TY - JOUR AU - Sanchez-Lengeling, B. AU - Aspuru-Guzik, A. PY - 2018 DA - 2018// TI - Inverse molecular design using machine learning: generative models for matter engineering JO - Science VL - 361 UR - https://doi.org/10.1126/science.aat2663 DO - 10.1126/science.aat2663 ID - Sanchez-Lengeling2018 ER - TY - JOUR AU - Vanhaelen, Q. AU - Lin, Y. -. C. AU - Zhavoronkov, A. PY - 2020 DA - 2020// TI - The advent of generative chemistry JO - ACS Med Chem Lett VL - 11 UR - https://doi.org/10.1021/acsmedchemlett.0c00088 DO - 10.1021/acsmedchemlett.0c00088 ID - Vanhaelen2020 ER - TY - JOUR AU - Joo, S. AU - Kim, M. S. AU - Yang, J. AU - Park, J. PY - 2020 DA - 2020// TI - Generative model for proposing drug candidates satisfying anticancer properties using a conditional variational autoencoder JO - ACS Omega VL - 5 UR - https://doi.org/10.1021/acsomega.0c01149 DO - 10.1021/acsomega.0c01149 ID - Joo2020 ER - TY - JOUR AU - Maziarka, Ł. AU - Pocha, A. AU - Kaczmarczyk, J. AU - Rataj, K. AU - Danel, T. AU - Warchoł, M. PY - 2020 DA - 2020// TI - Mol-CycleGAN: a generative model for molecular optimization JO - J Cheminform VL - 12 UR - https://doi.org/10.1186/s13321-019-0404-1 DO - 10.1186/s13321-019-0404-1 ID - Maziarka2020 ER - TY - JOUR AU - Zhavoronkov, A. AU - Ivanenkov, Y. A. AU - Aliper, A. AU - Veselov, M. S. AU - Aladinskiy, V. A. AU - Aladinskaya, A. V. AU - Terentiev, V. A. AU - Polykovskiy, D. A. AU - Kuznetsov, M. D. AU - Asadulaev, A. AU - Volkov, Y. AU - Zholus, A. AU - Shayakhmetov, R. R. AU - Zhebrak, A. AU - Minaeva, L. I. AU - Zagribelnyy, B. A. AU - Lee, L. H. AU - Soll, R. AU - Madge, G. AU - Xing, L. PY - 2019 DA - 2019// TI - Deep learning enables rapid identification of potent DDR1 kinase inhibitors JO - Nat Biotechnol UR - https://doi.org/10.1038/s41587-019-0224-x DO - 10.1038/s41587-019-0224-x ID - Zhavoronkov2019 ER - TY - JOUR AU - Bhowmik, D. AU - Gao, S. AU - Young, M. T. AU - Ramanathan, A. PY - 2018 DA - 2018// TI - Deep clustering of protein folding simulations JO - BMC Bioinform VL - 19 ID - Bhowmik2018 ER - TY - JOUR AU - Romero, R. AU - Ramanathan, A. AU - Yuen, T. AU - Bhowmik, D. AU - Mathew, M. AU - Munshi, L. B. AU - Javaid, S. AU - Bloch, M. AU - Lizneva, D. AU - Rahimova, A. AU - Khan, A. AU - Taneja, C. AU - Kim, S. -. M. AU - Sun, L. AU - New, M. AU - Haider, S. AU - Zaidi, M. PY - 2019 DA - 2019// TI - Mechanism of glucocerebrosidase activation and dysfunction in gaucher disease unraveled by molecular dynamics and deep learning JO - Proc Natl Acad Sci VL - 116 UR - https://doi.org/10.1073/pnas.1818411116 DO - 10.1073/pnas.1818411116 ID - Romero2019 ER - TY - JOUR AU - Chen, H. AU - Engkvist, O. AU - Wang, Y. AU - Olivecrona, M. AU - Blaschke, T. PY - 2018 DA - 2018// TI - The rise of deep learning in drug discovery JO - Drug Discov Today VL - 23 UR - https://doi.org/10.1016/j.drudis.2018.01.039 DO - 10.1016/j.drudis.2018.01.039 ID - Chen2018 ER - TY - STD TI - Goodfellow I, Pouget-Abadie J, Mirza M, Xu B, Warde-Farley D, Ozair S, Courville A, Bengio Y (2014) Generative adversarial nets. In: Ghahramani, Z., Welling, M., Cortes, C., Lawrence, N.D., Weinberger, K.Q. (eds.) Advances in Neural Information Processing Systems 27, vol. 2014-December, pp. 2672–2680. http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf UR - http://papers.nips.cc/paper/5423-generative-adversarial-nets.pdf ID - ref9 ER - TY - STD TI - Goodfellow I (2017) NIPS 2016 Tutorial: Generative Adversarial Networks. arxiv:1701.00160 UR - http://arxiv.org/abs/1701.00160 ID - ref10 ER - TY - STD TI - De Cao N, Kipf T (2018) MolGAN: An implicit generative model for small molecular graphs. ICML 2018 workshop on Theoretical Foundations and Applications of Deep Generative Models ID - ref11 ER - TY - STD TI - Guimaraes GL, Sanchez-Lengeling B, Outeiral C, Farias PLC, Aspuru-Guzik A (2017) Objective-Reinforced Generative Adversarial Networks (ORGAN) for Sequence Generation Models. arxiv:1705.10843 UR - http://arxiv.org/abs/1705.10843 ID - ref12 ER - TY - STD TI - Benhenda M (2017) ChemGAN challenge for drug discovery: can AI reproduce natural chemical diversity?. arxiv:1708.08227 UR - http://arxiv.org/abs/1708.08227 ID - ref13 ER - TY - STD TI - Arjovsky M, Chintala S, Bottou L (2017) Wasserstein GAN. arxiv:1701.07875 UR - http://arxiv.org/abs/1701.07875 ID - ref14 ER - TY - STD TI - Gulrajani I, Ahmed F, Arjovsky M, Dumoulin V, Courville A (2017) Improved Training of Wasserstein GANs. In: Advances in Neural Information Processing Systems 31, vol. 2017-December, pp. 5768–5778. arxiv:1704.00028 UR - http://arxiv.org/abs/1704.00028 ID - ref15 ER - TY - BOOK AU - Eiben, A. E. AU - Smith, J. E. PY - 2015 DA - 2015// TI - Introduction to evolutionary computing PB - Springer CY - Springer-Verlag GmbH Germany UR - https://doi.org/10.1007/978-3-662-44874-8 DO - 10.1007/978-3-662-44874-8 ID - Eiben2015 ER - TY - JOUR AU - Ramakrishnan, R. AU - Dral, P. O. AU - Rupp, M. AU - Lilienfeld, O. A. PY - 2014 DA - 2014// TI - Quantum chemistry structures and properties of 134 kilo molecules JO - Sci Data VL - 1 UR - https://doi.org/10.1038/sdata.2014.22 DO - 10.1038/sdata.2014.22 ID - Ramakrishnan2014 ER - TY - JOUR AU - Bickerton, G. R. AU - Paolini, G. V. AU - Besnard, J. AU - Muresan, S. AU - Hopkins, A. L. PY - 2012 DA - 2012// TI - Quantifying the chemical beauty of drugs JO - Nat Chem VL - 4 UR - https://doi.org/10.1038/nchem.1243 DO - 10.1038/nchem.1243 ID - Bickerton2012 ER - TY - STD TI - RDKit: Open-source cheminformatics. http://www.rdkit.org UR - http://www.rdkit.org ID - ref19 ER - TY - JOUR AU - Rogers, D. AU - Hahn, M. PY - 2010 DA - 2010// TI - Extended-connectivity fingerprints JO - J Chem Inf Model VL - 50 UR - https://doi.org/10.1021/ci100050t DO - 10.1021/ci100050t ID - Rogers2010 ER - TY - JOUR AU - Sterling, T. AU - Irwin, J. J. PY - 2015 DA - 2015// TI - ZINC 15 - Ligand discovery for everyone JO - J Chem Inf Model VL - 55 UR - https://doi.org/10.1021/acs.jcim.5b00559 DO - 10.1021/acs.jcim.5b00559 ID - Sterling2015 ER - TY - JOUR AU - Wildman, S. A. AU - Crippen, G. M. PY - 1999 DA - 1999// TI - Prediction of physicochemical parameters by atomic contributions JO - J Chem Inf Comput Sci VL - 39 UR - https://doi.org/10.1021/ci990307l DO - 10.1021/ci990307l ID - Wildman1999 ER - TY - JOUR AU - Veber, D. F. AU - Johnson, S. R. AU - Cheng, H. Y. AU - Smith, B. R. AU - Ward, K. W. AU - Kopple, K. D. PY - 2002 DA - 2002// TI - Molecular properties that influence the oral bioavailability of drug candidates JO - J Med Chem VL - 45 UR - https://doi.org/10.1021/jm020017n DO - 10.1021/jm020017n ID - Veber2002 ER - TY - STD TI - Zhao S, Liu Z, Lin J, Zhu J-Y, Han S (2020) Differentiable Augmentation for Data-Efficient GAN Training. arxiv:2006.10738 UR - http://arxiv.org/abs/2006.10738 ID - ref24 ER - TY - STD TI - Zhao Z, Zhang Z, Chen T, Singh S, Zhang H (2020) Image Augmentations for GAN Training. arxiv:2006.02595 UR - http://arxiv.org/abs/2006.02595 ID - ref25 ER - TY - JOUR AU - Virshup, A. M. AU - Contreras-García, J. AU - Wipf, P. AU - Yang, W. AU - Beratan, D. N. PY - 2013 DA - 2013// TI - Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds JO - J Am Chem Soc VL - 135 UR - https://doi.org/10.1021/ja401184g DO - 10.1021/ja401184g ID - Virshup2013 ER - TY - JOUR AU - Jensen, J. H. PY - 2019 DA - 2019// TI - A graph-based genetic algorithm and generative model/Monte Carlo tree search for the exploration of chemical space JO - Chem Sci VL - 10 UR - https://doi.org/10.1039/c8sc05372c DO - 10.1039/c8sc05372c ID - Jensen2019 ER - TY - JOUR AU - Brown, N. AU - McKay, B. AU - Gilardoni, F. AU - Gasteiger, J. PY - 2004 DA - 2004// TI - A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules JO - J Chem Inf Comput Sci VL - 44 UR - https://doi.org/10.1021/ci034290p DO - 10.1021/ci034290p ID - Brown2004 ER - TY - JOUR AU - Cho, H. Y. AU - Kim, Y. H. PY - 2019 DA - 2019// TI - Stabilized training of generative adversarial networks by a genetic algorithm JO - GECCO 2019 Companion - Proceedings of the 2019 Genetic and Evolutionary Computation Conference Companion VL - 1 UR - https://doi.org/10.1145/3319619.3326774 DO - 10.1145/3319619.3326774 ID - Cho2019 ER - TY - JOUR AU - Sun, M. AU - Zhao, S. AU - Gilvary, C. AU - Elemento, O. AU - Zhou, J. AU - Wang, F. PY - 2020 DA - 2020// TI - Graph convolutional networks for computational drug development and discovery JO - Brief Bioinform VL - 21 UR - https://doi.org/10.1093/bib/bbz042 DO - 10.1093/bib/bbz042 ID - Sun2020 ER - TY - JOUR AU - Ruddigkeit, L. AU - Deursen, R. AU - Blum, L. C. AU - Reymond, J. L. PY - 2012 DA - 2012// TI - Enumeration of 166 billion organic small molecules in the chemical universe database GDB-17 JO - J Chem Inf Model VL - 52 UR - https://doi.org/10.1021/ci300415d DO - 10.1021/ci300415d ID - Ruddigkeit2012 ER - TY - STD TI - Paszke A, Gross S, Chintala S, Chanan G, Yang E, DeVito Z, Lin Z, Desmaison A, Antiga L, Lerer A (2017) Automatic differentiation in pytorch. In: NIPS-W ID - ref32 ER - TY - STD TI - Kingma DP, Ba J (2017) Adam: A method for stochastic optimization. arxiv:1412.6980 UR - http://arxiv.org/abs/1412.6980 ID - ref33 ER - TY - JOUR AU - Ertl, P. AU - Schuffenhauer, A. PY - 2009 DA - 2009// TI - Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions JO - J Cheminform VL - 1 UR - https://doi.org/10.1186/1758-2946-1-8 DO - 10.1186/1758-2946-1-8 ID - Ertl2009 ER -