Conference proceeding
Can Large Language Models Classify and Generate Antimicrobial Resistance Genes?
PROCEEDINGS OF THE 24TH WORKSHOP ON BIOMEDICAL LANGUAGE PROCESSING, pp 240-248
01 Jan 2025
Abstract
This study explores the application of generative Large Language Models (LLMs) in DNA sequence analysis, highlighting their advantages over encoder-based models like DNABERT2 and Nucleotide Transformer. While encoder models excel in classification, they struggle to integrate external textual information. In contrast, generative LLMs can incorporate domain knowledge, such as BLASTn annotations, to improve classification accuracy even without fine-tuning. We evaluate this capability on antimicrobial resistance (AMR) gene classification, comparing generative LLMs with encoder-based baselines. Results show that LLMs significantly enhance classification when supplemented with textual information. Additionally, we demonstrate their potential in DNA sequence generation, further expanding their applicability. Our findings suggest that LLMs offer a novel paradigm for integrating biological sequences with external knowledge, bridging gaps in traditional classification methods.
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Details
- Title
- Can Large Language Models Classify and Generate Antimicrobial Resistance Genes?
- Creators
- Hyunwoo Yoo - Drexel UniversityHaebin Shin - KAIST AI, Seoul, South KoreaGail Rosen - Drexel University
- Contributors
- D Demner-Fushman (Editor)S Ananiadou (Editor)M Miwa (Editor)J Tsujii (Editor)
- Publication Details
- PROCEEDINGS OF THE 24TH WORKSHOP ON BIOMEDICAL LANGUAGE PROCESSING, pp 240-248
- Publisher
- Assoc Computational Linguistics-Acl
- Number of pages
- 9
- Grant note
- 2107108 / National Science Foundation (NSF); Instituto Politecnico Nacional - Mexico
- Resource Type
- Conference proceeding
- Language
- English
- Academic Unit
- Electrical and Computer Engineering
- Web of Science ID
- WOS:001616252100021
- Other Identifier
- 991022152238004721