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

arXiv: https://arxiv.org/abs/2308.16458 · HTML: https://mlsanity.com/paper/2308.16458/

## Key facts

- Cited by 25 papers in the map (data through 14 Oct 2026).
- Builds on 51 of its 63 references that are in the map.
- First posted on arXiv 31 Aug 2023.

## Builds on (most cited first, 30 of 51)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [Training a Helpful and Harmless Assistant with Reinforcement Learning from Human Feedback](https://mlsanity.com/paper/2204.05862/) (2022)
- [Program Synthesis with Large Language Models](https://mlsanity.com/paper/2108.07732/) (2021)
- [Training Compute-Optimal Large Language Models](https://mlsanity.com/paper/2203.15556/) (2022)
- [ToolLLM: Facilitating Large Language Models to Master 16000+ Real-world APIs](https://mlsanity.com/paper/2307.16789/) (2023)
- [Pythia: A Suite for Analyzing Large Language Models Across Training and Scaling](https://mlsanity.com/paper/2304.01373/) (2023)
- [Competition-Level Code Generation with AlphaCode](https://mlsanity.com/paper/2203.07814/) (2022)
- [Gorilla: Large Language Model Connected with Massive APIs](https://mlsanity.com/paper/2305.15334/) (2023)
- [LaMDA: Language Models for Dialog Applications](https://mlsanity.com/paper/2201.08239/) (2022)
- [A General Language Assistant as a Laboratory for Alignment](https://mlsanity.com/paper/2112.00861/) (2021)
- [Teaching Large Language Models to Self-Debug](https://mlsanity.com/paper/2304.05128/) (2023)
- [CodeT5: Identifier-aware Unified Pre-trained Encoder-Decoder Models for Code Understanding and Generation](https://mlsanity.com/paper/2109.00859/) (2021)
- [Measuring Coding Challenge Competence With APPS](https://mlsanity.com/paper/2105.09938/) (2021)
- [CodeGen: An Open Large Language Model for Code with Multi-Turn Program Synthesis](https://mlsanity.com/paper/2203.13474/) (2022)
- [GLM-130B: An Open Bilingual Pre-trained Model](https://mlsanity.com/paper/2210.02414/) (2022)
- [StarCoder: may the source be with you!](https://mlsanity.com/paper/2305.06161/) (2023)
- [WizardCoder: Empowering Code Large Language Models with Evol-Instruct](https://mlsanity.com/paper/2306.08568/) (2023)
- [InCoder: A Generative Model for Code Infilling and Synthesis](https://mlsanity.com/paper/2204.05999/) (2022)
- [DS-1000: A Natural and Reliable Benchmark for Data Science Code Generation](https://mlsanity.com/paper/2211.11501/) (2022)
- [CodeT: Code Generation with Generated Tests](https://mlsanity.com/paper/2207.10397/) (2022)
- [RepoBench: Benchmarking Repository-Level Code Auto-Completion Systems](https://mlsanity.com/paper/2306.03091/) (2023)
- [CodeT5+: Open Code Large Language Models for Code Understanding and Generation](https://mlsanity.com/paper/2305.07922/) (2023)
- [Grounded Copilot: How Programmers Interact with Code-Generating Models](https://mlsanity.com/paper/2206.15000/) (2022)
- [OctoPack: Instruction Tuning Code Large Language Models](https://mlsanity.com/paper/2308.07124/) (2023)
- [SantaCoder: don't reach for the stars!](https://mlsanity.com/paper/2301.03988/) (2023)

## Built on by (most cited first, 25 of 25)

- [OpenHands: An Open Platform for AI Software Developers as Generalist Agents](https://mlsanity.com/paper/2407.16741/) (2024)
- [BixBench: a Comprehensive Benchmark for LLM-based Agents in Computational Biology](https://mlsanity.com/paper/2503.00096/) (2025)
- [CodePDE: An Inference Framework for LLM-driven PDE Solver Generation](https://mlsanity.com/paper/2505.08783/) (2025)
- [Can Large Language Models Write Parallel Code?](https://mlsanity.com/paper/2401.12554/) (2024)
- [Virology Capabilities Test (VCT): A Multimodal Virology Q&A Benchmark](https://mlsanity.com/paper/2504.16137/) (2025)
- [MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science](https://mlsanity.com/paper/2506.04405/) (2025)
- [From Code Foundation Models to Agents and Applications: A Comprehensive Survey and Practical Guide to Code Intelligence](https://mlsanity.com/paper/2511.18538/) (2025)
- [Top General Performance = Top Domain Performance? DomainCodeBench: A Multi-domain Code Generation Benchmark](https://mlsanity.com/paper/2412.18573/) (2024)
- [BioAgents: Democratizing Bioinformatics Analysis with Multi-Agent Systems](https://mlsanity.com/paper/2501.06314/) (2025)
- [BioDSA-1K: Benchmarking Data Science Agents for Biomedical Research](https://mlsanity.com/paper/2505.16100/) (2025)
- [AutoNumerics: An Autonomous, PDE-Agnostic Multi-Agent Pipeline for Scientific Computing](https://mlsanity.com/paper/2602.17607/) (2026)
- [CHI-Bench: Can AI Agents Automate End-to-End, Long-Horizon, Policy-Rich Healthcare Workflows?](https://mlsanity.com/paper/2605.16679/) (2026)
- [ABC-Bench: An Agentic Bio-Capabilities Benchmark for Biosecurity](https://mlsanity.com/paper/2606.11150/) (2026)
- [Benchmarking AI Models in Software Engineering: A Review, Search Tool, and Unified Approach for Elevating Benchmark Quality](https://mlsanity.com/paper/2503.05860/) (2025)
- [Can LLM Agents Generate Real-World Evidence? Evaluating Observational Studies in Medical Databases](https://mlsanity.com/paper/2603.22767/) (2026)
- [Can Large Language Models Replace Data Scientists in Biomedical Research?](https://mlsanity.com/paper/2410.21591/) (2024)
- [Benchmarking LLM-based agents for single-cell omics analysis](https://mlsanity.com/paper/2508.13201/) (2025)
- [OLAF: An Open Life Science Analysis Framework for Conversational Bioinformatics Powered by Large Language Models](https://mlsanity.com/paper/2504.03976/) (2025)
- [Are LLMs Ready for Neural-integrated Mechanistic Modeling? A Benchmark and Agentic Framework](https://mlsanity.com/paper/2602.18008/) (2026)
- [IndustryCode: A Benchmark for Industry Code Generation](https://mlsanity.com/paper/2604.02729/) (2026)
- [MolViBench: Evaluating LLMs on Molecular Vibe Coding](https://mlsanity.com/paper/2605.02351/) (2026)
- [Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances](https://mlsanity.com/paper/2511.03354/) (2025)
- [MARBLE: Multi-Agent Reasoning for Bioinformatics Learning and Evolution](https://mlsanity.com/paper/2601.14349/) (2026)
- [SciCodePile: A 128GB Corpus and Executable Benchmark for Challenging Scientific Code Generation](https://mlsanity.com/paper/2607.19104/) (2026)
- [Bioinfoysis Technical Report](https://mlsanity.com/paper/2609.03871/) (2026)

## Abstract (arXiv)

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/.