HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignment

20 June 2024

Papers citing "HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignment"

50 / 51 papers shown

Title
Graph Machine Learning in the Era of Large Language Models (LLMs) Wenqi Fan Shijie Wang Jiani Huang Zhikai Chen Yu Song ... Haitao Mao Hui Liu Xiaorui Liu Dawei Yin Qing Li AI4CE 73 29 0 23 Apr 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 84 18 0 03 Mar 2024
Towards Versatile Graph Learning Approach: from the Perspective of Large Language Models Lanning Wei Jun Gao Huan Zhao Quanming Yao 56 1 0 18 Feb 2024
Towards 3D Molecule-Text Interpretation in Language Models Changhao Nai Zhiyuan Liu Yancheng Luo Xiang Wang Xiangnan He Kenji Kawaguchi Tat-Seng Chua Qi Tian AI4CE 62 48 0 25 Jan 2024
Large Language Models on Graphs: A Comprehensive Survey Bowen Jin Gang Liu Chi Han Meng Jiang Heng Ji Jiawei Han AI4CE 79 156 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-Feng Li 71 66 0 27 Nov 2023
A Survey of Graph Meets Large Language Model: Progress and Future Directions Yuhan Li Zhixun Li Peisong Wang Jia Li Xiangguo Sun Hongtao Cheng Jeffrey Xu Yu 83 58 0 21 Nov 2023
Rethinking Tokenizer and Decoder in Masked Graph Modeling for Molecules Zhiyuan Liu Yaorui Shi An Zhang Enzhi Zhang Kenji Kawaguchi Xiang Wang Tat-Seng Chua AI4CE 61 40 0 23 Oct 2023
MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter Zhiyuan Liu Changhao Nai Yancheng Luo Hao Fei Yixin Cao Kenji Kawaguchi Xiang Wang Tat-Seng Chua 60 90 0 19 Oct 2023
GraphGPT: Graph Instruction Tuning for Large Language Models Jiabin Tang Yuhao Yang Wei Wei Lei Shi Lixin Su Suqi Cheng Dawei Yin Chao Huang 91 139 0 19 Oct 2023
Talk like a Graph: Encoding Graphs for Large Language Models Bahare Fatemi Jonathan J. Halcrow Bryan Perozzi AI4CE 62 107 0 06 Oct 2023
Improved Baselines with Visual Instruction Tuning Haotian Liu Chunyuan Li Yuheng Li Yong Jae Lee VLM MLLM 108 2,672 0 05 Oct 2023
Fragment-based Pretraining and Finetuning on Molecular Graphs Kha-Dinh Luong Ambuj Singh AI4CE 40 12 0 05 Oct 2023
One for All: Towards Training One Graph Model for All Classification Tasks Hao Liu Jiarui Feng Lecheng Kong Ningyue Liang Dacheng Tao Yixin Chen Muhan Zhang AI4CE 57 124 0 29 Sep 2023
Graph Neural Prompting with Large Language Models Yijun Tian Huan Song Zichen Wang Haozhu Wang Ziqing Hu Fang Wang Nitesh Chawla Panpan Xu AI4CE 75 47 0 27 Sep 2023
The Rise and Potential of Large Language Model Based Agents: A Survey Zhiheng Xi Wenxiang Chen Xin Guo Wei He Yiwen Ding ... Wenjuan Qin Yongyan Zheng Xipeng Qiu Xuanjing Huan Tao Gui LM&MA LM&Ro 3DV AI4CE 92 919 0 14 Sep 2023
Motif-aware Attribute Masking for Molecular Graph Pre-training Eric Inae Gang Liu Meng Jiang AI4CE 72 14 0 08 Sep 2023
GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text Peng Liu Yiming Ren Jun Tao Zhixiang Ren AI4CE 51 82 0 14 Aug 2023
Llama 2: Open Foundation and Fine-Tuned Chat Models Hugo Touvron Louis Martin Kevin R. Stone Peter Albert Amjad Almahairi ... Sharan Narang Aurelien Rodriguez Robert Stojnic Sergey Edunov Thomas Scialom AI4MH ALM 267 11,791 0 18 Jul 2023
Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models Yin Fang Xiaozhuan Liang Ningyu Zhang Kangwei Liu Rui Huang Zhuo Chen Xiaohui Fan Huajun Chen 74 84 0 13 Jun 2023
Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective Jiatong Li Yunqing Liu Wenqi Fan Xiao Wei Hui Liu Jiliang Tang Qing Li 62 93 0 11 Jun 2023
MolFM: A Multimodal Molecular Foundation Model Yi Luo Kai Yang Massimo Hong Xingyi Liu Zaiqing Nie 50 39 0 06 Jun 2023
GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning Haiteng Zhao Shengchao Liu Chang Ma Hannan Xu Jie Fu Zhihong Deng Lingpeng Kong Qi Liu 57 64 0 28 May 2023
AlpacaFarm: A Simulation Framework for Methods that Learn from Human Feedback Yann Dubois Xuechen Li Rohan Taori Tianyi Zhang Ishaan Gulrajani Jimmy Ba Carlos Guestrin Percy Liang Tatsunori B. Hashimoto ALM 108 593 0 22 May 2023
DrugChat: Towards Enabling ChatGPT-Like Capabilities on Drug Molecule Graphs Youwei Liang Ruiyi Zhang Li Zhang Pengtao Xie LM&MA GNN 50 52 0 18 May 2023
MolXPT: Wrapping Molecules with Text for Generative Pre-training Zequn Liu Wei Zhang Yingce Xia Lijun Wu Shufang Xie Tao Qin Min Zhang Tie-Yan Liu 53 75 0 18 May 2023
Evaluating Object Hallucination in Large Vision-Language Models Yifan Li Yifan Du Kun Zhou Jinpeng Wang Wayne Xin Zhao Ji-Rong Wen MLLM LRM 273 768 0 17 May 2023
MiniGPT-4: Enhancing Vision-Language Understanding with Advanced Large Language Models Deyao Zhu Jun Chen Xiaoqian Shen Xiang Li Mohamed Elhoseiny VLM MLLM 126 2,007 0 20 Apr 2023
Visual Instruction Tuning Haotian Liu Chunyuan Li Qingyang Wu Yong Jae Lee SyDa VLM MLLM 437 4,715 0 17 Apr 2023
Vision-Language Models for Vision Tasks: A Survey Jingyi Zhang Jiaxing Huang Sheng Jin Shijian Lu VLM 124 528 0 03 Apr 2023
LLaMA: Open and Efficient Foundation Language Models Hugo Touvron Thibaut Lavril Gautier Izacard Xavier Martinet Marie-Anne Lachaux ... Faisal Azhar Aurelien Rodriguez Armand Joulin Edouard Grave Guillaume Lample ALM PILM 1.3K 13,100 0 27 Feb 2023
BLIP-2: Bootstrapping Language-Image Pre-training with Frozen Image Encoders and Large Language Models Junnan Li Dongxu Li Silvio Savarese Steven C. H. Hoi VLM MLLM 401 4,527 0 30 Jan 2023
Unifying Molecular and Textual Representations via Multi-task Language Modelling Dimitrios Christofidellis Giorgio Giannone Jannis Born Ole Winther Teodoro Laino Matteo Manica AI4CE 46 87 0 29 Jan 2023
Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing Shengchao Liu Weili Nie Chengpeng Wang Jiarui Lu Zhuoran Qiao Ling Liu Jian Tang Chaowei Xiao Anima Anandkumar 57 162 0 21 Dec 2022
Galactica: A Large Language Model for Science Ross Taylor Marcin Kardas Guillem Cucurull Thomas Scialom Anthony Hartshorn Elvis Saravia Andrew Poulton Viktor Kerkez Robert Stojnic ELM ReLM 98 763 0 16 Nov 2022
GLM-130B: An Open Bilingual Pre-trained Model Aohan Zeng Xiao Liu Zhengxiao Du Zihan Wang Hanyu Lai ... Jidong Zhai Wenguang Chen Peng Zhang Yuxiao Dong Jie Tang BDL LRM 342 1,090 0 05 Oct 2022
A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language Fuchun Sun Dazhao Du Zhao-Qing Yang Yujie Zhou Jiangmeng Li Anyi Rao Haoran Sun Zhiwu Lu Ji-Rong Wen 108 112 0 12 Sep 2022
Translation between Molecules and Natural Language Carl Edwards T. Lai Kevin Ros Garrett Honke Kyunghyun Cho Heng Ji 85 164 0 25 Apr 2022
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 164 316 0 07 Oct 2021
Motif-based Graph Self-Supervised Learning for Molecular Property Prediction Zaixin Zhang Qi Liu Hao Wang Chengqiang Lu Chee-Kong Lee SSL AI4CE 78 256 0 03 Oct 2021
Fantastically Ordered Prompts and Where to Find Them: Overcoming Few-Shot Prompt Order Sensitivity Yao Lu Max Bartolo Alastair Moore Sebastian Riedel Pontus Stenetorp AILaw LRM 385 1,177 0 18 Apr 2021
Benchmarking Graph Neural Networks Vijay Prakash Dwivedi Chaitanya K. Joshi Anh Tuan Luu T. Laurent Yoshua Bengio Xavier Bresson 393 939 0 02 Mar 2020
PyTorch: An Imperative Style, High-Performance Deep Learning Library Adam Paszke Sam Gross Francisco Massa Adam Lerer James Bradbury ... Sasank Chilamkurthy Benoit Steiner Lu Fang Junjie Bai Soumith Chintala ODL 401 42,299 0 03 Dec 2019
SciBERT: A Pretrained Language Model for Scientific Text Iz Beltagy Kyle Lo Arman Cohan 120 2,957 0 26 Mar 2019
How Powerful are Graph Neural Networks? Keyulu Xu Weihua Hu J. Leskovec Stefanie Jegelka GNN 228 7,638 0 01 Oct 2018
Hierarchical Graph Representation Learning with Differentiable Pooling Rex Ying Jiaxuan You Christopher Morris Xiang Ren William L. Hamilton J. Leskovec GNN 285 2,145 0 22 Jun 2018
Neural Discrete Representation Learning Aaron van den Oord Oriol Vinyals Koray Kavukcuoglu BDL SSL OCL 210 4,989 0 02 Nov 2017
Inductive Representation Learning on Large Graphs William L. Hamilton Z. Ying J. Leskovec 466 15,218 0 07 Jun 2017
MoleculeNet: A Benchmark for Molecular Machine Learning Zhenqin Wu Bharath Ramsundar Evan N. Feinberg Joseph Gomes C. Geniesse Aneesh S. Pappu K. Leswing Vijay S. Pande OOD 326 1,826 0 02 Mar 2017
Semi-Supervised Classification with Graph Convolutional Networks Thomas Kipf Max Welling GNN SSL 591 28,999 0 09 Sep 2016