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For: Zhu W, Zhang Y, Zhao D, Xu J, Wang L. HiGNN: A Hierarchical Informative Graph Neural Network for Molecular Property Prediction Equipped with Feature-Wise Attention. J Chem Inf Model 2023;63:43-55. [PMID: 36519623 DOI: 10.1021/acs.jcim.2c01099] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Number Cited by Other Article(s)
1
Chen L, Li B, Chen Y, Lin M, Zhang S, Li C, Pang Y, Wang L. ADCNet: a unified framework for predicting the activity of antibody-drug conjugates. Brief Bioinform 2025;26:bbaf228. [PMID: 40421657 DOI: 10.1093/bib/bbaf228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Revised: 02/25/2025] [Accepted: 04/28/2025] [Indexed: 05/28/2025]  Open
2
Yadalam PK, Ardila CM. Enhanced hierarchical attention networks for predictive interactome analysis of LncRNA and CircRNA in oral herpes virus. J Oral Biol Craniofac Res 2025;15:445-453. [PMID: 40144645 PMCID: PMC11938150 DOI: 10.1016/j.jobcr.2025.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Revised: 02/18/2025] [Accepted: 02/22/2025] [Indexed: 03/28/2025]  Open
3
Pala MA. Graph-Aware AURALSTM: An Attentive Unified Representation Architecture with BiLSTM for Enhanced Molecular Property Prediction. Mol Divers 2025:10.1007/s11030-025-11197-4. [PMID: 40279083 DOI: 10.1007/s11030-025-11197-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2025] [Accepted: 04/12/2025] [Indexed: 04/26/2025]
4
Gong X, Liu Q, Han R, Guo Y, Wang G. MIFS: An adaptive multipath information fused self-supervised framework for drug discovery. Neural Netw 2025;184:107088. [PMID: 39778297 DOI: 10.1016/j.neunet.2024.107088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 12/13/2024] [Accepted: 12/21/2024] [Indexed: 01/11/2025]
5
Zhang Y, Huang J, Li X, Sun W, Zhang N, Zhang J, Chen T, Wang L. Self-awareness of retrosynthesis via chemically inspired contrastive learning for reinforced molecule generation. Brief Bioinform 2025;26:bbaf185. [PMID: 40254835 PMCID: PMC12009711 DOI: 10.1093/bib/bbaf185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 03/19/2025] [Accepted: 03/30/2025] [Indexed: 04/22/2025]  Open
6
Pereira TO, Abbasi M, Arrais JP. ABIET: An explainable transformer for identifying functional groups in biological active molecules. Comput Biol Med 2025;187:109740. [PMID: 39894011 DOI: 10.1016/j.compbiomed.2025.109740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 12/18/2024] [Accepted: 01/21/2025] [Indexed: 02/04/2025]
7
Kianfar A, Razzaghi P, Asgari Z. Integrating convolutional layers and biformer network with forward-forward and backpropagation training. Sci Rep 2025;15:7230. [PMID: 40021838 PMCID: PMC11871031 DOI: 10.1038/s41598-025-92218-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2025] [Accepted: 02/26/2025] [Indexed: 03/03/2025]  Open
8
Lin B, Yan S, Zhen B. A machine learning method for predicting molecular antimicrobial activity. Sci Rep 2025;15:6559. [PMID: 39994442 PMCID: PMC11850884 DOI: 10.1038/s41598-025-91190-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 02/18/2025] [Indexed: 02/26/2025]  Open
9
Park J, Han M, Lee K, Park S. Hierarchical Graph Attention Network with Positive and Negative Attentions for Improved Interpretability: ISA-PN. J Chem Inf Model 2025;65:1115-1127. [PMID: 39654089 DOI: 10.1021/acs.jcim.4c01035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2025]
10
Ye W, Li J, Cai X. Mfgnn: Multi-Scale Feature-Attentive Graph Neural Networks for Molecular Property Prediction. J Comput Chem 2025;46:e70011. [PMID: 39840745 DOI: 10.1002/jcc.70011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 12/03/2024] [Accepted: 12/09/2024] [Indexed: 01/23/2025]
11
Nguyen LD, Nguyen QH, Trinh QH, Nguyen BP. From SMILES to Enhanced Molecular Property Prediction: A Unified Multimodal Framework with Predicted 3D Conformers and Contrastive Learning Techniques. J Chem Inf Model 2024;64:9173-9195. [PMID: 39641280 DOI: 10.1021/acs.jcim.4c01240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2024]
12
Zhao D, Zhang Y, Chen Y, Li B, Zhou W, Wang L. Highly Accurate and Explainable Predictions of Small-Molecule Antioxidants for Eight In Vitro Assays Simultaneously through an Alternating Multitask Learning Strategy. J Chem Inf Model 2024;64:9098-9110. [PMID: 38888465 DOI: 10.1021/acs.jcim.4c00748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
13
Si Z, Liu D, Nie W, Hu J, Wang C, Jiang T, Yu H, Fu Y. Data-Based Prediction of Redox Potentials via Introducing Chemical Features into the Transformer Architecture. J Chem Inf Model 2024;64:8453-8463. [PMID: 39513760 DOI: 10.1021/acs.jcim.4c01299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2024]
14
Kang Y, Xia Q, Jiang Y, Li Z. MVGNet: Prediction of PI3K Inhibitors Using Multitask Learning and Multiview Frameworks. ACS OMEGA 2024;9:45159-45168. [PMID: 39554430 PMCID: PMC11561616 DOI: 10.1021/acsomega.4c06224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 10/09/2024] [Accepted: 10/15/2024] [Indexed: 11/19/2024]
15
Lin M, Cai J, Wei Y, Peng X, Luo Q, Li B, Chen Y, Wang L. MalariaFlow: A comprehensive deep learning platform for multistage phenotypic antimalarial drug discovery. Eur J Med Chem 2024;277:116776. [PMID: 39173285 DOI: 10.1016/j.ejmech.2024.116776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 07/31/2024] [Accepted: 08/01/2024] [Indexed: 08/24/2024]
16
He G, Liu S, Liu Z, Wang C, Zhang K, Li H. Prototype-based contrastive substructure identification for molecular property prediction. Brief Bioinform 2024;25:bbae565. [PMID: 39494969 PMCID: PMC11533112 DOI: 10.1093/bib/bbae565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 08/11/2024] [Accepted: 10/22/2024] [Indexed: 11/05/2024]  Open
17
Zhu Y, Zhang Y, Li X, Wang L. 3MTox: A motif-level graph-based multi-view chemical language model for toxicity identification with deep interpretation. JOURNAL OF HAZARDOUS MATERIALS 2024;476:135114. [PMID: 38986414 DOI: 10.1016/j.jhazmat.2024.135114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/24/2024] [Accepted: 07/04/2024] [Indexed: 07/12/2024]
18
Liu Y, Yu Y, Wu B, Qian J, Mu H, Gu L, Zhou R, Zhang H, Wu H, Bu Y. A comprehensive prediction system for silkworm acute toxicity assessment of environmental and in-silico pesticides. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024;282:116759. [PMID: 39029220 DOI: 10.1016/j.ecoenv.2024.116759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 07/03/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
19
Zhang Q, Mao D, Tu Y, Wu YY. A New Fingerprint and Graph Hybrid Neural Network for Predicting Molecular Properties. J Chem Inf Model 2024;64:5853-5866. [PMID: 39052623 DOI: 10.1021/acs.jcim.4c00586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
20
Lavecchia A. Advancing drug discovery with deep attention neural networks. Drug Discov Today 2024;29:104067. [PMID: 38925473 DOI: 10.1016/j.drudis.2024.104067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/10/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
21
Samanipour S, Barron LP, van Herwerden D, Praetorius A, Thomas KV, O’Brien JW. Exploring the Chemical Space of the Exposome: How Far Have We Gone? JACS AU 2024;4:2412-2425. [PMID: 39055136 PMCID: PMC11267556 DOI: 10.1021/jacsau.4c00220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 05/29/2024] [Accepted: 05/31/2024] [Indexed: 07/27/2024]
22
Zhang R, Lin Y, Wu Y, Deng L, Zhang H, Liao M, Peng Y. MvMRL: a multi-view molecular representation learning method for molecular property prediction. Brief Bioinform 2024;25:bbae298. [PMID: 38920342 PMCID: PMC11200189 DOI: 10.1093/bib/bbae298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/09/2024] [Accepted: 06/07/2024] [Indexed: 06/27/2024]  Open
23
Kengkanna A, Ohue M. Enhancing property and activity prediction and interpretation using multiple molecular graph representations with MMGX. Commun Chem 2024;7:74. [PMID: 38580841 PMCID: PMC10997661 DOI: 10.1038/s42004-024-01155-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/07/2024]  Open
24
Song Z, Chen J, Cheng J, Chen G, Qi Z. Computer-Aided Molecular Design of Ionic Liquids as Advanced Process Media: A Review from Fundamentals to Applications. Chem Rev 2024;124:248-317. [PMID: 38108629 DOI: 10.1021/acs.chemrev.3c00223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
25
Maier JC, Wang CI, Jackson NE. Distilling coarse-grained representations of molecular electronic structure with continuously gated message passing. J Chem Phys 2024;160:024109. [PMID: 38193551 DOI: 10.1063/5.0179253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024]  Open
26
Zhang Y, Liu C, Liu M, Liu T, Lin H, Huang CB, Ning L. Attention is all you need: utilizing attention in AI-enabled drug discovery. Brief Bioinform 2023;25:bbad467. [PMID: 38189543 PMCID: PMC10772984 DOI: 10.1093/bib/bbad467] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 11/03/2023] [Accepted: 11/25/2023] [Indexed: 01/09/2024]  Open
27
Li B, Lin M, Chen T, Wang L. FG-BERT: a generalized and self-supervised functional group-based molecular representation learning framework for properties prediction. Brief Bioinform 2023;24:bbad398. [PMID: 37930026 DOI: 10.1093/bib/bbad398] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/25/2023] [Accepted: 10/14/2023] [Indexed: 11/07/2023]  Open
28
Han S, Fu H, Wu Y, Zhao G, Song Z, Huang F, Zhang Z, Liu S, Zhang W. HimGNN: a novel hierarchical molecular graph representation learning framework for property prediction. Brief Bioinform 2023;24:bbad305. [PMID: 37594313 DOI: 10.1093/bib/bbad305] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/18/2023] [Accepted: 08/04/2023] [Indexed: 08/19/2023]  Open
29
Hagg A, Kirschner KN. Open-Source Machine Learning in Computational Chemistry. J Chem Inf Model 2023;63:4505-4532. [PMID: 37466636 PMCID: PMC10430767 DOI: 10.1021/acs.jcim.3c00643] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Indexed: 07/20/2023]
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