lingzhi227 commited on
Commit
86dc2be
·
verified ·
1 Parent(s): 34bff4e

Upload README.md with huggingface_hub

Browse files
Files changed (1) hide show
  1. README.md +4 -3
README.md CHANGED
@@ -7,10 +7,10 @@ license: mit
7
  > **A growing benchmark for evaluating LLM agents on complex bioinformatics workflows.**
8
 
9
  [![Dataset on HF](https://img.shields.io/badge/Dataset-HuggingFace-yellow)](https://huggingface.co/datasets/lingzhi227/Extended-BioAgentBench)
10
- [![Tasks](https://img.shields.io/badge/Tasks-33-blue)]()
11
  [![Based on](https://img.shields.io/badge/Based%20on-BioAgentBench-green)](https://github.com/bioagent-bench/bioagent-bench)
12
 
13
- Building on [BioAgentBench](https://arxiv.org/abs/2601.21800) (10 tasks), this benchmark adds **33 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.
14
 
15
  **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.
16
 
@@ -21,7 +21,7 @@ Building on [BioAgentBench](https://arxiv.org/abs/2601.21800) (10 tasks), this b
21
  - **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)
22
  - **Real public data**: Every task uses published datasets with ground truth generated by validated reference pipelines
23
 
24
- ## Tasks (33 total)
25
 
26
  | # | Task ID | Name |
27
  |---|---------|------|
@@ -58,6 +58,7 @@ Building on [BioAgentBench](https://arxiv.org/abs/2601.21800) (10 tasks), this b
58
  | 41 | `rna-fusion` | RNA Fusion Detection from RNA-seq |
59
  | 42 | `spatial-transcriptomics` | Spatial Transcriptomics: Visium FFPE Brain Cancer Analy |
60
  | 43 | `taxonomic-profiling` | Multi-classifier Taxonomic Profiling of Metagenomic Rea |
 
61
 
62
  ## Quick start
63
 
 
7
  > **A growing benchmark for evaluating LLM agents on complex bioinformatics workflows.**
8
 
9
  [![Dataset on HF](https://img.shields.io/badge/Dataset-HuggingFace-yellow)](https://huggingface.co/datasets/lingzhi227/Extended-BioAgentBench)
10
+ [![Tasks](https://img.shields.io/badge/Tasks-34-blue)]()
11
  [![Based on](https://img.shields.io/badge/Based%20on-BioAgentBench-green)](https://github.com/bioagent-bench/bioagent-bench)
12
 
13
+ 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.
14
 
15
  **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.
16
 
 
21
  - **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)
22
  - **Real public data**: Every task uses published datasets with ground truth generated by validated reference pipelines
23
 
24
+ ## Tasks (34 total)
25
 
26
  | # | Task ID | Name |
27
  |---|---------|------|
 
58
  | 41 | `rna-fusion` | RNA Fusion Detection from RNA-seq |
59
  | 42 | `spatial-transcriptomics` | Spatial Transcriptomics: Visium FFPE Brain Cancer Analy |
60
  | 43 | `taxonomic-profiling` | Multi-classifier Taxonomic Profiling of Metagenomic Rea |
61
+ | 44 | `lcms-metabolomics` | LC-MS Untargeted Metabolomics: Urine Feature Discovery |
62
 
63
  ## Quick start
64