QizhiPei

QizhiPei

AI & ML interests

AI4Science, Natural Language Processing

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Posts 2

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🚀⭐️Introducing our new survey "Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey"

arxiv: https://arxiv.org/abs/2403.01528
github: https://github.com/QizhiPei/Awesome-Biomolecule-Language-Cross-Modeling

The integration of biomolecular modeling with natural language (BL) has emerged as a promising interdisciplinary area at the intersection of artificial intelligence, chemistry and biology. This approach leverages the rich, multifaceted descriptions of biomolecules contained within textual data sources to enhance our fundamental understanding and enable downstream computational tasks such as biomolecule property prediction. The fusion of the nuanced narratives expressed through natural language with the structural and functional specifics of biomolecules described via various molecular modeling techniques opens new avenues for comprehensively representing and analyzing biomolecules. By incorporating the contextual language data that surrounds biomolecules into their modeling, BL aims to capture a holistic view encompassing both the symbolic qualities conveyed through language as well as quantitative structural characteristics. In this review, we provide an extensive analysis of recent advancements achieved through cross modeling of biomolecules and natural language.


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BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations

BioT5 achieves superior performance on various biological tasks by integrating natural language. See more details at:

Paper: BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations (2310.07276)
Code: https://github.com/QizhiPei/BioT5
Model (base): QizhiPei/biot5-base
Model (molecule captioning): QizhiPei/biot5-base-mol2text
Model (Text-based Molecule Design): QizhiPei/biot5-base-text2mol