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Can Large Language Models Empower Molecular Property Prediction?

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arxiv 2307.07443 v1 pith:MPYHSGHJ submitted 2023-07-14 cs.LG cs.AIq-bio.QM

classification cs.LGcs.AIq-bio.QM
keywords llmsmolecularpredictionpropertyexplanationsmultiplesmilesclassification
verification ladder T0 review T1 audit T2 compute T3 formal
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Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at \url{https://github.com/ChnQ/LLM4Mol}.

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Cited by 2 Pith papers

Reviewed papers in the Pith corpus that reference this work. Sorted by Pith novelty score. Full citation record

  1. NOCL: Node-Oriented Conceptualization LLM for Graph Tasks without Message Passing

    cs.LG 2025-05 conditional novelty 5.0 of 10

    NOCL lets an LLM handle node, edge, and graph tasks on text and non-text graphs by compressing each node's description into one semantic embedding and turning the graph into a text prompt.

  2. ChemAU: Harness the Reasoning of LLMs in Chemical Research with Adaptive Uncertainty Estimation

    cs.AI 2025-06 reject novelty 4.0 of 10

    ChemAU adds a position penalty to token-level uncertainty estimates so that flagged reasoning steps are corrected by a fine-tuned chemistry model, reporting improved accuracy on GPQA, MMLU-Pro, and SuperGPQA chemistry...

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