@inproceedings{liu-etal-2024-geneverse,
title = "Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research",
author = "Liu, Tianyu and
Xiao, Yijia and
Luo, Xiao and
Xu, Hua and
Zheng, Wenjin and
Zhao, Hongyu",
editor = "Al-Onaizan, Yaser and
Bansal, Mohit and
Chen, Yun-Nung",
booktitle = "Findings of the Association for Computational Linguistics: EMNLP 2024",
month = nov,
year = "2024",
address = "Miami, Florida, USA",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/2024.findings-emnlp.277",
pages = "4819--4836",
abstract = "The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and proteomics is still limited. To fill this gap, we propose a collection of finetuned LLMs and multimodal LLMs (MLLMs), known as Geneverse, for three novel tasks in genomic and proteomic research. The models in Geneverse are trained and evaluated based on domain-specific datasets, and we use advanced parameter-efficient finetuning techniques to achieve the model adaptation for tasks including the generation of descriptions for gene functions, protein function inference from its structure, and marker gene selection from spatial transcriptomic data. We demonstrate that adapted LLMs and MLLMs perform well for these tasks and may outperform closed-source large-scale models based on our evaluations focusing on both truthfulness and structural correctness. All of the training strategies and base models we used are freely accessible. Our codes can be found at \url{https://github.com/HelloWorldLTY/Geneverse}.",
}
<?xml version="1.0" encoding="UTF-8"?>
<modsCollection xmlns="http://www.loc.gov/mods/v3">
<mods ID="liu-etal-2024-geneverse">
<titleInfo>
<title>Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research</title>
</titleInfo>
<name type="personal">
<namePart type="given">Tianyu</namePart>
<namePart type="family">Liu</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Yijia</namePart>
<namePart type="family">Xiao</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Xiao</namePart>
<namePart type="family">Luo</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Hua</namePart>
<namePart type="family">Xu</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Wenjin</namePart>
<namePart type="family">Zheng</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Hongyu</namePart>
<namePart type="family">Zhao</namePart>
<role>
<roleTerm authority="marcrelator" type="text">author</roleTerm>
</role>
</name>
<originInfo>
<dateIssued>2024-11</dateIssued>
</originInfo>
<typeOfResource>text</typeOfResource>
<relatedItem type="host">
<titleInfo>
<title>Findings of the Association for Computational Linguistics: EMNLP 2024</title>
</titleInfo>
<name type="personal">
<namePart type="given">Yaser</namePart>
<namePart type="family">Al-Onaizan</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Mohit</namePart>
<namePart type="family">Bansal</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<name type="personal">
<namePart type="given">Yun-Nung</namePart>
<namePart type="family">Chen</namePart>
<role>
<roleTerm authority="marcrelator" type="text">editor</roleTerm>
</role>
</name>
<originInfo>
<publisher>Association for Computational Linguistics</publisher>
<place>
<placeTerm type="text">Miami, Florida, USA</placeTerm>
</place>
</originInfo>
<genre authority="marcgt">conference publication</genre>
</relatedItem>
<abstract>The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and proteomics is still limited. To fill this gap, we propose a collection of finetuned LLMs and multimodal LLMs (MLLMs), known as Geneverse, for three novel tasks in genomic and proteomic research. The models in Geneverse are trained and evaluated based on domain-specific datasets, and we use advanced parameter-efficient finetuning techniques to achieve the model adaptation for tasks including the generation of descriptions for gene functions, protein function inference from its structure, and marker gene selection from spatial transcriptomic data. We demonstrate that adapted LLMs and MLLMs perform well for these tasks and may outperform closed-source large-scale models based on our evaluations focusing on both truthfulness and structural correctness. All of the training strategies and base models we used are freely accessible. Our codes can be found at https://github.com/HelloWorldLTY/Geneverse.</abstract>
<identifier type="citekey">liu-etal-2024-geneverse</identifier>
<location>
<url>https://aclanthology.org/2024.findings-emnlp.277</url>
</location>
<part>
<date>2024-11</date>
<extent unit="page">
<start>4819</start>
<end>4836</end>
</extent>
</part>
</mods>
</modsCollection>
%0 Conference Proceedings
%T Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research
%A Liu, Tianyu
%A Xiao, Yijia
%A Luo, Xiao
%A Xu, Hua
%A Zheng, Wenjin
%A Zhao, Hongyu
%Y Al-Onaizan, Yaser
%Y Bansal, Mohit
%Y Chen, Yun-Nung
%S Findings of the Association for Computational Linguistics: EMNLP 2024
%D 2024
%8 November
%I Association for Computational Linguistics
%C Miami, Florida, USA
%F liu-etal-2024-geneverse
%X The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs to genomics and proteomics is still limited. To fill this gap, we propose a collection of finetuned LLMs and multimodal LLMs (MLLMs), known as Geneverse, for three novel tasks in genomic and proteomic research. The models in Geneverse are trained and evaluated based on domain-specific datasets, and we use advanced parameter-efficient finetuning techniques to achieve the model adaptation for tasks including the generation of descriptions for gene functions, protein function inference from its structure, and marker gene selection from spatial transcriptomic data. We demonstrate that adapted LLMs and MLLMs perform well for these tasks and may outperform closed-source large-scale models based on our evaluations focusing on both truthfulness and structural correctness. All of the training strategies and base models we used are freely accessible. Our codes can be found at https://github.com/HelloWorldLTY/Geneverse.
%U https://aclanthology.org/2024.findings-emnlp.277
%P 4819-4836
Markdown (Informal)
[Geneverse: A Collection of Open-source Multimodal Large Language Models for Genomic and Proteomic Research](https://aclanthology.org/2024.findings-emnlp.277) (Liu et al., Findings 2024)
ACL