Evaluating Self-Supervised Learning for Molecular Graph Embeddings

Evaluating Self-Supervised Learning for Molecular Graph Embeddings

16 June 2022

Jian Tang

Qi Liu

Papers citing "Evaluating Self-Supervised Learning for Molecular Graph Embeddings"

18 / 18 papers shown

Title
Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction Sepideh Maleki Jan-Christian Huetter Kangway V Chuang Gabriele Scalia Tommaso Biancalani Tommaso Biancalani AI4CE 85 2 0 18 Dec 2024
Range-aware Positional Encoding via High-order Pretraining: Theory and Practice Viet Anh Nguyen Nhat-Khang Ngô Truong Son-Hy AI4CE 19 0 0 27 Sep 2024
Learning Molecular Representation in a Cell Gang Liu Srijit Seal John Arevalo Zhenwen Liang Anne E Carpenter Meng-Long Jiang Shantanu Singh 24 2 0 17 Jun 2024
Progress and Opportunities of Foundation Models in Bioinformatics Qing Li Zhihang Hu Yixuan Wang Lei Li Yimin Fan Irwin King Le Song Yu-Hu Li AI4CE 16 1 0 06 Feb 2024
Improving Self-supervised Molecular Representation Learning using Persistent Homology Yuankai Luo Lei Shi Veronika Thost SSL 14 8 0 29 Nov 2023
Graph Positional and Structural Encoder Semih Cantürk Renming Liu Olivier Lapointe-Gagné Vincent Létourneau Guy Wolf Dominique Beaini Ladislav Rampášek 25 13 0 14 Jul 2023
Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials Shengchao Liu Weitao Du Yanjing Li Zhuoxinran Li Zhiling Zheng ... Anima Anandkumar C. Borgs J. Chayes Hongyu Guo Jian Tang AI4CE 26 17 0 15 Jun 2023
A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining Shengchao Liu Weitao Du Zhiming Ma Hongyu Guo Jian Tang 22 29 0 28 May 2023
Probing Graph Representations Mohammad Sadegh Akhondzadeh Vijay Lingam Aleksandar Bojchevski 26 10 0 07 Mar 2023
Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language Philipp Seidl Andreu Vall Sepp Hochreiter G. Klambauer 55 35 0 06 Mar 2023
Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing Shengchao Liu Weili Nie Chengpeng Wang Jiarui Lu Zhuoran Qiao Ling Liu Jian Tang Chaowei Xiao Anima Anandkumar 21 148 0 21 Dec 2022
Flaky Performances when Pretraining on Relational Databases Shengchao Liu David Vazquez Jian Tang Pierre-Andre Noel 11 2 0 09 Nov 2022
Masked Autoencoders Are Scalable Vision Learners Kaiming He Xinlei Chen Saining Xie Yanghao Li Piotr Dollár Ross B. Girshick ViT TPM 258 7,337 0 11 Nov 2021
Pre-training Molecular Graph Representation with 3D Geometry Shengchao Liu Hanchen Wang Weiyang Liu Joan Lasenby Hongyu Guo Jian Tang 106 294 0 07 Oct 2021
On Feature Decorrelation in Self-Supervised Learning Tianyu Hua Wenxiao Wang Zihui Xue Sucheng Ren Yue Wang Hang Zhao SSL OOD 107 163 0 02 May 2021
Emerging Properties in Self-Supervised Vision Transformers Mathilde Caron Hugo Touvron Ishan Misra Hervé Jégou Julien Mairal Piotr Bojanowski Armand Joulin 283 5,723 0 29 Apr 2021
Decoupling the Role of Data, Attention, and Losses in Multimodal Transformers Lisa Anne Hendricks John F. J. Mellor R. Schneider Jean-Baptiste Alayrac Aida Nematzadeh 75 110 0 31 Jan 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 154 1,748 0 02 Mar 2017