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MHNfs:为低数据药物发现提供上下文生物活性预测

MHNfs: Prompting In-Context Bioactivity Predictions for Low-Data Drug Discovery.

作者信息

Schimunek Johannes, Luukkonen Sohvi, Klambauer Günter

机构信息

ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, A-4040 Linz, Austria.

出版信息

J Chem Inf Model. 2025 May 12;65(9):4243-4250. doi: 10.1021/acs.jcim.4c02373. Epub 2025 Apr 30.

DOI:10.1021/acs.jcim.4c02373
PMID:40302701
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12076497/
Abstract

Today's drug discovery increasingly relies on computational and machine learning approaches to identify novel candidates, yet data scarcity remains a significant challenge. To address this limitation, we present , an application specifically designed to predict molecular activity in low-data scenarios. At its core, leverages a state-of-the-art few-shot activity prediction model, named MHNfs, which has demonstrated strong performance across a large set of prediction tasks in the benchmark data set FS-Mol. The application features an intuitive interface that enables users to prompt the model for precise activity predictions based on a small number of known active and inactive molecules, akin to interactive interfaces for large language models. To evaluate its efficacy, we simulate real-world scenarios by recasting PubChem bioassays as few-shot prediction tasks. offers a streamlined and accessible solution for deploying advanced few-shot learning models, providing a valuable tool for accelerating drug discovery.

摘要

如今的药物发现越来越依赖于计算和机器学习方法来识别新的候选药物,但数据稀缺仍然是一个重大挑战。为了解决这一限制,我们展示了[具体名称未给出],这是一款专门设计用于预测低数据场景下分子活性的应用程序。其核心是利用了一种名为MHNfs的先进少样本活性预测模型,该模型在基准数据集FS-Mol中的大量预测任务中都表现出了强大的性能。该应用程序具有直观的界面,类似于大型语言模型的交互界面,用户可以根据少量已知的活性和非活性分子提示模型进行精确的活性预测。为了评估其有效性,我们通过将PubChem生物测定重新构建为少样本预测任务来模拟真实世界的场景。[具体名称未给出]为部署先进的少样本学习模型提供了一种简化且易于使用的解决方案,为加速药物发现提供了一个有价值的工具。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/da6622f73ef6/ci4c02373_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/9badaa8d8479/ci4c02373_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/29d6af8075a4/ci4c02373_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/1a37ac7db600/ci4c02373_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/0bda556f48cd/ci4c02373_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/da6622f73ef6/ci4c02373_0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/9badaa8d8479/ci4c02373_0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/29d6af8075a4/ci4c02373_0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/1a37ac7db600/ci4c02373_0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/0bda556f48cd/ci4c02373_0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/00cc/12076497/da6622f73ef6/ci4c02373_0005.jpg

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QSPRpred: a Flexible Open-Source Quantitative Structure-Property Relationship Modelling Tool.QSPRpred:一个灵活的开源定量结构-性质关系建模工具。
J Cheminform. 2024 Nov 14;16(1):128. doi: 10.1186/s13321-024-00908-y.
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The Goldilocks paradigm: comparing classical machine learning, large language models, and few-shot learning for drug discovery applications.
金发姑娘范式:比较经典机器学习、大语言模型和少样本学习在药物发现应用中的表现
Commun Chem. 2024 Jun 12;7(1):134. doi: 10.1038/s42004-024-01220-4.
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Chemprop: A Machine Learning Package for Chemical Property Prediction.Chemprop:一个用于化学性质预测的机器学习工具包。
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The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods.2023 年的 ChEMBL 数据库:一个涵盖多种生物活性数据类型和时间段的药物发现平台。
Nucleic Acids Res. 2024 Jan 5;52(D1):D1180-D1192. doi: 10.1093/nar/gkad1004.
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