DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier

15 May 2017

Papers citing "DeepGO: Predicting protein functions from sequence and interactions using a deep ontology-aware classifier"

29 / 29 papers shown

Title
Transformers trained on proteins can learn to attend to Euclidean distance Isaac Ellmen Constantin Schneider Matthew I.J. Raybould Charlotte M. Deane 88 0 0 03 Feb 2025
Informed deep hierarchical classification: a non-standard analysis inspired approach Lorenzo Fiaschi Marco Cococcioni 46 0 0 25 Sep 2024
ProteinRPN: Towards Accurate Protein Function Prediction with Graph-Based Region Proposals Shania Mitra Lei Huang Manolis Kellis ViT 21 0 0 01 Sep 2024
Clustering for Protein Representation Learning Ruijie Quan Wenguan Wang Fan Ma Hehe Fan Yi Yang 56 5 0 30 Mar 2024
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation Zuobai Zhang Jiarui Lu Vijil Chenthamarakshan Aurélie C. Lozano Payel Das Jian Tang 31 1 0 10 Feb 2024
VALUED -- Vision and Logical Understanding Evaluation Dataset Soumadeep Saha Saptarshi Saha Utpal Garain 33 0 0 21 Nov 2023
Insights Into the Inner Workings of Transformer Models for Protein Function Prediction M. Wenzel Erik Grüner Nils Strodthoff ViT 43 8 0 07 Sep 2023
DeepGATGO: A Hierarchical Pretraining-Based Graph-Attention Model for Automatic Protein Function Prediction Zihao Li Changkun Jiang Jianqiang Li 14 6 0 24 Jul 2023
A Review of Deep Learning Techniques for Protein Function Prediction Divyanshu Aggarwal Y. Hasija 24 1 0 27 Oct 2022
Isoform Function Prediction Using a Deep Neural Network Sara Ghazanfari Ali Rasteh S. Motahari M. Baghshah 29 0 0 05 Aug 2022
Transformer Neural Networks Attending to Both Sequence and Structure for Protein Prediction Tasks Anowarul Kabir Amarda Shehu ViT 40 3 0 17 Jun 2022
Deep Learning with Logical Constraints Eleonora Giunchiglia Mihaela C. Stoian Thomas Lukasiewicz NAI AI4CE 44 61 0 01 May 2022
An Effective GCN-based Hierarchical Multi-label classification for Protein Function Prediction Kyudam Choi Yurim Lee Cheongwon Kim MinSung Yoon 21 7 0 06 Dec 2021
Leveraging Sequence Embedding and Convolutional Neural Network for Protein Function Prediction Wei-Cheng Tseng Po-Han Chi Jiahong Wu Min Sun 24 0 0 01 Dec 2021
An Integrated Deep Learning and Dynamic Programming Method for Predicting Tumor Suppressor Genes, Oncogenes, and Fusion from PDB Structures Nishanth Anandanadarajah Chee-Hung Henry Chu R. Loganantharaj 38 2 0 17 May 2021
Multi-Label Classification Neural Networks with Hard Logical Constraints Eleonora Giunchiglia Thomas Lukasiewicz AILaw 54 43 0 24 Mar 2021
Cyberbiosecurity: DNA Injection Attack in Synthetic Biology Dor Farbiash Rami Puzis AAML 9 7 0 28 Nov 2020
Coherent Hierarchical Multi-Label Classification Networks Eleonora Giunchiglia Thomas Lukasiewicz AILaw 51 96 0 20 Oct 2020
Intrinsic-Extrinsic Convolution and Pooling for Learning on 3D Protein Structures Pedro Hermosilla M. Schäfer Matěj Lang Gloria Fackelmann Pere-Pau Vázquez Barbora Kozlíková M. Krone Tobias Ritschel Timo Ropinski 33 2 0 13 Jul 2020
Enzyme promiscuity prediction using hierarchy-informed multi-label classification Gian Marco Visani M. C. Hughes S. Hassoun 22 2 0 18 Feb 2020
AMP0: Species-Specific Prediction of Anti-microbial Peptides using Zero and Few Shot Learning Sadaf Gull F. Minhas 34 10 0 28 Oct 2019
Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations Xiang Yue Zhen Wang Jingong Huang Srinivasan Parthasarathy Soheil Moosavinasab Yungui Huang S. Lin Wen Zhang Ping Zhang Huan Sun GNN 21 325 0 12 Jun 2019
Using Ontologies To Improve Performance In Massively Multi-label Prediction Models E. Steinberg Peter J. Liu NoLa 29 4 0 28 May 2019
Deep learning in bioinformatics: introduction, application, and perspective in big data era Yu Li Chao Huang Lizhong Ding Zhongxiao Li Yijie Pan Xin Gao AI4CE 29 296 0 28 Feb 2019
Deep Robust Framework for Protein Function Prediction using Variable-Length Protein Sequences Ashish Ranjan M. S. Fahad David Fernández-Baca A. Deepak Sudhakar Tripathi 27 23 0 04 Nov 2018
DEEPGONET: Multi-label Prediction of GO Annotation for Protein from Sequence Using Cascaded Convolutional and Recurrent Network S. M. S. Islam Md Golam Moula Mehedi Hasan 28 2 0 31 Oct 2018
Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities Marinka Zitnik Francis Nguyen Bo Wang J. Leskovec Anna Goldenberg Michael M. Hoffman LM&MA AI4CE 16 457 0 30 Jun 2018
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction F. Z. Smaili Xin Gao Robert Hoehndorf 23 142 0 29 Apr 2018
ProLanGO: Protein Function Prediction Using Neural~Machine Translation Based on a Recurrent Neural Network Renzhi Cao Colton Freitas Leong Chan Miao Sun Haiqing Jiang Zhangxin Chen 30 169 0 19 Oct 2017