Title
A 3D-Shape Similarity-based Contrastive Approach to Molecular Representation Learning Austin O. Atsango N. Diamant Ziqing Lu Tommaso Biancalani Gabriele Scalia Kangway V Chuang 30 2 0 03 Nov 2022
Predicting Protein-Ligand Binding Affinity with Equivariant Line Graph Network Yi Yi Xu Wan Kangfei Zhao Ou-Yang Le Pei-Ying Zhao 24 1 0 27 Oct 2022
Artificial Intelligence in Material Engineering: A review on applications of AI in Material Engineering Lipichanda Goswami Manoj Deka Mohendra Roy AI4CE 37 19 0 15 Sep 2022
Grouping-matrix based Graph Pooling with Adaptive Number of Clusters Sung Moon Ko Sungjun Cho Dae-Woong Jeong Sehui Han Moontae Lee Ho Hin Lee 24 9 0 07 Sep 2022
ChemBERTa-2: Towards Chemical Foundation Models Walid Ahmad Elana Simon Seyone Chithrananda Gabriel Grand Bharath Ramsundar AI4CE 20 128 0 05 Sep 2022
TransPolymer: a Transformer-based language model for polymer property predictions Changwen Xu Yuyang Wang A. Farimani 27 86 0 03 Sep 2022
Graph neural networks for materials science and chemistry Patrick Reiser Marlen Neubert André Eberhard Luca Torresi Chen Zhou ... Houssam Metni Clint van Hoesel Henrik Schopmans T. Sommer Pascal Friederich GNN AI4CE 50 373 0 05 Aug 2022
Applying data technologies to combat AMR: current status, challenges, and opportunities on the way forward L. Chindelevitch E. Jauneikaite N. Wheeler K. Allel Bede Yaw Ansiri-Asafoakaa ... R. Stocker L. Unruh Daniel Waruingi H. Graz M. V. Dongen 30 4 0 05 Jul 2022
ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs Limei Wang Yi Liu Yu-Ching Lin Hao Liu Shuiwang Ji GNN 47 89 0 17 Jun 2022
Evaluating Self-Supervised Learning for Molecular Graph Embeddings Hanchen Wang Jean Kaddour Shengchao Liu Jian Tang Joan Lasenby Qi Liu 30 20 0 16 Jun 2022
An Empirical Study of Retrieval-enhanced Graph Neural Networks Dingmin Wang Shengchao Liu Hanchen Wang Bernardo Cuenca Grau Linfeng Song Jian Tang Song Le Qi Liu 21 0 0 01 Jun 2022
Representing Polymers as Periodic Graphs with Learned Descriptors for Accurate Polymer Property Predictions Evan R. Antoniuk Peggy Li B. Kailkhura A. Hiszpanski 27 31 0 27 May 2022
Tyger: Task-Type-Generic Active Learning for Molecular Property Prediction Kuangqi Zhou Kaixin Wang Jiashi Feng Jian Tang Tingyang Xu Xinchao Wang 29 1 0 23 May 2022
A graph representation of molecular ensembles for polymer property prediction Matteo Aldeghi Connor W. Coley AI4CE 25 43 0 17 May 2022
FP-GNN: a versatile deep learning architecture for enhanced molecular property prediction Hanxuan Cai Huimin Zhang Duancheng Zhao Jingxing Wu Ling Wang 36 123 0 08 May 2022
Self-focusing virtual screening with active design space pruning David E. Graff Matteo Aldeghi Joseph A. Morrone K. E. Jordan Edward O. Pyzer-Knapp Connor W. Coley 32 24 0 03 May 2022
Learning to Split for Automatic Bias Detection Yujia Bao Regina Barzilay 17 20 0 28 Apr 2022
MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design Yuanqi Du Tianfan Fu Jimeng Sun Shengchao Liu AI4CE 31 86 0 28 Mar 2022
CandidateDrug4Cancer: An Open Molecular Graph Learning Benchmark on Drug Discovery for Cancer Xianbin Ye Ziliang Li Fei Ma Z. Yi Pengyong Li Jun Wang Peng Gao Yixuan Qiao Guotong Xie 33 1 0 02 Mar 2022
Ligandformer: A Graph Neural Network for Predicting Compound Property with Robust Interpretation Jinjiang Guo Qi Liu Han Guo Xi Lu AI4CE 24 3 0 21 Feb 2022
Improving Molecular Contrastive Learning via Faulty Negative Mitigation and Decomposed Fragment Contrast Yuyang Wang Rishikesh Magar Chen Liang A. Farimani 46 78 0 18 Feb 2022
Learning to Discover Medicines T. Nguyen Thin Nguyen T. Tran 34 1 0 14 Feb 2022
Improving Molecular Representation Learning with Metric Learning-enhanced Optimal Transport Fang Wu Nicolas Courty Shuting Jin Stan Z. Li OOD OT 21 8 0 13 Feb 2022
Rxn Hypergraph: a Hypergraph Attention Model for Chemical Reaction Representation Mohammadamin Tavakoli Alexander Shmakov Francesco Ceccarelli Pierre Baldi GNN 39 8 0 02 Jan 2022
Graph-wise Common Latent Factor Extraction for Unsupervised Graph Representation Learning Thilini Cooray Ngai-man Cheung 27 6 0 16 Dec 2021
Genetic Algorithm for Constrained Molecular Inverse Design Yurim Lee Gydam Choi Minsug Yoon Cheongwon Kim 29 1 0 07 Dec 2021
Molecular Contrastive Learning with Chemical Element Knowledge Graph Yin Fang Qiang Zhang Haihong Yang Xiang Zhuang Shumin Deng Wen Zhang Minghai Qin Zhuo Chen Xiaohui Fan Huajun Chen 15 109 0 01 Dec 2021
AugLiChem: Data Augmentation Library of Chemical Structures for Machine Learning Rishikesh Magar Yuyang Wang Cooper Lorsung Chen Liang Hariharan Ramasubramanian Peiyuan Li A. Farimani 28 27 0 30 Nov 2021
Directional Message Passing on Molecular Graphs via Synthetic Coordinates Johannes Klicpera Chandan Yeshwanth Stephan Günnemann 42 35 0 08 Nov 2021
Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction Zhengkai Tu Connor W. Coley 30 90 0 19 Oct 2021
Relative Molecule Self-Attention Transformer Lukasz Maziarka Dawid Majchrowski Tomasz Danel Piotr Gaiñski Jacek Tabor Igor T. Podolak Pawel M. Morkisz Stanislaw Jastrzebski MedIm 40 34 0 12 Oct 2021
Ab-Initio Potential Energy Surfaces by Pairing GNNs with Neural Wave Functions Nicholas Gao Stephan Günnemann 27 36 0 11 Oct 2021
Learning 3D Representations of Molecular Chirality with Invariance to Bond Rotations Keir Adams L. Pattanaik Connor W. Coley 21 32 0 08 Oct 2021
3D Infomax improves GNNs for Molecular Property Prediction Hannes Stärk Dominique Beaini Gabriele Corso Prudencio Tossou Christian Dallago Stephan Günnemann Pietro Lió AI4CE 36 204 0 08 Oct 2021
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 126 302 0 07 Oct 2021
Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs Fang Wu Dragomir R. Radev Huabin Xing ViT 36 54 0 04 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 34 250 0 03 Oct 2021
PluGeN: Multi-Label Conditional Generation From Pre-Trained Models Maciej Wołczyk Magdalena Proszewska Lukasz Maziarka Maciej Ziȩba Patryk Wielopolski Rafał Kurczab Marek Śmieja DRL 27 5 0 18 Sep 2021
Geometric Deep Learning on Molecular Representations Kenneth Atz F. Grisoni G. Schneider AI4CE 34 287 0 26 Jul 2021
Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity Shuangli Li Jingbo Zhou Tong Xu Liang Huang Fan Wang Haoyi Xiong Weili Huang Dejing Dou Hui Xiong MLAU 27 165 0 21 Jul 2021
Quantitative Evaluation of Explainable Graph Neural Networks for Molecular Property Prediction Jiahua Rao Shuangjia Zheng Yuedong Yang 21 46 0 01 Jul 2021
Large-Scale Chemical Language Representations Capture Molecular Structure and Properties Jerret Ross Brian M. Belgodere Vijil Chenthamarakshan Inkit Padhi Youssef Mroueh Payel Das AI4CE 27 272 0 17 Jun 2021
Dual-view Molecule Pre-training Jinhua Zhu Yingce Xia Tao Qin Wen-gang Zhou Houqiang Li Tie-Yan Liu AI4CE 27 51 0 17 Jun 2021
Learning Stable Classifiers by Transferring Unstable Features Yujia Bao Shiyu Chang Regina Barzilay OOD 27 8 0 15 Jun 2021
Artificial Intelligence in Drug Discovery: Applications and Techniques Jianyuan Deng Zhibo Yang Iwao Ojima Dimitris Samaras Fusheng Wang AI4TS 35 100 0 09 Jun 2021
GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles O. Ganea L. Pattanaik Connor W. Coley Regina Barzilay K. Jensen W. Green Tommi Jaakkola AI4CE 30 135 0 08 Jun 2021
Graph2Graph Learning with Conditional Autoregressive Models Guan Wang F. Lauze Aasa Feragen CML GNN AI4CE 36 2 0 06 Jun 2021
SpreadGNN: Serverless Multi-task Federated Learning for Graph Neural Networks Chaoyang He Emir Ceyani Keshav Balasubramanian M. Annavaram Salman Avestimehr FedML 25 50 0 04 Jun 2021
Predict then Interpolate: A Simple Algorithm to Learn Stable Classifiers Yujia Bao Shiyu Chang Regina Barzilay 24 20 0 26 May 2021
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development Kexin Huang Tianfan Fu Wenhao Gao Yue Zhao Yusuf Roohani J. Leskovec Connor W. Coley Cao Xiao Jimeng Sun Marinka Zitnik OOD LM&MA 33 263 0 18 Feb 2021