MoleculeNet: A Benchmark for Molecular Machine Learning

2 March 2017

Papers citing "MoleculeNet: A Benchmark for Molecular Machine Learning"

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Title
Uniform Loss vs. Specialized Optimization: A Comparative Analysis in Multi-Task Learning Gabriel S. Gama Valdir Grassi Jr MoMe 40 0 0 15 May 2025
Schreier-Coset Graph Propagation Aryan Mishra Lizhen Lin 30 0 0 15 May 2025
Multi-Modal Molecular Representation Learning via Structure Awareness Rong Yin Ruyue Liu Xiaoshuai Hao Xingrui Zhou Y. Liu Can Ma Weiping Wang 29 0 0 09 May 2025
PyTDC: A multimodal machine learning training, evaluation, and inference platform for biomedical foundation models Alejandro Velez-Arce Marinka Zitnik 24 0 0 08 May 2025
Vision Graph Prompting via Semantic Low-Rank Decomposition Zixiang Ai Zichen Liu Jiahuan Zhou 48 0 0 07 May 2025
RISE: Radius of Influence based Subgraph Extraction for 3D Molecular Graph Explanation J. Qu Wenhan Gao Jiaxing Zhang Xufeng Liu Hua Wei Haibin Ling Y. Liu AI4CE 50 0 0 04 May 2025
From GNNs to Trees: Multi-Granular Interpretability for Graph Neural Networks Jie Yang Yuwen Wang Kaixuan Chen Tongya Zheng Yihe Zhou Zhenbang Xiao Ji Cao Mingli Song S. Liu AI4CE 44 1 0 01 May 2025
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks Xinyu Wang Jinbo Bi Minghu Song CLL 62 0 0 01 May 2025
Evaluating Effects of Augmented SELFIES for Molecular Understanding Using QK-LSTM Collin Beaudoin Swaroop Ghosh 33 0 0 29 Apr 2025
Learning Hierarchical Interaction for Accurate Molecular Property Prediction Huiyang Hong Xinkai Wu Hongyu Sun Chaoyang Xie Qi Wang Y. Li 31 0 0 28 Apr 2025
polyGen: A Learning Framework for Atomic-level Polymer Structure Generation Ayush Jain Rampi Ramprasad 40 0 0 24 Apr 2025
Unified Molecule Generation and Property Prediction Adam Izdebski Jan Olszewski Pankhil Gawade Krzysztof Koras Serra Korkmaz Valentin Rauscher Jakub M. Tomczak E. Szczurek 31 0 0 23 Apr 2025
Rethinking the generalization of drug target affinity prediction algorithms via similarity aware evaluation Chenbin Zhang Zhiqiang Hu Chuchu Jiang Wen Chen Jie Xu S. Zhang 19 0 0 13 Apr 2025
DMol: A Schedule-Driven Diffusion Model for Highly Efficient and Versatile Molecule Generation Peizhi Niu Yu-Hsiang Wang Vishal Rana Chetan Rupakheti Abhishek Pandey O. Milenkovic 28 0 0 08 Apr 2025
Improving Counterfactual Truthfulness for Molecular Property Prediction through Uncertainty Quantification Jonas Teufel Annika Leinweber Pascal Friederich 44 0 0 03 Apr 2025
Inductive Graph Representation Learning with Quantum Graph Neural Networks Arthur M. Faria Ignacio F. Graña Savvas Varsamopoulos GNN 62 0 0 31 Mar 2025
LGIN: Defining an Approximately Powerful Hyperbolic GNN Srinitish Srinivasan Omkumar CU AI4CE 43 0 0 31 Mar 2025
MolGround: A Benchmark for Molecular Grounding Jiaxin Wu Ting Zhang Rubing Chen Wengyu Zhang Chen Jason Zhang Xiaoyong Wei Li Qing 46 0 0 31 Mar 2025
Critical Iterative Denoising: A Discrete Generative Model Applied to Graphs Yoann Boget Alexandros Kalousis DiffM 58 0 0 27 Mar 2025
Improving Equivariant Networks with Probabilistic Symmetry Breaking Hannah Lawrence Vasco Portilheiro Yan Zhang Sékou-Oumar Kaba 40 3 0 27 Mar 2025
AugWard: Augmentation-Aware Representation Learning for Accurate Graph Classification Minjun Kim Jaehyeon Choi SeungJoo Lee Jinhong Jung U. Kang OOD GNN 57 1 0 27 Mar 2025
Graph neural networks extrapolate out-of-distribution for shortest paths Robert Nerem Samantha Chen Sanjoy Dasgupta Yusu Wang 42 0 0 24 Mar 2025
Chem42: a Family of chemical Language Models for Target-aware Ligand Generation A. Singh Engin Tekin Maryam Nadeem Nancy A. ElNaker Mohammad Amaan Sayeed Natalia Vassilieva Boulbaba Ben Amor 45 1 0 20 Mar 2025
On Local Posterior Structure in Deep Ensembles Mikkel Jordahn Jonas Vestergaard Jensen Mikkel N. Schmidt Michael Riis Andersen UQCV BDL OOD 51 0 0 17 Mar 2025
Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling Shuqi Lu Xiaohong Ji Bohang Zhang Lin Yao Siyuan Liu Zhifeng Gao Linfeng Zhang Guolin Ke AI4CE 46 1 0 13 Mar 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 50 6 0 12 Mar 2025
Backdoor Attacks on Discrete Graph Diffusion Models Jiawen Wang Samin Karim Yuan Hong Binghui Wang DiffM 65 0 0 08 Mar 2025
A Generalist Cross-Domain Molecular Learning Framework for Structure-Based Drug Discovery Yiheng Zhu Mingyang Li Junlong Liu Kun Fu J. Wu Q. Li Mingze Yin Jieping Ye Jian Wu Z. Wang 60 0 0 06 Mar 2025
Bridging Molecular Graphs and Large Language Models Runze Wang Mingqi Yang Yanming Shen 62 0 0 05 Mar 2025
All-atom Diffusion Transformers: Unified generative modelling of molecules and materials Chaitanya K. Joshi Xiang Fu Yi-Lun Liao Vahe Gharakhanyan Benjamin Kurt Miller Anuroop Sriram Zachary W. Ulissi DiffM 53 4 0 05 Mar 2025
GRAIN: Exact Graph Reconstruction from Gradients Maria Drencheva Ivo Petrov Maximilian Baader Dimitar I. Dimitrov Martin Vechev FedML 44 0 0 03 Mar 2025
LLM-Fusion: A Novel Multimodal Fusion Model for Accelerated Material Discovery Onur Boyar Indra Priyadarsini Seiji Takeda Lisa Hamada 42 0 0 02 Mar 2025
Edge Prompt Tuning for Graph Neural Networks Xingbo Fu Yinhan He Jundong Li 48 1 0 02 Mar 2025
GraphBridge: Towards Arbitrary Transfer Learning in GNNs Li Ju Xingyi Yang Qi Li Xinchao Wang 42 0 0 26 Feb 2025
Broadening Discovery through Structural Models: Multimodal Combination of Local and Structural Properties for Predicting Chemical Features Nikolai Rekut Alexey Orlov Klea Ziu Elizaveta Starykh Martin Takáč Aleksandr Beznosikov 54 0 0 25 Feb 2025
A Survey of Graph Transformers: Architectures, Theories and Applications Chaohao Yuan Kangfei Zhao Ercan Engin Kuruoglu Liang Wang Tingyang Xu Wenbing Huang Deli Zhao Hong Cheng Yu Rong 51 4 0 23 Feb 2025
RAG-Enhanced Collaborative LLM Agents for Drug Discovery Namkyeong Lee Edward De Brouwer Ehsan Hajiramezanali Tommaso Biancalani Chanyoung Park Gabriele Scalia 36 0 0 22 Feb 2025
Position: Graph Learning Will Lose Relevance Due To Poor Benchmarks Maya Bechler-Speicher Ben Finkelshtein Fabrizio Frasca Luis Muller Jan Tonshoff ... Michael M. Bronstein Mathias Niepert Bryan Perozzi Mikhail Galkin Christopher Morris OOD 97 2 0 21 Feb 2025
AI-Driven Discovery of High Performance Polymer Electrodes for Next-Generation Batteries Subhash V.S. Ganti Lukas Woelfel Christopher Kuenneth 49 0 0 20 Feb 2025
NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation Zhiyuan Liu Yanchen Luo Han Huang Enzhi Zhang Sihang Li Junfeng Fang Yaorui Shi X. Wang Kenji Kawaguchi Tat-Seng Chua 100 3 0 18 Feb 2025
From Abstract to Actionable: Pairwise Shapley Values for Explainable AI Jiaxin Xu Hung Chau Angela Burden TDI 50 0 0 18 Feb 2025
Locally-Deployed Chain-of-Thought (CoT) Reasoning Model in Chemical Engineering: Starting from 30 Experimental Data Tianhang Zhou Yingchun Niu Xingying Lan Chunming Xu LRM 39 0 0 17 Feb 2025
CL-MFAP: A Contrastive Learning-Based Multimodal Foundation Model for Molecular Property Prediction and Antibiotic Screening Gen Zhou Sugitha Janarthanan Yutong Lu Pingzhao Hu 35 0 0 16 Feb 2025
Generative Risk Minimization for Out-of-Distribution Generalization on Graphs Song Wang Zhen Tan Yaochen Zhu Chuxu Zhang Jundong Li OOD 96 0 0 11 Feb 2025
Graph Pseudotime Analysis and Neural Stochastic Differential Equations for Analyzing Retinal Degeneration Dynamics and Beyond Dai Shi Kuan Yan Lequan Lin Yue Zeng Ting Zhang D. Matsypura Mark C. Gillies Ling Zhu Junbin Gao 44 1 0 10 Feb 2025
Survey on Recent Progress of AI for Chemistry: Methods, Applications, and Opportunities Ding Hu Pengxiang Hua Zhen Huang 77 0 0 09 Feb 2025
No Metric to Rule Them All: Toward Principled Evaluations of Graph-Learning Datasets Corinna Coupette Jeremy Wayland Emily Simons Bastian Alexander Rieck 76 1 0 04 Feb 2025
GraphMinNet: Learning Dependencies in Graphs with Light Complexity Minimal Architecture Md. Atik Ahamed Andrew Cheng Q. Ye Q. Cheng GNN 53 0 0 01 Feb 2025
FIT-GNN: Faster Inference Time for GNNs Using Coarsening Shubhajit Roy Hrriday Ruparel Kishan Ved Anirban Dasgupta GNN AI4CE 62 0 0 28 Jan 2025
KAA: Kolmogorov-Arnold Attention for Enhancing Attentive Graph Neural Networks Taoran Fang Tianhong Gao Chunping Wang Yihao Shang Wei Chow Lei Chen Yang Yang 46 1 0 23 Jan 2025