The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
MoFlow: An Invertible Flow Model for Generating Molecular Graphs
Open accessAbstract
Generating molecular graphs with desired chemical properties driven by deep graph generative models provides a very promising way to accelerate drug discovery process. Such graph generative models usually consist of two steps: learning latent representations and generation of molecular graphs. However, to generate novel and chemically-valid molecular graphs from latent representations is very challenging because of the chemical constraints and combinatorial complexity of molecular graphs. In this paper, we propose MoFlow, a flow-based graph generative model to learn invertible mappings between molecular graphs and their latent representations. To generate molecular graphs, our MoFlow first generates bonds (edges) through a Glow based model, then generates atoms (nodes) given bonds by a novel graph conditional flow, and finally assembles them into a chemically valid molecular graph with a posthoc validity correction. Our MoFlow has merits including exact and tractable likelihood training, efficient one-pass embedding and generation, chemical validity guarantees, 100% reconstruction of training data, and good generalization ability. We validate our model by four tasks: molecular graph generation and reconstruction, visualization of the continuous latent space, property optimization, and constrained property optimization. Our MoFlow achieves state-of-the-art performance, which implies its potential efficiency and effectiveness to explore large chemical space for drug discovery.
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Cites
How to improve R&D productivity: the pharmaceutical industry's grand challenge
Paul, S. M., Mytelka, D. S., Dunwiddie, C. T., Persinger, C. C., Munos, B. H., Lindborg, S. R., & Schacht, A. L. (2010) · Nature Reviews Drug Discovery · doi:10.1038/nrd3078 · Cited by 3,566
Automatic Chemical Design Using a Data-Driven Continuous Representation of Molecules
Gómez-Bombarelli, R., Wei, J. N., Duvenaud, D., Hernández-Lobato, J. M., Sánchez-Lengeling, B., Sheberla, D., Aguilera-Iparraguirre, J., Hirzel, T. D., Adams, R. P., & Aspuru-Guzik, A. (2018) · ACS Central Science · doi:10.1021/acscentsci.7b00572 · Cited by 3,106
Quantum chemistry structures and properties of 134 kilo molecules
Ramakrishnan, R., Dral, P. O., Rupp, M., & von Lilienfeld, O. A. (2014) · Scientific Data · doi:10.1038/sdata.2014.22 · Cited by 1,966
Deep learning enables rapid identification of potent DDR1 kinase inhibitors
Zhavoronkov, A., Ivanenkov, Y. A., Aliper, A., Veselov, M. S., Aladinskiy, V. A., Aladinskaya, A. V., Terentiev, V. A., Polykovskiy, D. A., Kuznetsov, M. D., Asadulaev, A., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0224-x · Cited by 1,573
NICE: Non-linear Independent Components Estimation
Dinh, L., Krueger, D., & Bengio, Y. (2014) · arXiv · doi:10.48550/arxiv.1410.8516 · Cited by 1,493
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Cited by
Bandi, A., Adapa, P. V. S. R., & Kuchi, Y. E. V. P. K. (2023) · Future Internet · doi:10.3390/fi15080260 · Cited by 638
Self-Supervised Learning of Graph Neural Networks: A Unified Review
Xie, Y., Xu, Z., Zhang, J., Wang, Z., & Ji, S. (2023) · IEEE Transactions on Pattern Analysis and Machine Intelligence · doi:10.1109/tpami.2022.3170559 · Cited by 389
A Comprehensive Survey on Deep Graph Representation Learning
Ju, W., Fang, Z., Gu, Y., Liu, Z., Long, Q., Qiao, Z., Qin, Y., Shen, J., Sun, F., Xiao, Z., et al. (2024) · Neural Networks · doi:10.1016/j.neunet.2024.106207 · Cited by 341
Generative Models as an Emerging Paradigm in the Chemical Sciences
Anstine, D. M., & Isayev, O. (2023) · Journal of the American Chemical Society · doi:10.1021/jacs.2c13467 · Cited by 313
Deep generative molecular design reshapes drug discovery
Zeng, X., Wang, F., Luo, Y., Kang, S.-G., Tang, J., Lightstone, F. C., Fang, E. F., Cornell, W., Nussinov, R., & Cheng, F. (2022) · Cell Reports Medicine · doi:10.1016/j.xcrm.2022.100794 · Cited by 295
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Metadata
- Authors
- Zang, C., & Wang, F.
- Venue
- Proceedings of the 26th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining
- Publisher
- ACM
- Published
- 2020-08-20
- Pages
- 617-626
- OpenAlex
- W3036527662
- Cited by
- 227
- References
- 6
- FWCI
- 24.32
- Type
- conference paper
- Language
- en
- Open access
- bronze
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