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
Knowledge-augmented Pre-trained Language Models for Biomedical Relation Extraction Mario Sanger Ulf Leser 45 0 0 01 May 2025
Combining GCN Structural Learning with LLM Chemical Knowledge for Enhanced Virtual Screening Radia Berreziga Mohammed Brahimi Khairedine Kraim Hamid Azzoune 131 0 0 24 Apr 2025
LLM Agent Swarm for Hypothesis-Driven Drug Discovery Kevin Song Andrew Trotter Jake Y. Chen 22 0 0 24 Apr 2025
Enhancing TCR-Peptide Interaction Prediction with Pretrained Language Models and Molecular Representations Cong Qi Hanzhang Fang Siqi Jiang Tianxing Hu Wei Zhi 27 0 0 22 Apr 2025
Streamlining Biomedical Research with Specialized LLMs Linqing Chen Weilei Wang Yubin Xia Wentao Wu Peng Xu ... Lisha Zhang Fu Bian Zhongkai Ye Lidong Pei Changyang Tu 28 1 0 15 Apr 2025
Rethinking the generalization of drug target affinity prediction algorithms via similarity aware evaluation Chenbin Zhang Zhiqiang Hu Chuchu Jiang Wen Chen Jie Xu S. Zhang 30 0 0 13 Apr 2025
OmniScience: A Domain-Specialized LLM for Scientific Reasoning and Discovery Vignesh Prabhakar Md Amirul Islam Adam Atanas Yixuan Wang J. N. Han ... Rucha Apte Robert Clark Kang Xu Zihan Wang Kai Liu LRM 85 1 0 22 Mar 2025
Chem42: a Family of chemical Language Models for Target-aware Ligand Generation A. Singh Engin Tekin Maryam Nadeem Nancy A. ElNaker Mohammad Amaan Sayeed Natalia Vassilieva Boulbaba Ben Amor 47 1 0 20 Mar 2025
Uni-3DAR: Unified 3D Generation and Understanding via Autoregression on Compressed Spatial Tokens Shuqi Lu Haowei Lin Lin Yao Zhifeng Gao Xiaohong Ji W. Elwasif Linfeng Zhang Guolin Ke 48 0 0 20 Mar 2025
High-entropy Advantage in Neural Networks' Generalizability Entao Yang Xuzhi Zhang Yue Shang Ge Zhang AI4CE 63 0 0 17 Mar 2025
Exploiting Edited Large Language Models as General Scientific Optimizers Qitan Lv T. Liu Haoyu Wang 41 0 0 08 Mar 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu Jian Wu Yue Liu Mingze Yin Jieping Ye Jian Wu Zehua Wang 62 0 0 06 Mar 2025
LLM-Fusion: A Novel Multimodal Fusion Model for Accelerated Material Discovery Onur Boyar Indra Priyadarsini Seiji Takeda Lisa Hamada 42 0 0 02 Mar 2025
Broadening Discovery through Structural Models: Multimodal Combination of Local and Structural Properties for Predicting Chemical Features Nikolai Rekut Alexey Orlov Klea Ziu Elizaveta Starykh Martin Takáč Aleksandr Beznosikov 64 0 0 25 Feb 2025
CL-MFAP: A Contrastive Learning-Based Multimodal Foundation Model for Molecular Property Prediction and Antibiotic Screening Gen Zhou Sugitha Janarthanan Yutong Lu Pingzhao Hu 47 0 0 16 Feb 2025
Challenging reaction prediction models to generalize to novel chemistry John Bradshaw Anji Zhang Babak Mahjour David E. Graff Marwin H. S. Segler Connor W. Coley 40 1 0 11 Jan 2025
Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction Sepideh Maleki Jan-Christian Huetter Kangway V Chuang Gabriele Scalia Tommaso Biancalani Tommaso Biancalani AI4CE 90 2 0 18 Dec 2024
SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervision Kangjie Zheng Siyue Liang Junwei Yang Bin Feng Zequn Liu Wei Ju Zhiping Xiao Ming Zhang 73 1 0 07 Dec 2024
DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaboration Sizhe Liu Yaojie Lu Siyu Chen Xiyang Hu Jieyu Zhao Tianfan Fu Yue Zhao LLMAG 79 6 0 24 Nov 2024
MolMetaLM: a Physicochemical Knowledge-Guided Molecular Meta Language Model Yifan Wu Min Zeng Yang Li Yuyao Zhang Min Li 71 1 0 23 Nov 2024
NPGPT: Natural Product-Like Compound Generation with GPT-based Chemical Language Models Koh Sakano Kairi Furui Masahito Ohue 64 1 0 19 Nov 2024
Bio-xLSTM: Generative modeling, representation and in-context learning of biological and chemical sequences Niklas Schmidinger Lisa Schneckenreiter Philipp Seidl Johannes Schimunek Pieter-Jan Hoedt Johannes Brandstetter Andreas Mayr Sohvi Luukkonen Sepp Hochreiter G. Klambauer MedIm 61 4 0 06 Nov 2024
Adapting While Learning: Grounding LLMs for Scientific Problems with Intelligent Tool Usage Adaptation Bohan Lyu Yadi Cao Duncan Watson-Parris Leon Bergen Taylor Berg-Kirkpatrick Rose Yu 61 3 0 01 Nov 2024
Chemical Language Model Linker: blending text and molecules with modular adapters Yifan Deng Spencer S. Ericksen Anthony Gitter 30 1 0 26 Oct 2024
Multi-view biomedical foundation models for molecule-target and property prediction Parthasarathy Suryanarayanan Yunguang Qiu Shreyans Sethi Diwakar Mahajan Hongyang Li ... Bum Chul Kwon Pablo Meyer Feixiong Cheng Jianying Hu Joseph A. Morrone AI4CE 36 0 0 25 Oct 2024
nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder Maksim Kuznetsov Airat Valiev Alex Aliper Daniil Polykovskiy E. Tutubalina Rim Shayakhmetov Z. Miftahutdinov 27 0 0 11 Oct 2024
Smirk: An Atomically Complete Tokenizer for Molecular Foundation Models Alexius Wadell Anoushka Bhutani Venkatasubramanian Viswanathan 127 0 0 19 Sep 2024
Pre-Trained Language Models for Keyphrase Prediction: A Review Muhammad Umair Tangina Sultana Young-Koo Lee 32 4 0 02 Sep 2024
MaskMol: Knowledge-guided Molecular Image Pre-Training Framework for Activity Cliffs Zhixiang Cheng Hongxin Xiang Pengsen Ma Li Zeng Xin Jin ... Yang Deng Bosheng Song Xinxin Feng Changhui Deng Xiangxiang Zeng 28 0 0 02 Sep 2024
Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding Bing Hu Anita Layton Helen Chen MedIm 36 2 0 14 Aug 2024
LipidBERT: A Lipid Language Model Pre-trained on METiS de novo Lipid Library Tianhao Yu Cai Yao Zhuorui Sun Feng Shi Lin Zhang ... Xicheng Zhang Jiali Zou Wenshou Wang C. Lai Kai Wang 26 3 0 12 Aug 2024
Neural Network Emulator for Atmospheric Chemical ODE Zhi-Song Liu Petri S. Clusius Michael Boy 42 3 0 03 Aug 2024
UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation Jiayuan Zhu Yunli Qi Yongqiang Chen Quanming Yao 29 7 0 01 Aug 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 29 7 0 24 Jul 2024
Graph Transformers: A Survey Ahsan Shehzad Feng Xia Shagufta Abid Ciyuan Peng Shuo Yu Dongyu Zhang Karin Verspoor AI4CE 34 9 0 13 Jul 2024
MolTRES: Improving Chemical Language Representation Learning for Molecular Property Prediction Jun-Hyung Park Yeachan Kim Mingyu Lee Hyuntae Park SangKeun Lee 37 0 0 09 Jul 2024
Improving Performance Prediction of Electrolyte Formulations with Transformer-based Molecular Representation Model Indra Priyadarsini Vidushi Sharma Seiji Takeda Akihiro Kishimoto Lisa Hamada Hajime Shinohara 27 5 0 28 Jun 2024
PharmaGPT: Domain-Specific Large Language Models for Bio-Pharmaceutical and Chemistry Linqing Chen Weilei Wang Zilong Bai Peng Xu Yan Fang ... Lisha Zhang Fu Bian Zhongkai Ye Lidong Pei Changyang Tu AI4MH LM&MA 53 2 0 26 Jun 2024
MolFusion: Multimodal Fusion Learning for Molecular Representations via Multi-granularity Views Muzhen Cai Sendong Zhao Haochun Wang Yanrui Du Zewen Qiang Bing Qin Ting Liu 37 0 0 26 Jun 2024
RetroGFN: Diverse and Feasible Retrosynthesis using GFlowNets Piotr Gaiñski Michał Koziarski Krzysztof Maziarz Marwin H. S. Segler Jacek Tabor Marek Śmieja 52 3 0 26 Jun 2024
MatText: Do Language Models Need More than Text & Scale for Materials Modeling? Nawaf Alampara Santiago Miret K. Jablonka 56 9 0 25 Jun 2024
Efficient Evolutionary Search Over Chemical Space with Large Language Models Haorui Wang Marta Skreta C. Ser Wenhao Gao Lingkai Kong ... Yanqiao Zhu Yuanqi Du Alán Aspuru-Guzik Kirill Neklyudov Chao Zhang 47 12 0 23 Jun 2024
Efficient Sharpness-Aware Minimization for Molecular Graph Transformer Models Yili Wang Kaixiong Zhou Ninghao Liu Ying Wang Xin Wang 40 10 0 19 Jun 2024
Machine Learning Based Prediction of Proton Conductivity in Metal-Organic Frameworks Seunghee Han Byeong Gwan Lee Dae Woon Lim Jihan Kim AI4CE 22 2 0 18 Jun 2024
Learning Molecular Representation in a Cell Gang Liu Srijit Seal John Arevalo Zhenwen Liang Anne E Carpenter Meng Jiang Shantanu Singh 42 2 0 17 Jun 2024
A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery Yu Zhang Xiusi Chen Bowen Jin Sheng Wang Shuiwang Ji Wei Wang Jiawei Han 44 27 0 16 Jun 2024
In-Context Learning of Physical Properties: Few-Shot Adaptation to Out-of-Distribution Molecular Graphs Grzegorz Kaszuba Amirhossein D. Naghdi Dario Massa Stefanos Papanikolaou Andrzej Jaszkiewicz Piotr Sankowski AI4CE OODD 42 0 0 03 Jun 2024
LLM and GNN are Complementary: Distilling LLM for Multimodal Graph Learning Junjie Xu Zongyu Wu Min Lin Xiang Zhang Suhang Wang 30 11 0 03 Jun 2024
Adapting Differential Molecular Representation with Hierarchical Prompts for Multi-label Property Prediction Linjia Kang Songhua Zhou Shuyan Fang Shichao Liu Wen Zhang AI4CE 52 3 0 29 May 2024
Explainable Molecular Property Prediction: Aligning Chemical Concepts with Predictions via Language Models Zhenzhong Wang Zehui Lin Wanyu Lin Ming Yang Minggang Zeng Kay Chen Tan 28 3 0 25 May 2024