Papers citing 'Molecular Graph Convolutions: Moving Beyond Fingerprints'

Title
Learning Cell-Aware Hierarchical Multi-Modal Representations for Robust Molecular Modeling Mengran Li Z. Zang Wenbin Xing Junzhou Chen Ronghui Zhang Jiebo Luo Stan Z. Li AI4CE 270 0 0 26 Nov 2025
GraphCliff: Short-Long Range Gating for Subtle Differences but Critical Changes Hajung Kim Jueon Park Junseok Choe Sheunheun Baek Hyeon Hwang Jaewoo Kang 172 0 0 05 Nov 2025
If You Want to Be Robust, Be Wary of InitializationNeural Information Processing Systems (NeurIPS), 2025 Sofiane Ennadir J. Lutzeyer Michalis Vazirgiannis El Houcine Bergou AAML 112 4 0 26 Oct 2025
Enhancing Graph Classification Robustness with Singular Pooling Sofiane Ennadir Oleg Smirnov Yassine Abbahaddou Lele Cao J. Lutzeyer AAML 100 0 0 26 Oct 2025
Robustness Verification of Graph Neural Networks Via Lightweight Satisfiability Testing Chia-Hsuan Lu Tony Tan Michael Benedikt AAML OOD 96 1 0 21 Oct 2025
Symmetry and Generalisation in Neural Approximations of Renormalisation Transformations Cassidy Ashworth Pietro Lio Francesco Caso AI4CE 96 0 0 18 Oct 2025
Reasoning-Enhanced Large Language Models for Molecular Property Prediction Jiaxi Zhuang Yaorui Shi Jue Hou Yunong He Mingwei Ye ... Linfeng Zhang Linfeng Zhang Linfeng Zhang Guolin Ke Hengxing Cai LRM 152 2 0 11 Oct 2025
When Does Global Attention Help? A Unified Empirical Study on Atomistic Graph Learning Arindam Chowdhury Massimiliano Lupo Pasini 97 0 0 07 Oct 2025
Geometric Multi-color Message Passing Graph Neural Networks for Blood-brain Barrier Permeability Prediction T. Nguyen M. Rana Farjana Tasnim Mukta Chang-Guo Zhan D. Nguyen 249 0 0 25 Jul 2025
Leveraging Partial SMILES Validation Scheme for Enhanced Drug Design in Reinforcement Learning Frameworks Xinyu Wang Jinbo Bi Minghu Song CLL 284 1 0 01 May 2025
Large language models as uncertainty-calibrated optimizers for experimental discovery Bojana Ranković Ryan-Rhys Griffiths P. Schwaller BDL 1.0K 3 0 08 Apr 2025
NaFM: Pre-training a Foundation Model for Small-Molecule Natural Products Yuheng Ding Bo Qiang Yiran Zhou Jie Yu Qi Li Liangren Zhang Yusong Wang Zhenmin Liu 997 0 0 22 Mar 2025
Curvature Corrected Nonnegative Manifold Data Factorization Joyce A. Chew Willem Diepeveen Deanna Needell 165 1 0 24 Feb 2025
Survey on Recent Progress of AI for Chemistry: Methods, Applications, and Opportunities Ding Hu Pengxiang Hua Zhen Huang 526 2 0 09 Feb 2025
Hier-EgoPack: Hierarchical Egocentric Video Understanding with Diverse Task PerspectivesIEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), 2025 Simone Alberto Peirone Francesca Pistilli A. Alliegro Tatiana Tommasi Giuseppe Averta 95 3 0 04 Feb 2025
Generative quantum combinatorial optimization by means of a novel conditional generative quantum eigensolverDigital Discovery (DD), 2025 Shunya Minami Kouhei Nakaji Yohichi Suzuki Alán Aspuru-Guzik Tadashi Kadowaki AI4CE 162 10 0 28 Jan 2025
A Hybrid Supervised and Self-Supervised Graph Neural Network for Edge-Centric ApplicationsIEEE Transactions on Signal and Information Processing over Networks (TSIPN), 2025 Eugenio Borzone Leandro Di Persia Matias Gerard SSL 244 1 0 21 Jan 2025
Pre-training Graph Neural Networks on Molecules by Using Subgraph-Conditioned Graph Information BottleneckAAAI Conference on Artificial Intelligence (AAAI), 2024 Van Thuy Hoang O-Joun Lee AI4CE 257 8 0 20 Dec 2024
Globally Correlation-Aware Hard Negative GenerationInternational Journal of Computer Vision (IJCV), 2024 Wenjie Peng Hongxiang Huang Tianshui Chen Quhui Ke Gang Dai Shuangping Huang 318 6 0 20 Nov 2024
DiVR: incorporating context from diverse VR scenes for human trajectory prediction Franz Franco Gallo Hui-Yin Wu L. Sassatelli 193 3 0 13 Nov 2024
Contextual Representation Anchor Network to Alleviate Selection Bias in Few-Shot Drug Discovery Yao Yang Wei Liu Xiangxin Zhou Mingqian Li Qiang Zhang Hongyang Chen Xuemin Lin 214 1 0 28 Oct 2024
Congestion Forecast for Trains with Railroad-Graph-based Semi-Supervised Learning using Sparse Passenger Reports Soto Anno Kota Tsubouchi Masamichi Shimosaka AI4TS 60 0 0 23 Oct 2024
GraphCroc: Cross-Correlation Autoencoder for Graph Structural ReconstructionNeural Information Processing Systems (NeurIPS), 2024 Shijin Duan Ruyi Ding Jiaxing He A. A. Ding Yunsi Fei Xiaolin Xu 144 0 0 04 Oct 2024
When Molecular GAN Meets Byte-Pair EncodingInternational Conference on Advanced Data Mining and Applications (ADMA), 2024 Huidong Tang Chen Li Yasuhiko Morimoto 172 0 0 29 Sep 2024
Dumpling GNN: Hybrid GNN Enables Better ADC Payload Activity Prediction Based on Chemical Structure Shengjie Xu Lingxi Xie 107 1 0 23 Sep 2024
A Generative Framework for Predictive Modeling of Multiple Chronic Conditions Using Graph Variational Autoencoder and Bandit-Optimized Graph Neural NetworkIEEE journal of biomedical and health informatics (IEEE JBHI), 2024 Julian Carvajal Rico A. Alaeddini Syed Hasib Akhter Faruqui S. Fisher-Hoch J. McCormick 473 1 0 20 Sep 2024
Unlocking Potential Binders: Multimodal Pretraining DEL-Fusion for Denoising DNA-Encoded Libraries Chunbin Gu Mutian He Hanqun Cao Guangyong Chen Chang-Yu Hsieh Ge Liu AI4CE 207 2 0 07 Sep 2024
Reactzyme: A Benchmark for Enzyme-Reaction PredictionNeural Information Processing Systems (NeurIPS), 2024 Chenqing Hua Bozitao Zhong Sitao Luan Liang Hong Guy Wolf Doina Precup Shuangjia Zheng 190 12 0 24 Aug 2024
4D Diffusion for Dynamic Protein Structure Prediction with Reference Guided Motion Alignment Kaihui Cheng Ce Liu Qingkun Su Jun Wang Liwei Zhang Yining Tang Yao Yao Siyu Zhu Yuan Qi DiffM 147 0 0 22 Aug 2024
LipidBERT: A Lipid Language Model Pre-trained on METiS de novo Lipid Library Tianhao Yu Cai Yao Zhuorui Sun Feng Shi Lin Zhang ... Xicheng Zhang Jiali Zou Wenshou Wang C. Lai Kai Wang 113 5 0 12 Aug 2024
Molecular Topological Profile (MOLTOP) -- Simple and Strong Baseline for Molecular Graph Classification Jakub Adamczyk Wojciech Czech 231 5 0 16 Jul 2024
RetroGFN: Diverse and Feasible Retrosynthesis using GFlowNets Piotr Gaiñski Michał Koziarski Krzysztof Maziarz Marwin H. S. Segler Jacek Tabor Marek Śmieja 292 9 0 26 Jun 2024
Bayesian neural networks for predicting uncertainty in full-field material response G. Pasparakis Lori Graham-Brady Michael D. Shields AI4CE 216 13 0 21 Jun 2024
Efficient Sharpness-Aware Minimization for Molecular Graph Transformer ModelsInternational Conference on Learning Representations (ICLR), 2024 Yili Wang Kaixiong Zhou Ninghao Liu Ying Wang Xin Wang 146 12 0 19 Jun 2024
Enhancing Size Generalization in Graph Neural Networks through Disentangled Representation LearningInternational Conference on Machine Learning (ICML), 2024 Zheng Huang Qihui Yang Dawei Zhou Yujun Yan AI4CE 311 8 0 07 Jun 2024
GATE: How to Keep Out Intrusive Neighbors Nimrah Mustafa R. Burkholz 372 2 0 01 Jun 2024
LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework Yiran Qiao Xiang Ao Yang Liu Jiarong Xu Xiaoqian Sun Qing He 203 9 0 22 May 2024
Contrastive Dual-Interaction Graph Neural Network for Molecular Property PredictionIEEE journal of biomedical and health informatics (IEEE JBHI), 2024 Zexing Zhao Guangsi Shi Xiaopeng Wu Ruohua Ren Xiaojun Gao Fuyi Li 123 3 0 04 May 2024
4DBInfer: A 4D Benchmarking Toolbox for Graph-Centric Predictive Modeling on Relational DBs Minjie Wang Quan Gan David Wipf Zhenkun Cai Ning Li ... Chuan Lei Mu-Nan Zhang Weinan Zhang Christos Faloutsos Zheng Zhang 169 5 0 28 Apr 2024
Bounding the Expected Robustness of Graph Neural Networks Subject to Node Feature Attacks Yassine Abbahaddou Sofiane Ennadir J. Lutzeyer Michalis Vazirgiannis Henrik Bostrom AAML OOD 186 13 0 27 Apr 2024
SPGNN: Recognizing Salient Subgraph Patterns via Enhanced Graph Convolution and Pooling Zehao Dong Muhan Zhang Yixin Chen 154 0 0 21 Apr 2024
Transformers for molecular property prediction: Lessons learned from the past five years Afnan Sultan Jochen Sieg M. Mathea Andrea Volkamer AI4CE 141 20 0 05 Apr 2024
BloomGML: Graph Machine Learning through the Lens of Bilevel OptimizationInternational Conference on Artificial Intelligence and Statistics (AISTATS), 2024 Amber Yijia Zheng Tong He Yixuan Qiu Minjie Wang David Wipf 236 2 0 07 Mar 2024
GNN-VPA: A Variance-Preserving Aggregation Strategy for Graph Neural Networks Lisa Schneckenreiter Richard Freinschlag Florian Sestak Johannes Brandstetter Günter Klambauer Andreas Mayr 204 6 0 07 Mar 2024
Almost Surely Asymptotically Constant Graph Neural Networks Sam Adam-Day Michael Benedikt .Ismail .Ilkan Ceylan Ben Finkelshtein GNN 242 6 0 06 Mar 2024
A Backpack Full of Skills: Egocentric Video Understanding with Diverse Task Perspectives Simone Alberto Peirone Francesca Pistilli A. Alliegro Giuseppe Averta EgoV 282 8 0 05 Mar 2024
Teaching MLP More Graph Information: A Three-stage Multitask Knowledge Distillation Framework Junxian Li Bin Shi Erfei Cui Hua Wei Qinghua Zheng 226 1 0 02 Mar 2024
Graph Diffusion Policy Optimization Yijing Liu Chao Du Tianyu Pang Chongxuan Li Wei Chen Min Lin 188 14 0 26 Feb 2024
Pretraining Strategy for Neural Potentials Zehua Zhang Zijie Li A. Farimani AI4CE 244 0 0 24 Feb 2024
Overcoming Pitfalls in Graph Contrastive Learning Evaluation: Toward Comprehensive Benchmarks Qian Ma Hongliang Chi Hengrui Zhang Kay Liu Zhiwei Zhang Lu Cheng Suhang Wang Philip S. Yu Yao Ma 160 3 0 24 Feb 2024