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In  International Conference on Learning Representations, 2018."},{"key":"ref78\/cit78","unstructured":"Guacamol baselines. https:\/\/github.com\/BenevolentAI\/guacamol_baselines (accessed 2021\u201309\u201330)."},{"key":"ref79\/cit79","doi-asserted-by":"publisher","DOI":"10.1039\/D1SC00231G"},{"key":"ref80\/cit80","first-page":"045024","volume":"1","author":"Krenn M.","year":"2020","journal-title":"Mach. Learn.: Sci. Technol."},{"key":"ref81\/cit81","doi-asserted-by":"publisher","DOI":"10.1016\/j.neunet.2005.07.009"},{"key":"ref82\/cit82","first-page":"1015","author":"Srinivas N.","year":"2010","journal-title":"Proceedings of the 27th International Conference on International Conference on Machine Learning"},{"key":"ref83\/cit83","doi-asserted-by":"publisher","DOI":"10.1023\/A:1008306431147"},{"key":"ref84\/cit84","doi-asserted-by":"publisher","DOI":"10.1016\/S0169-409X(00)00129-0"},{"key":"ref85\/cit85","unstructured":"Ester, M.; Kriegel, H.P.; Sander, J.; Xu, X. 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