ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction

19 October 2020

Papers citing "ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction"

50 / 167 papers shown

Title
SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design Carl N. Edwards Aakanksha Naik Tushar Khot Martin Burke Heng Ji Tom Hope 33 14 0 19 Jun 2023
MUBen: Benchmarking the Uncertainty of Molecular Representation Models Yinghao Li Lingkai Kong Yuanqi Du Yue Yu Yuchen Zhuang Wenhao Mu Chao Zhang 29 9 0 14 Jun 2023
MolCAP: Molecular Chemical reActivity pretraining and prompted-finetuning enhanced molecular representation learning Yu Wang Jing-jing Zhang Junru Jin Leyi Wei 29 1 0 13 Jun 2023
Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective Jiatong Li Yunqing Liu Wenqi Fan Xiao Wei Hui Liu Jiliang Tang Qing Li 23 84 0 11 Jun 2023
MolFM: A Multimodal Molecular Foundation Model Yi Luo Kai Yang Massimo Hong Xingyi Liu Zaiqing Nie 38 37 0 06 Jun 2023
Adaptive Conformal Regression with Jackknife+ Rescaled Scores N. Deutschmann Mattia Rigotti María Rodríguez Martínez 26 10 0 31 May 2023
GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning Haiteng Zhao Shengchao Liu Chang Ma Hannan Xu Jie Fu Zhihong Deng Lingpeng Kong Qi Liu 23 60 0 28 May 2023
Prompt Engineering for Transformer-based Chemical Similarity Search Identifies Structurally Distinct Functional Analogues Clayton W. Kosonocky Aaron L. Feller Claus O. Wilke A. D. Ellington 14 0 0 17 May 2023
MolKD: Distilling Cross-Modal Knowledge in Chemical Reactions for Molecular Property Prediction Liang Zeng Lanqing Li Jian Li 45 3 0 03 May 2023
Computational modeling of semantic change Nina Tahmasebi Haim Dubossarsky 34 6 0 13 Apr 2023
ChemCrow: Augmenting large-language models with chemistry tools Andres M Bran Sam Cox Oliver Schilter Carlo Baldassari Andrew D. White P. Schwaller LLMAG 34 357 0 11 Apr 2023
SELFormer: Molecular Representation Learning via SELFIES Language Models Atakan Yüksel Erva Ulusoy Atabey Ünlü Tunca Dogan 25 55 0 10 Apr 2023
HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations Derek Jones Jonathan E. Allen Xiaohua Zhang Behnam Khaleghi Jaeyoung Kang Weihong Xu Niema Moshiri Tajana Rosing 22 3 0 27 Mar 2023
Automated patent extraction powers generative modeling in focused chemical spaces Akshay Subramanian Kevin P. Greenman Alexis Gervaix Tzuhsiung Yang Rafael Gómez-Bombarelli 38 6 0 14 Mar 2023
Deep Learning Methods for Small Molecule Drug Discovery: A Survey Wenhao Hu Yingying Liu Xuanyu Chen Wenhao Chai Hangyue Chen Hongwei Wang Gaoang Wang 66 10 0 01 Mar 2023
A Biomedical Knowledge Graph for Biomarker Discovery in Cancer Md. Rezaul Karim Lina Molinas Comet Oya Beyan Dietrich-Rebholz Schuhmann Stefan Decker 17 2 0 09 Feb 2023
Exploring QSAR Models for Activity-Cliff Prediction Markus Dablander Thierry Hanser R. Lambiotte Garrett M. Morris 17 23 0 31 Jan 2023
Ontology Pre-training for Poison Prediction Martin Glauer Fabian Neuhaus Till Mossakowski Janna Hastings 27 4 0 20 Jan 2023
Multi-Constraint Molecular Generation using Sparsely Labelled Training Data for Localized High-Concentration Electrolyte Diluent Screening J. Mailoa Xin Li J. Qiu Shengyu Zhang 17 0 0 12 Jan 2023
Structure-based drug discovery with deep learning Rıza Özçelik D. V. Tilborg José Jiménez-Luna F. Grisoni AI4CE 26 35 0 26 Dec 2022
MolCPT: Molecule Continuous Prompt Tuning to Generalize Molecular Representation Learning Cameron Diao Kaixiong Zhou Zirui Liu Xiao Huang Xia Hu 30 14 0 20 Dec 2022
Pre-trained Language Models for Keyphrase Generation: A Thorough Empirical Study Di Wu Wasi Uddin Ahmad Kai-Wei Chang 21 17 0 20 Dec 2022
BARTSmiles: Generative Masked Language Models for Molecular Representations Gayane Chilingaryan Hovhannes Tamoyan Ani Tevosyan N. Babayan L. Khondkaryan Karen Hambardzumyan Zaven Navoyan Hrant Khachatrian Armen Aghajanyan SSL 32 25 0 29 Nov 2022
BatmanNet: Bi-branch Masked Graph Transformer Autoencoder for Molecular Representation Zhen Wang Zheng Feng Yanjun Li Bowen Li Yongrui Wang C. Sha Min He Xiaolin Li AI4CE 35 9 0 25 Nov 2022
Group SELFIES: A Robust Fragment-Based Molecular String Representation Austin H. Cheng Andy Cai Santiago Miret Gustavo Malkomes Mariano Phielipp Alán Aspuru-Guzik 24 27 0 23 Nov 2022
Reducing Down(stream)time: Pretraining Molecular GNNs using Heterogeneous AI Accelerators Jenna A. Bilbrey Kristina M Herman Henry W Sprueill Soritis S. Xantheas Payel Das Manuel Lopez Roldan Mike Kraus Hatem Helal Sutanay Choudhury AI4CE 21 4 0 08 Nov 2022
Multimodal Model with Text and Drug Embeddings for Adverse Drug Reaction Classification Andrey Sakhovskiy E. Tutubalina 27 18 0 21 Oct 2022
Markup-to-Image Diffusion Models with Scheduled Sampling Yuntian Deng Noriyuki Kojima Alexander M. Rush DiffM 36 4 0 11 Oct 2022
Improving Molecular Pretraining with Complementary Featurizations Yanqiao Zhu Dingshuo Chen Yuanqi Du Yingze Wang Qiang Liu Shu Wu AI4CE 39 6 0 29 Sep 2022
polyBERT: A chemical language model to enable fully machine-driven ultrafast polymer informatics Christopher Kuenneth R. Ramprasad 28 101 0 29 Sep 2022
A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language Bing-Huang Su Dazhao Du Zhao-Qing Yang Yujie Zhou Jiangmeng Li Anyi Rao Haoran Sun Zhiwu Lu Ji-Rong Wen 44 107 0 12 Sep 2022
ChemBERTa-2: Towards Chemical Foundation Models Walid Ahmad Elana Simon Seyone Chithrananda Gabriel Grand Bharath Ramsundar AI4CE 6 128 0 05 Sep 2022
TransPolymer: a Transformer-based language model for polymer property predictions Changwen Xu Yuyang Wang A. Farimani 24 86 0 03 Sep 2022
Exploiting Pretrained Biochemical Language Models for Targeted Drug Design Gökçe Uludogan Elif Özkirimli K. Ülgen N. Karalı Arzucan Özgür 17 15 0 02 Sep 2022
Learning from flowsheets: A generative transformer model for autocompletion of flowsheets Gabriel Vogel Lukas Schulze Balhorn Artur M. Schweidtmann AI4CE 35 33 0 01 Aug 2022
Unified 2D and 3D Pre-Training of Molecular Representations Jinhua Zhu Yingce Xia Lijun Wu Shufang Xie Tao Qin Wen-gang Zhou Houqiang Li Tie-Yan Liu AI4CE 57 67 0 14 Jul 2022
Pre-training Transformers for Molecular Property Prediction Using Reaction Prediction J. Broberg Maria Bånkestad Erik Ylipää AI4CE 21 5 0 06 Jul 2022
SSM-DTA: Breaking the Barriers of Data Scarcity in Drug-Target Affinity Prediction Qizhi Pei Lijun Wu Jinhua Zhu Yingce Xia Shufang Xia Tao Qin Haiguang Liu Tie-Yan Liu Rui Yan 13 20 0 20 Jun 2022
3D Graph Contrastive Learning for Molecular Property Prediction Kisung Moon Sunyoung Kwon 18 17 0 31 May 2022
A graph representation of molecular ensembles for polymer property prediction Matteo Aldeghi Connor W. Coley AI4CE 25 43 0 17 May 2022
Chemical transformer compression for accelerating both training and inference of molecular modeling Yi Yu K. Börjesson 21 0 0 16 May 2022
Crystal Twins: Self-supervised Learning for Crystalline Material Property Prediction Rishikesh Magar Yuyang Wang Amir Barati Farimani 32 57 0 04 May 2022
Translation between Molecules and Natural Language Carl N. Edwards T. Lai Kevin Ros Garrett Honke Kyunghyun Cho Heng Ji 30 157 0 25 Apr 2022
Infusing Linguistic Knowledge of SMILES into Chemical Language Models Ingoo Lee Hojung Nam 21 6 0 20 Apr 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 31 86 0 28 Mar 2022
Accelerating Bayesian Optimization for Biological Sequence Design with Denoising Autoencoders Samuel Stanton Wesley J. Maddox Nate Gruver Phillip M. Maffettone E. Delaney Peyton Greenside A. Wilson BDL 38 89 0 23 Mar 2022
Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast Yuyang Wang Rishikesh Magar Chen Liang A. Farimani 43 78 0 18 Feb 2022
Learning to Discover Medicines T. Nguyen Thin Nguyen T. Tran 32 1 0 14 Feb 2022
Mitigating cold start problems in drug-target affinity prediction with interaction knowledge transferring T. Nguyen Thin Nguyen T. Tran 8 14 0 16 Jan 2022
Bringing Atomistic Deep Learning to Prime Time Nathan C. Frey S. Samsi Bharath Ramsundar Connor W. Coley V. Gadepally AI4CE 28 0 0 09 Dec 2021