GP-MoLFormer: A Foundation Model For Molecular Generation

4 April 2024

Jerret Ross

Brian M. Belgodere

Samuel C. Hoffman

Vijil Chenthamarakshan

Youssef Mroueh

Payel Das

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Papers citing "GP-MoLFormer: A Foundation Model For Molecular Generation"

39 / 39 papers shown

Title
Large Language Monkeys: Scaling Inference Compute with Repeated Sampling Bradley Brown Jordan Juravsky Ryan Ehrlich Ronald Clark Quoc V. Le Christopher Ré Azalia Mirhoseini ALM LRM 154 278 0 03 Jan 2025
Conditional Latent Space Molecular Scaffold Optimization for Accelerated Molecular Design O. Boyar Hiroyuki Hanada I. Takeuchi BDL 58 0 0 03 Nov 2024
A Large Encoder-Decoder Family of Foundation Models For Chemical Language Eduardo Soares Victor Shirasuna E. V. Brazil Renato F. G. Cerqueira Dmitry Zubarev Kristin Schmidt AI4CE 43 7 0 24 Jul 2024
Large language models, physics-based modeling, experimental measurements: the trinity of data-scarce learning of polymer properties Ning Liu S. Jafarzadeh B. Lattimer Shuna Ni Jim Lua Yue Yu AI4CE 58 1 0 03 Jul 2024
Domain-Agnostic Molecular Generation with Chemical Feedback Yin Fang Ningyu Zhang Zhuo Chen Lingbing Guo Xiaohui Fan Huajun Chen 60 14 0 26 Jan 2023
Group SELFIES: A Robust Fragment-Based Molecular String Representation Austin H. Cheng Andy Cai Santiago Miret Gustavo Malkomes Mariano Phielipp Alán Aspuru-Guzik 44 28 0 23 Nov 2022
LIMO: Latent Inceptionism for Targeted Molecule Generation Peter Eckmann Kunyang Sun Bo Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 58 46 0 17 Jun 2022
Memorization Without Overfitting: Analyzing the Training Dynamics of Large Language Models Kushal Tirumala Aram H. Markosyan Luke Zettlemoyer Armen Aghajanyan TDI 85 191 0 22 May 2022
Quantifying Memorization Across Neural Language Models Nicholas Carlini Daphne Ippolito Matthew Jagielski Katherine Lee Florian Tramèr Chiyuan Zhang PILM 77 603 0 15 Feb 2022
Scaling Laws for Neural Machine Translation Behrooz Ghorbani Orhan Firat Markus Freitag Ankur Bapna M. Krikun Xavier Garcia Ciprian Chelba Colin Cherry 54 100 0 16 Sep 2021
Deduplicating Training Data Makes Language Models Better Katherine Lee Daphne Ippolito A. Nystrom Chiyuan Zhang Douglas Eck Chris Callison-Burch Nicholas Carlini SyDa 329 611 0 14 Jul 2021
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties Jerret Ross Brian M. Belgodere Vijil Chenthamarakshan Inkit Padhi Youssef Mroueh Payel Das AI4CE 42 283 0 17 Jun 2021
Augmenting Molecular Deep Generative Models with Topological Data Analysis Representations Yair Schiff Vijil Chenthamarakshan Samuel C. Hoffman Karthikeyan N. Ramamurthy Payel Das MedIm 34 9 0 08 Jun 2021
RoFormer: Enhanced Transformer with Rotary Position Embedding Jianlin Su Yu Lu Shengfeng Pan Ahmed Murtadha Bo Wen Yunfeng Liu 137 2,307 0 20 Apr 2021
MARS: Markov Molecular Sampling for Multi-objective Drug Discovery Yutong Xie Chence Shi Hao Zhou Yuwei Yang Weinan Zhang Yong Yu Lei Li 63 142 0 18 Mar 2021
MolGrow: A Graph Normalizing Flow for Hierarchical Molecular Generation Maksim Kuznetsov Daniil Polykovskiy 45 41 0 03 Feb 2021
GraphDF: A Discrete Flow Model for Molecular Graph Generation Youzhi Luo Keqiang Yan Shuiwang Ji DRL 207 195 0 01 Feb 2021
Extracting Training Data from Large Language Models Nicholas Carlini Florian Tramèr Eric Wallace Matthew Jagielski Ariel Herbert-Voss ... Tom B. Brown D. Song Ulfar Erlingsson Alina Oprea Colin Raffel MLAU SILM 404 1,868 0 14 Dec 2020
Rethinking Attention with Performers K. Choromanski Valerii Likhosherstov David Dohan Xingyou Song Andreea Gane ... Afroz Mohiuddin Lukasz Kaiser David Belanger Lucy J. Colwell Adrian Weller 144 1,548 0 30 Sep 2020
Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention Angelos Katharopoulos Apoorv Vyas Nikolaos Pappas Franccois Fleuret 107 1,734 0 29 Jun 2020
Hierarchical Generation of Molecular Graphs using Structural Motifs Wengong Jin Regina Barzilay Tommi Jaakkola 52 283 0 08 Feb 2020
Scaling Laws for Neural Language Models Jared Kaplan Sam McCandlish T. Henighan Tom B. Brown B. Chess R. Child Scott Gray Alec Radford Jeff Wu Dario Amodei 449 4,662 0 23 Jan 2020
Improved Precision and Recall Metric for Assessing Generative Models Tuomas Kynkaanniemi Tero Karras S. Laine J. Lehtinen Timo Aila EGVM 75 844 0 15 Apr 2019
Mol-CycleGAN - a generative model for molecular optimization Łukasz Maziarka Agnieszka Pocha Jan Kaczmarczyk Krzysztof Rataj M. Warchoł 46 246 0 06 Feb 2019
Learning Multimodal Graph-to-Graph Translation for Molecular Optimization Wengong Jin Kevin Kaichuang Yang Regina Barzilay Tommi Jaakkola 70 226 0 03 Dec 2018
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models Daniil Polykovskiy Alexander Zhebrak Benjamín Sánchez-Lengeling Sergey Golovanov Oktai Tatanov ... Simon Johansson Hongming Chen Sergey I. Nikolenko Alán Aspuru-Guzik Alex Zhavoronkov ELM 228 644 0 29 Nov 2018
GuacaMol: Benchmarking Models for De Novo Molecular Design Nathan Brown Marco Fiscato Marwin H. S. Segler Alain C. Vaucher ELM 82 703 0 22 Nov 2018
Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction P. Schwaller Teodoro Laino John McGuinness A. Horváth Constantine Bekas A. Lee 89 730 0 06 Nov 2018
Optimization of Molecules via Deep Reinforcement Learning Zhenpeng Zhou S. Kearnes Li Li R. Zare Patrick F. Riley AI4CE 71 537 0 19 Oct 2018
Constrained Generation of Semantically Valid Graphs via Regularizing Variational Autoencoders Tengfei Ma Jie Chen Cao Xiao 103 208 0 07 Sep 2018
Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation Jiaxuan You Bowen Liu Rex Ying Vijay S. Pande J. Leskovec GNN 262 895 0 07 Jun 2018
MolGAN: An implicit generative model for small molecular graphs Nicola De Cao Thomas Kipf GNN GAN 112 917 0 30 May 2018
Fréchet ChemNet Distance: A metric for generative models for molecules in drug discovery Kristina Preuer Philipp Renz Thomas Unterthiner Sepp Hochreiter Günter Klambauer MedIm 76 333 0 26 Mar 2018
Syntax-Directed Variational Autoencoder for Structured Data H. Dai Yingtao Tian Bo Dai Steven Skiena Le Song 74 325 0 24 Feb 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 286 1,358 0 12 Feb 2018
Attention Is All You Need Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 443 129,831 0 12 Jun 2017
Molecular De Novo Design through Deep Reinforcement Learning Marcus Olivecrona T. Blaschke Ola Engkvist Hongming Chen BDL 92 1,003 0 25 Apr 2017
Grammar Variational Autoencoder Matt J. Kusner Brooks Paige José Miguel Hernández-Lobato BDL DRL 58 838 0 06 Mar 2017
Automatic chemical design using a data-driven continuous representation of molecules Rafael Gómez-Bombarelli Jennifer N. Wei David Duvenaud José Miguel Hernández-Lobato Benjamín Sánchez-Lengeling Dennis Sheberla J. Aguilera-Iparraguirre Timothy D. Hirzel Ryan P. Adams Alán Aspuru-Guzik 3DV 123 2,911 0 07 Oct 2016