MoleculeNet: A Benchmark for Molecular Machine Learning

2 March 2017

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

50 / 802 papers shown

Title
Range-aware Positional Encoding via High-order Pretraining: Theory and Practice Viet Anh Nguyen Nhat-Khang Ngô Truong Son-Hy AI4CE 27 0 0 27 Sep 2024
SciDFM: A Large Language Model with Mixture-of-Experts for Science Liangtai Sun Danyu Luo Da Ma Zihan Zhao Baocai Chen Zhennan Shen Su Zhu Lu Chen Xin Chen Kai Yu MoE 40 2 0 27 Sep 2024
On the Impact of Feature Heterophily on Link Prediction with Graph Neural Networks Jiong Zhu Gaotang Li Yao-An Yang Jing Zhu Xuehao Cui Danai Koutra 35 3 0 26 Sep 2024
Dumpling GNN: Hybrid GNN Enables Better ADC Payload Activity Prediction Based on Chemical Structure Shengjie Xu Lingxi Xie 23 0 0 23 Sep 2024
Smirk: An Atomically Complete Tokenizer for Molecular Foundation Models Alexius Wadell Anoushka Bhutani Venkatasubramanian Viswanathan 127 0 0 19 Sep 2024
Open Source Infrastructure for Automatic Cell Segmentation Aaron Rock Menezes Bharath Ramsundar SSeg VLM 31 0 0 12 Sep 2024
Efficient Training of Transformers for Molecule Property Prediction on Small-scale Datasets Shivesh Prakash 33 0 0 07 Sep 2024
Advancing Machine Learning in Industry 4.0: Benchmark Framework for Rare-event Prediction in Chemical Processes Vikram Sudarshan Warren D. Seider 54 1 0 31 Aug 2024
Cross-Modal Learning for Chemistry Property Prediction: Large Language Models Meet Graph Machine Learning Sakhinana Sagar Srinivas Venkataramana Runkana AI4CE 38 1 0 27 Aug 2024
Leveraging Chemistry Foundation Models to Facilitate Structure Focused Retrieval Augmented Generation in Multi-Agent Workflows for Catalyst and Materials Design Nathaniel H. Park Tiffany J. Callahan James L. Hedrick Tim Erdmann Sara Capponi AI4CE 33 1 0 21 Aug 2024
Molecular Graph Representation Learning Integrating Large Language Models with Domain-specific Small Models Tianyu Zhang Yuxiang Ren Chengbin Hou Hairong Lv Xuegong Zhang AI4CE 34 1 0 19 Aug 2024
Advancements in Molecular Property Prediction: A Survey of Single and Multimodal Approaches Tanya Liyaqat T. Ahmad Chandni Saxena 32 2 0 18 Aug 2024
Graph Classification with GNNs: Optimisation, Representation and Inductive Bias P. Krishna Kumar a H. G. Ramaswamy 29 0 0 17 Aug 2024
Drug Discovery SMILES-to-Pharmacokinetics Diffusion Models with Deep Molecular Understanding Bing Hu Anita Layton Helen Chen MedIm 38 2 0 14 Aug 2024
Sampling Foundational Transformer: A Theoretical Perspective Viet Anh Nguyen Minh Lenhat Khoa Nguyen Duong Duc Hieu Dao Huu Hung Truong Son-Hy 44 0 0 11 Aug 2024
DIVE: Subgraph Disagreement for Graph Out-of-Distribution Generalization Xin Sun Liang Wang Qiang Liu Shu Wu Zilei Wang Liang Wang OOD CML 38 5 0 08 Aug 2024
Question Rephrasing for Quantifying Uncertainty in Large Language Models: Applications in Molecular Chemistry Tasks Zizhang Chen Pengyu Hong Sandeep Madireddy 32 1 0 07 Aug 2024
Invariant Graph Learning Meets Information Bottleneck for Out-of-Distribution Generalization Wenyu Mao Jiancan Wu Haoyang Liu Yongduo Sui Xiang Wang OOD 39 2 0 03 Aug 2024
UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation Jiayuan Zhu Yunli Qi Yongqiang Chen Quanming Yao 29 7 0 01 Aug 2024
Non-convolutional Graph Neural Networks Yuanqing Wang N. Scherer-Negenborn GNN 35 3 0 31 Jul 2024
Quantum Long Short-Term Memory for Drug Discovery Liang Zhang Yin Xu Mohan Wu Liang Wang Hua Xu VLM 23 2 0 29 Jul 2024
Small Molecule Optimization with Large Language Models Philipp Guevorguian Menua Bedrosian Tigran Fahradyan Gayane Chilingaryan Hrant Khachatrian Armen Aghajanyan 40 1 0 26 Jul 2024
A Large Encoder-Decoder Family of Foundation Models For Chemical Language Eduardo Soares Victor Shirasuna E. V. Brazil Renato F. G. Cerqueira Dmitry Zubarev Kristin Schmidt AI4CE 29 7 0 24 Jul 2024
Diff4VS: HIV-inhibiting Molecules Generation with Classifier Guidance Diffusion for Virtual Screening Jiaqing Lyu Changjie Chen Bing Liang Yijia Zhang 39 0 0 20 Jul 2024
Questionable practices in machine learning Gavin Leech Juan J. Vazquez Misha Yagudin Niclas Kupper Laurence Aitchison 53 4 0 17 Jul 2024
Molecular Topological Profile (MOLTOP) -- Simple and Strong Baseline for Molecular Graph Classification Jakub Adamczyk Wojciech Czech 42 2 0 16 Jul 2024
Improving Graph Out-of-distribution Generalization on Real-world Data Can Xu Yao Cheng Jianxiang Yu Haosen Wang Jingsong Lv Xiang Li OOD 36 0 0 14 Jul 2024
Empowering Graph Invariance Learning with Deep Spurious Infomax Tianjun Yao Yongqiang Chen Zhenhao Chen Kai Hu Zhiqiang Shen Anton van den Hengel OOD 45 6 0 13 Jul 2024
Any-Property-Conditional Molecule Generation with Self-Criticism using Spanning Trees Alexia Jolicoeur-Martineau A. Baratin Kisoo Kwon Boris Knyazev Yan Zhang 40 1 0 12 Jul 2024
MolTRES: Improving Chemical Language Representation Learning for Molecular Property Prediction Jun-Hyung Park Yeachan Kim Mingyu Lee Hyuntae Park SangKeun Lee 40 0 0 09 Jul 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 45 1 0 03 Jul 2024
Knowledge-Aware Parsimony Learning: A Perspective from Relational Graphs Quanming Yao Yongqi Zhang Yaqing Wang Nan Yin James Kwok Qiang Yang 31 0 0 29 Jun 2024
Improving the Expressiveness of $K$ -hop Message-Passing GNNs by Injecting Contextualized Substructure Information Tianjun Yao Yiongxu Wang Kun Zhang Shangsong Liang 38 11 0 27 Jun 2024
MolFusion: Multimodal Fusion Learning for Molecular Representations via Multi-granularity Views Muzhen Cai Sendong Zhao Haochun Wang Yanrui Du Zewen Qiang Bing Qin Ting Liu 37 0 0 26 Jun 2024
Enabling Regional Explainability by Automatic and Model-agnostic Rule Extraction Yu Chen Tianyu Cui Alexander Capstick Nan Fletcher-Loyd Payam Barnaghi 38 0 0 25 Jun 2024
Generative Modelling of Structurally Constrained Graphs Manuel Madeira Clément Vignac D. Thanou Pascal Frossard DiffM 53 0 0 25 Jun 2024
Uni-Mol2: Exploring Molecular Pretraining Model at Scale Xiaohong Ji Zhen Wang Zhifeng Gao Hang Zheng Linfeng Zhang Guolin Ke Weinan E AI4CE 48 6 0 21 Jun 2024
Unifying Unsupervised Graph-Level Anomaly Detection and Out-of-Distribution Detection: A Benchmark Yili Wang Yixin Liu Xu Shen Chenyu Li Kaize Ding Rui Miao Ying Wang Shirui Pan Xin Wang 42 8 0 21 Jun 2024
HIGHT: Hierarchical Graph Tokenization for Graph-Language Alignment Yongqiang Chen Quanming Yao Juzheng Zhang James Cheng Yatao Bian 35 4 0 20 Jun 2024
Younger: The First Dataset for Artificial Intelligence-Generated Neural Network Architecture Zhengxin Yang Wanling Gao Luzhou Peng Yunyou Huang Fei Tang Jianfeng Zhan 33 0 0 20 Jun 2024
Efficient Sharpness-Aware Minimization for Molecular Graph Transformer Models Yili Wang Kaixiong Zhou Ninghao Liu Ying Wang Xin Wang 43 10 0 19 Jun 2024
MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction Yuyan Liu Sirui Ding Sheng Zhou Wenqi Fan Qiaoyu Tan 42 7 0 18 Jun 2024
A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery Yu Zhang Xiusi Chen Bowen Jin Sheng Wang Shuiwang Ji Wei Wang Jiawei Han 44 27 0 16 Jun 2024
A Unified Graph Selective Prompt Learning for Graph Neural Networks Bo Jiang Hao Wu Ziyan Zhang Beibei Wang Jin Tang 44 1 0 15 Jun 2024
Automated Molecular Concept Generation and Labeling with Large Language Models Shichang Zhang Botao Xia Zimin Zhang Qianli Wu Fang Sun Ziniu Hu Yizhou Sun 43 0 0 13 Jun 2024
SciKnowEval: Evaluating Multi-level Scientific Knowledge of Large Language Models Kehua Feng Keyan Ding Weijie Wang Xiang Zhuang Zeyuan Wang Ming Qin Yu Zhao Jianhua Yao Qiang Zhang H. Chen ELM 45 6 0 13 Jun 2024
A Comprehensive Graph Pooling Benchmark: Effectiveness, Robustness and Generalizability Pengyun Wang Junyu Luo Yanxin Shen Siyu Heng Xiao Luo 49 1 0 13 Jun 2024
SIU: A Million-Scale Structural Small Molecule-Protein Interaction Dataset for Unbiased Bioactivity Prediction Yanwen Huang Bowen Gao Yinjun Jia Hongbo Ma Wei-Ying Ma Ya-Qin Zhang Yanyan Lan 23 0 0 13 Jun 2024
MoleculeCLA: Rethinking Molecular Benchmark via Computational Ligand-Target Binding Analysis Shikun Feng Jiaxin Zheng Yinjun Jia Yanwen Huang Fengfeng Zhou Wei-Ying Ma Yanyan Lan 34 0 0 13 Jun 2024
Expressivity and Generalization: Fragment-Biases for Molecular GNNs Tom Wollschlager Niklas Kemper Leon Hetzel Johanna Sommer Stephan Günnemann 48 4 0 12 Jun 2024