Benchmarking large language models for identifying transcription factor regulatory interactions
The literature-based TF-target interactions ground truth were obtained from TRRUST v2 human dataset (www.grnpedia.org/trrust). The experimental derived TF-target interactions ground truth were obtained from TFLink Home Sapiens small-scale interaction table (https://tflink.net/). Processed TF-target interactions data and the analytical pipeline has been compiled as an interactive Python notebook file and is available at https://github.com/pengpclab/LLM-TF-interactions.
Authors
- Edward Ray (ORCID: https://orcid.org/0000-0002-0921-7623)
- Xiuzhen Huang (ORCID: https://orcid.org/0000-0003-0498-3131)
- Jason H. Moore (ORCID: https://orcid.org/0000-0002-5015-1099)
- Xiaojiang Cui (ORCID: https://orcid.org/0000-0002-6843-736X)
- Andrew J. Hung (ORCID: https://orcid.org/0000-0002-7201-6736)
- Pei-Chen Peng (ORCID: https://orcid.org/0000-0002-5004-4322)
- Yi-Wen Hsiao
- Yimeng He
- L.H. Noël
Institutions
- Cedars-Sinai Medical Center (US)
Publication Details
- Journal
- Bioinformatics
- Published
- 2025-12-09
- DOI
- https://doi.org/10.1093/bioinformatics/btaf653
- Primary Topic
- Genomics and Chromatin Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 0.00