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README.md
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> **A growing benchmark for evaluating LLM agents on complex bioinformatics workflows.**
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[](https://huggingface.co/datasets/lingzhi227/Extended-BioAgentBench)
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[](https://github.com/bioagent-bench/bioagent-bench)
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Building on [BioAgentBench](https://arxiv.org/abs/2601.21800) (10 tasks), this benchmark adds **
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**This benchmark is actively growing** — new tasks are added continuously to cover more domains, increase complexity, and push the boundaries of what AI agents can do in bioinformatics.
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- **Domain-specific traps**: Tasks include steps where default parameters silently produce wrong results (e.g., Tn5 shift correction in ATAC-seq, Medaka model selection for Nanopore)
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- **Real public data**: Every task uses published datasets with ground truth generated by validated reference pipelines
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## Tasks (
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| # | Task ID | Name |
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| 41 | `rna-fusion` | RNA Fusion Detection from RNA-seq |
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| 42 | `spatial-transcriptomics` | Spatial Transcriptomics: Visium FFPE Brain Cancer Analy |
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| 43 | `taxonomic-profiling` | Multi-classifier Taxonomic Profiling of Metagenomic Rea |
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## Quick start
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> **A growing benchmark for evaluating LLM agents on complex bioinformatics workflows.**
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[](https://huggingface.co/datasets/lingzhi227/Extended-BioAgentBench)
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[]()
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[](https://github.com/bioagent-bench/bioagent-bench)
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Building on [BioAgentBench](https://arxiv.org/abs/2601.21800) (10 tasks), this benchmark adds **34 new tasks** that test LLM agents on increasingly complex, multi-tool bioinformatics pipelines. Tasks span 6 domains and range from simple linear workflows to depth-8 diamond DAGs with 16+ CLI tools.
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**This benchmark is actively growing** — new tasks are added continuously to cover more domains, increase complexity, and push the boundaries of what AI agents can do in bioinformatics.
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- **Domain-specific traps**: Tasks include steps where default parameters silently produce wrong results (e.g., Tn5 shift correction in ATAC-seq, Medaka model selection for Nanopore)
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- **Real public data**: Every task uses published datasets with ground truth generated by validated reference pipelines
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## Tasks (34 total)
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| # | Task ID | Name |
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| 41 | `rna-fusion` | RNA Fusion Detection from RNA-seq |
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| 42 | `spatial-transcriptomics` | Spatial Transcriptomics: Visium FFPE Brain Cancer Analy |
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| 43 | `taxonomic-profiling` | Multi-classifier Taxonomic Profiling of Metagenomic Rea |
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| 44 | `lcms-metabolomics` | LC-MS Untargeted Metabolomics: Urine Feature Discovery |
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## Quick start
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