Bayesian Flow Network Framework for Chemistry Tasks.

IF 5.6 2区 化学 Q1 CHEMISTRY, MEDICINAL Journal of Chemical Information and Modeling Pub Date : 2025-02-10 Epub Date: 2025-01-21 DOI:10.1021/acs.jcim.4c01792
Nianze Tao, Minori Abe
{"title":"Bayesian Flow Network Framework for Chemistry Tasks.","authors":"Nianze Tao, Minori Abe","doi":"10.1021/acs.jcim.4c01792","DOIUrl":null,"url":null,"abstract":"<p><p>In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working with discrete data. A new accuracy schedule is proposed to improve sampling quality by significantly reducing reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity, even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.</p>","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":" ","pages":"1178-1187"},"PeriodicalIF":5.6000,"publicationDate":"2025-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Information and Modeling ","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jcim.4c01792","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/21 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}
引用次数: 0

Abstract

In this work, we introduce ChemBFN, a language model that handles chemistry tasks based on Bayesian flow networks working with discrete data. A new accuracy schedule is proposed to improve sampling quality by significantly reducing reconstruction loss. We show evidence that our method is appropriate for generating molecules with satisfied diversity, even when a smaller number of sampling steps is used. A classifier-free guidance method is adapted for conditional generation. It is also worthwhile to point out that after generative training, our model can be fine-tuned on regression and classification tasks with state-of-the-art performance, which opens the gate of building all-in-one models in a single module style. Our model has been open sourced at https://github.com/Augus1999/bayesian-flow-network-for-chemistry.

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
化学任务的贝叶斯流网络框架。
在这项工作中,我们介绍了ChemBFN,一种基于贝叶斯流网络处理离散数据的化学任务的语言模型。提出了一种新的精度计划,通过显著减少重构损失来提高采样质量。我们证明,即使使用较少的采样步骤,我们的方法也适用于产生具有满意多样性的分子。采用无分类器的制导方法进行条件生成。同样值得指出的是,经过生成训练,我们的模型可以在回归和分类任务上进行微调,具有最先进的性能,这为以单一模块风格构建一体化模型打开了大门。我们的模型已经在https://github.com/Augus1999/bayesian-flow-network-for-chemistry上开源了。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
CiteScore
9.80
自引率
10.70%
发文量
529
审稿时长
1.4 months
期刊介绍: The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.
期刊最新文献
Identification of Small-Molecule Inhibitors for Enterovirus A71 IRES by Structure-Based Virtual Screening. SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases. Accelerated Hydration Site Localization and Thermodynamic Profiling. Applying Molecular Dynamics Simulations to Unveil the Anisotropic Growth Mechanism of Gold Nanorods: Advances and Perspectives. GLMCyp: A Deep Learning-Based Method for CYP450-Mediated Reaction Site Prediction.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1