ML-Bench: Evaluating Large Language Models and Agents for Machine Learning Tasks on Repository-Level Code
On the map: LLM agents and tool use → Software engineering coding agents
Abstract (arXiv)
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.
Key facts. Cited by 63 papers in the map (data through 7 Oct 2026). Placed in Software engineering coding agents, one of 16 directions in LLM agents and tool use. Builds on 16 of its 25 references that are in the map. First posted on arXiv 16 Nov 2023.
Builds on
16 of 25 references.
References · 16
- 2021Evaluating Large Language Models Trained on Codecited by 8,053
- 2023Reflexion: Language Agents with Verbal Reinforcement Learningcited by 4,064
- 2021Program Synthesis with Large Language Modelscited by 3,509
- 2023SWE-bench: Can Language Models Resolve Real-World GitHub Issues?cited by 3,193
- 2022Competition-Level Code Generation with AlphaCodecited by 1,427
- 2020CodeBERT: A Pre-Trained Model for Programming and Natural Languagescited by 1,286
- 2021Measuring Coding Challenge Competence With APPScited by 879
- 2022DS-1000: A Natural and Reliable Benchmark for Data Science Code Generationcited by 442
- 2023RepoCoder: Repository-Level Code Completion Through Iterative Retrieval and Generationcited by 357
- 2023RepoBench: Benchmarking Repository-Level Code Auto-Completion Systemscited by 346
- 2023MLAgentBench: Evaluating Language Agents on Machine Learning Experimentationcited by 339
- 2023CodeT5+: Open Code Large Language Models for Code Understanding and Generationcited by 327
4 more
- 2022MultiPL-E: A Scalable and Extensible Approach to Benchmarking Neural Code Generationcited by 132
- 2023Agents: An Open-source Framework for Autonomous Language Agentscited by 116
- 2022PanGu-Coder: Program Synthesis with Function-Level Language Modelingcited by 47
- 2023Measuring The Impact Of Programming Language Distributioncited by 32
Built on by
Citing papers per year: 2023: 1; 2024: 15; 2025: 31; 2026: 16.
63 papers.
Sort:
By area:
- 2024OpenHands: An Open Platform for AI Software Developers as Generalist Agentscited by 956
- 2024MLE-bench: Evaluating Machine Learning Agents on Machine Learning Engineeringcited by 429
- 2024ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discoverycited by 208
- 2025Deep Research Agents: A Systematic Examination And Roadmapcited by 122
- 2024DSBench: How Far Are Data Science Agents from Becoming Data Science Experts?cited by 119
- 2025MLGym: A New Framework and Benchmark for Advancing AI Research Agentscited by 111
- 2025BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biologycited by 75
- 2024AutoKaggle: A Multi-Agent Framework for Autonomous Data Science Competitionscited by 70
- 2025Paper2Code: Automating Code Generation from Scientific Papers in Machine Learningcited by 67
- 2025LLM Agents for Education: Advances and Applicationscited by 59
- 2025LLM Agents Making Agent Toolscited by 45
- 2025SciReplicate-Bench: Benchmarking LLMs in Agent-driven Algorithmic Reproduction from Research Paperscited by 42
38 more
- 2025EnvBench: A Benchmark for Automated Environment Setupcited by 36
- 2024Efficient Tool Use with Chain-of-Abstraction Reasoningcited by 33
- 2026AIRS-Bench: a Suite of Tasks for Frontier AI Research Science Agentscited by 32
- 2025KramaBench: A Benchmark for AI Systems on Data-to-Insight Pipelines over Data Lakescited by 30
- 2025GitTaskBench: A Benchmark for Code Agents Solving Real-World Tasks Through Code Repository Leveragingcited by 25
- 2024AAAR-1.0: Assessing AI's Potential to Assist Researchcited by 24
- 2024Kolb-Based Experiential Learning for Generalist Agents with Human-Level Kaggle Data Science Performancecited by 22
- 2025MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Sciencecited by 22
- 2025Large Language Model-based Data Science Agent: A Surveycited by 22
- 2024CodePori: Large-Scale System for Autonomous Software Development Using Multi-Agent Technologycited by 21
- 2024BudgetMLAgent: A Cost-Effective LLM Multi-Agent system for Automating Machine Learning Taskscited by 19
- 2025RepoMaster: Autonomous Exploration and Understanding of GitHub Repositories for Complex Task Solvingcited by 19
- 2025InnovatorBench: Evaluating Agents' Ability to Conduct Innovative LLM Researchcited by 18
- 2024AIGS: Generating Science from AI-Powered Automated Falsificationcited by 17
- 2025ML-Dev-Bench: Comparative Analysis of AI Agents on ML development workflowscited by 16
- 2025TimeSeriesGym: A Scalable Benchmark for (Time Series) Machine Learning Engineering Agentscited by 14
- 2025The Measurement Imbalance in Agentic AI Evaluation Undermines Industry Productivity Claimscited by 13
- 2025Reinforcement Learning for Machine Learning Engineering Agentscited by 13
- 2025Evolutionary Perspectives on the Evaluation of LLM-Based AI Agents: A Comprehensive Surveycited by 12
- 2025Software Development Life Cycle Perspective: A Survey of Benchmarks for Code Large Language Models and Agentscited by 11
- 2025EvaLearn: Quantifying the Learning Capability and Efficiency of LLMs via Sequential Problem Solvingcited by 10
- 2026AI4AI-Bench: Benchmarking LLM Agents in Algorithmic Design for Recursive Self-Improvementcited by 10
- 2024Exploring the Limitations of Large Language Models in Compositional Relation Reasoningcited by 9
- 2024LLM vs. Lawyers: Identifying a Subset of Summary Judgments in a Large UK Case Law Datasetcited by 8
- 2025LLM-REVal: Can We Trust LLM Reviewers Yet?cited by 8
- 2023Enhancing Open-Domain Task-Solving Capability of LLMs via Autonomous Tool Integration from GitHubcited by 7
- 2025SPIO: Ensemble and Selective Strategies via LLM-Based Multi-Agent Planning in Automated Data Sciencecited by 7
- 2025OSS-Bench: Benchmark Generator for Coding LLMscited by 6
- 2024From Linguistic Giants to Sensory Maestros: A Survey on Cross-Modal Reasoning with Large Language Modelscited by 4
- 2025From Standalone LLMs to Integrated Intelligence: A Survey of Compound Al Systemscited by 4
- 2025Gistify! Codebase-Level Understanding via Runtime Executioncited by 4
- 2025Agint: Agentic Graph Compilation for Software Engineering Agentscited by 4
- 2026FormulaCode: Evaluating Agentic Optimization on Large Codebasescited by 4
- 2026PDEAgent-Bench: A Multi-Metric, Multi-Library Benchmark for PDE Solver Generationcited by 4
- 2026DeltaML-Bench: Evaluating Machine Learning Agents on Real-World Research Repositoriescited by 4
- 2025Benchmarking AI Models in Software Engineering: A Review, Search Tool, and Unified Approach for Elevating Benchmark Qualitycited by 3
- 2025Code2Bench: Scaling Source and Rigor for Dynamic Benchmark Constructioncited by 3
- 2025ReX-MLE: The Autonomous Agent Benchmark for Medical Imaging Challengescited by 3
50 most cited of 63 All 63 (JSON)
- 2026Reward-rate Policy Gradient for Efficient Machine Learning Engineering Agents28 Sep 2026
- 2026ORCA: Evaluating LLMs on Data Science Code Translation25 Sep 2026
- 2026RECLAIM: Can Agents Reproduce the Claims of Machine Learning Papers?23 Sep 2026
- 2026PaperDoctor: Evidence-Grounded and Actionable Feedback for Scientific Papers in Progress15 Sep 2026
- 2026PaperCompiler: Faithful Paper-to-Code Generation via Repository-Level Specification Compilation2 Sep 2026
- 2026AI4AI-Bench: Benchmarking LLM Agents in Algorithmic Design for Recursive Self-Improvement20 Aug 2026
- 2026DeltaML-Bench: Evaluating Machine Learning Agents on Real-World Research Repositories20 Aug 2026
- 2026AgentHPOBench: A Benchmark For Evaluating LLM Agents as Sequential Hyperparameter Optimizers31 Jul 2026
- 2026Matryoshka Agent: Unfolding Sub-Agents for Long-Horizon Machine Learning Engineering27 Jul 2026
- 2026ProfiliTable: Profiling-Driven Tabular Data Processing via Agentic Workflows12 May 2026
- 2026PDEAgent-Bench: A Multi-Metric, Multi-Library Benchmark for PDE Solver Generation10 May 2026
- 2026Business Utility of Large Language Models as Exploratory Data Analysis Agents8 May 2026
38 more
- 2026FormulaCode: Evaluating Agentic Optimization on Large Codebases16 Mar 2026
- 2026Compiling Large Multi-Modal Requirement Documents into Runnable Software Systems: From an Agentic Test-Driven Perspective14 Feb 2026
- 2026AIRS-Bench: a Suite of Tasks for Frontier AI Research Science Agents6 Feb 2026
- 2026Learning When to Trust LLM Priors: A Validated Framework for Semantic Prior Integration29 Jan 2026
- 2025ReX-MLE: The Autonomous Agent Benchmark for Medical Imaging Challenges19 Dec 2025
- 2025Agint: Agentic Graph Compilation for Software Engineering Agents24 Nov 2025
- 2025InnovatorBench: Evaluating Agents' Ability to Conduct Innovative LLM Research31 Oct 2025
- 2025Gistify! Codebase-Level Understanding via Runtime Execution30 Oct 2025
- 2025LLM-REVal: Can We Trust LLM Reviewers Yet?14 Oct 2025
- 2025Reinforcement Learning for Machine Learning Engineering Agents1 Sep 2025
- 2025GitTaskBench: A Benchmark for Code Agents Solving Real-World Tasks Through Code Repository Leveraging26 Aug 2025
- 2025Code2Bench: Scaling Source and Rigor for Dynamic Benchmark Construction10 Aug 2025
- 2025Mockingbird: How does LLM perform in general machine learning tasks?6 Aug 2025
- 2025Large Language Model-based Data Science Agent: A Survey2 Aug 2025
- 2025Deep Research Agents: A Systematic Examination And Roadmap22 Jun 2025
- 2025Evolutionary Perspectives on the Evaluation of LLM-Based AI Agents: A Comprehensive Survey6 Jun 2025
- 2025KramaBench: A Benchmark for AI Systems on Data-to-Insight Pipelines over Data Lakes6 Jun 2025
- 2025From Standalone LLMs to Integrated Intelligence: A Survey of Compound Al Systems5 Jun 2025
- 2025MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science4 Jun 2025
- 2025EvaLearn: Quantifying the Learning Capability and Efficiency of LLMs via Sequential Problem Solving3 Jun 2025
- 2025The Measurement Imbalance in Agentic AI Evaluation Undermines Industry Productivity Claims1 Jun 2025
- 2025RepoMaster: Autonomous Exploration and Understanding of GitHub Repositories for Complex Task Solving27 May 2025
- 2025TimeSeriesGym: A Scalable Benchmark for (Time Series) Machine Learning Engineering Agents19 May 2025
- 2025OSS-Bench: Benchmark Generator for Coding LLMs18 May 2025
- 2025Software Development Life Cycle Perspective: A Survey of Benchmarks for Code Large Language Models and Agents8 May 2025
- 2025Paper2Code: Automating Code Generation from Scientific Papers in Machine Learning24 Apr 2025
- 2025SciReplicate-Bench: Benchmarking LLMs in Agent-driven Algorithmic Reproduction from Research Papers31 Mar 2025
- 2025SPIO: Ensemble and Selective Strategies via LLM-Based Multi-Agent Planning in Automated Data Science30 Mar 2025
- 2025EnvBench: A Benchmark for Automated Environment Setup18 Mar 2025
- 2025LLM Agents for Education: Advances and Applications14 Mar 2025
- 2025Benchmarking AI Models in Software Engineering: A Review, Search Tool, and Unified Approach for Elevating Benchmark Quality7 Mar 2025
- 2025BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology28 Feb 2025
- 2025MLGym: A New Framework and Benchmark for Advancing AI Research Agents20 Feb 2025
- 2025LLM Agents Making Agent Tools17 Feb 2025
- 2025ML-Dev-Bench: Comparative Analysis of AI Agents on ML development workflows3 Feb 2025
- 2024AIGS: Generating Science from AI-Powered Automated Falsification17 Nov 2024
- 2024BudgetMLAgent: A Cost-Effective LLM Multi-Agent system for Automating Machine Learning Tasks12 Nov 2024
- 2024Kolb-Based Experiential Learning for Generalist Agents with Human-Level Kaggle Data Science Performance5 Nov 2024
50 newest of 63 All 63 (JSON)
- 2024OpenHands: An Open Platform for AI Software Developers as Generalist Agentscited by 956
- 2024MLE-bench: Evaluating Machine Learning Agents on Machine Learning Engineeringcited by 429
- 2024ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discoverycited by 208
- 2025Deep Research Agents: A Systematic Examination And Roadmapcited by 122
- 2025MLGym: A New Framework and Benchmark for Advancing AI Research Agentscited by 111
- 2025BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biologycited by 75
- 2025LLM Agents for Education: Advances and Applicationscited by 59
- 2025LLM Agents Making Agent Toolscited by 45
- 2025SciReplicate-Bench: Benchmarking LLMs in Agent-driven Algorithmic Reproduction from Research Paperscited by 42
- 2026AIRS-Bench: a Suite of Tasks for Frontier AI Research Science Agentscited by 32
- 2025GitTaskBench: A Benchmark for Code Agents Solving Real-World Tasks Through Code Repository Leveragingcited by 25
- 2024Kolb-Based Experiential Learning for Generalist Agents with Human-Level Kaggle Data Science Performancecited by 22
12 most cited of 36 All 36 (JSON)
- 2026Reward-rate Policy Gradient for Efficient Machine Learning Engineering Agents28 Sep 2026
- 2026RECLAIM: Can Agents Reproduce the Claims of Machine Learning Papers?23 Sep 2026
- 2026PaperDoctor: Evidence-Grounded and Actionable Feedback for Scientific Papers in Progress15 Sep 2026
- 2026AI4AI-Bench: Benchmarking LLM Agents in Algorithmic Design for Recursive Self-Improvement20 Aug 2026
- 2026DeltaML-Bench: Evaluating Machine Learning Agents on Real-World Research Repositories20 Aug 2026
- 2026AgentHPOBench: A Benchmark For Evaluating LLM Agents as Sequential Hyperparameter Optimizers31 Jul 2026
- 2026ProfiliTable: Profiling-Driven Tabular Data Processing via Agentic Workflows12 May 2026
- 2026Business Utility of Large Language Models as Exploratory Data Analysis Agents8 May 2026
- 2026FormulaCode: Evaluating Agentic Optimization on Large Codebases16 Mar 2026
- 2026Compiling Large Multi-Modal Requirement Documents into Runnable Software Systems: From an Agentic Test-Driven Perspective14 Feb 2026
- 2026AIRS-Bench: a Suite of Tasks for Frontier AI Research Science Agents6 Feb 2026
- 2025ReX-MLE: The Autonomous Agent Benchmark for Medical Imaging Challenges19 Dec 2025
12 newest of 36 All 36 (JSON)
- 2024DSBench: How Far Are Data Science Agents from Becoming Data Science Experts?cited by 119
- 2024Efficient Tool Use with Chain-of-Abstraction Reasoningcited by 33
- 2025MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Sciencecited by 22
- 2024Exploring the Limitations of Large Language Models in Compositional Relation Reasoningcited by 9
- 2025SPIO: Ensemble and Selective Strategies via LLM-Based Multi-Agent Planning in Automated Data Sciencecited by 7
- 2024From Linguistic Giants to Sensory Maestros: A Survey on Cross-Modal Reasoning with Large Language Modelscited by 4
- 2025MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science4 Jun 2025
- 2025SPIO: Ensemble and Selective Strategies via LLM-Based Multi-Agent Planning in Automated Data Science30 Mar 2025
- 2024From Linguistic Giants to Sensory Maestros: A Survey on Cross-Modal Reasoning with Large Language Models19 Sep 2024
- 2024DSBench: How Far Are Data Science Agents from Becoming Data Science Experts?12 Sep 2024
- 2024Exploring the Limitations of Large Language Models in Compositional Relation Reasoning5 Mar 2024
- 2024Efficient Tool Use with Chain-of-Abstraction Reasoning30 Jan 2024
- 2024AutoKaggle: A Multi-Agent Framework for Autonomous Data Science Competitionscited by 70
- 2025Paper2Code: Automating Code Generation from Scientific Papers in Machine Learningcited by 67
- 2025EnvBench: A Benchmark for Automated Environment Setupcited by 36
- 2025KramaBench: A Benchmark for AI Systems on Data-to-Insight Pipelines over Data Lakescited by 30
- 2024AAAR-1.0: Assessing AI's Potential to Assist Researchcited by 24
- 2025RepoMaster: Autonomous Exploration and Understanding of GitHub Repositories for Complex Task Solvingcited by 19
- 2024AIGS: Generating Science from AI-Powered Automated Falsificationcited by 17
- 2025EvaLearn: Quantifying the Learning Capability and Efficiency of LLMs via Sequential Problem Solvingcited by 10
- 2024LLM vs. Lawyers: Identifying a Subset of Summary Judgments in a Large UK Case Law Datasetcited by 8
- 2025LLM-REVal: Can We Trust LLM Reviewers Yet?cited by 8
- 2025OSS-Bench: Benchmark Generator for Coding LLMscited by 6
- 2025From Standalone LLMs to Integrated Intelligence: A Survey of Compound Al Systemscited by 4
12 most cited of 21 All 21 (JSON)
- 2026ORCA: Evaluating LLMs on Data Science Code Translation25 Sep 2026
- 2026PaperCompiler: Faithful Paper-to-Code Generation via Repository-Level Specification Compilation2 Sep 2026
- 2026Matryoshka Agent: Unfolding Sub-Agents for Long-Horizon Machine Learning Engineering27 Jul 2026
- 2026PDEAgent-Bench: A Multi-Metric, Multi-Library Benchmark for PDE Solver Generation10 May 2026
- 2026Learning When to Trust LLM Priors: A Validated Framework for Semantic Prior Integration29 Jan 2026
- 2025LLM-REVal: Can We Trust LLM Reviewers Yet?14 Oct 2025
- 2025Code2Bench: Scaling Source and Rigor for Dynamic Benchmark Construction10 Aug 2025
- 2025Mockingbird: How does LLM perform in general machine learning tasks?6 Aug 2025
- 2025KramaBench: A Benchmark for AI Systems on Data-to-Insight Pipelines over Data Lakes6 Jun 2025
- 2025From Standalone LLMs to Integrated Intelligence: A Survey of Compound Al Systems5 Jun 2025
- 2025EvaLearn: Quantifying the Learning Capability and Efficiency of LLMs via Sequential Problem Solving3 Jun 2025
- 2025RepoMaster: Autonomous Exploration and Understanding of GitHub Repositories for Complex Task Solving27 May 2025
12 newest of 21 All 21 (JSON)
Similar, not cited
Close in wording, no citation either way
- 2025LMR-BENCH: Evaluating LLM Agent's Ability on Reproducing Language Modeling Research
- 2025DataSciBench: An LLM Agent Benchmark for Data Science
- 2025MRG-Bench: Evaluating and Exploring the Requirements of Context for Repository-Level Code Generation
- 2024Large Language Model Evaluation Via Multi AI Agents: Preliminary results
- 2025CSR-Bench: Benchmarking LLM Agents in Deployment of Computer Science Research Repositories
- 2025CodeJudgeBench: Benchmarking LLM-as-a-Judge for Coding Tasks
- 2026Narrowing the Complexity Gap in the Evaluation of Large Language Models ↗
- 2025Automatically Benchmarking LLM Code Agents through Agent-Driven Annotation and Evaluation