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GP-MoLFormer: A Foundation Model For Molecular Generation

Digital Discovery (DD), 2024

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"

41 / 41 papers shown

Title
ChemOrch: Empowering LLMs with Chemical Intelligence via Synthetic Instructions Yue Huang Zhengzhe Jiang Xiaonan Luo Kehan Guo Haomin Zhuang ... Shuhao Zhang Mihir Surve Nitesh Chawla Olaf Wiest Xiangliang Zhang SyDa AI4CE 36 0 0 20 Sep 2025
NovoMolGen: Rethinking Molecular Language Model Pretraining Kamran Chitsaz Roshan Balaji Quentin Fournier Nirav Pravinbhai Bhatt Sarath Chandar AI4CE 144 0 0 19 Aug 2025
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 518 526 0 03 Jan 2025
Conditional Latent Space Molecular Scaffold Optimization for Accelerated Molecular Design O. Boyar Hiroyuki Hanada I. Takeuchi BDL 172 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 176 12 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 148 3 0 03 Jul 2024
Domain-Agnostic Molecular Generation with Chemical FeedbackInternational Conference on Learning Representations (ICLR), 2023 Yin Fang Ningyu Zhang Zhuo Chen Lingbing Guo Xiaohui Fan Huajun Chen 253 21 0 26 Jan 2023
Group SELFIES: A Robust Fragment-Based Molecular String RepresentationDigital Discovery (DD), 2022 Austin H. Cheng Andy Cai Santiago Miret Gustavo Malkomes Mariano Phielipp Alán Aspuru-Guzik 151 38 0 23 Nov 2022
LIMO: Latent Inceptionism for Targeted Molecule GenerationInternational Conference on Machine Learning (ICML), 2022 Peter Eckmann Kunyang Sun Bo Zhao Mudong Feng Michael K. Gilson Rose Yu BDL 148 53 0 17 Jun 2022
Memorization Without Overfitting: Analyzing the Training Dynamics of Large Language ModelsNeural Information Processing Systems (NeurIPS), 2022 Kushal Tirumala Aram H. Markosyan Luke Zettlemoyer Armen Aghajanyan TDI 191 233 0 22 May 2022
Quantifying Memorization Across Neural Language ModelsInternational Conference on Learning Representations (ICLR), 2022 Nicholas Carlini Daphne Ippolito Matthew Jagielski Katherine Lee Florian Tramèr Chiyuan Zhang PILM 280 741 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 148 125 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 522 732 0 14 Jul 2021
Large-Scale Chemical Language Representations Capture Molecular Structure and PropertiesNature Machine Intelligence (Nat. Mach. Intell.), 2021 Jerret Ross Brian M. Belgodere Vijil Chenthamarakshan Inkit Padhi Youssef Mroueh Payel Das AI4CE 190 391 0 17 Jun 2021
Augmenting Molecular Deep Generative Models with Topological Data Analysis RepresentationsIEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2021 Yair Schiff Vijil Chenthamarakshan Samuel C. Hoffman Karthikeyan N. Ramamurthy Payel Das MedIm 159 10 0 08 Jun 2021
RoFormer: Enhanced Transformer with Rotary Position Embedding Jianlin Su Yu Lu Shengfeng Pan Ahmed Murtadha Bo Wen Yunfeng Liu 645 3,483 0 20 Apr 2021
MARS: Markov Molecular Sampling for Multi-objective Drug DiscoveryInternational Conference on Learning Representations (ICLR), 2021 Yutong Xie Chence Shi Hao Zhou Yuwei Yang Weinan Zhang Yong Yu Lei Li 172 166 0 18 Mar 2021
MolGrow: A Graph Normalizing Flow for Hierarchical Molecular GenerationAAAI Conference on Artificial Intelligence (AAAI), 2021 Maksim Kuznetsov Daniil Polykovskiy 142 52 0 03 Feb 2021
GraphDF: A Discrete Flow Model for Molecular Graph GenerationInternational Conference on Machine Learning (ICML), 2021 Youzhi Luo Keqiang Yan Shuiwang Ji DRL 364 233 0 01 Feb 2021
Extracting Training Data from Large Language ModelsUSENIX Security Symposium (USENIX Security), 2020 Nicholas Carlini Florian Tramèr Eric Wallace Matthew Jagielski Ariel Herbert-Voss ... Tom B. Brown Basel Alomair Ulfar Erlingsson Alina Oprea Colin Raffel MLAU SILM 932 2,317 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 524 1,840 0 30 Sep 2020
Transformers are RNNs: Fast Autoregressive Transformers with Linear Attention Angelos Katharopoulos Apoorv Vyas Nikolaos Pappas Franccois Fleuret 554 2,151 0 29 Jun 2020
Hierarchical Generation of Molecular Graphs using Structural MotifsInternational Conference on Machine Learning (ICML), 2020 Wengong Jin Regina Barzilay Tommi Jaakkola 218 322 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 1.4K 6,160 0 23 Jan 2020
Improved Precision and Recall Metric for Assessing Generative Models Tuomas Kynkaanniemi Tero Karras S. Laine J. Lehtinen Timo Aila EGVM 323 1,007 0 15 Apr 2019
Mol-CycleGAN - a generative model for molecular optimization Łukasz Maziarka Agnieszka Pocha Jan Kaczmarczyk Krzysztof Rataj M. Warchoł 145 267 0 06 Feb 2019
Learning Multimodal Graph-to-Graph Translation for Molecular Optimization Wengong Jin Kevin Kaichuang Yang Regina Barzilay Tommi Jaakkola 282 245 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 480 733 0 29 Nov 2018
GuacaMol: Benchmarking Models for De Novo Molecular DesignJournal of Chemical Information and Modeling (JCIM), 2018 Nathan Brown Marco Fiscato Marwin H. S. Segler Alain C. Vaucher ELM 241 784 0 22 Nov 2018
Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction PredictionACS Central Science (ACS Cent. Sci.), 2018 P. Schwaller Teodoro Laino John McGuinness A. Horváth Constantine Bekas A. Lee 260 823 0 06 Nov 2018
Optimization of Molecules via Deep Reinforcement Learning Zhenpeng Zhou S. Kearnes Li Li R. Zare Patrick F. Riley AI4CE 288 586 0 19 Oct 2018
Constrained Generation of Semantically Valid Graphs via Regularizing Variational Autoencoders Tengfei Ma Jie Chen Cao Xiao 232 218 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 625 951 0 07 Jun 2018
MolGAN: An implicit generative model for small molecular graphs Nicola De Cao Thomas Kipf GNN GAN 405 1,000 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 317 381 0 26 Mar 2018
Syntax-Directed Variational Autoencoder for Structured Data H. Dai Yingtao Tian Bo Dai Steven Skiena Le Song 197 341 0 24 Feb 2018
Junction Tree Variational Autoencoder for Molecular Graph Generation Wengong Jin Regina Barzilay Tommi Jaakkola 782 1,497 0 12 Feb 2018
Attention Is All You NeedNeural Information Processing Systems (NeurIPS), 2017 Ashish Vaswani Noam M. Shazeer Niki Parmar Jakob Uszkoreit Llion Jones Aidan Gomez Lukasz Kaiser Illia Polosukhin 3DV 2.0K 152,933 0 12 Jun 2017
Molecular De Novo Design through Deep Reinforcement Learning Marcus Olivecrona T. Blaschke Ola Engkvist Hongming Chen BDL 301 1,101 0 25 Apr 2017
Grammar Variational Autoencoder Matt J. Kusner Brooks Paige José Miguel Hernández-Lobato BDL DRL 257 891 0 06 Mar 2017
Automatic chemical design using a data-driven continuous representation of moleculesACS Central Science (ACS Cent. Sci.), 2016 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 498 3,151 0 07 Oct 2016