ChemBERTa-2: Towards Chemical Foundation Models

5 September 2022

Papers citing "ChemBERTa-2: Towards Chemical Foundation Models"

50 / 56 papers shown

Title
DeepGDel: Deep Learning-based Gene Deletion Prediction Framework for Growth-Coupled Production in Genome-Scale Metabolic Models Ziwei Yang T. Tamura 27 0 0 08 Apr 2025
High-entropy Advantage in Neural Networks' Generalizability Entao Yang Xuzhi Zhang Yue Shang Ge Zhang AI4CE 66 0 0 17 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 66 0 0 25 Feb 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi Xuben Wang Kenji Kawaguchi Tat-Seng Chua 102 3 0 18 Feb 2025
From Generalist to Specialist: A Survey of Large Language Models for Chemistry Yang Han Ziping Wan Lu Chen Kai Yu Xin Chen LM&MA 35 1 0 31 Dec 2024
Solaris: A Foundation Model of the Sun Harris Abdul Majid Pietro Sittoni Francesco Tudisco 69 0 0 25 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
A Transformer Based Generative Chemical Language AI Model for Structural Elucidation of Organic Compounds Xiaofeng Tan 19 1 0 13 Oct 2024
Smirk: An Atomically Complete Tokenizer for Molecular Foundation Models Alexius Wadell Anoushka Bhutani Venkatasubramanian Viswanathan 150 0 0 19 Sep 2024
Towards understanding evolution of science through language model series Junjie Dong Zhuoqi Lyu Qing Ke AI4TS 35 0 0 15 Sep 2024
Regression with Large Language Models for Materials and Molecular Property Prediction Ryan Jacobs Maciej P. Polak Lane E. Schultz Hamed Mahdavi V. Honavar Dane Morgan 31 2 0 09 Sep 2024
Efficient Training of Transformers for Molecule Property Prediction on Small-scale Datasets Shivesh Prakash 33 0 0 07 Sep 2024
Cross-Modal Learning for Chemistry Property Prediction: Large Language Models Meet Graph Machine Learning Sakhinana Sagar Srinivas Venkataramana Runkana AI4CE 41 1 0 27 Aug 2024
Leveraging Chemistry Foundation Models to Facilitate Structure Focused Retrieval Augmented Generation in Multi-Agent Workflows for Catalyst and Materials Design Nathaniel H. Park Tiffany J. Callahan James L. Hedrick Tim Erdmann Sara Capponi AI4CE 33 1 0 21 Aug 2024
Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding Bing Hu Anita Layton Helen Chen MedIm 41 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
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
MatText: Do Language Models Need More than Text & Scale for Materials Modeling? Nawaf Alampara Santiago Miret Kevin Maik Jablonka 58 9 0 25 Jun 2024
MolX: Enhancing Large Language Models for Molecular Learning with A Multi-Modal Extension Khiem Le Zhichun Guo Kaiwen Dong Xiaobao Huang B. Nan Roshni G. Iyer Xiangliang Zhang Olaf Wiest Wei Wang Nitesh V. Chawla 41 8 0 10 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
FusionDTI: Fine-grained Binding Discovery with Token-level Fusion for Drug-Target Interaction Zhaohan Meng Zaiqiao Meng I. Ounis 51 4 0 03 Jun 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
Could Chemical LLMs benefit from Message Passing Jiaqing Xie Ziheng Chi 41 0 0 14 May 2024
$$\texttt{MiniMol}$: A Parameter-Efficient Foundation Model for Molecular Learning$ $\texttt{MiniMol}$ : A Parameter-Efficient Foundation Model for Molecular Learning Kerstin Klaser Bla.zej Banaszewski S. Maddrell-Mander Callum McLean Luis Muller Alipanah Parviz Shenyang Huang Andrew Fitzgibbon AI4CE 48 5 0 23 Apr 2024
An Evaluation Benchmark for Adverse Drug Event Prediction from Clinical Trial Results A. Yazdani Alban Bornet Boya Zhang Philipp Khlebnikov P. Amini Douglas Teodoro Douglas Teodoro ELM 18 0 0 19 Apr 2024
Are large language models superhuman chemists? Adrian Mirza Nawaf Alampara Sreekanth Kunchapu Benedict Emoekabu Aswanth Krishnan ... Leanne M. Stafast Dinga Wonanke Michael Pieler P. Schwaller Kevin Maik Jablonka ELM AI4MH LRM LM&MA 31 5 0 01 Apr 2024
Re-Simulation-based Self-Supervised Learning for Pre-Training Foundation Models Philip Harris Michael Kagan J. Krupa B. Maier Nathaniel Woodward 38 13 0 11 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
On the Challenges and Opportunities in Generative AI Laura Manduchi Kushagra Pandey Robert Bamler Ryan Cotterell Sina Daubener ... F. Wenzel Frank Wood Stephan Mandt Vincent Fortuin Vincent Fortuin 56 17 0 28 Feb 2024
Self-Guided Masked Autoencoders for Domain-Agnostic Self-Supervised Learning Johnathan Xie Yoonho Lee Annie S. Chen Chelsea Finn 25 3 0 22 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
Structure-Aware E(3)-Invariant Molecular Conformer Aggregation Networks D. M. Nguyen Nina Lukashina Tai Nguyen An T. Le TrungTin Nguyen Nhat Ho Jan Peters Daniel Sonntag Viktor Zaverkin Mathias Niepert 36 5 0 03 Feb 2024
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 16 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 30 58 0 27 Nov 2023
PepLand: a large-scale pre-trained peptide representation model for a comprehensive landscape of both canonical and non-canonical amino acids Ruochi Zhang Haoran Wu Yuting Xiu Kewei Li Ningning Chen Yu Wang Yan Wang Xin Gao Fengfeng Zhou AI4TS 36 2 0 08 Nov 2023
An Interdisciplinary Outlook on Large Language Models for Scientific Research James Boyko Joseph Cohen Nathan Fox Maria Han Veiga Jennifer I-Hsiu Li ... Andreas H. Rauch Kenneth N. Reid Soumi Tribedi Anastasia Visheratina Xin Xie 38 18 0 03 Nov 2023
Transferring a molecular foundation model for polymer property predictions Pei Zhang Logan T. Kearney D. Bhowmik Zachary R. Fox Amit K. Naskar John P. Gounley AI4CE 28 7 0 25 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
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
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 21 13 0 20 Sep 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 27 1 0 25 Jul 2023
CTAGE: Curvature-Based Topology-Aware Graph Embedding for Learning Molecular Representations Yili Chen Zhengyu Li Zheng Wan Hui Yu Xian Wei 23 0 0 25 Jul 2023
SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design Carl Edwards Aakanksha Naik Tushar Khot Martin D. 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 32 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 31 1 0 13 Jun 2023
Grammar Prompting for Domain-Specific Language Generation with Large Language Models Bailin Wang Zi Wang Xuezhi Wang Yuan Cao Rif A. Saurous Yoon Kim ReLM LRM 35 52 0 30 May 2023
Computational modeling of semantic change Nina Tahmasebi Haim Dubossarsky 34 6 0 13 Apr 2023
SELFormer: Molecular Representation Learning via SELFIES Language Models Atakan Yüksel Erva Ulusoy Atabey Ünlü Tunca Dogan 27 55 0 10 Apr 2023