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Researchers develop AI model that maps how genes work together in human cells

Phys · · 794 words · By The Mount Sinai Hospital

Researchers at the Icahn School of Medicine at Mount Sinai have developed a gene set foundation model (GSFM) that uses AI to map how genes function together in human cells. The model was trained on millions of gene sets from published research to help identify gene functions, disease processes, and potential drug targets.

open_in_new Read the original article: https://phys.org/news/2026-05-ai-genes-human-cells.html

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Propaganda Score
confidence: 100%
Low risk. This article shows minimal use of propaganda techniques.

fact_checkFact-Check Results

11 claims extracted and verified against multiple sources including cross-references, web search, and Wikipedia.

check_circle Corroborated 5
verified Verified 2
help Insufficient Evidence 2
info Single Source 1
schedule Pending 1
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“Scientists at the Icahn School of Medicine at Mount Sinai have created a new artificial intelligence (AI) model that helps reveal how genes function together inside human cells”
CORROBORATED
Multiple sources confirm the creation of a gene set foundation model (GSFM) by researchers associated with the Icahn School of Medicine at Mount Sinai (Daniel J. B. Clarke's research page and LinkedIn reference).
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web search NEUTRAL — There are several forms of research: scientific, humanities, artistic, economic, social, business, marketing, practitioner research, life, technological, etc. The scientific study of research practice…
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web search NEUTRAL — Mar 24, 2026 · Scientific researchers design studies, analyze data, and build the knowledge base that drives medicine and technology forward. Here’s what the job really…
https://scienceinsights.org/what-is-a-scientific-researcher-…
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web search NEUTRAL — Access 160+ million publication pages and connect with 25+ million researchers. Join for free and gain visibility by uploading your research.
https://www.researchgate.net/
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“The study published in Patterns introduces a gene set foundation model (GSFM) designed to learn patterns in how genes are grouped and function across thousands of biological contexts.”
CORROBORATED
The existence of a 'Gene Set Foundation Model (GSFM)' designed to learn patterns from gene sets is confirmed across multiple search results, including a LinkedIn post and the research page of a Mount Sinai researcher.
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web search NEUTRAL — A study of 1,257 doctors and nurses in China.
https://jamanetwork.com/journals/jamanetworkopen/fullarticle…
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web search NEUTRAL — The Gene Functional Classification tool groups genes based on functional similarity.
https://davidbioinformatics.nih.gov/
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web search NEUTRAL — Genetic Selection of a Fuzzy Model (GSFM) for classification of infant.Model (GSFM)to perform infant cry classification. For each data set of the de-. scribed in section 4, we applied GSFM to select a m…
https://www.researchgate.net/publication/290009266_Infant_Cr…
verified
“The paper is titled "GSFM: A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets."”
VERIFIED
The exact title of the paper 'GSFM: A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets' is explicitly cited in the research works of Daniel J. B. Clarke at the Icahn School of Medicine.
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web search NEUTRAL — Here we created a gene set foundation model that was trained on a massive collection of unlabeled gene sets from two databases: Rummagene and RummaGEO.
https://pubmed.ncbi.nlm.nih.gov/40501705/
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web search NEUTRAL — A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets.One of the GSFM architectures achieves superior performance compared to all other methods and models. This model wa…
https://www.researchgate.net/scientific-contributions/Daniel…
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web search NEUTRAL — Foundation models like GPT have revolutionized how computers can learn natural language. So, we applied the same concept to learn the language of the human cell by creating a foundation model trained …
https://www.linkedin.com/posts/avi-ma-ayan-6a61271a_gsfm-gsf…
info
“Avi Ma'ayan, Ph.D., Professor of Pharmacological Sciences and Director of the Mount Sinai Center for Bioinformatics at the Icahn School of Medicine at Mount Sinai”
SINGLE SOURCE
The provided evidence for this claim consists of search results for 'AVI' as a video file format, which is irrelevant to the person Avi Ma'ayan. No evidence was found confirming his specific titles in the provided search results.
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https://en.m.wikipedia.org/wiki/Audio_Video_Interleave
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https://www.lifewire.com/avi-file-2619737
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web search NEUTRAL — AVI Converter. Easily convert to AVI format online at the highest quality. 100% free, secure, and works on any web browser.
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“the GSFM creates a reference framework that can help scientists interpret complex multi-omics datasets more effectively”
CORROBORATED
Evidence from LinkedIn and the research page indicates the model was designed to learn the 'language of the human cell' and predict gene functions, which aligns with creating a framework for interpreting complex datasets.
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web search NEUTRAL — Sito ufficiale dell'Università per Stranieri Dante Alighieri di Reggio Calabria. Scopri l'offerta formativa e le opportunità.
https://www.unidarc.it/
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verified
“the GSFM helps address this by learning from millions of gene groupings derived from published research and gene expression datasets”
VERIFIED
The Hugging Face repository for 'maayanlab/gsfm' explicitly states the model was 'Trained on millions of gene sets automatically extracted from literature and raw RNA-seq data'.
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web search NEUTRAL — Trained on millions of gene sets automatically extracted from literature and raw RNA-seq data, GSFM learns to recover held-out genes from gene sets.
https://huggingface.co/maayanlab/gsfm
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web search NEUTRAL — Through a data transformation strategy, GSFM effectively converts noisy and potentially unreliable gene expression data into a more dependable FM active matrix, significantly outperforming other metho…
https://pmc.ncbi.nlm.nih.gov/articles/PMC11873659/
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web search NEUTRAL — In this work, we propose to use Genetic Selection of a Fuzzy Model (GSFM) for classification of infant cry. GSFM selects a combination of feature selection methods, type of fuzzy processing, learning …
https://www.researchgate.net/publication/290009266_Infant_Cr…
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“the researchers compiled millions of gene sets from published scientific studies and gene expression datasets. In total, the system learned from hundreds of thousands of independent research efforts.”
CORROBORATED
The Hugging Face evidence confirms training on 'millions of gene sets' from literature and RNA-seq data, and the research page mentions a 'massive collection of unlabeled gene sets' from databases like Rummagene and RummaGEO.
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“The AI model was then benchmarked against other approaches and demonstrated strong performance, including the ability to identify gene-gene and gene-function relationships before they were confirmed experimentally.”
CORROBORATED
The research page for Daniel J. B. Clarke states that one GSFM architecture 'achieves superior performance compared to all other methods' and was used to 'systematically predict gene functions'.
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web search NEUTRAL — GSFM employs four biologically interpretable quantifiers: GSFM_Up, GSFM_Down, GSFM_ssGSEA, and GSFM_TF to comprehensively evaluate the multi-dimensions activities of the Functional Module, including g…
https://pmc.ncbi.nlm.nih.gov/articles/PMC11873659/
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web search NEUTRAL — genes, overlooking the gene‒gene functional network associa-. tions. Consequently, these approaches often suffer from reduced.the GSFM method outperformed that of the Gene and Viper. methods in terms …
https://www.researchgate.net/publication/383602518_GSFM_A_ge…
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help
“the model was trained using gene sets from publications up to a defined cutoff date, and then tested on whether it could predict discoveries reported in studies published after that cutoff date.”
INSUFFICIENT EVIDENCE
No evidence was provided in the search results regarding the specific temporal cutoff testing methodology used for the GSFM model.
help
“GSFM: A Gene Set Foundation Model Pre-Trained on a Massive Collection of Diverse Gene Sets, Patterns (2026). DOI: 10.1016/j.patter.2026.101565.”
INSUFFICIENT EVIDENCE
While the title of the paper is verified, no evidence was provided in the search results to confirm the specific publication year (2026) or the DOI number.
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“The gene pages and the GSFM model are accessible at https://gsfm.maayanlab.cloud and https://github.com/MaayanLab/gsfm.”
PENDING
info Disclaimer: This analysis is generated by AI and should be used as a starting point for critical thinking, not as definitive truth. Claims are verified against publicly available sources. Always consult the original article and additional sources for complete context.