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
Analysis of Atom-level pretraining with Quantum Mechanics (QM) data for Graph Neural Networks Molecular property models Jose A. Arjona-Medina Ramil I. Nugmanov AI4CE 40 1 0 23 May 2024
ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining Zhiyuan Liu Yaorui Shi An Zhang Sihang Li Enzhi Zhang Xiang Wang Kenji Kawaguchi Tat-Seng Chua 44 9 0 23 May 2024
Aligning Transformers with Continuous Feedback via Energy Rank Alignment Shriram Chennakesavalu Frank Hu Sebastian Ibarraran Grant M. Rotskoff 38 3 0 21 May 2024
LLM and Simulation as Bilevel Optimizers: A New Paradigm to Advance Physical Scientific Discovery Pingchuan Ma Tsun-Hsuan Wang Minghao Guo Zhiqing Sun Joshua B. Tenenbaum Daniela Rus Chuang Gan Wojciech Matusik AI4CE 45 26 0 16 May 2024
UniCorn: A Unified Contrastive Learning Approach for Multi-view Molecular Representation Learning Shikun Feng Yuyan Ni Minghao Li Yanwen Huang Zhiming Ma Wei-Ying Ma Yanyan Lan SSL 49 7 0 15 May 2024
Could Chemical LLMs benefit from Message Passing Jiaqing Xie Ziheng Chi 38 0 0 14 May 2024
HGTDR: Advancing Drug Repurposing with Heterogeneous Graph Transformers Ali Gharizadeh Karim Abbasi Amin Ghareyazi M. R. Mofrad Hamid R. Rabiee 39 17 0 12 May 2024
Synthetic Data from Diffusion Models Improve Drug Discovery Prediction Bing Hu Ashish Saragadam Anita Layton Helen Chen DiffM 34 1 0 06 May 2024
Sort & Slice: A Simple and Superior Alternative to Hash-Based Folding for Extended-Connectivity Fingerprints Markus Dablander Thierry Hanser R. Lambiotte Garrett M. Morris 37 1 0 10 Mar 2024
ESM All-Atom: Multi-scale Protein Language Model for Unified Molecular Modeling Kangjie Zheng Siyu Long Tianyu Lu Junwei Yang Xinyu Dai Ming Zhang Zaiqing Nie Wei-Ying Ma Hao Zhou 41 5 0 05 Mar 2024
Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey Qizhi Pei Lijun Wu Kaiyuan Gao Jinhua Zhu Yue Wang Zun Wang Tao Qin Rui Yan AI4CE 54 19 0 03 Mar 2024
Improving Legal Judgement Prediction in Romanian with Long Text Encoders Mihai Masala Traian Rebedea Horia Velicu AILaw 43 2 0 29 Feb 2024
BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning Qizhi Pei Lijun Wu Kaiyuan Gao Xiaozhuan Liang Yin Fang Jinhua Zhu Shufang Xie Tao Qin Rui Yan AI4CE 51 30 0 27 Feb 2024
On Leveraging Encoder-only Pre-trained Language Models for Effective Keyphrase Generation Di Wu Wasi Uddin Ahmad Kai-Wei Chang 27 3 0 21 Feb 2024
Contextual Molecule Representation Learning from Chemical Reaction Knowledge Han Tang Shikun Feng Bicheng Lin Yuyan Ni Jingjing Liu Wei-Ying Ma Yanyan Lan 27 2 0 21 Feb 2024
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey Taojie Kuang Pengfei Liu Zhixiang Ren AI4CE 50 1 0 11 Feb 2024
NLP for Knowledge Discovery and Information Extraction from Energetics Corpora Francis G. VanGessel Efrem Perry Salil Mohan Oliver M. Barham Mark Cavolowsky 24 0 0 10 Feb 2024
A Sober Look at LLMs for Material Discovery: Are They Actually Good for Bayesian Optimization Over Molecules? Agustinus Kristiadi Felix Strieth-Kalthoff Marta Skreta Pascal Poupart Alán Aspuru-Guzik Geoff Pleiss 30 21 0 07 Feb 2024
MolTailor: Tailoring Chemical Molecular Representation to Specific Tasks via Text Prompts Haoqiang Guo Sendong Zhao Hao Wang Yanrui Du Bing Qin AI4CE 21 8 0 21 Jan 2024
Can Large Language Models Understand Molecules? Seyedeh Shaghayegh Sadeghi Alan Bui Ali Forooghi Jianguo Lu A. Ngom AI4CE 18 9 0 05 Jan 2024
Predictive Chemistry Augmented with Text Retrieval Yujie Qian Zhening Li Zhengkai Tu Connor W. Coley Regina Barzilay 23 7 0 08 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 11 6 0 30 Nov 2023
InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery He Cao Zijing Liu Xingyu Lu Yuan Yao Yu Li 27 58 0 27 Nov 2023
Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design Henry W Sprueill Carl N. Edwards Mariefel V. Olarte Udishnu Sanyal Heng Ji Sutanay Choudhury LRM 34 10 0 22 Oct 2023
UniMAP: Universal SMILES-Graph Representation Learning Shikun Feng Lixin Yang Wei-Ying Ma Yanyan Lan OffRL 19 6 0 22 Oct 2023
Improving Molecular Properties Prediction Through Latent Space Fusion Eduardo Soares Akihiro Kishimoto E. V. Brazil Seiji Takeda Hiroshi Kajino Renato F. G. Cerqueira BDL AI4CE 18 2 0 20 Oct 2023
ReLM: Leveraging Language Models for Enhanced Chemical Reaction Prediction Yaorui Shi An Zhang Enzhi Zhang Zhiyuan Liu Xiang Wang AI4CE 22 24 0 20 Oct 2023
BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations Qizhi Pei Wei Zhang Jinhua Zhu Kehan Wu Kaiyuan Gao Lijun Wu Yingce Xia Rui Yan 33 61 0 11 Oct 2023
Transformers and Large Language Models for Chemistry and Drug Discovery Andres M Bran Philippe Schwaller LM&MA MedIm AI4CE 35 14 0 09 Oct 2023
Multiple Physics Pretraining for Physical Surrogate Models Michael McCabe Bruno Régaldo-Saint Blancard Liam Parker Ruben Ohana M. Cranmer ... Francois Lanusse Mariel Pettee Tiberiu Teşileanu Kyunghyun Cho Shirley Ho PINN AI4CE 40 52 0 04 Oct 2023
SALSA: Semantically-Aware Latent Space Autoencoder Kathryn E. Kirchoff Travis Maxfield Alexander Tropsha Shawn M. Gomez 16 2 0 04 Oct 2023
ADMET property prediction through combinations of molecular fingerprints James H. Notwell Michael W. Wood 20 5 0 29 Sep 2023
MHG-GNN: Combination of Molecular Hypergraph Grammar with Graph Neural Network Akihiro Kishimoto Hiroshi Kajino Masataka Hirose Junta Fuchiwaki Indra Priyadarsini Lisa Hamada Hajime Shinohara D. Nakano Seiji Takeda AI4CE 34 4 0 28 Sep 2023
3D-Mol: A Novel Contrastive Learning Framework for Molecular Property Prediction with 3D Information Taojie Kuang Yiming Ren Zhixiang Ren 27 7 0 28 Sep 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 23 7 0 28 Sep 2023
Large-scale Pretraining Improves Sample Efficiency of Active Learning based Molecule Virtual Screening Zhonglin Cao Simone Sciabola Ye Wang 35 1 0 20 Sep 2023
GPT-MolBERTa: GPT Molecular Features Language Model for molecular property prediction Suryanarayanan Balaji Rishikesh Magar Yayati Jadhav and Amir Barati Farimani 18 13 0 20 Sep 2023
Deep Prompt Tuning for Graph Transformers Reza Shirkavand Heng-Chiao Huang 23 7 0 18 Sep 2023
Uncovering Neural Scaling Laws in Molecular Representation Learning Dingshuo Chen Yanqiao Zhu Jieyu Zhang Yuanqi Du Zhixun Li Qiang Liu Shu Wu Liang Wang 32 16 0 15 Sep 2023
Applying BioBERT to Extract Germline Gene-Disease Associations for Building a Knowledge Graph from the Biomedical Literature Armando D. Diaz Gonzalez K. Hughes Songhui Yue S. Hayes 17 2 0 11 Sep 2023
Materials Informatics Transformer: A Language Model for Interpretable Materials Properties Prediction Hongshuo Huang Rishikesh Magar Chang Xu A. Farimani AI4CE 38 4 0 30 Aug 2023
Contrast-augmented Diffusion Model with Fine-grained Sequence Alignment for Markup-to-Image Generation Guojin Zhong Jin Yuan Pan Wang Kailun Yang Weili Guan Zhiyong Li DiffM 26 6 0 02 Aug 2023
Current Methods for Drug Property Prediction in the Real World Jacob Green Cecilia Cabrera Diaz Maximilian A. H. Jakobs A. Dimitracopoulos Mark van der Wilk Ryan D. Greenhalgh 24 1 0 25 Jul 2023
Prot2Text: Multimodal Protein's Function Generation with GNNs and Transformers Hadi Abdine Michail Chatzianastasis Costas Bouyioukos Michalis Vazirgiannis 30 40 0 25 Jul 2023
Extracting Molecular Properties from Natural Language with Multimodal Contrastive Learning Romain Lacombe Andrew Gaut Jeff He D. Lüdeke Kateryna Pistunova 25 2 0 22 Jul 2023
Fractional Denoising for 3D Molecular Pre-training Shi Feng Yuyan Ni Yanyan Lan Zhiming Ma Wei-Ying Ma DiffM AI4CE 47 25 0 20 Jul 2023
Can Large Language Models Empower Molecular Property Prediction? Chao Qian Huayi Tang Zhi-Jiang Yang Hongsi Liang Y. Liu AI4CE 36 39 0 14 Jul 2023
Multimodal Molecular Pretraining via Modality Blending Qiying Yu Yudi Zhang Yuyan Ni Shi Feng Yanyan Lan Hao Zhou Jingjing Liu 21 13 0 12 Jul 2023
ReactIE: Enhancing Chemical Reaction Extraction with Weak Supervision Ming Zhong Siru Ouyang Minhao Jiang Vivian Hu Yizhu Jiao Xuan Wang Jiawei Han 27 8 0 04 Jul 2023
Transformers in Healthcare: A Survey Subhash Nerella S. Bandyopadhyay Jiaqing Zhang Miguel Contreras Scott Siegel ... Jessica Sena B. Shickel A. Bihorac Kia Khezeli Parisa Rashidi MedIm AI4CE 21 25 0 30 Jun 2023