{"id":6171,"date":"2020-10-20T16:07:03","date_gmt":"2020-10-20T15:07:03","guid":{"rendered":"https:\/\/www.blopig.com\/blog\/?p=6171"},"modified":"2020-11-02T12:44:41","modified_gmt":"2020-11-02T12:44:41","slug":"neurips-2020-chemistry-biology-papers","status":"publish","type":"post","link":"https:\/\/www.blopig.com\/blog\/2020\/10\/neurips-2020-chemistry-biology-papers\/","title":{"rendered":"NeurIPS 2020: Chemistry \/ Biology papers"},"content":{"rendered":"\n

Another blog post, another look at accepted papers for a major ML conference. NeurIPS joins the other major machine learning conferences (and others) in moving virtual this year, running from 6th – 12th December 2020. In a continuation of past posts (ICML 2020<\/a>, NeurIPS 2019<\/a>), I will highlight several of potential interest to the chem-\/bio-informatics communities<\/p>\n\n\n\n

The list of accepted papers can be found here<\/a>, with 1,903 papers accepted out of 9,467 submissions (20% acceptance rate). <\/p>\n\n\n\n

In addition to the main conference, there are several workshops highly related to the type of research undertaken in OPIG: Machine Learning in Structural Biology<\/a> and Machine Learning for Molecules<\/a>.<\/p>\n\n\n\n

The usual caveat: given the large number of papers, these were selected either by “accident” (i.e. I stumbled across them in one way or another) or through a basic search (e.g. Ctrl+f “molecule”). If you find any I have missed, please reach out and I will update accordingly.<\/p>\n\n\n\n\n\n\n\n

Title:<\/strong> RetroXpert: Decompose Retrosynthesis Prediction like A Chemist
Authors:<\/strong> Chaochao Yan (The University of Texas at Arlington) \u00b7 Qianggang Ding (Tsinghua University) \u00b7 Peilin Zhao (Tencent AI Lab) \u00b7 Shuangjia Zheng (SUN YAT-SEN UNIVERSITY) \u00b7 JINYU YANG (The University of Texas at Arlington) \u00b7 Yang Yu (Tencent AI Lab) \u00b7 Junzhou Huang (University of Texas at Arlington \/ Tencent AI Lab)
Preprint: <\/strong>https:\/\/chemrxiv.org\/articles\/preprint\/Interpretable_Retrosynthesis_Prediction_in_Two_Steps\/11869692\/3<\/a><\/p>\n\n\n\n

Title:<\/strong> GROVER: Self-Supervised Message Passing Transformer on Large-scale Molecular Graphs
Authors:<\/strong> Yu Rong (Tencent AI Lab) \u00b7 Yatao Bian (Tencent AI Lab) \u00b7 Tingyang Xu (Tencent AI Lab) \u00b7 Weiyang Xie (Tencent AI Lab) \u00b7 Ying WEI (Tencent AI Lab) \u00b7 Wenbing Huang (Tsinghua University) \u00b7 Junzhou Huang (University of Texas at Arlington \/ Tencent AI Lab)
Preprint:<\/strong> https:\/\/arxiv.org\/abs\/2007.02835<\/a><\/p>\n\n\n\n

Title:<\/strong> Reinforced Molecular Optimization with Neighborhood-Controlled Grammars
Authors:<\/strong> Chencheng Xu (Tsinghua University) \u00b7 Qiao Liu (Tsinghua University) \u00b7 Minlie Huang (Tsinghua University) \u00b7 Tao Jiang (University of California – Riverside)
Preprint:<\/strong> N\/A<\/p>\n\n\n\n

Title:<\/strong> Guiding Deep Molecular Optimization with Genetic Exploration
Authors:<\/strong> Sung-Soo Ahn (KAIST) \u00b7 Junsu Kim (KAIST) \u00b7 Hankook Lee (Korea Advanced Institute of Science and Technology) \u00b7 Jinwoo Shin (KAIST)
Preprint:<\/strong> https:\/\/arxiv.org\/abs\/2007.04897<\/a><\/p>\n\n\n\n

Title:<\/strong> Barking up the right tree: an approach to search over molecule synthesis DAGs
Authors:<\/strong> John Bradshaw (University of Cambridge\/MPI IS T\u00fcbingen) \u00b7 Brooks Paige (University College London) \u00b7 Matt Kusner (University College London) \u00b7 Marwin Segler (BenevolentAI) \u00b7 Jos\u00e9 Miguel Hern\u00e1ndez-Lobato (University of Cambridge)
ICML Workshop version:<\/strong> https:\/\/logicalreasoninggnn.github.io\/papers\/4.pdf<\/a><\/p>\n\n\n\n

Title:<\/strong> Sample-Efficient Optimization in the Latent Space of Deep Generative Models via Weighted Retraining
Authors:<\/strong> Austin Tripp (University of Cambridge) \u00b7 Erik Daxberger (University of Cambridge) \u00b7 Jos\u00e9 Miguel Hern\u00e1ndez-Lobato (University of Cambridge)
Preprint:<\/strong> https:\/\/arxiv.org\/abs\/2006.09191<\/a><\/p>\n\n\n\n

Title:<\/strong> TorsionNet: A Reinforcement Learning Approach to Sequential Conformer Search
Authors:<\/strong> Tarun Gogineni (University of Michigan) \u00b7 Ziping Xu (University of Michigan) \u00b7 Exequiel Punzalan (University of Michigan) \u00b7 Runxuan Jiang (University of Michigan) \u00b7 Joshua Kammeraad (University of Michigan) \u00b7 Ambuj Tewari (University of Michigan) \u00b7 Paul Zimmerman (University of Michigan)
Preprint:<\/strong> https:\/\/arxiv.org\/abs\/2006.07078<\/a><\/p>\n\n\n\n

Title:<\/strong> Attribution for Graph Neural Networks
Authors:<\/strong> Benjamin Sanchez-Lengeling (Google Research) \u00b7 Jennifer Wei (Google Research) \u00b7 Brian Lee (Google Inc.) \u00b7 Emily Reif (Google) \u00b7 Peter Wang (Columbia University) \u00b7 Wesley Wei Qian (University of Illinois at Urbana-Champaign) \u00b7 Kevin McCloskey (Google) \u00b7 Lucy Colwell (Google) \u00b7 Alexander Wiltschko (Google Brain)
Preprint:<\/strong> N\/A<\/p>\n\n\n\n

Title:<\/strong> Modern Hopfield Networks and Attention for Immune Repertoire Classification
Authors:<\/strong> Michael Widrich (LIT AI Lab \/ University Linz) \u00b7 Bernhard Sch\u00e4fl (JKU Linz) \u00b7 Milena Pavlovi\u0107 (Department of Informatics, University of Oslo) \u00b7 Hubert Ramsauer (LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Austria) \u00b7 Lukas Gruber (Johannes Kepler University) \u00b7 Markus Holzleitner (LIT AI Lab \/ University Linz) \u00b7 Johannes Brandstetter (LIT AI Lab \/ University Linz) \u00b7 Geir Kjetil Sandve (Department of Informatics, University of Oslo) \u00b7 Victor Greiff (Department of Immunology, University of Oslo) \u00b7 Sepp Hochreiter (LIT AI Lab \/ University Linz \/ IARAI) \u00b7 G\u00fcnter Klambauer (LIT AI Lab \/ University Linz)
Preprint:<\/strong> https:\/\/arxiv.org\/abs\/2007.13505<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"

Another blog post, another look at accepted papers for a major ML conference. NeurIPS joins the other major machine learning conferences (and others) in moving virtual this year, running from 6th – 12th December 2020. In a continuation of past posts (ICML 2020, NeurIPS 2019), I will highlight several of potential interest to the chem-\/bio-informatics […]<\/p>\n","protected":false},"author":50,"featured_media":0,"comment_status":"closed","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"nf_dc_page":"","wikipediapreview_detectlinks":true,"_monsterinsights_skip_tracking":false,"_monsterinsights_sitenote_active":false,"_monsterinsights_sitenote_note":"","_monsterinsights_sitenote_category":0,"ngg_post_thumbnail":0,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[187,52,189],"tags":[248,131,325,172,326,134],"ppma_author":[535],"class_list":["post-6171","post","type-post","status-publish","format-standard","hentry","category-cheminformatics","category-conferences","category-machine-learning","tag-conference","tag-conformer-generation","tag-de-novo-design","tag-machine-learning","tag-reactions-retrosynthesis","tag-small-molecules"],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"authors":[{"term_id":535,"user_id":50,"is_guest":0,"slug":"fergus2","display_name":"Fergus Imrie","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/19c18fa7f4d0a2aecc5f69760c6a9f2fc9b493dfe45b1fd333ccb447db9d6a90?s=96&d=mm&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/6171","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/users\/50"}],"replies":[{"embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/comments?post=6171"}],"version-history":[{"count":3,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/6171\/revisions"}],"predecessor-version":[{"id":6193,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/posts\/6171\/revisions\/6193"}],"wp:attachment":[{"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/media?parent=6171"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/categories?post=6171"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/tags?post=6171"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.blopig.com\/blog\/wp-json\/wp\/v2\/ppma_author?post=6171"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}