Unifying Molecular and Textual Representations via Multi-task Language Modelling

29 January 2023

Dimitrios Christofidellis

Papers citing "Unifying Molecular and Textual Representations via Multi-task Language Modelling"

50 / 58 papers shown

Title
Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning Xuan Lin Qingrui Liu Hongxin Xiang Daojian Zeng Xiangxiang Zeng 40 1 0 05 May 2025
GOLLuM: Gaussian Process Optimized LLMs -- Reframing LLM Finetuning through Bayesian Optimization Bojana Ranković P. Schwaller BDL 235 0 0 08 Apr 2025
We Need Improved Data Curation and Attribution in AI for Scientific Discovery Mara Graziani Antonio Foncubierta Dimitrios Christofidellis Irina Espejo Morales Malina Molnar Marvin Alberts Matteo Manica Jannis Born 55 0 0 03 Apr 2025
Uni-3DAR: Unified 3D Generation and Understanding via Autoregression on Compressed Spatial Tokens Shuqi Lu Haowei Lin Lin Yao Zhifeng Gao Xiaohong Ji Weinan E Linfeng Zhang Guolin Ke 53 0 0 20 Mar 2025
GraphT5: Unified Molecular Graph-Language Modeling via Multi-Modal Cross-Token Attention Sangyeup Kim Nayeon Kim Yinhua Piao Sun Kim 49 0 0 07 Mar 2025
RAG-Enhanced Collaborative LLM Agents for Drug Discovery Namkyeong Lee Edward De Brouwer Ehsan Hajiramezanali Tommaso Biancalani Chanyoung Park Gabriele Scalia 46 0 0 22 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 37 1 0 31 Dec 2024
GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules Teng Xiao Chao Cui Huaisheng Zhu V. Honavar AI4CE CLIP 42 0 0 16 Nov 2024
Regress, Don't Guess -- A Regression-like Loss on Number Tokens for Language Models Jonas Zausinger Lars Pennig Kacper Chlodny Vincent Limbach Anna Ketteler Thorben Prein Vishwa Mohan Singh Michael Morris Danziger Jannis Born 37 1 0 04 Nov 2024
Exploring Optimal Transport-Based Multi-Grained Alignments for Text-Molecule Retrieval Zijun Min Bingshuai Liu Li Zhang Jia Song Jinsong Su Song He Xiaochen Bo OT 75 1 0 04 Nov 2024
LLaMo: Large Language Model-based Molecular Graph Assistant Jinyoung Park Minseong Bae Dohwan Ko Hyunwoo J. Kim 42 1 0 31 Oct 2024
Chemical Language Model Linker: blending text and molecules with modular adapters Yifan Deng Spencer S. Ericksen Anthony Gitter 35 1 0 26 Oct 2024
Chain-of-Thoughts for Molecular Understanding Yunhui Jang Jaehyung Kim Sungsoo Ahn LRM AI4CE 38 1 0 08 Oct 2024
Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity Hyosoon Jang Yunhui Jang Jaehyung Kim Sungsoo Ahn 30 2 0 04 Oct 2024
Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model Yuran Xiang Haiteng Zhao Chang Ma Zhi-Hong Deng 34 0 0 19 Aug 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 13 0 23 Jun 2024
HIGHT: Hierarchical Graph Tokenization for Graph-Language Alignment Yongqiang Chen Quanming Yao Juzheng Zhang James Cheng Yatao Bian 36 4 0 20 Jun 2024
PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomes He Cao Yanjun Shao Zhiyuan Liu Zijing Liu Xiangru Tang Yuan Yao Yu Li AI4CE 35 5 0 19 Jun 2024
MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction Yuyan Liu Sirui Ding Sheng Zhou Wenqi Fan Qiaoyu Tan 42 8 0 18 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 49 29 0 16 Jun 2024
Learning Multi-view Molecular Representations with Structured and Unstructured Knowledge Yizhen Luo Kai Yang Massimo Hong Xing Yi Liu Zikun Nie Hao Zhou Zaiqing Nie 51 2 0 14 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
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 10 0 23 May 2024
ALMol: Aligned Language-Molecule Translation LLMs through Offline Preference Contrastive Optimisation Dimitris Gkoumas 39 0 0 14 May 2024
Data-Efficient Molecular Generation with Hierarchical Textual Inversion Seojin Kim Jaehyun Nam Sihyun Yu Younghoon Shin Jinwoo Shin 45 2 0 05 May 2024
Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generation Yikun Zhang Geyan Ye Chaohao Yuan Bo Han Long-Kai Huang Jianhua Yao Wei Liu Yu Rong 42 3 0 23 Apr 2024
A Self-feedback Knowledge Elicitation Approach for Chemical Reaction Predictions Pengfei Liu Jun Tao Zhixiang Ren 22 0 0 15 Apr 2024
AlloyBERT: Alloy Property Prediction with Large Language Models Akshat Chaudhari Chakradhar Guntuboina Hongshuo Huang A. Farimani 40 4 0 28 Mar 2024
Instruction Multi-Constraint Molecular Generation Using a Teacher-Student Large Language Model Peng Zhou Jianmin Wang Chunyan Li Zixu Wang Yiping Liu ... Xibao Cai Houtim Lai Wei Liu Longyue Wang Xiangxiang Zeng 21 0 0 20 Mar 2024
MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular Comprehension Xingyu Lu He Cao Zijing Liu Shengyuan Bai Leqing Chen Yuan Yao Hai-Tao Zheng Yu Li HILM 21 7 0 13 Mar 2024
3M-Diffusion: Latent Multi-Modal Diffusion for Text-Guided Generation of Molecular Graphs Huaisheng Zhu Teng Xiao V. Honavar DiffM 45 1 0 11 Mar 2024
Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule Yi Xiao Xiangxin Zhou Qiang Liu Liang Wang AI4CE 37 3 0 07 Mar 2024
DRAK: Unlocking Molecular Insights with Domain-Specific Retrieval-Augmented Knowledge in LLMs Jinzhe Liu Xiangsheng Huang Zhuo Chen Yin Fang 52 3 0 04 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 62 19 0 03 Mar 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 31 0 27 Feb 2024
L+M-24: Building a Dataset for Language + Molecules @ ACL 2024 Carl Edwards Qingyun Wang Lawrence Zhao Heng Ji 40 18 0 22 Feb 2024
ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback Henry W Sprueill Carl Edwards Khushbu Agarwal Mariefel V. Olarte Udishnu Sanyal Conrad Johnston Hongbin Liu Heng Ji Sutanay Choudhury LRM 36 8 0 15 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 43 21 0 07 Feb 2024
MolTC: Towards Molecular Relational Modeling In Language Models Junfeng Fang Shuai Zhang Chang Wu Zhengyi Yang Zhiyuan Liu Sihang Li Kun Wang Wenjie Du Xiang Wang 39 19 0 06 Feb 2024
From Words to Molecules: A Survey of Large Language Models in Chemistry Chang Liao Yemin Yu Yu Mei Ying Wei 33 16 0 02 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
Large Language Models on Graphs: A Comprehensive Survey Bowen Jin Gang Liu Chi Han Meng Jiang Heng Ji Jiawei Han AI4CE 42 141 0 05 Dec 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 33 58 0 27 Nov 2023
ReactionT5: a large-scale pre-trained model towards application of limited reaction data Tatsuya Sagawa Ryosuke Kojima AI4CE 13 7 0 12 Nov 2023
Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design Henry W Sprueill Carl Edwards Mariefel V. Olarte Udishnu Sanyal Heng Ji Sutanay Choudhury LRM 34 10 0 22 Oct 2023
MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter Zhiyuan Liu Sihang Li Yancheng Luo Hao Fei Yixin Cao Kenji Kawaguchi Xiang Wang Tat-Seng Chua 38 82 0 19 Oct 2023
Transformers and Large Language Models for Chemistry and Drug Discovery Andres M Bran Philippe Schwaller LM&MA MedIm AI4CE 38 14 0 09 Oct 2023
Language models in molecular discovery Chaoqi Wang Yibo Jiang Chenghao Yang Han Liu Yuxin Chen 30 7 0 28 Sep 2023
From Artificially Real to Real: Leveraging Pseudo Data from Large Language Models for Low-Resource Molecule Discovery Yuhan Chen Nuwa Xi Yanrui Du Hao Wang Jianyu Chen Sendong Zhao Bing Qin 27 10 0 11 Sep 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 15 0 19 Jun 2023