TY - STD TI - Radford A, Wu J, Child R, Luan D, Amodei D, Sutskever I. Language models are unsupervised multitask learners. https://cdn.openai.com/better-language-models/language_models_are_unsupervised_multitask_learners.pdf UR - https://cdn.openai.com/better-language-models/language_models_are_unsupervised_multitask_learners.pdf ID - ref1 ER - TY - STD TI - Karras T, Aila T, Laine S, Lehtinen J (2018) Progressive growing of GANs for improved quality, stability, and variation. arXiv:1710.10196 [cs, stat]. http://arxiv.org/abs/1710.10196. Accessed 19 Feb 2020 UR - http://arxiv.org/abs/1710.10196 ID - ref2 ER - TY - STD TI - Pan Y, Qiu Z, Yao T, Li H, Mei T (2018) To create what you tell: generating videos from captions. arXiv:1804.08264 [cs]. http://arxiv.org/abs/1804.08264. Accessed 19 Feb 2020 UR - http://arxiv.org/abs/1804.08264 ID - ref3 ER - TY - STD TI - Huang CZA, Cooijmans T, Roberts A, Courville A, Eck D (2019) Counterpoint by convolution. arXiv:1903.07227 [cs, eess, stat]. http://arxiv.org/abs/1903.07227. Accessed 19 Feb 2020 UR - http://arxiv.org/abs/1903.07227 ID - ref4 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 - JOUR AU - Chen, H. AU - Kogej, T. AU - Engkvist, O. PY - 2018 DA - 2018// TI - Cheminformatics in drug discovery, an industrial perspective JO - Mol Inform VL - 37 UR - https://doi.org/10.1002/minf.201800041 DO - 10.1002/minf.201800041 ID - Chen2018 ER - TY - JOUR AU - David, L. PY - 2019 DA - 2019// TI - Applications of deep-learning in exploiting large-scale and heterogeneous compound data in industrial pharmaceutical research JO - Front Pharmacol UR - https://doi.org/10.3389/fphar.2019.01303 DO - 10.3389/fphar.2019.01303 ID - David2019 ER - TY - JOUR AU - Hochreiter, S. AU - Schmidhuber, J. PY - 1997 DA - 1997// TI - Long short-term memory JO - Neural Comput VL - 9 UR - https://doi.org/10.1162/neco.1997.9.8.1735 DO - 10.1162/neco.1997.9.8.1735 ID - Hochreiter1997 ER - TY - JOUR AU - Gaulton, A. PY - 2017 DA - 2017// TI - The ChEMBL database in 2017 JO - Nucleic Acids Res VL - 45 UR - https://doi.org/10.1093/nar/gkw1074 DO - 10.1093/nar/gkw1074 ID - Gaulton2017 ER - TY - JOUR AU - Arús-Pous, J. PY - 2019 DA - 2019// TI - Randomized SMILES strings improve the quality of molecular generative models JO - J Cheminform VL - 11 UR - https://doi.org/10.1186/s13321-019-0393-0 DO - 10.1186/s13321-019-0393-0 ID - Arús-Pous2019 ER - TY - JOUR AU - Segler, M. H. S. AU - Kogej, T. AU - Tyrchan, C. AU - Waller, M. P. PY - 2018 DA - 2018// TI - Generating focused molecule libraries for drug discovery with recurrent neural networks JO - ACS Cent Sci VL - 4 UR - https://doi.org/10.1021/acscentsci.7b00512 DO - 10.1021/acscentsci.7b00512 ID - Segler2018 ER - TY - JOUR AU - Awale, M. AU - Sirockin, F. AU - Stiefl, N. AU - Reymond, J. -. L. PY - 2019 DA - 2019// TI - Drug analogs from fragment-based long short-term memory generative neural networks JO - J Chem Inf Model VL - 59 UR - https://doi.org/10.1021/acs.jcim.8b00902 DO - 10.1021/acs.jcim.8b00902 ID - Awale2019 ER - TY - JOUR AU - Olivecrona, M. AU - Blaschke, T. AU - Engkvist, O. AU - Chen, H. PY - 2017 DA - 2017// TI - Molecular de-novo design through deep reinforcement learning JO - J Cheminform VL - 9 UR - https://doi.org/10.1186/s13321-017-0235-x DO - 10.1186/s13321-017-0235-x ID - Olivecrona2017 ER - TY - JOUR AU - Blaschke, T. AU - Olivecrona, M. AU - Engkvist, O. AU - Bajorath, J. AU - Chen, H. PY - 2018 DA - 2018// TI - Application of generative autoencoder in de novo molecular design JO - Mol Inform VL - 37 UR - https://doi.org/10.1002/minf.201700123 DO - 10.1002/minf.201700123 ID - Blaschke2018 ER - TY - JOUR AU - Gómez-Bombarelli, R. PY - 2018 DA - 2018// TI - Automatic chemical design using a data-driven continuous representation of molecules JO - ACS Cent Sci. VL - 4 UR - https://doi.org/10.1021/acscentsci.7b00572 DO - 10.1021/acscentsci.7b00572 ID - Gómez-Bombarelli2018 ER - TY - JOUR AU - Kotsias, P. -. C. AU - Arús-Pous, J. AU - Chen, H. AU - Engkvist, O. AU - Tyrchan, C. AU - Bjerrum, E. J. PY - 2020 DA - 2020// TI - Direct steering of de novo molecular generation with descriptor conditional recurrent neural networks JO - Nat Mach Intell VL - 2 UR - https://doi.org/10.1038/s42256-020-0174-5 DO - 10.1038/s42256-020-0174-5 ID - Kotsias2020 ER - TY - JOUR AU - Sanchez-Lengeling, B. AU - Outeiral, C. AU - Guimaraes, G. L. AU - Aspuru-Guzik, A. PY - 2017 DA - 2017// TI - Optimizing distributions over molecular space. An objective-reinforced generative adversarial network for inverse-design chemistry (ORGANIC) JO - ChemRxiv UR - https://doi.org/10.26434/chemrxiv.5309668.v3 DO - 10.26434/chemrxiv.5309668.v3 ID - Sanchez-Lengeling2017 ER - TY - JOUR AU - Prykhodko, O. PY - 2019 DA - 2019// TI - A de novo molecular generation method using latent vector based generative adversarial network JO - J Cheminform VL - 11 UR - https://doi.org/10.1186/s13321-019-0397-9 DO - 10.1186/s13321-019-0397-9 ID - Prykhodko2019 ER - TY - JOUR AU - Weininger, D. PY - 1988 DA - 1988// TI - SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules JO - J Chem Inf Comput Sci VL - 28 UR - https://doi.org/10.1021/ci00057a005 DO - 10.1021/ci00057a005 ID - Weininger1988 ER - TY - STD TI - Li Y, Vinyals O, Dyer C, Pascanu R, Battaglia P (2018) Learning deep generative models of graphs. arXiv:1803.03324 [cs, stat]. http://arxiv.org/abs/1803.03324. Accessed 18 Feb 2020 UR - http://arxiv.org/abs/1803.03324 ID - ref20 ER - TY - JOUR AU - Li, Y. AU - Zhang, L. AU - Liu, Z. PY - 2018 DA - 2018// TI - Multi-objective de novo drug design with conditional graph generative model JO - J Cheminform VL - 10 UR - https://doi.org/10.1186/s13321-018-0287-6 DO - 10.1186/s13321-018-0287-6 ID - Li2018 ER - TY - STD TI - Bjerrum EJ (2017) SMILES enumeration as data augmentation for neural network modeling of molecules. arXiv:1703.07076 [cs]. http://arxiv.org/abs/1703.07076. Accessed 19 Feb 2020 UR - http://arxiv.org/abs/1703.07076 ID - ref22 ER - TY - JOUR AU - Weininger, D. AU - Weininger, A. AU - Weininger, J. L. PY - 1989 DA - 1989// TI - SMILES. 2. Algorithm for generation of unique SMILES notation JO - J Chem Inf Comput Sci VL - 29 UR - https://doi.org/10.1021/ci00062a008 DO - 10.1021/ci00062a008 ID - Weininger1989 ER - TY - JOUR AU - Grisoni, F. AU - Moret, M. AU - Lingwood, R. AU - Schneider, G. PY - 2020 DA - 2020// TI - Bidirectional molecule generation with recurrent neural networks JO - J Chem Inf Model VL - 60 UR - https://doi.org/10.1021/acs.jcim.9b00943 DO - 10.1021/acs.jcim.9b00943 ID - Grisoni2020 ER - TY - JOUR AU - Lim, J. AU - Hwang, S. -. Y. AU - Moon, S. AU - Kim, S. AU - Kim, W. Y. PY - 2020 DA - 2020// TI - Scaffold-based molecular design with a graph generative model JO - Chem Sci VL - 11 UR - https://doi.org/10.1039/C9SC04503A DO - 10.1039/C9SC04503A ID - Lim2020 ER - TY - JOUR AU - Li, Y. AU - Hu, J. AU - Wang, Y. AU - Zhou, J. AU - Zhang, L. AU - Liu, Z. PY - 2020 DA - 2020// TI - DeepScaffold: a comprehensive tool for Scaffold-based de novo drug discovery using deep learning JO - J Chem Inf Model VL - 60 UR - https://doi.org/10.1021/acs.jcim.9b00727 DO - 10.1021/acs.jcim.9b00727 ID - Li2020 ER - TY - JOUR AU - Hughes, J. P. AU - Rees, S. AU - Kalindjian, S. B. AU - Philpott, K. L. PY - 2011 DA - 2011// TI - Principles of early drug discovery JO - Br J Pharmacol VL - 162 UR - https://doi.org/10.1111/j.1476-5381.2010.01127.x DO - 10.1111/j.1476-5381.2010.01127.x ID - Hughes2011 ER - TY - JOUR AU - Hajduk, P. J. AU - Galloway, W. R. J. D. AU - Spring, D. R. PY - 2011 DA - 2011// TI - A question of library design JO - Nature VL - 470 UR - https://doi.org/10.1038/470042a DO - 10.1038/470042a ID - Hajduk2011 ER - TY - JOUR AU - Tyrchan, C. AU - Evertsson, E. PY - 2017 DA - 2017// TI - Matched molecular pair analysis in short: algorithms, applications and limitations JO - Comput Struct Biotechnol J VL - 15 UR - https://doi.org/10.1016/j.csbj.2016.12.003 DO - 10.1016/j.csbj.2016.12.003 ID - Tyrchan2017 ER - TY - JOUR AU - Hussain, J. AU - Rea, C. PY - 2010 DA - 2010// TI - Computationally efficient algorithm to identify matched molecular pairs (MMPs) in large data sets JO - J Chem Inf Model VL - 50 UR - https://doi.org/10.1021/ci900450m DO - 10.1021/ci900450m ID - Hussain2010 ER - TY - JOUR AU - Ertl, P. PY - 2003 DA - 2003// TI - Cheminformatics analysis of organic substituents: identification of the most common substituents, calculation of substituent properties, and automatic identification of drug-like bioisosteric groups JO - J Chem Inf Comput Sci VL - 43 UR - https://doi.org/10.1021/ci0255782 DO - 10.1021/ci0255782 ID - Ertl2003 ER - TY - JOUR AU - Ertl, P. PY - 2020 DA - 2020// TI - Craig plot 2.0: an interactive navigation in the substituent bioisosteric space JO - J Cheminform VL - 12 UR - https://doi.org/10.1186/s13321-020-0412-1 DO - 10.1186/s13321-020-0412-1 ID - Ertl2020 ER - TY - JOUR AU - Sun, J. PY - 2017 DA - 2017// TI - ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics JO - J Cheminform VL - 9 UR - https://doi.org/10.1186/s13321-017-0203-5 DO - 10.1186/s13321-017-0203-5 ID - Sun2017 ER - TY - JOUR AU - Probst, D. AU - Reymond, J. -. L. PY - 2020 DA - 2020// TI - Visualization of very large high-dimensional data sets as minimum spanning trees JO - J Cheminform VL - 12 UR - https://doi.org/10.1186/s13321-020-0416-x DO - 10.1186/s13321-020-0416-x ID - Probst2020 ER - TY - JOUR AU - Lewell, X. Q. AU - Judd, D. B. AU - Watson, S. P. AU - Hann, M. M. PY - 1998 DA - 1998// TI - RECAP retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry JO - J Chem Inf Comput Sci VL - 38 UR - https://doi.org/10.1021/ci970429i DO - 10.1021/ci970429i ID - Lewell1998 ER - TY - JOUR AU - Congreve, M. AU - Carr, R. AU - Murray, C. AU - Jhoti, H. PY - 2003 DA - 2003// TI - A ‘Rule of Three’ for fragment-based lead discovery? JO - Drug Discov Today VL - 8 UR - https://doi.org/10.1016/S1359-6446(03)02831-9 DO - 10.1016/S1359-6446(03)02831-9 ID - Congreve2003 ER - TY - JOUR AU - Tropsha, A. PY - 2010 DA - 2010// TI - Best practices for QSAR model development, validation, and exploitation JO - Mol Inform VL - 29 UR - https://doi.org/10.1002/minf.201000061 DO - 10.1002/minf.201000061 ID - Tropsha2010 ER - TY - JOUR AU - Lyu, J. PY - 2019 DA - 2019// TI - Ultra-large library docking for discovering new chemotypes JO - Nature VL - 566 UR - https://doi.org/10.1038/s41586-019-0917-9 DO - 10.1038/s41586-019-0917-9 ID - Lyu2019 ER - TY - JOUR AU - Schneider, G. AU - Fechner, U. PY - 2005 DA - 2005// TI - Computer-based de novo design of drug-like molecules JO - Nat Rev Drug Discov VL - 4 UR - https://doi.org/10.1038/nrd1799 DO - 10.1038/nrd1799 ID - Schneider2005 ER - TY - JOUR AU - Arús-Pous, J. AU - Blaschke, T. AU - Ulander, S. AU - Reymond, J. -. L. AU - Chen, H. AU - Engkvist, O. PY - 2019 DA - 2019// TI - Exploring the GDB-13 chemical space using deep generative models JO - J Cheminform VL - 11 UR - https://doi.org/10.1186/s13321-019-0341-z DO - 10.1186/s13321-019-0341-z ID - Arús-Pous2019 ER - TY - STD TI - Luong M-T, Pham H, Manning CD (2015) Effective approaches to attention-based neural machine translation. arXiv:1508.04025 [cs]. http://arxiv.org/abs/1508.04025. Accessed 19 Feb 2020 UR - http://arxiv.org/abs/1508.04025 ID - ref41 ER - TY - JOUR AU - Bemis, G. W. AU - Murcko, M. A. PY - 1996 DA - 1996// TI - The properties of known drugs. 1. Molecular frameworks JO - J Med Chem VL - 39 UR - https://doi.org/10.1021/jm9602928 DO - 10.1021/jm9602928 ID - Bemis1996 ER - TY - JOUR AU - Wilkens, S. J. AU - Janes, J. AU - Su, A. I. PY - 2005 DA - 2005// TI - HierS: hierarchical Scaffold clustering using topological chemical graphs JO - J Med Chem VL - 48 UR - https://doi.org/10.1021/jm049032d DO - 10.1021/jm049032d ID - Wilkens2005 ER - TY - JOUR AU - Gupta, A. AU - Müller, A. T. AU - Huisman, B. J. H. AU - Fuchs, J. A. AU - Schneider, P. AU - Schneider, G. PY - 2018 DA - 2018// TI - Generative recurrent networks for de novo drug design JO - Mol Inform VL - 37 UR - https://doi.org/10.1002/minf.201700111 DO - 10.1002/minf.201700111 ID - Gupta2018 ER - TY - STD TI - Hinton GE, Srivastava N, Krizhevsky A, Sutskever I, Salakhutdinov RR (2012) Improving neural networks by preventing co-adaptation of feature detectors,” arXiv:1207.0580 [cs]. http://arxiv.org/abs/1207.0580. Accessed 19 Feb 2020 UR - http://arxiv.org/abs/1207.0580 ID - ref45 ER - TY - STD TI - Bahdanau D, Cho K, Bengio Y (2016) Neural machine translation by jointly learning to align and translate. arXiv:1409.0473 [cs, stat]. http://arxiv.org/abs/1409.0473. Accessed 19 Feb 2020 UR - http://arxiv.org/abs/1409.0473 ID - ref46 ER - TY - STD TI - Vaswani A et al (2017) Attention is all you need. arXiv:1706.03762 [cs]. http://arxiv.org/abs/1706.03762. Accessed 19 Feb 2020 UR - http://arxiv.org/abs/1706.03762 ID - ref47 ER - TY - JOUR AU - Butina, D. PY - 1999 DA - 1999// TI - Unsupervised data base clustering based on daylight’s fingerprint and tanimoto similarity: a fast and automated way to cluster small and large data sets JO - J Chem Inf Comput Sci VL - 39 UR - https://doi.org/10.1021/ci9803381 DO - 10.1021/ci9803381 ID - Butina1999 ER - TY - JOUR AU - Varoquaux, G. AU - Buitinck, L. AU - Louppe, G. AU - Grisel, O. AU - Pedregosa, F. AU - Mueller, A. PY - 2015 DA - 2015// TI - Scikit-learn: machine learning without learning the machinery JO - GetMobile Mobile Comp Comm VL - 19 UR - https://doi.org/10.1145/2786984.2786995 DO - 10.1145/2786984.2786995 ID - Varoquaux2015 ER - TY - STD TI - Akiba T, Sano S, Yanase T, Ohta T, Koyama M (2019) Optuna: a next-generation hyperparameter optimization framework. arXiv:1907.10902 [cs, stat]. http://arxiv.org/abs/1907.10902. Accessed 19 Feb 2020 UR - http://arxiv.org/abs/1907.10902 ID - ref50 ER - TY - STD TI - Paszke A et al (2017) Automatic differentiation in PyTorch. https://openreview.net/forum?id=BJJsrmfCZ. Accessed 18 Feb 2020 UR - https://openreview.net/forum?id=BJJsrmfCZ ID - ref51 ER - TY - STD TI - Landrum G (2020) rdkit/rdkit: 2019_09_3 (Q3 2019) Release. Zenodo ID - ref52 ER - TY - JOUR AU - Zaharia, M. PY - 2016 DA - 2016// TI - Apache Spark: a unified engine for big data processing JO - Commun ACM VL - 59 UR - https://doi.org/10.1145/2934664 DO - 10.1145/2934664 ID - Zaharia2016 ER -