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Generative Models for Automatic Chemical Design

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Machine Learning Meets Quantum Physics

Part of the book series: Lecture Notes in Physics ((LNP,volume 968))

Abstract

Materials discovery is decisive for tackling urgent challenges related to energy, the environment, health care, and many others. In chemistry, conventional methodologies for innovation usually rely on expensive and incremental strategies to optimize properties from molecular structures. On the other hand, inverse approaches map properties to structures, thus expediting the design of novel useful compounds. In this chapter, we examine the way in which current deep generative models are addressing the inverse chemical discovery paradigm. We begin by revisiting early inverse design algorithms. Then, we introduce generative models for molecular systems and categorize them according to their architecture and molecular representation. Using this classification, we review the evolution and performance of important molecular generation schemes reported in the literature. Finally, we conclude highlighting the prospects and challenges of generative models as cutting edge tools in materials discovery.

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References

  1. D.P. Tabor, L.M. Roch, S.K. Saikin, C. Kreisbeck, D. Sheberla, J.H. Montoya, S. Dwaraknath, M. Aykol, C. Ortiz, H. Tribukait, C. Amador-Bedolla, C.J. Brabec, B. Maruyama, K.A. Persson, A. Aspuru-Guzik, Nat. Rev. Mater. 3(5), 5 (2018)

    Article  ADS  Google Scholar 

  2. R.F. Gibson, Compos. Struct. 92(12), 2793 (2010)

    Article  Google Scholar 

  3. H. Chen, O. Engkvist, Y. Wang, M. Olivecrona, T. Blaschke, Drug Discov. Today 23(6), 1241 (2018)

    Article  Google Scholar 

  4. J. A. DiMasi, H. G. Grabowski, R. W. Hansen, J. Health Econ. 47, 20 (2016)

    Article  Google Scholar 

  5. B. K. Shoichet, Nature 432(7019), 862 (2004)

    Article  ADS  Google Scholar 

  6. J. Greeley, T.F. Jaramillo, J. Bonde, I. Chorkendorff, J.K. Nørskov, Nat. Mater. 5(11), 909 (2006)

    Article  ADS  Google Scholar 

  7. S.V. Alapati, J.K. Johnson, D.S. Sholl, J. Phys. Chem. B 110(17), 8769 (2006)

    Article  Google Scholar 

  8. W. Setyawan, R.M. Gaume, S. Lam, R.S. Feigelson, S. Curtarolo, ACS Comb. Sci. 13(4), 382 (2011)

    Article  Google Scholar 

  9. S. Subramaniam, M. Mehrotra, D. Gupta, Bioinformation 3(1), 14 (2008)

    Article  Google Scholar 

  10. R. Armiento, B. Kozinsky, M. Fornari, G. Ceder, Phys. Rev. B 84(1) (2011)

    Google Scholar 

  11. A. Jain, G. Hautier, C.J. Moore, S.P. Ong, C.C. Fischer, T. Mueller, K.A. Persson, G. Ceder, Comput. Mater. Sci. 50(8), 2295 (2011)

    Article  Google Scholar 

  12. S. Curtarolo, G.L.W. Hart, M.B. Nardelli, N. Mingo, S. Sanvito, O. Levy, Nat. Mater. 12(3), 191 (2013)

    Article  ADS  Google Scholar 

  13. E.O. Pyzer-Knapp, C. Suh, R. Gómez-Bombarelli, J. Aguilera-Iparraguirre, A.A.A. Aspuru-Guzik, R. Gomez-Bombarelli, J. Aguilera-Iparraguirre, A.A.A. Aspuru-Guzik, D.R. Clarke, Annu. Rev. Mater. Res. 45(1), 195 (2015)

    Article  ADS  Google Scholar 

  14. R. Gómez-Bombarelli, J. Aguilera-Iparraguirre, T.D. Hirzel, D. Duvenaud, D. Maclaurin, M.A. Blood-Forsythe, H.S. Chae, M. Einzinger, D.-G. Ha, T. Wu, G. Markopoulos, S. Jeon, H. Kang, H. Miyazaki, M. Numata, S. Kim, W. Huang, S.I. Hong, M. Baldo, R.P. Adams, A. Aspuru-Guzik, Nat. Mater. 15(10), 1120 (2016)

    Article  ADS  Google Scholar 

  15. D. Morgan, G. Ceder, S. Curtarolo, Meas. Sci. Technol. 16(1), 296 (2004)

    Article  ADS  Google Scholar 

  16. C. Ortiz, O. Eriksson, M. Klintenberg, Comput. Mater. Sci. 44(4), 1042 (2009)

    Article  Google Scholar 

  17. L. Yu, A. Zunger, Phys. Rev. Lett. 108(6) (2012)

    Google Scholar 

  18. K. Yang, W. Setyawan, S. Wang, M.B. Nardelli, S. Curtarolo, Nat. Mater. 11(7), 614 (2012)

    Article  ADS  Google Scholar 

  19. L.-C. Lin, A.H. Berger, R.L. Martin, J. Kim, J.A. Swisher, K. Jariwala, C.H. Rycroft, A.S. Bhown, M.W. Deem, M. Haranczyk, B. Smit, Nat. Mater. 11(7), 633 (2012)

    Article  ADS  Google Scholar 

  20. N. Mounet, M. Gibertini, P. Schwaller, D. Campi, A. Merkys, A. Marrazzo, T. Sohier, I.E. Castelli, A. Cepellotti, G. Pizzi, et al., Nat. Nanotechnol. 13(3), 246 (2018)

    Article  ADS  Google Scholar 

  21. R. Potyrailo, K. Rajan, K. Stoewe, I. Takeuchi, B. Chisholm, H. Lam, ACS Comb. Sci. 13(6), 579 (2011)

    Article  Google Scholar 

  22. A. Jain, Y. Shin, K.A. Persson, Nat. Rev. Mater. 1(1) (2016)

    Google Scholar 

  23. National Science and Technology Council (US), Materials Genome Initiative for Global Competitiveness (Executive Office of the President, National Science and Technology Council, Washington, 2011)

    Google Scholar 

  24. S. Curtarolo, W. Setyawan, S. Wang, J. Xue, K. Yang, R.H. Taylor, L.J. Nelson, G.L. Hart, S. Sanvito, M. Buongiorno-Nardelli, N. Mingo, O. Levy, Comput. Mater. Sci. 58, 227 (2012)

    Article  Google Scholar 

  25. C.E. Calderon, J.J. Plata, C. Toher, C. Oses, O. Levy, M. Fornari, A. Natan, M.J. Mehl, G. Hart, M.B. Nardelli, S. Curtarolo, Comput. Mater. Sci. 108, 233 (2015)

    Article  Google Scholar 

  26. A. Jain, S.P. Ong, G. Hautier, W. Chen, W.D. Richards, S. Dacek, S. Cholia, D. Gunter, D. Skinner, G. Ceder, K.A. Persson, APL Mater. 1(1), 011002 (2013)

    Article  ADS  Google Scholar 

  27. J.E. Saal, S. Kirklin, M. Aykol, B. Meredig, C. Wolverton, JOM 65(11), 1501 (2013)

    Article  Google Scholar 

  28. B. Sanchez-Lengeling, A. Aspuru-Guzik, Science 361(6400), 360 (2018)

    Article  ADS  Google Scholar 

  29. A. Zunger, Nat. Rev. Chem. 2(4), 0121 (2018)

    Article  Google Scholar 

  30. P.G. Polishchuk, T.I. Madzhidov, A. Varnek, J. Comput. Aided Mol. Des. 27(8), 675 (2013)

    Article  ADS  Google Scholar 

  31. A.M. Virshup, J. Contreras-García, P. Wipf, W. Yang, D.N. Beratan, J. Am. Chem. Soc. 135(19), 7296 (2013)

    Article  Google Scholar 

  32. K.G. Joback, Designing Molecules Possessing Desired Physical Property Values. Ph.D. Thesis, Massachusetts Institute of Technology, 1989

    Google Scholar 

  33. C. Kuhn, D.N. Beratan, J. Phys. Chem. 100(25), 10595 (1996)

    Article  Google Scholar 

  34. D.J. Wales, H.A. Scheraga, Science 285(5432), 1368 (1999)

    Article  Google Scholar 

  35. J. Schön, M. Jansen, Z. Kristallogr. Cryst. Mater. 216(6) (2001)

    Google Scholar 

  36. R. Gani, E. Brignole, Fluid Phase Equilib. 13, 331 (1983)

    Article  Google Scholar 

  37. S.R. Marder, D.N. Beratan, L.T. Cheng, Science 252(5002), 103 (1991)

    Article  ADS  Google Scholar 

  38. P.M. Holmblad, J.H. Larsen, I. Chorkendorff, L.P. Nielsen, F. Besenbacher, I. Stensgaard, E. Lægsgaard, P. Kratzer, B. Hammer, J.K. Nøskov, Catal. Lett. 40(3–4), 131 (1996)

    Article  Google Scholar 

  39. O. Sigmund, S. Torquato, J. Mech. Phys. Solids 45(6), 1037 (1997)

    Article  ADS  MathSciNet  Google Scholar 

  40. C. Wolverton, A. Zunger, B. Schönfeld, Solid State Commun. 101(7), 519 (1997)

    Article  ADS  Google Scholar 

  41. N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, E. Teller, J. Chem. Phys. 21(6), 1087 (1953)

    Article  ADS  Google Scholar 

  42. R. Kaplow, T.A. Rowe, B.L. Averbach, Phys. Rev. 168(3), 1068 (1968)

    Article  ADS  Google Scholar 

  43. V. Gerold, J. Kern, Acta Metall. 35(2), 393 (1987)

    Article  Google Scholar 

  44. R.L. McGreevy, L. Pusztai, Mol. Simul. 1(6), 359 (1988)

    Article  Google Scholar 

  45. A. Franceschetti, A. Zunger, Nature 402(6757), 60 (1999)

    Article  ADS  Google Scholar 

  46. J.H. Holland, Adaptation in Natural and Artificial Systems (MIT Press, Cambridge, 1992)

    Book  Google Scholar 

  47. R. Judson, E. Jaeger, A. Treasurywala, M. Peterson, J. Comput. Chem. 14(11), 1407 (1993)

    Article  Google Scholar 

  48. R.C. Glen, A.W.R. Payne, J. Comput. Aided Mol. Des. 9(2), 181 (1995)

    Article  ADS  Google Scholar 

  49. V. Venkatasubramanian, K. Chan, J. Caruthers, Comput. Chem. Eng. 18(9), 833 (1994)

    Article  Google Scholar 

  50. V. Venkatasubramanian, K. Chan, J.M. Caruthers, J. Chem. Inf. Model. 35(2), 188 (1995)

    Article  Google Scholar 

  51. A.L. Parrill, Drug Discov. Today 1(12), 514 (1996)

    Article  Google Scholar 

  52. G. Schneider, M.-L. Lee, M. Stahl, P. Schneider, J. Comput. Aided Mol. Des. 14(5), 487 (2000)

    Article  ADS  Google Scholar 

  53. D.B. Gordon, S.L. Mayo, Structure 7(9), 1089 (1999)

    Article  Google Scholar 

  54. M.T. Reetz, Proc. Natl. Acad. Sci. 101(16), 5716 (2004)

    Article  ADS  Google Scholar 

  55. D. Wolf, O. Buyevskaya, M. Baerns, Appl. Catal. A 200(1–2), 63 (2000)

    Article  Google Scholar 

  56. G.H. Jóhannesson, T. Bligaard, A.V. Ruban, H.L. Skriver, K.W. Jacobsen, J.K. Nørskov, Phys. Rev. Lett. 88(25) (2002)

    Google Scholar 

  57. S.V. Dudiy, A. Zunger, Phys. Rev. Lett. 97(4) (2006)

    Google Scholar 

  58. P. Piquini, P.A. Graf, A. Zunger, Phys. Rev. Lett. 100(18) (2008)

    Google Scholar 

  59. M. d’Avezac, J.-W. Luo, T. Chanier, A. Zunger, Phys. Rev. Lett. 108(2) (2012)

    Google Scholar 

  60. L. Zhang, J.-W. Luo, A. Saraiva, B. Koiller, A. Zunger, Nat. Commun. 4(1) (2013)

    Google Scholar 

  61. L. Yu, R.S. Kokenyesi, D.A. Keszler, A. Zunger, Adv. Energy Mater. 3(1), 43 (2012)

    Article  Google Scholar 

  62. T. Brodmeier, E. Pretsch, J. Comput. Chem. 15(6), 588 (1994)

    Article  Google Scholar 

  63. S.M. Woodley, P.D. Battle, J.D. Gale, C.R.A. Catlow, Phys. Chem. Chem. Phys. 1(10), 2535 (1999)

    Article  Google Scholar 

  64. C.W. Glass, A.R. Oganov, N. Hansen, Comput. Phys. Commun. 175(11–12), 713 (2006)

    Article  ADS  Google Scholar 

  65. A.R. Oganov, C.W. Glass, J. Chem. Phys. 124(24), 244704 (2006)

    Article  ADS  Google Scholar 

  66. N.S. Froemming, G. Henkelman, J. Chem. Phys. 131(23), 234103 (2009)

    Article  ADS  Google Scholar 

  67. L.B. Vilhelmsen, B. Hammer, J. Chem. Phys. 141(4), 044711 (2014)

    Article  ADS  Google Scholar 

  68. G.L.W. Hart, V. Blum, M.J. Walorski, A. Zunger, Nat. Mater. 4(5), 391 (2005)

    Article  ADS  Google Scholar 

  69. V. Blum, G.L.W. Hart, M.J. Walorski, A. Zunger, Phys. Rev. B 72(16) (2005)

    Google Scholar 

  70. C. Rupakheti, A. Virshup, W. Yang, D.N. Beratan, J. Chem. Inf. Model. 55(3), 529 (2015)

    Article  Google Scholar 

  71. J.L. Reymond, Acc. Chem. Res. 48(3), 722 (2015)

    Article  Google Scholar 

  72. T.C. Le, D.A. Winkler, Chem. Rev. 116(10), 6107 (2016)

    Article  Google Scholar 

  73. P.C. Jennings, S. Lysgaard, J.S. Hummelshøj, T. Vegge, T. Bligaard, npj Comput. Mater. 5(1) (2019)

    Google Scholar 

  74. O.A. von Lilienfeld, R.D. Lins, U. Rothlisberger, Phys. Rev. Lett. 95(15) (2005)

    Google Scholar 

  75. V. Marcon, O.A. von Lilienfeld, D. Andrienko, J. Chem. Phys. 127(6), 064305 (2007)

    Article  ADS  Google Scholar 

  76. M. Wang, X. Hu, D.N. Beratan, W. Yang, J. Am. Chem. Soc. 128(10), 3228 (2006)

    Article  Google Scholar 

  77. P. Hohenberg, W. Kohn, Phys. Rev. 136(3B), B864 (1964)

    Article  ADS  Google Scholar 

  78. D. Xiao, W. Yang, D.N. Beratan, J. Chem. Phys. 129(4), 044106 (2008)

    Article  ADS  Google Scholar 

  79. D. Balamurugan, W. Yang, D.N. Beratan, J. Chem. Phys. 129(17), 174105 (2008)

    Article  ADS  Google Scholar 

  80. S. Keinan, X. Hu, D.N. Beratan, W. Yang, J. Phys. Chem. A 111(1), 176 (2007)

    Article  Google Scholar 

  81. X. Hu, D.N. Beratan, W. Yang, J. Chem. Phys. 129(6), 064102 (2008)

    Article  ADS  Google Scholar 

  82. F.D. Vleeschouwer, W. Yang, D.N. Beratan, P. Geerlings, F.D. Proft, Phys. Chem. Chem. Phys. 14(46), 16002 (2012)

    Article  Google Scholar 

  83. G.E. Hinton, T.J. Sejnowski, in Parallel Distributed Processing: Explorations in the Microstructure of Cognition, Vol. 1, ed. by D.E. Rumelhart, J.L. McClelland, C. PDP Research Group (MIT Press, Cambridge, 1986), pp. 282–317

    Google Scholar 

  84. G.E. Hinton, T.J. Sejnowski, in Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition (1983)

    Google Scholar 

  85. P. Smolensky, in Parallel Distributed Processing: Explorations in the Microstructure of Cognition, Vol. 1, ed. by D.E. Rumelhart, J.L. McClelland, C. PDP Research Group (MIT Press, Cambridge, 1986), pp. 194–281

    Google Scholar 

  86. G.E. Hinton, S. Osindero, Y.-W. Teh, Neural Comput. 18(7), 1527 (2006)

    Article  MathSciNet  Google Scholar 

  87. R. Salakhutdinov, G. Hinton, in Proceedings of the Twelth International Conference on Artificial Intelligence and Statistics. PMLR, vol. 5, 2009, pp. 448–455

    Google Scholar 

  88. I. Goodfellow, Y. Bengio, A. Courville, Deep Learning (MIT Press, Cambridge, 2016)

    MATH  Google Scholar 

  89. T. Karras, T. Aila, S. Laine, J. Lehtinen (2017). arXiv:1710.10196

    Google Scholar 

  90. I.J. Goodfellow, J. Pouget-Abadie, M. Mirza, B. Xu, D. Warde-Farley, S. Ozair, A. Courville, Y. Bengio (2014). arXiv:1406.2661

    Google Scholar 

  91. L.A. Gatys, A.S. Ecker, M. Bethge (2015). arXiv:1508.06576

    Google Scholar 

  92. C. Ledig, L. Theis, F. Huszar, J. Caballero, A. Cunningham, A. Acosta, A. Aitken, A. Tejani, J. Totz, Z. Wang, W. Shi (2016). arXiv:1609.04802

    Google Scholar 

  93. S.R. Bowman, L. Vilnis, O. Vinyals, A.M. Dai, R. Jozefowicz, S. Bengio, G. Brain (2015), pp. 1–15. arXiv:1511.06349

    Google Scholar 

  94. K. Xu, J. Ba, R. Kiros, K. Cho, A. Courville, R. Salakhutdinov, R. Zemel, Y. Bengio (2015). arXiv:1502.03044

    Google Scholar 

  95. S. Mehri, K. Kumar, I. Gulrajani, R. Kumar, S. Jain, J. Sotelo, A. Courville, Y. Bengio (2016). arXiv:1612.07837

    Google Scholar 

  96. A. van den Oord, S. Dieleman, H. Zen, K. Simonyan, O. Vinyals, A. Graves, N. Kalchbrenner, A. Senior, K. Kavukcuoglu (2016). arXiv:1609.03499

    Google Scholar 

  97. C. Vondrick, H. Pirsiavash, A. Torralba (2016). arXiv:1609.02612

    Google Scholar 

  98. A. Radford, L. Metz, S. Chintala (2015). arXiv:1511.06434

    Google Scholar 

  99. J. Engel, M. Hoffman, A. Roberts (2017). arXiv:1711.05772

    Google Scholar 

  100. Y. LeCun, Y. Bengio, G. Hinton, Nature 521(7553), 436 (2015)

    Article  ADS  Google Scholar 

  101. D.P. Kingma, M. Welling (2013). arXiv:1312.6114

    Google Scholar 

  102. M. Arjovsky, S. Chintala, L. Bottou (2017). arXiv:1701.07875

    Google Scholar 

  103. I. Tolstikhin, O. Bousquet, S. Gelly, B. Schölkopf, B. Schoelkopf (2017). arXiv:1711.01558

    Google Scholar 

  104. P.K. Rubenstein, B. Schoelkopf, I. Tolstikhin, B. Schölkopf, I. Tolstikhin (2018). arXiv:1802.03761

    Google Scholar 

  105. M. Mirza, S. Osindero (2014). arXiv:1411.1784

    Google Scholar 

  106. X. Chen, Y. Duan, R. Houthooft, J. Schulman, I. Sutskever, P. Abbeel (2016). arXiv:1606.03657

    Google Scholar 

  107. T. Che, Y. Li, A.P. Jacob, Y. Bengio, W. Li (2016). arXiv:1612.02136

    Google Scholar 

  108. A. Odena, C. Olah, J. Shlens (2016). arXiv:1610.09585

    Google Scholar 

  109. X. Mao, Q. Li, H. Xie, R. Y. K. Lau, Z. Wang, S.P. Smolley (2016). arXiv:1611.04076

    Google Scholar 

  110. R.D. Hjelm, A.P. Jacob, T. Che, A. Trischler, K. Cho, Y. Bengio (2017). arXiv:1702.08431

    Google Scholar 

  111. J. Zhao, M. Mathieu, Y. LeCun (2016). arXiv:1609.03126

    Google Scholar 

  112. S. Nowozin, B. Cseke, R. Tomioka (2016). arXiv:1606.00709

    Google Scholar 

  113. J. Donahue, P. Krähenbühl, T. Darrell (2016). arXiv:1605.09782

    Google Scholar 

  114. D. Berthelot, T. Schumm, L. Metz (2017). arXiv:1703.10717

    Google Scholar 

  115. I. Gulrajani, F. Ahmed, M. Arjovsky, V. Dumoulin, A. Courville (2017). arXiv:1704.00028

    Google Scholar 

  116. Z. Yi, H. Zhang, P. Tan, M. Gong (2017). arXiv:1704.02510

    Google Scholar 

  117. M. Lucic, K. Kurach, M. Michalski, S. Gelly, O. Bousquet (2017). arXiv:1711.10337

    Google Scholar 

  118. A. van den Oord, N. Kalchbrenner, K. Kavukcuoglu (2016). arXiv:1601.06759

    Google Scholar 

  119. A. van den Oord, N. Kalchbrenner, O. Vinyals, L. Espeholt, A. Graves, K. Kavukcuoglu (2016). arXiv:1606.05328

    Google Scholar 

  120. T. Salimans, A. Karpathy, X. Chen, D.P. Kingma (2017). arXiv:1701.05517

    Google Scholar 

  121. N. Kalchbrenner, A. van den Oord, K. Simonyan, I. Danihelka, O. Vinyals, A. Graves, K. Kavukcuoglu (2016). arXiv:1610.00527

    Google Scholar 

  122. N. Kalchbrenner, L. Espeholt, K. Simonyan, A. van den Oord, A. Graves, K. Kavukcuoglu (2016). arXiv:1610.10099

    Google Scholar 

  123. R. Gómez-Bombarelli, J.N. Wei, D. Duvenaud, J.M. Hernández-Lobato, B. Sánchez-Lengeling, D. Sheberla, J. Aguilera-Iparraguirre, T.D. Hirzel, R.P. Adams, A. Aspuru-Guzik, ACS Cent. Sci. 4(2), 268 (2018)

    Article  Google Scholar 

  124. D.R. Hartree, Math. Proc. Cambridge Philos. Soc. 24(01), 89 (1928)

    Article  ADS  Google Scholar 

  125. V. Fock, Z. Phys. A At. Nucl. 61(1–2), 126 (1930)

    ADS  Google Scholar 

  126. W. Kohn, L.J. Sham, Phys. Rev. 140(4A), A1133 (1965)

    Article  ADS  Google Scholar 

  127. R. Todeschini, V. Consonni, Handbook of Molecular Descriptors. Methods and Principles in Medicinal Chemistry (Wiley-VCH, Weinheim, 2000)

    Google Scholar 

  128. D. Rogers, M. Hahn, J. Chem. Inf. Model. 50(5), 742 (2010)

    Article  Google Scholar 

  129. K. Hansen, F. Biegler, R. Ramakrishnan, W. Pronobis, O.A. von Lilienfeld, K.-R. Müller, A. Tkatchenko, J. Phys. Chem. Lett. 6(12), 2326 (2015)

    Article  Google Scholar 

  130. M. Rupp, A. Tkatchenko, K.-R. Müller, O.A. von Lilienfeld, Phys. Rev. Lett. 108(5), 058301 (2012)

    Article  ADS  Google Scholar 

  131. K.T. Schütt, F. Arbabzadah, S. Chmiela, K.R. Müller, A. Tkatchenko, Nat. Commun. 8, 13890 (2017)

    Article  ADS  Google Scholar 

  132. H. Huo, M. Rupp (2017). arXiv:1704.06439

    Google Scholar 

  133. D. Weininger, J. Chem. Inf. Model. 28(1), 31 (1988)

    Article  Google Scholar 

  134. S. Kearnes, K. McCloskey, M. Berndl, V. Pande, P. Riley, J. Comput. Aided Mol. Des. 30(8), 595 (2016)

    Article  ADS  Google Scholar 

  135. D.K. Duvenaud, D. Maclaurin, J. Aguilera-Iparraguirre, R. Gómez-Bombarelli, T. Hirzel, A. Aspuru-Guzik, R.P. Adams, Advances in Neural Information Processing Systems (2015), pp. 2215–2223

    Google Scholar 

  136. J. Gilmer, S.S. Schoenholz, P.F. Riley, O. Vinyals, G.E. Dahl (2017). arXiv:1704.01212

    Google Scholar 

  137. S. Hochreiter, J. Schmidhuber, Neural Comput. 9(8), 1735 (1997)

    Article  Google Scholar 

  138. J. Chung, C. Gulcehre, K. Cho, Y. Bengio (2014). arXiv:1412.3555

    Google Scholar 

  139. M. Popova, O. Isayev, A. Tropsha, Sci. Adv. 4(7), eaap7885 (2018)

    Google Scholar 

  140. H. Ikebata, K. Hongo, T. Isomura, R. Maezono, R. Yoshida, J. Comput. Aided Mol. Des. 31(4), 379 (2017)

    Article  ADS  Google Scholar 

  141. P. Ertl, R. Lewis, E. Martin, V. Polyakov (2017). arXiv:1712.07449

    Google Scholar 

  142. M.H.S. Segler, T. Kogej, C. Tyrchan, M.P. Waller, ACS Cent. Sci. 4(1), 120 (2018)

    Article  Google Scholar 

  143. A. Gupta, A.T. Müller, B.J.H. Huisman, J.A. Fuchs, P. Schneider, G. Schneider, Mol. Inf. 37(1–2), 1700111 (2017)

    Google Scholar 

  144. T. Ching, D.S. Himmelstein, B.K. Beaulieu-Jones, A.A. Kalinin, B.T. Do, G.P. Way, E. Ferrero, P.-M. Agapow, M. Zietz, M.M. Hoffman, W. Xie, G.L. Rosen, B.J. Lengerich, J. Israeli, J. Lanchantin, S. Woloszynek, A.E. Carpenter, A. Shrikumar, J. Xu, E.M. Cofer, C.A. Lavender, S.C. Turaga, A.M. Alexandari, Z. Lu, D.J. Harris, D. DeCaprio, Y. Qi, A. Kundaje, Y. Peng, L.K. Wiley, M.H.S. Segler, S.M. Boca, S.J. Swamidass, A. Huang, A. Gitter, C.S. Greene, J. R. Soc. Interface 15(141), 20170387 (2018)

    Article  Google Scholar 

  145. N. Jaques, S. Gu, D. Bahdanau, J.M. Hernández-Lobato, R.E. Turner, D. Eck, in Proceedings of the 34th International Conference on Machine Learning Research, vol. 70, ed. by D. Precup, Y.W. Teh (PMLR, International Convention Centre, Sydney, 2017), pp. 1645–1654

    Google Scholar 

  146. M. Olivecrona, T. Blaschke, O. Engkvist, H. Chen, J. Cheminf. 9(1), 48 (2017)

    Article  Google Scholar 

  147. S. Kang, K. Cho, J. Chem. Inf. Model. 59(1), 43 (2018)

    Article  Google Scholar 

  148. B. Sattarov, I.I. Baskin, D. Horvath, G. Marcou, E.J. Bjerrum, A. Varnek, J. Chem. Inf. Model. 59(3), 1182 (2019)

    Article  Google Scholar 

  149. S. Sinai, E. Kelsic, G.M. Church, M.A. Nowak (2017), pp. 1–6. arXiv:1712.03346

    Google Scholar 

  150. S. Kwon, S. Yoon, in Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - ACM-BCB ’17 (ACM Press, New York, 2017), pp. 203–212

    Google Scholar 

  151. K. Kim, S. Kang, J. Yoo, Y. Kwon, Y. Nam, D. Lee, I. Kim, Y.-S. Choi, Y. Jung, S. Kim, W.-J. Son, J. Son, H.S. Lee, S. Kim, J. Shin, S. Hwang, npj Comput. Mater. 4(1) (2018)

    Google Scholar 

  152. V. Mallet, C.G. Oliver, N. Moitessier, J. Waldispuhl (2019). arXiv:1905.12033

    Google Scholar 

  153. J. Lim, S. Ryu, J.W. Kim, W.Y. Kim, J. Cheminf. 10(1) (2018)

    Google Scholar 

  154. G.L. Guimaraes, B. Sanchez-Lengeling, C. Outeiral, P.L.C. Farias, A. Aspuru-Guzik, C. Outeiral, P.L.C. Farias, A. Aspuru-Guzik (2017). arXiv:1705.10843

    Google Scholar 

  155. B. Sanchez-Lengeling, C. Outeiral, G.L.L. Guimaraes, A.A. Aspuru-Guzik (2017), pp. 1–18. chemRxiv:5309668

    Google Scholar 

  156. E. Putin, A. Asadulaev, Y. Ivanenkov, V. Aladinskiy, B. Sanchez-Lengeling, A. Aspuru-Guzik, A. Zhavoronkov, J. Chem. Inf. Model. 58(6), 1194 (2018)

    Article  Google Scholar 

  157. O. Mendez-Lucio, B. Baillif, D.-A. Clevert, D. Rouquié, J. Wichard (2018). chemrXiv:7294388

    Google Scholar 

  158. N. Killoran, L.J. Lee, A. Delong, D. Duvenaud, B.J. Frey (2017). arXiv:1712.06148

    Google Scholar 

  159. A. Kadurin, S. Nikolenko, K. Khrabrov, A. Aliper, A. Zhavoronkov, Mol. Pharm. 14(9), 3098 (2017)

    Article  Google Scholar 

  160. A. Kadurin, A. Aliper, A. Kazennov, P. Mamoshina, Q. Vanhaelen, K. Khrabrov, A. Zhavoronkov, Oncotarget 8(7), 10883 (2017)

    Article  Google Scholar 

  161. T. Blaschke, M. Olivecrona, O. Engkvist, J. Bajorath, H. Chen, Mol. Inf. 37(1–2), 1700123 (2018)

    Article  Google Scholar 

  162. D. Polykovskiy, A. Zhebrak, D. Vetrov, Y. Ivanenkov, V. Aladinskiy, P. Mamoshina, M. Bozdaganyan, A. Aliper, A. Zhavoronkov, A. Kadurin, Mol. Pharm. 15(10), 4398 (2018)

    Article  Google Scholar 

  163. J. Mueller, D. Gifford, T. Jaakkola, in Proceedings of the 34th International Conference on Machine Learning Research, vol. 70, ed. by D. Precup, Y.W. Teh (PMLR, International Convention Centre, Sydney, 2017), pp. 2536–2544

    Google Scholar 

  164. J.P. Janet, L. Chan, H.J. Kulik, J. Phys. Chem. Lett. 9(5), 1064 (2018)

    Article  Google Scholar 

  165. M.J. Kusner, B. Paige, J.M. Hernández-Lobato (2017). arXiv:1703.01925

    Google Scholar 

  166. H. Dai, Y. Tian, B. Dai, S. Skiena, L. Song (2018). arXiv:1802.08786

    Google Scholar 

  167. R. Winter, F. Montanari, F. Noé, D.-A. Clevert, Chem. Sci. 10(6), 1692 (2019)

    Article  Google Scholar 

  168. W. Jin, R. Barzilay, T. Jaakkola (2018). arXiv:1802.04364

    Google Scholar 

  169. E.J. Bjerrum (2017). arXiv:1703.07076

    Google Scholar 

  170. Z. Alperstein, A. Cherkasov, J.T. Rolfe (2019). arXiv:1905.13343

    Google Scholar 

  171. A. Lusci, G. Pollastri, P. Baldi, J. Chem. Inf. Model. 53(7), 1563 (2013)

    Article  Google Scholar 

  172. J. Bruna, W. Zaremba, A. Szlam, Y. LeCun (2013). arXiv:1312.6203

    Google Scholar 

  173. C.W. Coley, R. Barzilay, W.H. Green, T.S. Jaakkola, K.F. Jensen, J. Chem. Inf. Model. 57(8), 1757 (2017)

    Article  Google Scholar 

  174. P. Hop, B. Allgood, J. Yu, Mol. Pharmaceutics 15(10), 4371 (2018)

    Article  Google Scholar 

  175. K. Yang, K. Swanson, W. Jin, C. Coley, P. Eiden, H. Gao, A. Guzman-Perez, T. Hopper, B. Kelley, M. Mathea, A. Palmer, V. Settels, T. Jaakkola, K. Jensen, R. Barzilay (2019). arXiv:1904.01561

    Google Scholar 

  176. J. You, R. Ying, X. Ren, W.L. Hamilton, J. Leskovec (2018). arXiv:1802.08773

    Google Scholar 

  177. Y. Li, L. Zhang, Z. Liu (2018). arXiv:1801.07299

    Google Scholar 

  178. T.N. Kipf, M. Welling (2016). arXiv:1611.07308

    Google Scholar 

  179. M. Simonovsky, N. Komodakis (2018). arXiv:1802.03480

    Google Scholar 

  180. A. Grover, A. Zweig, S. Ermon (2018). arXiv:1803.10459

    Google Scholar 

  181. B. Samanta, A. De, N. Ganguly, M. Gomez-Rodriguez (2018). arXiv:1802.05283

    Google Scholar 

  182. Q. Liu, M. Allamanis, M. Brockschmidt, A.L. Gaunt (2018). arXiv:1805.09076

    Google Scholar 

  183. T. Ma, J. Chen, C. Xiao (2018). arXiv:1809.02630

    Google Scholar 

  184. W. Jin, K. Yang, R. Barzilay, T. Jaakkola, International Conference on Learning Representations (2019)

    Google Scholar 

  185. W. Jin, R. Barzilay, T.S. Jaakkola (2019). chemrXiv:8266745

    Google Scholar 

  186. R. Assouel, M. Ahmed, M.H. Segler, A. Saffari, Y. Bengio (2018). arXiv:1811.09766

    Google Scholar 

  187. J. Lim, S.-Y. Hwang, S. Kim, S. Moon, W.Y. Kim (2019). arXiv:1905.13639

    Google Scholar 

  188. Z. Zhou, S. Kearnes, L. Li, R.N. Zare, P. Riley (2018). arXiv:1810.08678

    Google Scholar 

  189. S. Kearnes, L. Li, P. Riley (2019). arXiv:1904.08915

    Google Scholar 

  190. S. Liu, T. Chandereng, Y. Liang (2018). arXiv:1806.09206

    Google Scholar 

  191. M. Krenn, F. Häse, A. Nigam, P. Friederich, A. Aspuru-Guzik (2019). arXiv:1905.13741

    Google Scholar 

  192. X. Guo, L. Wu, L. Zhao (2018). arXiv:1805.09980

    Google Scholar 

  193. A. Bojchevski, O. Shchur, D. Zügner, S. Günnemann (2018). arXiv:1803.00816

    Google Scholar 

  194. Y. Xiong, Y. Zhang, H. Fu, W. Wang, Y. Zhu, P.S. Yu, Database Systems for Advanced Applications (Springer International Publishing, Cham, 2019), pp. 536–552

    Book  Google Scholar 

  195. N. De Cao, T. Kipf (2018). arXiv:1805.11973

    Google Scholar 

  196. E. Jang, S. Gu, B. Poole (2016). arXiv:1611.01144

    Google Scholar 

  197. M.J. Kusner, J.M. Hernández-Lobato (2016). arXiv:1611.04051

    Google Scholar 

  198. S. Pölsterl, C. Wachinger (2019). arXiv:1905.10310

    Google Scholar 

  199. K. Xu, W. Hu, J. Leskovec, S. Jegelka (2018). arXiv:1810.00826

    Google Scholar 

  200. Ł. Maziarka, A. Pocha, J. Kaczmarczyk, K. Rataj, M. Warchoł (2019). arXiv:1902.02119

    Google Scholar 

  201. S. Fan, B. Huang (2019). arXiv:1906.03220

    Google Scholar 

  202. M. Neuhaus, H. Bunke, Bridging the Gap Between Graph Edit Distance and Kernel Machines (World Scientific Publishing, River Edge, 2007)

    Book  MATH  Google Scholar 

  203. Y. Li, O. Vinyals, C. Dyer, R. Pascanu, P. Battaglia (2018). arXiv:1803.03324

    Google Scholar 

  204. T.A. Schieber, L. Carpi, A. Díaz-Guilera, P.M. Pardalos, C. Masoller, M.G. Ravetti, Nat. Commun. 8, 13928 (2017)

    Article  ADS  Google Scholar 

  205. H. Choi, H. Lee, Y. Shen, Y. Shi (2018). arXiv:1807.00252

    Google Scholar 

  206. S.I. Ktena, S. Parisot, E. Ferrante, M. Rajchl, M. Lee, B. Glocker, D. Rueckert (2017). arXiv:1703.02161

    Google Scholar 

  207. K. Do, T. Tran, T. Nguyen, S. Venkatesh (2018). arXiv:1804.00293

    Google Scholar 

  208. S. Ryu, J. Lim, W.Y. Kim (2018). arXiv:1805.10988

    Google Scholar 

  209. H. Kajino (2018). arXiv:1809.02745

    Google Scholar 

  210. L. Theis, A. van den Oord, M. Bethge (2015). arXiv:1511.01844

    Google Scholar 

  211. K. Preuer, P. Renz, T. Unterthiner, S. Hochreiter, G. Klambauer, J. Chem. Inf. Model. 58(9), 1736 (2018)

    Article  Google Scholar 

  212. D. Polykovskiy, A. Zhebrak, B. Sanchez-Lengeling, S. Golovanov, O. Tatanov, S. Belyaev, R. Kurbanov, A. Artamonov, V. Aladinskiy, M. Veselov, A. Kadurin, S. Nikolenko, A. Aspuru-Guzik, A. Zhavoronkov (2018). arXiv:1811.12823

    Google Scholar 

  213. Z. Wu, B. Ramsundar, E.N. Feinberg, J. Gomes, C. Geniesse, A.S. Pappu, K. Leswing, V. Pande, Chem. Sci. 9(2), 513 (2018)

    Article  Google Scholar 

  214. N. Brown, M. Fiscato, M.H. Segler, A.C. Vaucher, J. Chem. Inf. Model. 59(3), 1096 (2019)

    Article  Google Scholar 

  215. F. Häse, L.M. Roch, C. Kreisbeck, A. Aspuru-Guzik (2018). arXiv:1801.01469

    Google Scholar 

  216. N.W.A. Gebauer, M. Gastegger, K.T. Schütt (2018). arXiv:1810.11347

    Google Scholar 

  217. F. Noé, H. Wu (2018). arXiv:1812.01729

    Google Scholar 

  218. N.W.A. Gebauer, M. Gastegger, K.T. Schütt (2019). arXiv:1906.00957

    Google Scholar 

  219. M.S. Jørgensen, H.L. Mortensen, S.A. Meldgaard, E.L. Kolsbjerg, T.L. Jacobsen, K.H. Sørensen, B. Hammer (2019). arXiv:1902.10501

    Google Scholar 

  220. E. Mansimov, O. Mahmood, S. Kang, K. Cho (2019). arXiv:1904.00314

    Google Scholar 

  221. K. Madhawa, K. Ishiguro, K. Nakago, M. Abe (2019). arXiv:1905.11600

    Google Scholar 

  222. J. Wang, S. Olsson, C. Wehmeyer, A. Perez, N.E. Charron, G. de Fabritiis, F. Noe, C. Clementi (2018). arXiv:1812.01736

    Google Scholar 

  223. W. Wang, R. Gómez-Bombarelli (2018). arXiv:1812.02706

    Google Scholar 

  224. J. Bradshaw, M.J. Kusner, B. Paige, M.H.S. Segler, J.M. Hernández-Lobato, International Conference on Learning Representations (2019)

    Google Scholar 

  225. J. Bradshaw, B. Paige, M.J. Kusner, M.H.S. Segler, J.M. Hernández-Lobato (2019). arXiv:1906.05221

    Google Scholar 

  226. A.J. Riesselman, J.B. Ingraham, D.S. Marks, Nat. Methods 15(10), 816 (2018)

    Article  Google Scholar 

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Acknowledgements

D.S.-K. acknowledges the MIT Nicole and Ingo Wender Fellowship and the MIT Robert Rose Presidential Fellowship for financial support. R.G.-B. thanks MIT DMSE and Toyota Faculty Chair for support.

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Schwalbe-Koda, D., Gómez-Bombarelli, R. (2020). Generative Models for Automatic Chemical Design. In: Schütt, K., Chmiela, S., von Lilienfeld, O., Tkatchenko, A., Tsuda, K., Müller, KR. (eds) Machine Learning Meets Quantum Physics. Lecture Notes in Physics, vol 968. Springer, Cham. https://doi.org/10.1007/978-3-030-40245-7_21

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