specifically, we formulate an online target generative classifier to induce the target distribution into distinctive Gaussian components weighted by their class priors to mitigate source data bias and enhance target class discriminability. We further propose a structure similarity regularization framework to alleviate target class distribution bias and further improve target class discriminability. Experimental results show that our proposed GeT is effective and achieves consistent improvements under various DA settings with and without class distribution bias. Our code is available at: https://lulusindazc.github.io/getproject/.

Open World Object Detection (OWOD) is a challenging and realistic task that extends beyond the scope of standard Object Detection task. It involves detecting both known and unknown objects while integrating learned knowledge for future tasks. However, the level of "unknownness" varies significantly depending on the context. For example, a tree is typically considered part of the background in a self-driving scene, but it may be significant in a household context. We argue that this contextual information should already be embedded within the known classes. In other words, there should be a semantic or latent structure relationship between the known and unknown items to be discovered. Motivated by this observation, we propose Hyp-OW, a method that learns and models hierarchical representation of known items through a SuperClass Regularizer. Leveraging this representation allows us to effectively detect unknown objects using a similarity distance-based relabeling module. Extensive experiments on benchmark datasets demonstrate the effectiveness of Hyp-OW, achieving improvement in both known and unknown detection (up to 6 percent). These findings are particularly pronounced in our newly designed benchmark, where a strong hierarchical structure exists between known and unknown objects. Our code can be found at https://github.com/tldoan/-HYP-OW-AAAI-2024-

Structure-based drug design (SBDD) aims to discover drug candidates by finding molecules (ligands) that bind tightly to a disease-related protein (targets), which is the primary approach to computer-aided drug discovery. Recently, applying deep generative models for three-dimensional (3D) molecular design conditioned on protein pockets to solve SBDD has attracted much attention, but their formulation as probabilistic modeling often leads to unsatisfactory optimization performance. On the other hand, traditional combinatorial optimization methods such as genetic algorithms (GA) have demonstrated state-of-the-art performance in various molecular optimization tasks. However, they do not utilize protein target structure to inform design steps but rely on a random-walk-like exploration, which leads to unstable performance and no knowledge transfer between different tasks despite the similar binding physics. To achieve a more stable and efficient SBDD, we propose Reinforced Genetic Algorithm (RGA) that uses neural models to prioritize the profitable design steps and suppress random-walk behavior. The neural models take the 3D structure of the targets and ligands as inputs and are pre-trained using native complex structures to utilize the knowledge of the shared binding physics from different targets and then fine-tuned during optimization. We conduct thorough empirical studies on optimizing binding affinity to various disease targets and show that RGA outperforms the baselines in terms of docking scores and is more robust to random initializations. The ablation study also indicates that the training on different targets helps improve performance by leveraging the shared underlying physics of the binding processes. The code is available at https://github.com/futianfan/reinforced-genetic-algorithm.

Estimating a dense depth map from a single view is geometrically ill-posed, and state-of-the-art methods rely on learning depth's relation with visual appearance using deep neural networks. On the other hand, Structure from Motion (SfM) leverages multi-view constraints to produce very accurate but sparse maps, as matching across images is typically limited by locally discriminative texture. In this work, we combine the strengths of both approaches by proposing a novel test-time refinement (TTR) method, denoted as SfM-TTR, that boosts the performance of single-view depth networks at test time using SfM multi-view cues. Specifically, and differently from the state of the art, we use sparse SfM point clouds as test-time self-supervisory signal, fine-tuning the network encoder to learn a better representation of the test scene. Our results show how the addition of SfM-TTR to several state-of-the-art self-supervised and supervised networks improves significantly their performance, outperforming previous TTR baselines mainly based on photometric multi-view consistency. The code is available at https://github.com/serizba/SfM-TTR.

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

Modern methods mainly regard lane detection as a problem of pixel-wise segmentation, which is struggling to address the problem of challenging scenarios and speed. Inspired by human perception, the recognition of lanes under severe occlusion and extreme lighting conditions is mainly based on contextual and global information. Motivated by this observation, we propose a novel, simple, yet effective formulation aiming at extremely fast speed and challenging scenarios. Specifically, we treat the process of lane detection as a row-based selecting problem using global features. With the help of row-based selecting, our formulation could significantly reduce the computational cost. Using a large receptive field on global features, we could also handle the challenging scenarios. Moreover, based on the formulation, we also propose a structural loss to explicitly model the structure of lanes. Extensive experiments on two lane detection benchmark datasets show that our method could achieve the state-of-the-art performance in terms of both speed and accuracy. A light-weight version could even achieve 300+ frames per second with the same resolution, which is at least 4x faster than previous state-of-the-art methods. Our code will be made publicly available.

Structure information is critical for understanding the semantics of text-rich images, such as documents, tables, and charts. Existing Multimodal Large Language Models (MLLMs) for Visual Document Understanding are equipped with text recognition ability but lack general structure understanding abilities for text-rich document images. In this work, we emphasize the importance of structure information in Visual Document Understanding and propose the Unified Structure Learning to boost the performance of MLLMs. Our Unified Structure Learning comprises structure-aware parsing tasks and multi-grained text localization tasks across 5 domains: document, webpage, table, chart, and natural image. To better encode structure information, we design a simple and effective vision-to-text module H-Reducer, which can not only maintain the layout information but also reduce the length of visual features by merging horizontal adjacent patches through convolution, enabling the LLM to understand high-resolution images more efficiently. Furthermore, by constructing structure-aware text sequences and multi-grained pairs of texts and bounding boxes for publicly available text-rich images, we build a comprehensive training set DocStruct4M to support structure learning. Finally, we construct a small but high-quality reasoning tuning dataset DocReason25K to trigger the detailed explanation ability in the document domain. Our model DocOwl 1.5 achieves state-of-the-art performance on 10 visual document understanding benchmarks, improving the SOTA performance of MLLMs with a 7B LLM by more than 10 points in 5/10 benchmarks. Our codes, models, and datasets are publicly available at https://github.com/X-PLUG/mPLUG-DocOwl/tree/main/DocOwl1.5.

Multi-modal recommendation has gained traction as items possess rich attributes like text and images. Semantic ID-based approaches effectively discretize this information into compact tokens. However, two challenges persist: (1) Suboptimal Tokenization: existing methods (e.g., RQ-VAE) lack disentanglement between shared cross-modal semantics and modality-specific details, causing redundancy or collapse; (2) Architecture-Data Mismatch: vanilla Transformers treat semantic IDs as flat streams, ignoring the hierarchy of user interactions, items, and tokens. Expanding items into multiple tokens amplifies length and noise, biasing attention toward local details over holistic semantics. We propose Hi-SAM, a Hierarchical Structure-Aware Multi-modal framework with two designs: (1) Disentangled Semantic Tokenizer (DST): unifies modalities via geometry-aware alignment and quantizes them via a coarse-to-fine strategy. Shared codebooks distill consensus while modality-specific ones recover nuances from residuals, enforced by mutual information minimization; (2) Hierarchical Memory-Anchor Transformer (HMAT): splits positional encoding into inter- and intra-item subspaces via Hierarchical RoPE to restore hierarchy. It inserts Anchor Tokens to condense items into compact memory, retaining details for the current item while accessing history only through compressed summaries. Experiments on real-world datasets show consistent improvements over SOTA baselines, especially in cold-start scenarios. Deployed on a large-scale social platform serving millions of users, Hi-SAM achieved a 6.55% gain in the core online metric.

Semi-supervised image segmentation has attracted great attention recently. The key is how to leverage unlabeled images in the training process. Most methods maintain consistent predictions of the unlabeled images under variations (e.g., adding noise/perturbations, or creating alternative versions) in the image and/or model level. In most image-level variation, medical images often have prior structure information, which has not been well explored. In this paper, we propose novel dual structure-aware image filterings (DSAIF) as the image-level variations for semi-supervised medical image segmentation. Motivated by connected filtering that simplifies image via filtering in structure-aware tree-based image representation, we resort to the dual contrast invariant Max-tree and Min-tree representation. Specifically, we propose a novel connected filtering that removes topologically equivalent nodes (i.e. connected components) having no siblings in the Max/Min-tree. This results in two filtered images preserving topologically critical structure. Applying the proposed DSAIF to mutually supervised networks decreases the consensus of their erroneous predictions on unlabeled images. This helps to alleviate the confirmation bias issue of overfitting to noisy pseudo labels of unlabeled images, and thus effectively improves the segmentation performance. Extensive experimental results on three benchmark datasets demonstrate that the proposed method significantly/consistently outperforms some state-of-the-art methods. The source codes will be publicly available.

Graph structure learning aims to learn connectivity in a graph from data. It is particularly important for many computer vision related tasks since no explicit graph structure is available for images for most cases. A natural way to construct a graph among images is to treat each image as a node and assign pairwise image similarities as weights to corresponding edges. It is well known that pairwise similarities between images are sensitive to the noise in feature representations, leading to unreliable graph structures. We address this problem from the viewpoint of statistical tests. By viewing the feature vector of each node as an independent sample, the decision of whether creating an edge between two nodes based on their similarity in feature representation can be thought as a {it single} statistical test. To improve the robustness in the decision of creating an edge, multiple samples are drawn and integrated by {it multiple} statistical tests to generate a more reliable similarity measure, consequentially more reliable graph structure. The corresponding elegant matrix form named B-Attention is designed for efficiency. The effectiveness of multiple tests for graph structure learning is verified both theoretically and empirically on multiple clustering and ReID benchmark datasets. Source codes are available at https://github.com/Thomas-wyh/B-Attention.

Image inpainting has made significant advances in recent years. However, it is still challenging to recover corrupted images with both vivid textures and reasonable structures. Some specific methods only tackle regular textures while losing holistic structures due to the limited receptive fields of convolutional neural networks (CNNs). On the other hand, attention-based models can learn better long-range dependency for the structure recovery, but they are limited by the heavy computation for inference with large image sizes. To address these issues, we propose to leverage an additional structure restorer to facilitate the image inpainting incrementally. The proposed model restores holistic image structures with a powerful attention-based transformer model in a fixed low-resolution sketch space. Such a grayscale space is easy to be upsampled to larger scales to convey correct structural information. Our structure restorer can be integrated with other pretrained inpainting models efficiently with the zero-initialized residual addition. Furthermore, a masking positional encoding strategy is utilized to improve the performance with large irregular masks. Extensive experiments on various datasets validate the efficacy of our model compared with other competitors. Our codes are released in https://github.com/DQiaole/ZITS_inpainting.

Recent advancements in video autoencoders (Video AEs) have significantly improved the quality and efficiency of video generation. In this paper, we propose a novel and compact video autoencoder, VidTwin, that decouples video into two distinct latent spaces: Structure latent vectors, which capture overall content and global movement, and Dynamics latent vectors, which represent fine-grained details and rapid movements. Specifically, our approach leverages an Encoder-Decoder backbone, augmented with two submodules for extracting these latent spaces, respectively. The first submodule employs a Q-Former to extract low-frequency motion trends, followed by downsampling blocks to remove redundant content details. The second averages the latent vectors along the spatial dimension to capture rapid motion. Extensive experiments show that VidTwin achieves a high compression rate of 0.20% with high reconstruction quality (PSNR of 28.14 on the MCL-JCV dataset), and performs efficiently and effectively in downstream generative tasks. Moreover, our model demonstrates explainability and scalability, paving the way for future research in video latent representation and generation. Our code has been released at https://github.com/microsoft/VidTok/tree/main/vidtwin.

When an AI agent calls an API and hits a validation error, it needs more than what went wrong -- it needs what to do next. A self-reflective API returns, on validation failure, a machine-readable recovery\_feedback.suggestions[] payload sufficient for the agent to repair the request and retry without external reasoning. On a leak-audited pilot (N{=}30 per cell, 3 LLMs, 10 adversarial tasks), structured suggestions lift task-completion rate by +36.7--40.0pp over plain-English diagnoses on Anthropic models (Fisher's exact p le 0.0022), at 1.8--2.2times better per-success token efficiency. The lift is not significant on gpt-4o-mini (p{=}0.435); a second-domain replication on a billing API confirms the pattern. The comparison only holds after auditing two undocumented classes of answer leakage in LLM benchmarks. We shipaudit\_prompt\_leakage.py as reusable CI infrastructure. Code and data: https://github.com/arquicanedo/self-reflective-apis.

Organic crystal structure prediction (CSP) is a requirement for computational modelling of organic solids, but traditionally costs several CPU-years per molecule. Generative models such as OXtal dramatically reduce this cost by sampling stable organic crystal structures directly. However, OXtal forgoes explicit lattice parametrization in favour of modelling large crops of the bulk material with expensive triangle layers, which can incur a computational cost of minutes per molecule. In this paper, we reduce this to seconds with Clari, a large-scale flow matching model that generates redundancy-free unit cells and replaces triangle layers with pure pair-bias attention. Clari requires only atom types and bonds as input and does not need an RDKit-sanitizable input molecule, which expands its applicability to challenging chemistries such as fullerenes, metal complexes, and atom clusters. We further ablate key design choices such as auxiliary losses, timestep distributions, noise priors, and self-conditioning. On OXtal's test sets, we surpass OXtal's solve rate while obtaining a speedup of 15-30times. Because Clari also models explicit hydrogens, it supports inference-time scaling via direct energy ranking, without any decoration or relaxation step. When generating 150 crystals and selecting the top-30 by energy, we further improve solve rate while maintaining a speedup of 5-8times. We also introduce the CSD Teaching Subset as a new test split of diverse and complex molecules for future benchmarking. Our contributions enable CSP within seconds, making large-scale virtual screening of organic solids practical. Code is available at https://github.com/aspuru-guzik-group/clari.

Self-supervised learning on large-scale multi-modal datasets allows learning semantically meaningful embeddings in a joint multi-modal representation space without relying on human annotations. These joint embeddings enable zero-shot cross-modal tasks like retrieval and classification. However, these methods often struggle to generalize well on out-of-domain data as they ignore the semantic structure present in modality-specific embeddings. In this context, we propose a novel Semantic-Structure-Preserving Consistency approach to improve generalizability by preserving the modality-specific relationships in the joint embedding space. To capture modality-specific semantic relationships between samples, we propose to learn multiple anchors and represent the multifaceted relationship between samples with respect to their relationship with these anchors. To assign multiple anchors to each sample, we propose a novel Multi-Assignment Sinkhorn-Knopp algorithm. Our experimentation demonstrates that our proposed approach learns semantically meaningful anchors in a self-supervised manner. Furthermore, our evaluation on MSR-VTT and YouCook2 datasets demonstrates that our proposed multi-anchor assignment based solution achieves state-of-the-art performance and generalizes to both inand out-of-domain datasets. Code: https://github.com/Swetha5/Multi_Sinkhorn_Knopp

Large-scale vision-language models (VLMs) such as CLIP have gained popularity for their generalizable and expressive multimodal representations. By leveraging large-scale training data with diverse textual metadata, VLMs acquire open-vocabulary capabilities, solving tasks beyond their training scope. This paper investigates the temporal awareness of VLMs, assessing their ability to position visual content in time. We introduce TIME10k, a benchmark dataset of over 10,000 images with temporal ground truth, and evaluate the time-awareness of 37 VLMs by a novel methodology. Our investigation reveals that temporal information is structured along a low-dimensional, non-linear manifold in the VLM embedding space. Based on this insight, we propose methods to derive an explicit ``timeline'' representation from the embedding space. These representations model time and its chronological progression and thereby facilitate temporal reasoning tasks. Our timeline approaches achieve competitive to superior accuracy compared to a prompt-based baseline while being computationally efficient. All code and data are available at https://tekayanidham.github.io/timeline-page/.

As a branch of time series forecasting, stock movement forecasting is one of the challenging problems for investors and researchers. Since Transformer was introduced to analyze financial data, many researchers have dedicated themselves to forecasting stock movement using Transformer or attention mechanisms. However, existing research mostly focuses on individual stock information but ignores stock market information and high noise in stock data. In this paper, we propose a novel method using the attention mechanism in which both stock market information and individual stock information are considered. Meanwhile, we propose a novel EMD-based algorithm for reducing short-term noise in stock data. Two randomly selected exchange-traded funds (ETFs) spanning over ten years from US stock markets are used to demonstrate the superior performance of the proposed attention-based method. The experimental analysis demonstrates that the proposed attention-based method significantly outperforms other state-of-the-art baselines. Code is available at https://github.com/DurandalLee/ACEFormer.

The consensus that GCN, GraphSAGE, GAT, and EvolveGCN outperform feature-only baselines on the Elliptic Bitcoin Dataset is widely cited but has not been rigorously stress-tested under a leakage-free evaluation protocol. We perform a seed-matched inductive-versus-transductive comparison and find that this consensus does not hold. Under a strictly inductive protocol, Random Forest on raw features achieves F1 = 0.821 and outperforms all evaluated GNNs, while GraphSAGE reaches F1 = 0.689 +/- 0.017. A paired controlled experiment reveals a 39.5-point F1 gap attributable to training-time exposure to test-period adjacency. Additionally, edge-shuffle ablations show that randomly wired graphs outperform the real transaction graph, indicating that the dataset's topology can be misleading under temporal distribution shift. Hybrid models combining GNN embeddings with raw features provide only marginal gains and remain substantially below feature-only baselines. We release code, checkpoints, and a strict-inductive protocol to enable reproducible, leakage-free evaluation.

Stereo depth estimation is fundamental to underwater robotic perception, yet suffers from severe domain shifts caused by wavelength-dependent light attenuation, scattering, and refraction. Recent approaches leverage monocular foundation models with GRU-based iterative refinement for underwater adaptation; however, the sequential gating and local convolutional kernels in GRUs necessitate multiple iterations for long-range disparity propagation, limiting performance in large-disparity and textureless underwater regions. In this paper, we propose StereoAdapter-2, which replaces the conventional ConvGRU updater with a novel ConvSS2D operator based on selective state space models. The proposed operator employs a four-directional scanning strategy that naturally aligns with epipolar geometry while capturing vertical structural consistency, enabling efficient long-range spatial propagation within a single update step at linear computational complexity. Furthermore, we construct UW-StereoDepth-80K, a large-scale synthetic underwater stereo dataset featuring diverse baselines, attenuation coefficients, and scattering parameters through a two-stage generative pipeline combining semantic-aware style transfer and geometry-consistent novel view synthesis. Combined with dynamic LoRA adaptation inherited from StereoAdapter, our framework achieves state-of-the-art zero-shot performance on underwater benchmarks with 17% improvement on TartanAir-UW and 7.2% improvment on SQUID, with real-world validation on the BlueROV2 platform demonstrates the robustness of our approach. Code: https://github.com/AIGeeksGroup/StereoAdapter-2. Website: https://aigeeksgroup.github.io/StereoAdapter-2.

We present SIGMA-GEN, a unified framework for multi-identity preserving image generation. Unlike prior approaches, SIGMA-GEN is the first to enable single-pass multi-subject identity-preserved generation guided by both structural and spatial constraints. A key strength of our method is its ability to support user guidance at various levels of precision -- from coarse 2D or 3D boxes to pixel-level segmentations and depth -- with a single model. To enable this, we introduce SIGMA-SET27K, a novel synthetic dataset that provides identity, structure, and spatial information for over 100k unique subjects across 27k images. Through extensive evaluation we demonstrate that SIGMA-GEN achieves state-of-the-art performance in identity preservation, image generation quality, and speed. Code and visualizations at https://oindrilasaha.github.io/SIGMA-Gen/

Music structure analysis (MSA) underpins music understanding and controllable generation, yet progress has been limited by small, inconsistent corpora. We present SongFormer, a scalable framework that learns from heterogeneous supervision. SongFormer (i) fuses short- and long-window self-supervised audio representations to capture both fine-grained and long-range dependencies, and (ii) introduces a learned source embedding to enable training with partial, noisy, and schema-mismatched labels. To support scaling and fair evaluation, we release SongFormDB, the largest MSA corpus to date (over 10k tracks spanning languages and genres), and SongFormBench, a 300-song expert-verified benchmark. On SongFormBench, SongFormer sets a new state of the art in strict boundary detection (HR.5F) and achieves the highest functional label accuracy, while remaining computationally efficient; it surpasses strong baselines and Gemini 2.5 Pro on these metrics and remains competitive under relaxed tolerance (HR3F). Code, datasets, and model are publicly available.

We introduce EvoGit, a decentralized multi-agent framework for collaborative software development driven by autonomous code evolution. EvoGit deploys a population of independent coding agents, each proposing edits to a shared codebase without centralized coordination, explicit message passing, or shared memory. Instead, all coordination emerges through a Git-based phylogenetic graph that tracks the full version lineage and enables agents to asynchronously read from and write to the evolving code repository. This graph-based structure supports fine-grained branching, implicit concurrency, and scalable agent interaction while preserving a consistent historical record. Human involvement is minimal but strategic: users define high-level goals, periodically review the graph, and provide lightweight feedback to promote promising directions or prune unproductive ones. Experiments demonstrate EvoGit's ability to autonomously produce functional and modular software artifacts across two real-world tasks: (1) building a web application from scratch using modern frameworks, and (2) constructing a meta-level system that evolves its own language-model-guided solver for the bin-packing optimization problem. Our results underscore EvoGit's potential to establish a new paradigm for decentralized, automated, and continual software development. EvoGit is open-sourced at https://github.com/BillHuang2001/evogit.

Abstractive summarization of scientific papers has always been a research focus, yet existing methods face two main challenges. First, most summarization models rely on Encoder-Decoder architectures that treat papers as sequences of words, thus fail to fully capture the structured information inherent in scientific papers. Second, existing research often use keyword mapping or feature engineering to identify the structural information, but these methods struggle with the structural flexibility of scientific papers and lack robustness across different disciplines. To address these challenges, we propose a two-stage abstractive summarization framework that leverages automatic recognition of structural functions within scientific papers. In the first stage, we standardize chapter titles from numerous scientific papers and construct a large-scale dataset for structural function recognition. A classifier is then trained to automatically identify the key structural components (e.g., Background, Methods, Results, Discussion), which provides a foundation for generating more balanced summaries. In the second stage, we employ Longformer to capture rich contextual relationships across sections and generating context-aware summaries. Experiments conducted on two domain-specific scientific paper summarization datasets demonstrate that our method outperforms advanced baselines, and generates more comprehensive summaries. The code and dataset can be accessed at https://github.com/tongbao96/code-for-SFR-AS.

The RNA structure-function relationship has recently garnered significant attention within the deep learning community, promising to grow in importance as nucleic acid structure models advance. However, the absence of standardized and accessible benchmarks for deep learning on RNA 3D structures has impeded the development of models for RNA functional characteristics. In this work, we introduce a set of seven benchmarking datasets for RNA structure-function prediction, designed to address this gap. Our library builds on the established Python library rnaglib, and offers easy data distribution and encoding, splitters and evaluation methods, providing a convenient all-in-one framework for comparing models. Datasets are implemented in a fully modular and reproducible manner, facilitating for community contributions and customization. Finally, we provide initial baseline results for all tasks using a graph neural network. Source code: https://github.com/cgoliver/rnaglib Documentation: https://rnaglib.org

Calibrating large-scale camera arrays, such as those in dome-based setups, is time-intensive and typically requires dedicated captures of known patterns. While extrinsics in such arrays are fixed due to the physical setup, intrinsics often vary across sessions due to factors like lens adjustments or temperature changes. In this paper, we propose a dense-feature-driven multi-frame calibration method that refines intrinsics directly from scene data, eliminating the necessity for additional calibration captures. Our approach enhances traditional Structure-from-Motion (SfM) pipelines by introducing an extrinsics regularization term to progressively align estimated extrinsics with ground-truth values, a dense feature reprojection term to reduce keypoint errors by minimizing reprojection loss in the feature space, and an intrinsics variance term for joint optimization across multiple frames. Experiments on the Multiface dataset show that our method achieves nearly the same precision as dedicated calibration processes, and significantly enhances intrinsics and 3D reconstruction accuracy. Fully compatible with existing SfM pipelines, our method provides an efficient and practical plug-and-play solution for large-scale camera setups. Our code is publicly available at: https://github.com/YJJfish/Multi-Cali-Anything

Structure-based drug discovery, encompassing the tasks of protein-ligand docking and pocket-aware 3D drug design, represents a core challenge in drug discovery. However, no existing work can deal with both tasks to effectively leverage the duality between them, and current methods for each task are hindered by challenges in modeling 3D information and the limitations of available data. To address these issues, we propose 3DMolFormer, a unified dual-channel transformer-based framework applicable to both docking and 3D drug design tasks, which exploits their duality by utilizing docking functionalities within the drug design process. Specifically, we represent 3D pocket-ligand complexes using parallel sequences of discrete tokens and continuous numbers, and we design a corresponding dual-channel transformer model to handle this format, thereby overcoming the challenges of 3D information modeling. Additionally, we alleviate data limitations through large-scale pre-training on a mixed dataset, followed by supervised and reinforcement learning fine-tuning techniques respectively tailored for the two tasks. Experimental results demonstrate that 3DMolFormer outperforms previous approaches in both protein-ligand docking and pocket-aware 3D drug design, highlighting its promising application in structure-based drug discovery. The code is available at: https://github.com/HXYfighter/3DMolFormer .

Understanding how humans perceive visual complexity is a key area of study in visual cognition. Previous approaches to modeling visual complexity assessments have often resulted in intricate, difficult-to-interpret algorithms that employ numerous features or sophisticated deep learning architectures. While these complex models achieve high performance on specific datasets, they often sacrifice interpretability, making it challenging to understand the factors driving human perception of complexity. Recently (Shen, et al. 2024) proposed an interpretable segmentation-based model that accurately predicted complexity across various datasets, supporting the idea that complexity can be explained simply. In this work, we investigate the failure of their model to capture structural, color and surprisal contributions to complexity. To this end, we propose Multi-Scale Sobel Gradient (MSG) which measures spatial intensity variations, Multi-Scale Unique Color (MUC) which quantifies colorfulness across multiple scales, and surprise scores generated using a Large Language Model. We test our features on existing benchmarks and a novel dataset (Surprising Visual Genome) containing surprising images from Visual Genome. Our experiments demonstrate that modeling complexity accurately is not as simple as previously thought, requiring additional perceptual and semantic factors to address dataset biases. Our model improves predictive performance while maintaining interpretability, offering deeper insights into how visual complexity is perceived and assessed. Our code, analysis and data are available at https://github.com/Complexity-Project/Complexity-in-Complexity.

Despite the significant advancements in pre-training methods for point cloud understanding, directly capturing intricate shape information from irregular point clouds without reliance on external data remains a formidable challenge. To address this problem, we propose GPSFormer, an innovative Global Perception and Local Structure Fitting-based Transformer, which learns detailed shape information from point clouds with remarkable precision. The core of GPSFormer is the Global Perception Module (GPM) and the Local Structure Fitting Convolution (LSFConv). Specifically, GPM utilizes Adaptive Deformable Graph Convolution (ADGConv) to identify short-range dependencies among similar features in the feature space and employs Multi-Head Attention (MHA) to learn long-range dependencies across all positions within the feature space, ultimately enabling flexible learning of contextual representations. Inspired by Taylor series, we design LSFConv, which learns both low-order fundamental and high-order refinement information from explicitly encoded local geometric structures. Integrating the GPM and LSFConv as fundamental components, we construct GPSFormer, a cutting-edge Transformer that effectively captures global and local structures of point clouds. Extensive experiments validate GPSFormer's effectiveness in three point cloud tasks: shape classification, part segmentation, and few-shot learning. The code of GPSFormer is available at https://github.com/changshuowang/GPSFormer.

We algorithmically determine the regions and facets of all dimensions of the canonical polyhedral complex, the universal object into which a ReLU network decomposes its input space. We show that the locations of the vertices of the canonical polyhedral complex along with their signs with respect to layer maps determine the full facet structure across all dimensions. We present an algorithm which calculates this full combinatorial structure, making use of our theorems that the dual complex to the canonical polyhedral complex is cubical and it possesses a multiplication compatible with its facet structure. The resulting algorithm is numerically stable, polynomial time in the number of intermediate neurons, and obtains accurate information across all dimensions. This permits us to obtain, for example, the true topology of the decision boundaries of networks with low-dimensional inputs. We run empirics on such networks at initialization, finding that width alone does not increase observed topology, but width in the presence of depth does. Source code for our algorithms is accessible online at https://github.com/mmasden/canonicalpoly.

Given an incomplete image without additional constraint, image inpainting natively allows for multiple solutions as long as they appear plausible. Recently, multiplesolution inpainting methods have been proposed and shown the potential of generating diverse results. However, these methods have difficulty in ensuring the quality of each solution, e.g. they produce distorted structure and/or blurry texture. We propose a two-stage model for diverse inpainting, where the first stage generates multiple coarse results each of which has a different structure, and the second stage refines each coarse result separately by augmenting texture. The proposed model is inspired by the hierarchical vector quantized variational auto-encoder (VQ-VAE), whose hierarchical architecture isentangles structural and textural information. In addition, the vector quantization in VQVAE enables autoregressive modeling of the discrete distribution over the structural information. Sampling from the distribution can easily generate diverse and high-quality structures, making up the first stage of our model. In the second stage, we propose a structural attention module inside the texture generation network, where the module utilizes the structural information to capture distant correlations. We further reuse the VQ-VAE to calculate two feature losses, which help improve structure coherence and texture realism, respectively. Experimental results on CelebA-HQ, Places2, and ImageNet datasets show that our method not only enhances the diversity of the inpainting solutions but also improves the visual quality of the generated multiple images. Code and models are available at: https://github.com/USTC-JialunPeng/Diverse-Structure-Inpainting.

In this paper, we design a simple yet powerful deep network architecture, U^2-Net, for salient object detection (SOD). The architecture of our U^2-Net is a two-level nested U-structure. The design has the following advantages: (1) it is able to capture more contextual information from different scales thanks to the mixture of receptive fields of different sizes in our proposed ReSidual U-blocks (RSU), (2) it increases the depth of the whole architecture without significantly increasing the computational cost because of the pooling operations used in these RSU blocks. This architecture enables us to train a deep network from scratch without using backbones from image classification tasks. We instantiate two models of the proposed architecture, U^2-Net (176.3 MB, 30 FPS on GTX 1080Ti GPU) and U^2-Net^{dagger} (4.7 MB, 40 FPS), to facilitate the usage in different environments. Both models achieve competitive performance on six SOD datasets. The code is available: https://github.com/NathanUA/U-2-Net.

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.

While large language models have made significant strides in code generation, the pass rate of the generated code is bottlenecked on subtle errors, often requiring human intervention to pass tests, especially for complex problems. Existing LLM-based debugging systems treat generated programs as monolithic units, failing to address bugs at multiple levels of granularity, from low-level syntax errors to high-level algorithmic flaws. In this paper, we introduce Multi-Granularity Debugger (MGDebugger), a hierarchical code debugger by isolating, identifying, and resolving bugs at various levels of granularity. MGDebugger decomposes problematic code into a hierarchical tree structure of subfunctions, with each level representing a particular granularity of error. During debugging, it analyzes each subfunction and iteratively resolves bugs in a bottom-up manner. To effectively test each subfunction, we propose an LLM-simulated Python executor, which traces code execution and tracks important variable states to pinpoint errors accurately. Extensive experiments demonstrate that MGDebugger outperforms existing debugging systems, achieving an 18.9% improvement in accuracy over seed generations in HumanEval and a 97.6% repair success rate in HumanEvalFix. Furthermore, MGDebugger effectively fixes bugs across different categories and difficulty levels, demonstrating its robustness and effectiveness.

Code provides a general syntactic structure to build complex programs and perform precise computations when paired with a code interpreter - we hypothesize that language models (LMs) can leverage code-writing to improve Chain of Thought reasoning not only for logic and arithmetic tasks, but also for semantic ones (and in particular, those that are a mix of both). For example, consider prompting an LM to write code that counts the number of times it detects sarcasm in an essay: the LM may struggle to write an implementation for "detect_sarcasm(string)" that can be executed by the interpreter (handling the edge cases would be insurmountable). However, LMs may still produce a valid solution if they not only write code, but also selectively "emulate" the interpreter by generating the expected output of "detect_sarcasm(string)". In this work, we propose Chain of Code (CoC), a simple yet surprisingly effective extension that improves LM code-driven reasoning. The key idea is to encourage LMs to format semantic sub-tasks in a program as flexible pseudocode that the interpreter can explicitly catch undefined behaviors and hand off to simulate with an LM (as an "LMulator"). Experiments demonstrate that Chain of Code outperforms Chain of Thought and other baselines across a variety of benchmarks; on BIG-Bench Hard, Chain of Code achieves 84%, a gain of 12% over Chain of Thought. In a nutshell, CoC broadens the scope of reasoning questions that LMs can answer by "thinking in code".

Text-guided image editing with diffusion models has achieved remarkable quality but suffers from prohibitive latency, hindering real-world applications. We introduce FlashEdit, a novel framework designed to enable high-fidelity, real-time image editing. Its efficiency stems from three key innovations: (1) a One-Step Inversion-and-Editing (OSIE) pipeline that bypasses costly iterative processes; (2) a Background Shield (BG-Shield) technique that guarantees background preservation by selectively modifying features only within the edit region; and (3) a Sparsified Spatial Cross-Attention (SSCA) mechanism that ensures precise, localized edits by suppressing semantic leakage to the background. Extensive experiments demonstrate that FlashEdit maintains superior background consistency and structural integrity, while performing edits in under 0.2 seconds, which is an over 150times speedup compared to prior multi-step methods. Our code will be made publicly available at https://github.com/JunyiWuCode/FlashEdit.

We introduce MonkeyOCR, a vision-language model for document parsing that advances the state of the art by leveraging a Structure-Recognition-Relation (SRR) triplet paradigm. This design simplifies what would otherwise be a complex multi-tool pipeline (as in MinerU's modular approach) and avoids the inefficiencies of processing full pages with giant end-to-end models (e.g., large multimodal LLMs like Qwen-VL). In SRR, document parsing is abstracted into three fundamental questions - "Where is it?" (structure), "What is it?" (recognition), and "How is it organized?" (relation) - corresponding to layout analysis, content identification, and logical ordering. This focused decomposition balances accuracy and speed: it enables efficient, scalable processing without sacrificing precision. To train and evaluate this approach, we introduce the MonkeyDoc (the most comprehensive document parsing dataset to date), with 3.9 million instances spanning over ten document types in both Chinese and English. Experiments show that MonkeyOCR outperforms MinerU by an average of 5.1%, with particularly notable improvements on challenging content such as formulas (+15.0%) and tables (+8.6%). Remarkably, our 3B-parameter model surpasses much larger and top-performing models, including Qwen2.5-VL (72B) and Gemini 2.5 Pro, achieving state-of-the-art average performance on English document parsing tasks. In addition, MonkeyOCR processes multi-page documents significantly faster (0.84 pages per second compared to 0.65 for MinerU and 0.12 for Qwen2.5-VL-7B). The 3B model can be efficiently deployed for inference on a single NVIDIA 3090 GPU. Code and models will be released at https://github.com/Yuliang-Liu/MonkeyOCR.

Image restoration in adverse weather conditions is a difficult task in computer vision. In this paper, we propose a novel transformer-based framework called GridFormer which serves as a backbone for image restoration under adverse weather conditions. GridFormer is designed in a grid structure using a residual dense transformer block, and it introduces two core designs. First, it uses an enhanced attention mechanism in the transformer layer. The mechanism includes stages of the sampler and compact self-attention to improve efficiency, and a local enhancement stage to strengthen local information. Second, we introduce a residual dense transformer block (RDTB) as the final GridFormer layer. This design further improves the network's ability to learn effective features from both preceding and current local features. The GridFormer framework achieves state-of-the-art results on five diverse image restoration tasks in adverse weather conditions, including image deraining, dehazing, deraining & dehazing, desnowing, and multi-weather restoration. The source code and pre-trained models will be released.

Neural video codecs (NVCs), leveraging the power of end-to-end learning, have demonstrated remarkable coding efficiency improvements over traditional video codecs. Recent research has begun to pay attention to the quality structures in NVCs, optimizing them by introducing explicit hierarchical designs. However, less attention has been paid to the reference structure design, which fundamentally should be aligned with the hierarchical quality structure. In addition, there is still significant room for further optimization of the hierarchical quality structure. To address these challenges in NVCs, we propose EHVC, an efficient hierarchical neural video codec featuring three key innovations: (1) a hierarchical multi-reference scheme that draws on traditional video codec design to align reference and quality structures, thereby addressing the reference-quality mismatch; (2) a lookahead strategy to utilize an encoder-side context from future frames to enhance the quality structure; (3) a layer-wise quality scale with random quality training strategy to stabilize quality structures during inference. With these improvements, EHVC achieves significantly superior performance to the state-of-the-art NVCs. Code will be released in: https://github.com/bytedance/NEVC.

Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but lack the structural knowledge essential for many biological applications. To address this, we integrate structural insights from pre-trained protein graph neural networks (pGNNs) into pLMs through a latent-level contrastive learning task. This task aligns residue representations from pLMs with those from pGNNs across multiple proteins, enriching pLMs with inter-protein structural knowledge. Additionally, we incorporate a physical-level task that infuses intra-protein structural knowledge by optimizing pLMs to predict structural tokens. The proposed dual-task framework effectively incorporates both inter-protein and intra-protein structural knowledge into pLMs. Given the variability in the quality of protein structures in PDB, we further introduce a residue loss selection module, which uses a small model trained on high-quality structures to select reliable yet challenging residue losses for the pLM to learn. Applying our structure alignment method to the state-of-the-art ESM2 and AMPLIFY results in notable performance gains across a wide range of tasks, including a 12.7% increase in ESM2 contact prediction. The data, code, and resulting SaESM2 and SaAMPLIFY models will be released on Hugging Face.

Building credible simulators from data is difficult because structure design, parameter calibration, and out-of-distribution (OOD) robustness are tightly coupled. We introduce SOCIA (Simulation Orchestration for Computational Intelligence with Agents), a framework that treats simulator construction as joint structure-parameter co-optimization: it elicits mechanism-rich blueprints, exposes explicit tunable parameters, and instantiates a calibration schema, producing an executable simulator with built-in calibration hooks. SOCIA couples Bayesian Optimization for sample-efficient point calibration with Simulation-Based Inference for uncertainty-aware fitting; diagnostics trigger targeted structural edits in an outer refinement loop to co-optimize design and parameters under tight budgets. Across three diverse tasks, SOCIA consistently outperforms strong baselines, excelling on both in-distribution (ID) fitting and OOD shift. Ablations that weaken structure, calibration design, or tuning yield near-monotone degradations, underscoring the necessity of unified structure-parameter optimization. We will release the code soon.

Large Language Models are transforming software development by automatically generating code. Current prompting techniques such as Chain-of-Thought (CoT) suggest tasks step by step and the reasoning process follows a linear structure, which hampers the understanding of complex programming problems, particularly those requiring hierarchical solutions. Inspired by the principle of modularization in software development, in this work, we propose a novel prompting technique, called MoT, to enhance the code generation performance of LLMs. At first, MoT exploits modularization principles to decompose complex programming problems into smaller, independent reasoning steps, enabling a more structured and interpretable problem-solving process. This hierarchical structure improves the LLM's ability to comprehend complex programming problems. Then, it structures the reasoning process using an MLR Graph (Multi-Level Reasoning Graph), which hierarchically organizes reasoning steps. This approach enhances modular understanding and ensures better alignment between reasoning steps and the generated code, significantly improving code generation performance. Our experiments on two advanced LLMs (GPT-4o-mini and DeepSeek-R1), comparing MoT to six baseline prompting techniques across six widely used datasets, HumanEval, HumanEval-ET, HumanEval+, MBPP, MBPP-ET, and MBPP+, demonstrate that MoT significantly outperforms existing baselines (e.g., CoT and SCoT), achieving Pass@1 scores ranging from 58.1% to 95.1%. The experimental results confirm that MoT significantly enhances the performance of LLM-based code generation.

When reading a document, glancing at the spatial layout of a document is an initial step to understand it roughly. Traditional document layout analysis (DLA) methods, however, offer only a superficial parsing of documents, focusing on basic instance detection and often failing to capture the nuanced spatial and logical relations between instances. These limitations hinder DLA-based models from achieving a gradually deeper comprehension akin to human reading. In this work, we propose a novel graph-based Document Structure Analysis (gDSA) task. This task requires that model not only detects document elements but also generates spatial and logical relations in form of a graph structure, allowing to understand documents in a holistic and intuitive manner. For this new task, we construct a relation graph-based document structure analysis dataset (GraphDoc) with 80K document images and 4.13M relation annotations, enabling training models to complete multiple tasks like reading order, hierarchical structures analysis, and complex inter-element relation inference. Furthermore, a document relation graph generator (DRGG) is proposed to address the gDSA task, which achieves performance with 57.6% at mAP_g@0.5 for a strong benchmark baseline on this novel task and dataset. We hope this graphical representation of document structure can mark an innovative advancement in document structure analysis and understanding. The new dataset and code will be made publicly available at https://yufanchen96.github.io/projects/GraphDoc.

For a two-player imperfect-information extensive-form game (IIEFG) with K time steps and a player action space of size U, the game tree complexity is U^{2K}, causing existing IIEFG solvers to struggle with large or infinite (U,K), e.g., differential games with continuous action spaces. To partially address this scalability challenge, we focus on an important class of 2p0s games where the informed player (P1) knows the payoff while the uninformed player (P2) only has a belief over the set of I possible payoffs. Such games encompass a wide range of scenarios in sports, defense, cybersecurity, and finance. We prove that under mild conditions, P1's (resp. P2's) equilibrium strategy at any infostate concentrates on at most I (resp. I+1) action prototypes. When Ill U, this equilibrium structure causes the game tree complexity to collapse to I^K for P1 when P2 plays pure best responses, and (I+1)^K for P2 in a dual game where P1 plays pure best responses. We then show that exploiting this structure in standard learning modes, i.e., model-free multiagent reinforcement learning and model predictive control, is straightforward, leading to significant improvements in learning accuracy and efficiency from SOTA IIEFG solvers. Our demonstration solves a 22-player football game (K=10, U=infty) where the attacking team has to strategically conceal their intention until a critical moment in order to exploit information advantage. Code is available at https://github.com/ghimiremukesh/cams/tree/iclr

Unsupervised Multiplex Graph Learning (UMGL) aims to learn node representations on various edge types without manual labeling. However, existing research overlooks a key factor: the reliability of the graph structure. Real-world data often exhibit a complex nature and contain abundant task-irrelevant noise, severely compromising UMGL's performance. Moreover, existing methods primarily rely on contrastive learning to maximize mutual information across different graphs, limiting them to multiplex graph redundant scenarios and failing to capture view-unique task-relevant information. In this paper, we focus on a more realistic and challenging task: to unsupervisedly learn a fused graph from multiple graphs that preserve sufficient task-relevant information while removing task-irrelevant noise. Specifically, our proposed Information-aware Unsupervised Multiplex Graph Fusion framework (InfoMGF) uses graph structure refinement to eliminate irrelevant noise and simultaneously maximizes view-shared and view-unique task-relevant information, thereby tackling the frontier of non-redundant multiplex graph. Theoretical analyses further guarantee the effectiveness of InfoMGF. Comprehensive experiments against various baselines on different downstream tasks demonstrate its superior performance and robustness. Surprisingly, our unsupervised method even beats the sophisticated supervised approaches. The source code and datasets are available at https://github.com/zxlearningdeep/InfoMGF.

This paper presents a pioneering methodology, termed StructTuning, to efficiently transform foundation Large Language Models (LLMs) into domain specialists. It significantly minimizes the training corpus requirement to a mere 0.3% while achieving an impressive 50% of traditional knowledge injection performance. Our method is inspired by the educational processes for human students, particularly how structured domain knowledge from textbooks is absorbed and then applied to tackle real-world challenges through specific exercises. Based on this, we propose a novel two-stage knowledge injection strategy: Structure-aware Continual Pre-Training (SCPT) and Structure-aware Supervised Fine-Tuning (SSFT). In the SCPT phase, we organize the training data into an auto-generated taxonomy of domain knowledge, enabling LLMs to effectively memorize textual segments linked to specific expertise within the taxonomy's architecture. Subsequently, in the SSFT phase, we explicitly prompt models to reveal the underlying knowledge structure in their outputs, leveraging this structured domain insight to address practical problems adeptly. Our ultimate method has undergone extensive evaluations across model architectures and scales, using closed-book question-answering tasks on LongBench and MMedBench datasets. Remarkably, our method matches 50% of the improvement displayed by the state-of-the-art MMedLM2 on MMedBench, but with only 0.3% quantity of the training corpus. This breakthrough showcases the potential to scale up our StructTuning for stronger domain-specific LLMs. Code will be made public soon.

Fine-tuning pre-trained language models (PLMs) has recently shown a potential to improve knowledge graph completion (KGC). However, most PLM-based methods focus solely on encoding textual information, neglecting the long-tailed nature of knowledge graphs and their various topological structures, e.g., subgraphs, shortest paths, and degrees. We claim that this is a major obstacle to achieving higher accuracy of PLMs for KGC. To this end, we propose a Subgraph-Aware Training framework for KGC (SATKGC) with two ideas: (i) subgraph-aware mini-batching to encourage hard negative sampling and to mitigate an imbalance in the frequency of entity occurrences during training, and (ii) new contrastive learning to focus more on harder in-batch negative triples and harder positive triples in terms of the structural properties of the knowledge graph. To the best of our knowledge, this is the first study to comprehensively incorporate the structural inductive bias of the knowledge graph into fine-tuning PLMs. Extensive experiments on three KGC benchmarks demonstrate the superiority of SATKGC. Our code is available.

Autoregressive language models demonstrate excellent performance in various scenarios. However, the inference efficiency is limited by its one-step-one-word generation mode, which has become a pressing problem recently as the models become increasingly larger. Speculative decoding employs a "draft and then verify" mechanism to allow multiple tokens to be generated in one step, realizing lossless acceleration. Existing methods mainly adopt fixed heuristic draft structures, which fail to adapt to different situations to maximize the acceptance length during verification. To alleviate this dilemma, we proposed OPT-Tree, an algorithm to construct adaptive and scalable draft trees. It searches the optimal tree structure that maximizes the mathematical expectation of the acceptance length in each decoding step. Experimental results reveal that OPT-Tree outperforms the existing draft structures and achieves a speed-up ratio of up to 3.2 compared with autoregressive decoding. If the draft model is powerful enough and the node budget is sufficient, it can generate more than ten tokens in a single step. Our code is available at https://github.com/Jikai0Wang/OPT-Tree.

The impressive performance of large language models (LLMs) on code-related tasks has shown the potential of fully automated software development. In light of this, we introduce a new software engineering task, namely Natural Language to code Repository (NL2Repo). This task aims to generate an entire code repository from its natural language requirements. To address this task, we propose a simple yet effective framework CodeS, which decomposes NL2Repo into multiple sub-tasks by a multi-layer sketch. Specifically, CodeS includes three modules: RepoSketcher, FileSketcher, and SketchFiller. RepoSketcher first generates a repository's directory structure for given requirements; FileSketcher then generates a file sketch for each file in the generated structure; SketchFiller finally fills in the details for each function in the generated file sketch. To rigorously assess CodeS on the NL2Repo task, we carry out evaluations through both automated benchmarking and manual feedback analysis. For benchmark-based evaluation, we craft a repository-oriented benchmark, SketchEval, and design an evaluation metric, SketchBLEU. For feedback-based evaluation, we develop a VSCode plugin for CodeS and engage 30 participants in conducting empirical studies. Extensive experiments prove the effectiveness and practicality of CodeS on the NL2Repo task.

Ribonucleic acid (RNA) plays a variety of crucial roles in fundamental biological processes. Recently, RNA has become an interesting drug target, emphasizing the need to improve our understanding of its structures and functions. Over the years, sequencing technologies have produced an enormous amount of unlabeled RNA data, which hides important knowledge and potential. Motivated by the successes of protein language models, we introduce RiboNucleic Acid Language Model (RiNALMo) to help unveil the hidden code of RNA. RiNALMo is the largest RNA language model to date with 650 million parameters pre-trained on 36 million non-coding RNA sequences from several available databases. RiNALMo is able to extract hidden knowledge and capture the underlying structure information implicitly embedded within the RNA sequences. RiNALMo achieves state-of-the-art results on several downstream tasks. Notably, we show that its generalization capabilities can overcome the inability of other deep learning methods for secondary structure prediction to generalize on unseen RNA families. The code has been made publicly available on https://github.com/lbcb-sci/RiNALMo.

Real-world text can be damaged by corrosion issues caused by environmental or human factors, which hinder the preservation of the complete styles of texts, e.g., texture and structure. These corrosion issues, such as graffiti signs and incomplete signatures, bring difficulties in understanding the texts, thereby posing significant challenges to downstream applications, e.g., scene text recognition and signature identification. Notably, current inpainting techniques often fail to adequately address this problem and have difficulties restoring accurate text images along with reasonable and consistent styles. Formulating this as an open problem of text image inpainting, this paper aims to build a benchmark to facilitate its study. In doing so, we establish two specific text inpainting datasets which contain scene text images and handwritten text images, respectively. Each of them includes images revamped by real-life and synthetic datasets, featuring pairs of original images, corrupted images, and other assistant information. On top of the datasets, we further develop a novel neural framework, Global Structure-guided Diffusion Model (GSDM), as a potential solution. Leveraging the global structure of the text as a prior, the proposed GSDM develops an efficient diffusion model to recover clean texts. The efficacy of our approach is demonstrated by thorough empirical study, including a substantial boost in both recognition accuracy and image quality. These findings not only highlight the effectiveness of our method but also underscore its potential to enhance the broader field of text image understanding and processing. Code and datasets are available at: https://github.com/blackprotoss/GSDM.

Transformers have been recently explored for 3D point cloud understanding with impressive progress achieved. A large number of points, over 0.1 million, make the global self-attention infeasible for point cloud data. Thus, most methods propose to apply the transformer in a local region, e.g., spherical or cubic window. However, it still contains a large number of Query-Key pairs, which requires high computational costs. In addition, previous methods usually learn the query, key, and value using a linear projection without modeling the local 3D geometric structure. In this paper, we attempt to reduce the costs and model the local geometry prior by developing a new transformer block, named ConDaFormer. Technically, ConDaFormer disassembles the cubic window into three orthogonal 2D planes, leading to fewer points when modeling the attention in a similar range. The disassembling operation is beneficial to enlarging the range of attention without increasing the computational complexity, but ignores some contexts. To provide a remedy, we develop a local structure enhancement strategy that introduces a depth-wise convolution before and after the attention. This scheme can also capture the local geometric information. Taking advantage of these designs, ConDaFormer captures both long-range contextual information and local priors. The effectiveness is demonstrated by experimental results on several 3D point cloud understanding benchmarks. Code is available at https://github.com/LHDuan/ConDaFormer .

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

Image-based fashion design with AI techniques has attracted increasing attention in recent years. We focus on a new fashion design task, where we aim to transfer a reference appearance image onto a clothing image while preserving the structure of the clothing image. It is a challenging task since there are no reference images available for the newly designed output fashion images. Although diffusion-based image translation or neural style transfer (NST) has enabled flexible style transfer, it is often difficult to maintain the original structure of the image realistically during the reverse diffusion, especially when the referenced appearance image greatly differs from the common clothing appearance. To tackle this issue, we present a novel diffusion model-based unsupervised structure-aware transfer method to semantically generate new clothes from a given clothing image and a reference appearance image. In specific, we decouple the foreground clothing with automatically generated semantic masks by conditioned labels. And the mask is further used as guidance in the denoising process to preserve the structure information. Moreover, we use the pre-trained vision Transformer (ViT) for both appearance and structure guidance. Our experimental results show that the proposed method outperforms state-of-the-art baseline models, generating more realistic images in the fashion design task. Code and demo can be found at https://github.com/Rem105-210/DiffFashion.

In this paper, we propose a new class of metric for table structure recognition (TSR) evaluation, called grid table similarity (GriTS). Unlike prior metrics, GriTS evaluates the correctness of a predicted table directly in its natural form as a matrix. To create a similarity measure between matrices, we generalize the two-dimensional largest common substructure (2D-LCS) problem, which is NP-hard, to the 2D most similar substructures (2D-MSS) problem and propose a polynomial-time heuristic for solving it. This algorithm produces both an upper and a lower bound on the true similarity between matrices. We show using evaluation on a large real-world dataset that in practice there is almost no difference between these bounds. We compare GriTS to other metrics and empirically validate that matrix similarity exhibits more desirable behavior than alternatives for TSR performance evaluation. Finally, GriTS unifies all three subtasks of cell topology recognition, cell location recognition, and cell content recognition within the same framework, which simplifies the evaluation and enables more meaningful comparisons across different types of TSR approaches. Code will be released at https://github.com/microsoft/table-transformer.

Estimating the structure of directed acyclic graphs (DAGs, also known as Bayesian networks) is a challenging problem since the search space of DAGs is combinatorial and scales superexponentially with the number of nodes. Existing approaches rely on various local heuristics for enforcing the acyclicity constraint. In this paper, we introduce a fundamentally different strategy: We formulate the structure learning problem as a purely continuous optimization problem over real matrices that avoids this combinatorial constraint entirely. This is achieved by a novel characterization of acyclicity that is not only smooth but also exact. The resulting problem can be efficiently solved by standard numerical algorithms, which also makes implementation effortless. The proposed method outperforms existing ones, without imposing any structural assumptions on the graph such as bounded treewidth or in-degree. Code implementing the proposed algorithm is open-source and publicly available at https://github.com/xunzheng/notears.