SMILES Enumeration as Data Augmentation for Neural Network Modeling of Molecules

21 March 2017

Papers citing "SMILES Enumeration as Data Augmentation for Neural Network Modeling of Molecules"

50 / 74 papers shown

Title
Evaluating Effects of Augmented SELFIES for Molecular Understanding Using QK-LSTM Collin Beaudoin Swaroop Ghosh 49 0 0 29 Apr 2025
Unified Molecule Generation and Property Prediction Adam Izdebski Jan Olszewski Pankhil Gawade Krzysztof Koras Serra Korkmaz Valentin Rauscher Jakub M. Tomczak E. Szczurek 36 0 0 23 Apr 2025
MetaMolGen: A Neural Graph Motif Generation Model for De Novo Molecular Design Zimo Yan Jie Zhang Zheng Xie Chang-rui Liu Yong-Jin Liu Yiping Song 42 0 0 22 Apr 2025
NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models Koh Sakano Kairi Furui Masahito Ohue 64 1 0 19 Nov 2024
SAFE setup for generative molecular design Yassir El Mesbahi Emmanuel Noutahi 36 0 0 26 Oct 2024
GUISE: Graph GaUssIan Shading watErmark Renyi Yang 29 0 0 14 Oct 2024
A Hitchhiker's Guide to Deep Chemical Language Processing for Bioactivity Prediction Rıza Özçelik F. Grisoni 37 2 0 16 Jul 2024
BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning Artem Zholus Maksim Kuznetsov Roman Schutski Rim Shayakhmetov Daniil Polykovskiy Sarath Chandar Alex Zhavoronkov DiffM AI4CE 40 5 0 06 Jun 2024
Saturn: Sample-efficient Generative Molecular Design using Memory Manipulation Jeff Guo Philippe Schwaller Mamba 56 7 0 27 May 2024
Synthetic data enables faster annotation and robust segmentation for multi-object grasping in clutter Dongmyoung Lee Wei Chen Nicolás Rojas 24 2 0 24 Jan 2024
Empirical Evidence for the Fragment level Understanding on Drug Molecular Structure of LLMs Xiuyuan Hu Guoqing Liu Yang Zhao Hao Zhang 30 1 0 15 Jan 2024
Large Language Models on Graphs: A Comprehensive Survey Bowen Jin Gang Liu Chi Han Meng Jiang Heng Ji Jiawei Han AI4CE 42 138 0 05 Dec 2023
Transfer Learning across Different Chemical Domains: Virtual Screening of Organic Materials with Deep Learning Models Pretrained on Small Molecule and Chemical Reaction Data Chengwei Zhang Yushuang Zhai Ziyang Gong Hongliang Duan Yuan-Bin She Yun-Fang Yang An Su 19 7 0 30 Nov 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 30 7 0 28 Sep 2023
Data augmentation for machine learning of chemical process flowsheets Lukas Schulze Balhorn Edwin Hirtreiter Lynn Luderer Artur M. Schweidtmann AI4CE 20 1 0 07 Feb 2023
Recent advances in artificial intelligence for retrosynthesis Zipeng Zhong Mingli Song Zunlei Feng Tiantao Liu Lingxiang Jia Shaolun Yao Tingjun Hou Mingli Song 34 5 0 14 Jan 2023
Bidirectional Generation of Structure and Properties Through a Single Molecular Foundation Model Jinho Chang Jong Chul Ye AI4CE 22 30 0 19 Nov 2022
Deep learning methods for drug response prediction in cancer: predominant and emerging trends A. Partin Thomas Brettin Yitan Zhu Oleksandr Narykov Austin R. Clyde Jamie Overbeek Department of Materials Science 13 54 0 18 Nov 2022
Towards automatic generation of Piping and Instrumentation Diagrams (P&IDs) with Artificial Intelligence Edwin Hirtreiter Lukas Schulze Balhorn Artur M. Schweidtmann AI4CE 19 14 0 26 Oct 2022
Investigation of chemical structure recognition by encoder-decoder models in learning progress Katsuhisa Morita T. Mizuno Hiroyuki Kusuhara 19 8 0 24 Oct 2022
Faster and more diverse de novo molecular optimization with double-loop reinforcement learning using augmented SMILES E. Bjerrum Christian Margreitter Thomas Blaschke Raquel Lopez-Rios de Castro 40 12 0 22 Oct 2022
Pre-training Transformers for Molecular Property Prediction Using Reaction Prediction J. Broberg Maria Bånkestad Erik Ylipää AI4CE 21 5 0 06 Jul 2022
A smile is all you need: Predicting limiting activity coefficients from SMILES with natural language processing Benedikt Winter Clemens Winter J. Schilling A. Bardow 33 28 0 15 Jun 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 41 86 0 28 Mar 2022
Regression Transformer: Concurrent sequence regression and generation for molecular language modeling Jannis Born Matteo Manica 13 91 0 01 Feb 2022
Rxn Hypergraph: a Hypergraph Attention Model for Chemical Reaction Representation Mohammadamin Tavakoli Alexander Shmakov Francesco Ceccarelli Pierre Baldi GNN 39 8 0 02 Jan 2022
AugLiChem: Data Augmentation Library of Chemical Structures for Machine Learning Rishikesh Magar Yuyang Wang Cooper Lorsung Chen Liang Hariharan Ramasubramanian Peiyuan Li A. Farimani 28 27 0 30 Nov 2021
Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction Zhengkai Tu Connor W. Coley 30 90 0 19 Oct 2021
Analysis of training and seed bias in small molecules generated with a conditional graph-based variational autoencoder -- Insights for practical AI-driven molecule generation Seung-gu Kang Joseph A. Morrone J. Weber Wendy D. Cornell 13 7 0 19 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 27 272 0 17 Jun 2021
Evening the Score: Targeting SARS-CoV-2 Protease Inhibition in Graph Generative Models for Therapeutic Candidates Jenna A. Bilbrey Logan T. Ward Sutanay Choudhury Neeraj Kumar Ganesh Sivaraman 29 1 0 07 May 2021
TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks Anna Weber Jannis Born María Rodríguez Martínez 19 129 0 21 Apr 2021
Artificial Intelligence based Autonomous Molecular Design for Medical Therapeutic: A Perspective R. P. Joshi Neeraj Kumar 16 2 0 10 Feb 2021
Benchmarking Deep Graph Generative Models for Optimizing New Drug Molecules for COVID-19 Logan T. Ward Jenna A. Bilbrey Sutanay Choudhury Neeraj Kumar Ganesh Sivaraman GNN 32 3 0 09 Feb 2021
MolGrow: A Graph Normalizing Flow for Hierarchical Molecular Generation Maksim Kuznetsov Daniil Polykovskiy 35 40 0 03 Feb 2021
High throughput screening with machine learning O. Gurbych M. Druchok Dzvenymyra Yarish Sofiya Garkot 19 6 0 15 Dec 2020
Advanced Graph and Sequence Neural Networks for Molecular Property Prediction and Drug Discovery Zhengyang Wang Meng Liu Youzhi Luo Zhao Xu Yaochen Xie ... Lei Cai Q. Qi Zhuoning Yuan Tianbao Yang Shuiwang Ji 36 100 0 02 Dec 2020
Predicting Chemical Properties using Self-Attention Multi-task Learning based on SMILES Representation Sangrak Lim Yong Oh Lee 27 17 0 19 Oct 2020
$PaccMann$^{RL}$ on SARS-CoV-2: Designing antiviral candidates with conditional generative models$ PaccMann $^{RL}$ on SARS-CoV-2: Designing antiviral candidates with conditional generative models Jannis Born Matteo Manica Joris Cadow Greta Markert N. Mill Modestas Filipavicius María Rodríguez Martínez 37 4 0 27 May 2020
Improving Deep Learning Models via Constraint-Based Domain Knowledge: a Brief Survey Andrea Borghesi Federico Baldo M. Milano AI4CE 16 35 0 19 May 2020
Continuous Representation of Molecules Using Graph Variational Autoencoder Mohammadamin Tavakoli Pierre Baldi BDL GNN DRL 13 9 0 17 Apr 2020
State-of-the-Art Augmented NLP Transformer models for direct and single-step retrosynthesis Igor V. Tetko Pavel Karpov R. V. Deursen Guillaume Godin 19 6 0 05 Mar 2020
Exploring Chemical Space using Natural Language Processing Methodologies for Drug Discovery Hakime Öztürk Arzucan Özgür P. Schwaller Teodoro Laino Elif Özkirimli 35 116 0 10 Feb 2020
Big-Data Science in Porous Materials: Materials Genomics and Machine Learning Kevin Maik Jablonka D. Ongari S. M. Moosavi B. Smit AI4CE 31 350 0 18 Jan 2020
SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery Shion Honda Shoi Shi H. Ueda MedIm 22 172 0 12 Nov 2019
Mixup-breakdown: a consistency training method for improving generalization of speech separation models Max W. Y. Lam Jun Wang Dan Su Dong Yu 33 22 0 28 Oct 2019
Deep Generative Model for Sparse Graphs using Text-Based Learning with Augmentation in Generative Examination Networks R. V. Deursen Guillaume Godin 19 1 0 24 Sep 2019
GEN: Highly Efficient SMILES Explorer Using Autodidactic Generative Examination Networks R. V. Deursen P. Ertl Igor V. Tetko Guillaume Godin 16 32 0 10 Sep 2019
Toxicity Prediction by Multimodal Deep Learning Abdul Karim Jaspreet Singh Avinash Mishra A. Dehzangi M. A. Hakim Newton Abdul Sattar 13 14 0 19 Jul 2019
Generative Models for Automatic Chemical Design Daniel Schwalbe-Koda Rafael Gómez-Bombarelli MedIm AI4CE 32 81 0 02 Jul 2019