arXiv subjects

Xiangru Tang

Publications and source records attributed to Xiangru Tang.

At least 73 records · Page 4Linked to original sources

arXiv2025

LocAgent: Graph-Guided LLM Agents for Code Localization

Code localization--identifying precisely where in a codebase changes need to be made--is a fundamental yet challenging task in software maintenance. Existing approaches struggle to efficiently navigate complex codebases when identifying relevant code sections. The challenge lies in bridging natural language problem descriptions with the appropriate code elements, often requiring reasoning across hierarchical structures and multiple dependencies. We introduce LocAgent, a framework that addresses code localization through graph-based representation. By parsing codebases into directed heterogeneous graphs, LocAgent creates a lightweight representation that captures code structures (files, classes, functions) and their dependencies (imports, invocations, inheritance), enabling LLM agents to effectively search and locate relevant entities through powerful multi-hop reasoning. Experimental results on real-world benchmarks demonstrate that our approach significantly enhances accuracy in code localization. Notably, our method with the fine-tuned Qwen-2.5-Coder-Instruct-32B model achieves comparable results to SOTA proprietary models at greatly reduced cost (approximately 86% reduction), reaching up to 92.7% accuracy on file-level localization while improving downstream GitHub issue resolution success rates by 12% for multiple attempts (Pass@10). Our code is available at https://github.com/gersteinlab/LocAgent.

cs.SE↗

arXiv2025

OpenHands: An Open Platform for AI Software Developers as Generalist Agents

Software is one of the most powerful tools that we humans have at our disposal; it allows a skilled programmer to interact with the world in complex and profound ways. At the same time, thanks to improvements in large language models (LLMs), there has also been a rapid development in AI agents that interact with and affect change in their surrounding environments. In this paper, we introduce OpenHands (f.k.a. OpenDevin), a platform for the development of powerful and flexible AI agents that interact with the world in similar ways to those of a human developer: by writing code, interacting with a command line, and browsing the web. We describe how the platform allows for the implementation of new agents, safe interaction with sandboxed environments for code execution, coordination between multiple agents, and incorporation of evaluation benchmarks. Based on our currently incorporated benchmarks, we perform an evaluation of agents over 15 challenging tasks, including software engineering (e.g., SWE-BENCH) and web browsing (e.g., WEBARENA), among others. Released under the permissive MIT license, OpenHands is a community project spanning academia and industry with more than 2.1K contributions from over 188 contributors.

cs.SE↗

arXiv2025

MultiAgentBench: Evaluating the Collaboration and Competition of LLM agents

Large Language Models (LLMs) have shown remarkable capabilities as autonomous agents, yet existing benchmarks either focus on single-agent tasks or are confined to narrow domains, failing to capture the dynamics of multi-agent coordination and competition. In this paper, we introduce MultiAgentBench, a comprehensive benchmark designed to evaluate LLM-based multi-agent systems across diverse, interactive scenarios. Our framework measures not only task completion but also the quality of collaboration and competition using novel, milestone-based key performance indicators. Moreover, we evaluate various coordination protocols (including star, chain, tree, and graph topologies) and innovative strategies such as group discussion and cognitive planning. Notably, gpt-4o-mini reaches the average highest task score, graph structure performs the best among coordination protocols in the research scenario, and cognitive planning improves milestone achievement rates by 3%. Code and datasets are public available at https://github.com/MultiagentBench/MARBLE.

cs.MA↗

arXiv2025

MMVU: Measuring Expert-Level Multi-Discipline Video Understanding

We introduce MMVU, a comprehensive expert-level, multi-discipline benchmark for evaluating foundation models in video understanding. MMVU includes 3,000 expert-annotated questions spanning 27 subjects across four core disciplines: Science, Healthcare, Humanities & Social Sciences, and Engineering. Compared to prior benchmarks, MMVU features three key advancements. First, it challenges models to apply domain-specific knowledge and perform expert-level reasoning to analyze specialized-domain videos, moving beyond the basic visual perception typically assessed in current video benchmarks. Second, each example is annotated by human experts from scratch. We implement strict data quality controls to ensure the high quality of the dataset. Finally, each example is enriched with expert-annotated reasoning rationals and relevant domain knowledge, facilitating in-depth analysis. We conduct an extensive evaluation of 32 frontier multimodal foundation models on MMVU. The latest System-2-capable models, o1 and Gemini 2.0 Flash Thinking, achieve the highest performance among the tested models. However, they still fall short of matching human expertise. Through in-depth error analyses and case studies, we offer actionable insights for future advancements in expert-level, knowledge-intensive video understanding for specialized domains.

cs.CV↗

arXiv2025

ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/chemagent

cs.CL↗

arXiv2024

ChemSafetyBench: Benchmarking LLM Safety on Chemistry Domain

The advancement and extensive application of large language models (LLMs) have been remarkable, including their use in scientific research assistance. However, these models often generate scientifically incorrect or unsafe responses, and in some cases, they may encourage users to engage in dangerous behavior. To address this issue in the field of chemistry, we introduce ChemSafetyBench, a benchmark designed to evaluate the accuracy and safety of LLM responses. ChemSafetyBench encompasses three key tasks: querying chemical properties, assessing the legality of chemical uses, and describing synthesis methods, each requiring increasingly deeper chemical knowledge. Our dataset has more than 30K samples across various chemical materials. We incorporate handcrafted templates and advanced jailbreaking scenarios to enhance task diversity. Our automated evaluation framework thoroughly assesses the safety, accuracy, and appropriateness of LLM responses. Extensive experiments with state-of-the-art LLMs reveal notable strengths and critical vulnerabilities, underscoring the need for robust safety measures. ChemSafetyBench aims to be a pivotal tool in developing safer AI technologies in chemistry. Our code and dataset are available at https://github.com/HaochenZhao/SafeAgent4Chem. Warning: this paper contains discussions on the synthesis of controlled chemicals using AI models.

cs.CL↗

arXiv2024

FinDVer: Explainable Claim Verification over Long and Hybrid-Content Financial Documents

We introduce FinDVer, a comprehensive benchmark specifically designed to evaluate the explainable claim verification capabilities of LLMs in the context of understanding and analyzing long, hybrid-content financial documents. FinDVer contains 2,400 expert-annotated examples, divided into three subsets: information extraction, numerical reasoning, and knowledge-intensive reasoning, each addressing common scenarios encountered in real-world financial contexts. We assess a broad spectrum of LLMs under long-context and RAG settings. Our results show that even the current best-performing system, GPT-4o, still lags behind human experts. We further provide in-depth analysis on long-context and RAG setting, Chain-of-Thought reasoning, and model reasoning errors, offering insights to drive future advancements. We believe that FinDVer can serve as a valuable benchmark for evaluating LLMs in claim verification over complex, expert-domain documents.

cs.CL↗

arXiv2024

Data Interpreter: An LLM Agent For Data Science

Large Language Model (LLM)-based agents have shown effectiveness across many applications. However, their use in data science scenarios requiring solving long-term interconnected tasks, dynamic data adjustments and domain expertise remains challenging. Previous approaches primarily focus on individual tasks, making it difficult to assess the complete data science workflow. Moreover, they struggle to handle real-time changes in intermediate data and fail to adapt dynamically to evolving task dependencies inherent to data science problems. In this paper, we present Data Interpreter, an LLM-based agent designed to automatically solve various data science problems end-to-end. Our Data Interpreter incorporates two key modules: 1) Hierarchical Graph Modeling, which breaks down complex problems into manageable subproblems, enabling dynamic node generation and graph optimization; and 2) Programmable Node Generation, a technique that refines and verifies each subproblem to iteratively improve code generation results and robustness. Extensive experiments consistently demonstrate the superiority of Data Interpreter. On InfiAgent-DABench, it achieves a 25% performance boost, raising accuracy from 75.9% to 94.9%. For machine learning and open-ended tasks, it improves performance from 88% to 95%, and from 60% to 97%, respectively. Moreover, on the MATH dataset, Data Interpreter achieves remarkable performance with a 26% improvement compared to state-of-the-art baselines. The code is available at https://github.com/geekan/MetaGPT.

cs.AI↗

arXiv2024

ML-Bench: Evaluating Large Language Models and Agents for Machine Learning Tasks on Repository-Level Code

Despite Large Language Models (LLMs) like GPT-4 achieving impressive results in function-level code generation, they struggle with repository-scale code understanding (e.g., coming up with the right arguments for calling routines), requiring a deeper comprehension of complex file interactions. Also, recently, people have developed LLM agents that attempt to interact with repository code (e.g., compiling and evaluating its execution), prompting the need to evaluate their performance. These gaps have motivated our development of ML-Bench, a benchmark rooted in real-world programming applications that leverage existing code repositories to perform tasks. Addressing the need for LLMs to interpret long code contexts and translate instructions into precise, executable scripts, ML-Bench encompasses annotated 9,641 examples across 18 GitHub repositories, challenging LLMs to accommodate user-specified arguments and documentation intricacies effectively. To evaluate both LLMs and AI agents, two setups are employed: ML-LLM-Bench for assessing LLMs' text-to-code conversion within a predefined deployment environment, and ML-Agent-Bench for testing autonomous agents in an end-to-end task execution within a Linux sandbox environment. Our findings indicate that while GPT-4o leads with a Pass@5 rate surpassing 50%, there remains significant scope for improvement, highlighted by issues such as hallucinated outputs and difficulties with bash script generation. Notably, in the more demanding ML-Agent-Bench, GPT-4o achieves a 76.47% success rate, reflecting the efficacy of iterative action and feedback in complex task resolution. Our code, dataset, and models are available at https://github.com/gersteinlab/ML-bench.

cs.CL↗

arXiv2024

DocMath-Eval: Evaluating Math Reasoning Capabilities of LLMs in Understanding Long and Specialized Documents

Recent LLMs have demonstrated remarkable performance in solving exam-like math word problems. However, the degree to which these numerical reasoning skills are effective in real-world scenarios, particularly in expert domains, is still largely unexplored. This paper introduces DocMath-Eval, a comprehensive benchmark specifically designed to evaluate the numerical reasoning capabilities of LLMs in the context of understanding and analyzing specialized documents containing both text and tables. We conduct an extensive evaluation of 48 LLMs with Chain-of-Thought and Program-of-Thought prompting methods, aiming to comprehensively assess the capabilities and limitations of existing LLMs in DocMath-Eval. We found that even the current best-performing system (i.e., GPT-4o) still significantly lags behind human experts in solving complex numerical reasoning problems grounded in long contexts. We believe that DocMath-Eval can serve as a valuable benchmark for evaluating LLMs' capabilities in solving challenging numerical reasoning problems within expert domains.

cs.CL↗

arXiv2024

Step-Back Profiling: Distilling User History for Personalized Scientific Writing

Large language models (LLM) excel at a variety of natural language processing tasks, yet they struggle to generate personalized content for individuals, particularly in real-world scenarios like scientific writing. Addressing this challenge, we introduce STEP-BACK PROFILING to personalize LLMs by distilling user history into concise profiles, including essential traits and preferences of users. To conduct the experiments, we construct a Personalized Scientific Writing (PSW) dataset to study multi-user personalization. PSW requires the models to write scientific papers given specialized author groups with diverse academic backgrounds. As for the results, we demonstrate the effectiveness of capturing user characteristics via STEP-BACK PROFILING for collaborative writing. Moreover, our approach outperforms the baselines by up to 3.6 points on the general personalization benchmark (LaMP), including 7 personalization LLM tasks. Our ablation studies validate the contributions of different components in our method and provide insights into our task definition. Our dataset and code are available at \url{https://github.com/gersteinlab/step-back-profiling}.

cs.CL↗

arXiv2024

Data Preparation for Deep Learning based Code Smell Detection: A Systematic Literature Review

Code Smell Detection (CSD) plays a crucial role in improving software quality and maintainability. And Deep Learning (DL) techniques have emerged as a promising approach for CSD due to their superior performance. However, the effectiveness of DL-based CSD methods heavily relies on the quality of the training data. Despite its importance, little attention has been paid to analyzing the data preparation process. This systematic literature review analyzes the data preparation techniques used in DL-based CSD methods. We identify 36 relevant papers published by December 2023 and provide a thorough analysis of the critical considerations in constructing CSD datasets, including data requirements, collection, labeling, and cleaning. We also summarize seven primary challenges and corresponding solutions in the literature. Finally, we offer actionable recommendations for preparing and accessing high-quality CSD data, emphasizing the importance of data diversity, standardization, and accessibility. This survey provides valuable insights for researchers and practitioners to harness the full potential of DL techniques in CSD.

cs.SE↗

arXiv2024

A Survey of Generative AI for de novo Drug Design: New Frontiers in Molecule and Protein Generation

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.

q-bio.BM↗

arXiv2024

Unveiling the Spectrum of Data Contamination in Language Models: A Survey from Detection to Remediation

Data contamination has garnered increased attention in the era of large language models (LLMs) due to the reliance on extensive internet-derived training corpora. The issue of training corpus overlap with evaluation benchmarks--referred to as contamination--has been the focus of significant recent research. This body of work aims to identify contamination, understand its impacts, and explore mitigation strategies from diverse perspectives. However, comprehensive studies that provide a clear pathway from foundational concepts to advanced insights are lacking in this nascent field. Therefore, we present a comprehensive survey in the field of data contamination, laying out the key issues, methodologies, and findings to date, and highlighting areas in need of further research and development. In particular, we begin by examining the effects of data contamination across various stages and forms. We then provide a detailed analysis of current contamination detection methods, categorizing them to highlight their focus, assumptions, strengths, and limitations. We also discuss mitigation strategies, offering a clear guide for future research. This survey serves as a succinct overview of the most recent advancements in data contamination research, providing a straightforward guide for the benefit of future research endeavors.

cs.CL↗

arXiv2024

PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomes

Multimodal Large Language Models (MLLMs) have seen growing adoption across various scientific disciplines. These advancements encourage the investigation of molecule-text modeling within synthetic chemistry, a field dedicated to designing and conducting chemical reactions to synthesize new compounds with desired properties and applications. Current approaches, however, often neglect the critical role of multiple molecule graph interaction in understanding chemical reactions, leading to suboptimal performance in synthetic chemistry tasks. This study introduces PRESTO(Progressive Pretraining Enhances Synthetic Chemistry Outcomes), a new framework that bridges the molecule-text modality gap by integrating a comprehensive benchmark of pretraining strategies and dataset configurations. It progressively improves multimodal LLMs through cross-modal alignment and multi-graph understanding. Our extensive experiments demonstrate that PRESTO offers competitive results in downstream synthetic chemistry tasks. The code can be found at https://github.com/IDEA-XL/PRESTO.

cs.LG↗

arXiv2024

MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning

Large language models (LLMs), despite their remarkable progress across various general domains, encounter significant barriers in medicine and healthcare. This field faces unique challenges such as domain-specific terminologies and reasoning over specialized knowledge. To address these issues, we propose MedAgents, a novel multi-disciplinary collaboration framework for the medical domain. MedAgents leverages LLM-based agents in a role-playing setting that participate in a collaborative multi-round discussion, thereby enhancing LLM proficiency and reasoning capabilities. This training-free framework encompasses five critical steps: gathering domain experts, proposing individual analyses, summarising these analyses into a report, iterating over discussions until a consensus is reached, and ultimately making a decision. Our work focuses on the zero-shot setting, which is applicable in real-world scenarios. Experimental results on nine datasets (MedQA, MedMCQA, PubMedQA, and six subtasks from MMLU) establish that our proposed MedAgents framework excels at mining and harnessing the medical expertise within LLMs, as well as extending its reasoning abilities. Our code can be found at https://github.com/gersteinlab/MedAgents.

cs.CL↗

arXiv2024

BioCoder: A Benchmark for Bioinformatics Code Generation with Large Language Models

Pre-trained large language models (LLMs) have significantly improved code generation. As these models scale up, there is an increasing need for the output to handle more intricate tasks and to be appropriately specialized to particular domains. Here, we target bioinformatics due to the amount of domain knowledge, algorithms, and data operations this discipline requires. We present BioCoder, a benchmark developed to evaluate LLMs in generating bioinformatics-specific code. BioCoder spans much of the field, covering cross-file dependencies, class declarations, and global variables. It incorporates 1,026 Python functions and 1,243 Java methods extracted from GitHub, along with 253 examples from the Rosalind Project, all pertaining to bioinformatics. Using topic modeling, we show that the overall coverage of the included code is representative of the full spectrum of bioinformatics calculations. BioCoder incorporates a fuzz-testing framework for evaluation. We have applied it to evaluate various models including InCoder, CodeGen, CodeGen2, SantaCoder, StarCoder, StarCoder+, InstructCodeT5+, GPT-3.5, and GPT- 4. Furthermore, we fine-tuned one model (StarCoder), demonstrating that our training dataset can enhance the performance on our testing benchmark (by >15% in terms of Pass@K under certain prompt configurations and always >3%). The results highlight two key aspects of successful models: (1) Successful models accommodate a long prompt (> 2,600 tokens) with full context, including functional dependencies. (2) They contain domain-specific knowledge of bioinformatics, beyond just general coding capability. This is evident from the performance gain of GPT-3.5/4 compared to the smaller models on our benchmark (50% vs. up to 25%). Availability and implementation: Code is available at: https://github.com/gersteinlab/biocoder and https://biocoder-benchmark. github.io/.

cs.LG↗

arXiv2024

Struc-Bench: Are Large Language Models Really Good at Generating Complex Structured Data?

Despite the remarkable capabilities of Large Language Models (LLMs) like GPT-4, producing complex, structured tabular data remains challenging. Our study assesses LLMs' proficiency in structuring tables and introduces a novel fine-tuning method, cognizant of data structures, to bolster their performance. We unveil Struc-Bench, a comprehensive benchmark featuring prominent LLMs (GPT-NeoX-20B, GPT-3.5, GPT-4, and Vicuna), which spans text tables, HTML, and LaTeX formats. Our proposed FormatCoT aids in crafting format-specific instructions from the intended outputs to populate this benchmark. Addressing the gap in task-centered evaluation, we propose two innovative metrics, P-Score (Prompting Score) and H-Score (Heuristical Score), to more accurately gauge LLM performance. Our experiments show that applying our structure-aware fine-tuning to LLaMA-7B leads to substantial performance gains, outshining its LLM counterparts across most measures. In-depth error analysis and creating an ability map across six dimensions -- coverage, formatting, reasoning, comprehension, pragmatics, and hallucination -- highlight areas for future enhancements and suggest forthcoming research trajectories. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

cs.CL↗