Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs

4 October 2021

Papers citing "Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs"

24 / 24 papers shown

Title
Addressing Model Overcomplexity in Drug-Drug Interaction Prediction With Molecular Fingerprints Manel Gil-Sorribes Alexis Molina 39 0 0 30 Mar 2025
MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model Sumin Ha Jun Hyeong Kim Yinhua Piao Sun Kim 44 0 0 23 Feb 2025
Revisiting Self-Supervised Heterogeneous Graph Learning from Spectral Clustering Perspective Yujie Mo Zhihe Lu Runpeng Yu Xiaofeng Zhu Xinchao Wang 79 1 0 01 Dec 2024
FARM: Functional Group-Aware Representations for Small Molecules Thao Nguyen Kuan-Hao Huang Ge Liu Martin Burke Ying Diao Heng Ji 20 0 0 02 Oct 2024
Molecular Graph Representation Learning via Structural Similarity Information Chengyu Yao Hong Huang Hang Gao Fengge Wu Haiming Chen Junsuo Zhao 26 0 0 13 Sep 2024
Question Rephrasing for Quantifying Uncertainty in Large Language Models: Applications in Molecular Chemistry Tasks Zizhang Chen Pengyu Hong Sandeep Madireddy 22 1 0 07 Aug 2024
Large language models, physics-based modeling, experimental measurements: the trinity of data-scarce learning of polymer properties Ning Liu S. Jafarzadeh B. Lattimer Shuna Ni Jim Lua Yue Yu AI4CE 40 1 0 03 Jul 2024
Towards DNA-Encoded Library Generation with GFlowNets Michal Koziarski Mohammed Abukalam Vedant Shah Louis Vaillancourt Doris Alexandra Schuetz Moksh Jain A. V. D. Sloot Mathieu Bourgey A. Marinier Yoshua Bengio 29 4 0 15 Apr 2024
Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey Taojie Kuang Pengfei Liu Zhixiang Ren AI4CE 47 1 0 11 Feb 2024
From Words to Molecules: A Survey of Large Language Models in Chemistry Chang Liao Yemin Yu Yu Mei Ying Wei 25 16 0 02 Feb 2024
Harnessing the Power of Neural Operators with Automatically Encoded Conservation Laws Ning Liu Yiming Fan Xianyi Zeng Milan Klöwer Lu Zhang Yue Yu AI4CE 24 8 0 18 Dec 2023
Neural Atoms: Propagating Long-range Interaction in Molecular Graphs through Efficient Communication Channel Xuan Li Zhanke Zhou Jiangchao Yao Yu Rong Lu Zhang Bo Han 31 3 0 02 Nov 2023
A Hierarchical Training Paradigm for Antibody Structure-sequence Co-design Fang Wu Stan Z. Li 27 17 0 30 Oct 2023
Atom-Motif Contrastive Transformer for Molecular Property Prediction Wentao Yu Shuo Chen Chen Gong Gang Niu Masashi Sugiyama ViT 37 2 0 11 Oct 2023
Transformers and Large Language Models for Chemistry and Drug Discovery Andres M Bran Philippe Schwaller LM&MA MedIm AI4CE 32 14 0 09 Oct 2023
Hierarchical Grammar-Induced Geometry for Data-Efficient Molecular Property Prediction Minghao Guo Veronika Thost Samuel W Song A. Balachandran Payel Das Jie Chen Wojciech Matusik AI4CE 18 0 0 04 Sep 2023
CTAGE: Curvature-Based Topology-Aware Graph Embedding for Learning Molecular Representations Yili Chen Zhengyu Li Zheng Wan Hui Yu Xian Wei 21 0 0 25 Jul 2023
Atomic and Subgraph-aware Bilateral Aggregation for Molecular Representation Learning Jiahao Chen Yurou Liu Jiangmeng Li Bing-Huang Su Jirong Wen 23 0 0 22 May 2023
InstructBio: A Large-scale Semi-supervised Learning Paradigm for Biochemical Problems Fang Wu Huiling Qin Siyuan Li Stan Z. Li Xianyuan Zhan Jinbo Xu 21 5 0 08 Apr 2023
Rethinking Explaining Graph Neural Networks via Non-parametric Subgraph Matching Fang Wu Siyuan Li Xurui Jin Yinghui Jiang Dragomir R. Radev Z. Niu Stan Z. Li 24 10 0 07 Jan 2023
Integration of Pre-trained Protein Language Models into Geometric Deep Learning Networks Fang Wu Yujun Tao Dragomir R. Radev Jinbo Xu Stan Z. Li AI4CE 27 32 0 07 Dec 2022
Reducing Down(stream)time: Pretraining Molecular GNNs using Heterogeneous AI Accelerators Jenna A. Bilbrey Kristina M Herman Henry W Sprueill Soritis S. Xantheas Payel Das Manuel Lopez Roldan Mike Kraus Hatem Helal Sutanay Choudhury AI4CE 21 4 0 08 Nov 2022
Relative Molecule Self-Attention Transformer Lukasz Maziarka Dawid Majchrowski Tomasz Danel Piotr Gaiñski Jacek Tabor Igor T. Podolak Pawel M. Morkisz Stanislaw Jastrzebski MedIm 34 34 0 12 Oct 2021
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 172 1,775 0 02 Mar 2017