Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models

13 June 2023

Ningyu Zhang

Huajun Chen

Papers citing "Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models"

50 / 57 papers shown

Title
Benchmarking Retrieval-Augmented Generation for Chemistry Xianrui Zhong Bowen Jin Siru Ouyang Yanzhen Shen Qiao Jin Yin Fang Zhiyong Lu Jiawei Han 3DV 31 1 0 12 May 2025
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
Agentic AI for Scientific Discovery: A Survey of Progress, Challenges, and Future Directions Mourad Gridach Jay Nanavati Khaldoun Zine El Abidine Lenon Mendes Christina Mack 54 6 0 12 Mar 2025
ProtTeX: Structure-In-Context Reasoning and Editing of Proteins with Large Language Models Zicheng Ma Chuanliu Fan Zhicong Wang Zhenyu Chen Xiaohan Lin Yong Li Shihao Feng Jun Zhang Ziqiang Cao Y. Gao 50 0 0 11 Mar 2025
RAG-Enhanced Collaborative LLM Agents for Drug Discovery Namkyeong Lee Edward De Brouwer Ehsan Hajiramezanali Tommaso Biancalani Chanyoung Park Gabriele Scalia 48 0 0 22 Feb 2025
A Survey of Large Language Models for Healthcare: from Data, Technology, and Applications to Accountability and Ethics Kai He Rui Mao Qika Lin Yucheng Ruan Xiang Lan Mengling Feng Min Zhang LM&MA AILaw 107 155 0 28 Jan 2025
ChemDFM-X: Towards Large Multimodal Model for Chemistry Zihan Zhao B. Chen Jingpiao Li Lu Chen Liyang Wen ... Ziping Wan Yansi Li Zhongyang Dai Xin Chen Kai Yu AI4CE 58 3 0 03 Jan 2025
GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules Teng Xiao Chao Cui Huaisheng Zhu V. Honavar AI4CE CLIP 42 0 0 16 Nov 2024
Exploring Hierarchical Molecular Graph Representation in Multimodal LLMs Chengxin Hu Hao Li Yihe Yuan Jing Li Ivor Tsang 51 0 0 07 Nov 2024
LLM4Mat-Bench: Benchmarking Large Language Models for Materials Property Prediction Andre Niyongabo Rubungo Kangming Li Jason Hattrick-Simpers Adji Bousso Dieng 39 6 0 31 Oct 2024
LLaMo: Large Language Model-based Molecular Graph Assistant Jinyoung Park Minseong Bae Dohwan Ko Hyunwoo J. Kim 42 1 0 31 Oct 2024
MutaPLM: Protein Language Modeling for Mutation Explanation and Engineering Yizhen Luo Zikun Nie Massimo Hong Suyuan Zhao Hao Zhou Zaiqing Nie 45 0 0 30 Oct 2024
Chemical Language Model Linker: blending text and molecules with modular adapters Yifan Deng Spencer S. Ericksen Anthony Gitter 37 1 0 26 Oct 2024
Data Quality Control in Federated Instruction-tuning of Large Language Models Yaxin Du Guangyi Liu Fengting Yuchi W. Zhao Jingjing Qu Yunhong Wang Siheng Chen ALM FedML 58 0 0 15 Oct 2024
InstructBioMol: Advancing Biomolecule Understanding and Design Following Human Instructions Xiang Zhuang Keyan Ding Tianwen Lyu Yinuo Jiang Xiaotong Li ... Ming Qin Kehua Feng Jike Wang Qiang Zhang Huajun Chen 38 3 0 10 Oct 2024
Chain-of-Thoughts for Molecular Understanding Yunhui Jang Jaehyung Kim Sungsoo Ahn LRM AI4CE 41 1 0 08 Oct 2024
Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity Hyosoon Jang Yunhui Jang Jaehyung Kim Sungsoo Ahn 32 2 0 04 Oct 2024
SciSafeEval: A Comprehensive Benchmark for Safety Alignment of Large Language Models in Scientific Tasks Tianhao Li Jingyu Lu Chuangxin Chu Tianyu Zeng Yujia Zheng ... Xuejing Yuan Xingkai Wang Keyan Ding Huajun Chen Qiang Zhang ELM 47 3 0 02 Oct 2024
SciDFM: A Large Language Model with Mixture-of-Experts for Science Liangtai Sun Danyu Luo Da Ma Zihan Zhao Baocai Chen Zhennan Shen Su Zhu Lu Chen Xin Chen Kai Yu MoE 43 2 0 27 Sep 2024
AlpaPICO: Extraction of PICO Frames from Clinical Trial Documents Using LLMs Madhusudan Ghosh Shrimon Mukherjee Asmit Ganguly Partha Basuchowdhuri S. Naskar Debasis Ganguly 38 7 0 15 Sep 2024
An Investigation of Warning Erroneous Chat Translations in Cross-lingual Communication Yunmeng Li Jun Suzuki Makoto Morishita Kaori Abe Kentaro Inui 65 1 0 28 Aug 2024
Question Rephrasing for Quantifying Uncertainty in Large Language Models: Applications in Molecular Chemistry Tasks Zizhang Chen Pengyu Hong Sandeep Madireddy 37 1 0 07 Aug 2024
UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation Jiayuan Zhu Yunli Qi Yongqiang Chen Quanming Yao 36 7 0 01 Aug 2024
HIGHT: Hierarchical Graph Tokenization for Graph-Language Alignment Yongqiang Chen Quanming Yao Juzheng Zhang James Cheng Yatao Bian 41 4 0 20 Jun 2024
SciKnowEval: Evaluating Multi-level Scientific Knowledge of Large Language Models Kehua Feng Keyan Ding Weijie Wang Xiang Zhuang Zeyuan Wang Ming Qin Yu Zhao Jianhua Yao Qiang Zhang H. Chen ELM 50 6 0 13 Jun 2024
SciRIFF: A Resource to Enhance Language Model Instruction-Following over Scientific Literature David Wadden Kejian Shi Jacob Morrison Aakanksha Naik Shruti Singh ... Luca Soldaini Shannon Zejiang Shen Doug Downey Hannaneh Hajishirzi Arman Cohan 55 11 0 10 Jun 2024
Peer Review as A Multi-Turn and Long-Context Dialogue with Role-Based Interactions Cheng Tan Dongxin Lyu Siyuan Li Zhangyang Gao Jingxuan Wei Siqi Ma Zicheng Liu Stan Z. Li LLMAG 53 10 0 09 Jun 2024
A Fine-tuning Dataset and Benchmark for Large Language Models for Protein Understanding Yiqing Shen Zan Chen Michail Mamalakis Luhan He Haiyang Xia Tianbin Li Yanzhou Su Junjun He Yu Guang Wang AI4MH 35 9 0 08 Jun 2024
RLSF: Reinforcement Learning via Symbolic Feedback Piyush Jha Prithwish Jana Arnav Arora Vijay Ganesh LRM 49 3 0 26 May 2024
A Self-feedback Knowledge Elicitation Approach for Chemical Reaction Predictions Pengfei Liu Jun Tao Zhixiang Ren 32 0 0 15 Apr 2024
ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction Mingyu Jin Haochen Xue Zhenting Wang Boming Kang Ruosong Ye Kaixiong Zhou Mengnan Du Yongfeng Zhang LLMAG 40 11 0 30 Mar 2024
Bioinformatics and Biomedical Informatics with ChatGPT: Year One Review Jinge Wang Zien Cheng Qiuming Yao Li Liu Dong Xu Gangqing Hu LM&MA AI4CE 43 7 0 22 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
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
LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset Botao Yu Frazier N. Baker Ziqi Chen Xia Ning Huan Sun LM&MA 55 42 0 14 Feb 2024
From Words to Molecules: A Survey of Large Language Models in Chemistry Chang Liao Yemin Yu Yu Mei Ying Wei 38 16 0 02 Feb 2024
Improving Medical Reasoning through Retrieval and Self-Reflection with Retrieval-Augmented Large Language Models Minbyul Jeong Jiwoong Sohn Mujeen Sung Jaewoo Kang 25 29 0 27 Jan 2024
Towards 3D Molecule-Text Interpretation in Language Models Sihang Li Zhiyuan Liu Yancheng Luo Xiang Wang Xiangnan He Kenji Kawaguchi Tat-Seng Chua Qi Tian AI4CE 37 43 0 25 Jan 2024
Speak It Out: Solving Symbol-Related Problems with Symbol-to-Language Conversion for Language Models Yile Wang Sijie Cheng Zixin Sun Peng Li Yang Liu ReLM LRM 32 4 0 22 Jan 2024
Quokka: An Open-source Large Language Model ChatBot for Material Science Xianjun Yang Stephen D. Wilson Linda R. Petzold OSLM 37 2 0 02 Jan 2024
DrugAssist: A Large Language Model for Molecule Optimization Geyan Ye Xibao Cai Houtim Lai Xing Wang Junhong Huang Longyue Wang Wei Liu Xian Zeng 56 26 0 28 Dec 2023
Large Language Models on Graphs: A Comprehensive Survey Bowen Jin Gang Liu Chi Han Meng Jiang Heng Ji Jiawei Han AI4CE 44 141 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 38 58 0 27 Nov 2023
nach0: Multimodal Natural and Chemical Languages Foundation Model M. Livne Z. Miftahutdinov E. Tutubalina Maksim Kuznetsov Daniil Polykovskiy ... Aastha Jhunjhunwala Anthony Costa Alex Aliper Alán Aspuru-Guzik Alex Zhavoronkov AI4CE 27 13 0 21 Nov 2023
Structured Chemistry Reasoning with Large Language Models Siru Ouyang Zhuosheng Zhang Bing Yan Xuan Liu Yejin Choi Jiawei Han Lianhui Qin LRM 31 14 0 16 Nov 2023
DARWIN Series: Domain Specific Large Language Models for Natural Science Tong Xie Yuwei Wan Wei Huang Zhenyu Yin Yixuan Liu ... Chunyu Kit Clara Grazian Wenjie Zhang Imran Razzak B. Hoex ELM ALM AI4CE 30 27 0 25 Aug 2023
Emergent autonomous scientific research capabilities of large language models Daniil A. Boiko R. MacKnight Gabe Gomes ELM LM&Ro AI4CE LLMAG 109 119 0 11 Apr 2023