Gene Set Summarization Using Large Language Models. Joachimiak, M. P., Caufield, J. H., Harris, N. L., Kim, H., & Mungall, C. J. May, 2023.
doi  abstract   bibtex   
Molecular biologists frequently interpret gene lists derived from high-throughput experiments and computational analysis. This is typically done as a statistical enrichment analysis that measures the over- or under-representation of biological function terms associated with genes or their properties, based on curated assertions from a knowledge base (KB) such as the Gene Ontology (GO). Interpreting gene lists can also be framed as a textual summarization task, enabling the use of Large Language Models (LLMs), potentially utilizing scientific texts directly and avoiding reliance on a KB. We developed SPINDOCTOR (Structured Prompt Interpolation of Natural Language Descriptions of Controlled Terms for Ontology Reporting), a method that uses GPT models to perform gene set function summarization as a complement to standard enrichment analysis. This method can use different sources of gene functional information: (1) structured text derived from curated ontological KB annotations, (2) ontology-free narrative gene summaries, or (3) direct model retrieval. We demonstrate that these methods are able to generate plausible and biologically valid summary GO term lists for gene sets. However, GPT-based approaches are unable to deliver reliable scores or p-values and often return terms that are not statistically significant. Crucially, these methods were rarely able to recapitulate the most precise and informative term from standard enrichment, likely due to an inability to generalize and reason using an ontology. Results are highly nondeterministic, with minor variations in prompt resulting in radically different term lists. Our results show that at this point, LLM-based methods are unsuitable as a replacement for standard term enrichment analysis and that manual curation of ontological assertions remains necessary.
@misc{joachimiakGeneSetSummarization2023,
  title = {Gene {{Set Summarization}} Using {{Large Language Models}}},
  author = {Joachimiak, Marcin P. and Caufield, J. Harry and Harris, Nomi L. and Kim, Hyeongsik and Mungall, Christopher J.},
  year = {2023},
  month = may,
  number = {arXiv:2305.13338},
  eprint = {2305.13338},
  primaryclass = {cs, q-bio},
  publisher = {arXiv},
  doi = {10.48550/arXiv.2305.13338},
  urldate = {2024-03-13},
  abstract = {Molecular biologists frequently interpret gene lists derived from high-throughput experiments and computational analysis. This is typically done as a statistical enrichment analysis that measures the over- or under-representation of biological function terms associated with genes or their properties, based on curated assertions from a knowledge base (KB) such as the Gene Ontology (GO). Interpreting gene lists can also be framed as a textual summarization task, enabling the use of Large Language Models (LLMs), potentially utilizing scientific texts directly and avoiding reliance on a KB. We developed SPINDOCTOR (Structured Prompt Interpolation of Natural Language Descriptions of Controlled Terms for Ontology Reporting), a method that uses GPT models to perform gene set function summarization as a complement to standard enrichment analysis. This method can use different sources of gene functional information: (1) structured text derived from curated ontological KB annotations, (2) ontology-free narrative gene summaries, or (3) direct model retrieval. We demonstrate that these methods are able to generate plausible and biologically valid summary GO term lists for gene sets. However, GPT-based approaches are unable to deliver reliable scores or p-values and often return terms that are not statistically significant. Crucially, these methods were rarely able to recapitulate the most precise and informative term from standard enrichment, likely due to an inability to generalize and reason using an ontology. Results are highly nondeterministic, with minor variations in prompt resulting in radically different term lists. Our results show that at this point, LLM-based methods are unsuitable as a replacement for standard term enrichment analysis and that manual curation of ontological assertions remains necessary.},
  archiveprefix = {arxiv},
  keywords = {Computer Science - Artificial Intelligence,Computer Science - Computation and Language,Quantitative Biology - Genomics,Quantitative Biology - Quantitative Methods},
  groups = {Ontologies and AI},
  timestamp = {2024-03-13T12:53:17Z},
  file = {joachimiakGeneSetSummarization2023.pdf:/home/upal/Zotero/storage/UTPS843R/joachimiakGeneSetSummarization2023.pdf:application/pdf;arXiv.org Snapshot:/home/upal/Zotero/storage/GN4JWCDQ/2305.html:text/html}
}

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