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Register a new userDrug-Target Interaction Prediction with Graph Attention networks
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Motivation: Predicting Drug-Target Interaction (DTI) is a well-studied topic in bioinformatics due to its relevance in the fields of proteomics and pharmaceutical research. Although many machine learning methods have been successfully applied in this task, few of them aim at leveraging the inherent heterogeneous graph structure in the DTI network to address the challenge. For better learning and interpreting the DTI topological structure and the similarity, it is desirable to have methods specifically for predicting interactions from the graph structure. Results: We present an end-to-end framework, DTI-GAT (Drug-Target Interaction prediction with Graph Attention networks) for DTI predictions. DTI-GAT incorporates a deep neural network architecture that operates on graph-structured data with the attention mechanism, which leverages both the interaction patterns and the features of drug and protein sequences. DTI-GAT facilitates the interpretation of the DTI topological structure by assigning different attention weights to each node with the self-attention mechanism. Experimental evaluations show that DTI-GAT outperforms various state-of-the-art systems on the binary DTI prediction problem. Moreover, the independent study results further demonstrate that our model can be generalized better than other conventional methods. Availability: The source code and all datasets are available at https://github.com/Haiyang-W/DTI-GRAPH
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Accurately predicting the binding affinity between drugs and proteins is an essential step for computational drug discovery. Since graph neural networks (GNNs) have demonstrated remarkable success in various graph-related tasks, GNNs have been considered as a promising tool to improve the binding affinity prediction in recent years. However, most of the existing GNN architectures can only encode the topological graph structure of drugs and proteins without considering the relative spatial information among their atoms. Whereas, different from other graph datasets such as social networks and commonsense knowledge graphs, the relative spatial position and chemical bonds among atoms have significant impacts on the binding affinity. To this end, in this paper, we propose a diStance-aware Molecule graph Attention Network (S-MAN) tailored to drug-target binding affinity prediction. As a dedicated solution, we first propose a position encoding mechanism to integrate the topological structure and spatial position information into the constructed pocket-ligand graph. Moreover, we propose a novel edge-node hierarchical attentive aggregation structure which has edge-level aggregation and node-level aggregation. The hierarchical attentive aggregation can capture spatial dependencies among atoms, as well as fuse the position-enhanced information with the capability of discriminating multiple spatial relations among atoms. Finally, we conduct extensive experiments on two standard datasets to demonstrate the effectiveness of S-MAN.
We introduce Bi-GNN for modeling biological link prediction tasks such as drug-drug interaction (DDI) and protein-protein interaction (PPI). Taking drug-drug interaction as an example, existing methods using machine learning either only utilize the link structure between drugs without using the graph representation of each drug molecule, or only leverage the individual drug compound structures without using graph structure for the higher-level DDI graph. The key idea of our method is to fundamentally view the data as a bi-level graph, where the highest level graph represents the interaction between biological entities (interaction graph), and each biological entity itself is further expanded to its intrinsic graph representation (representation graphs), where the graph is either flat like a drug compound or hierarchical like a protein with amino acid level graph, secondary structure, tertiary structure, etc. Our model not only allows the usage of information from both the high-level interaction graph and the low-level representation graphs, but also offers a baseline for future research opportunities to address the bi-level nature of the data.
Properties of molecules are indicative of their functions and thus are useful in many applications. With the advances of deep learning methods, computational approaches for predicting molecular properties are gaining increasing momentum. However, there lacks customized and advanced methods and comprehensive tools for this task currently. Here we develop a suite of comprehensive machine learning methods and tools spanning different computational models, molecular representations, and loss functions for molecular property prediction and drug discovery. Specifically, we represent molecules as both graphs and sequences. Built on these representations, we develop novel deep models for learning from molecular graphs and sequences. In order to learn effectively from highly imbalanced datasets, we develop advanced loss functions that optimize areas under precision-recall curves. Altogether, our work not only serves as a comprehensive tool, but also contributes towards developing novel and advanced graph and sequence learning methodologies. Results on both online and offline antibiotics discovery and molecular property prediction tasks show that our methods achieve consistent improvements over prior methods. In particular, our methods achieve #1 ranking in terms of both ROC-AUC and PRC-AUC on the AI Cures Open Challenge for drug discovery related to COVID-19. Our software is released as part of the MoleculeX library under AdvProp.
Drug-drug interaction(DDI) prediction is an important task in the medical health machine learning community. This study presents a new method, multi-view graph contrastive representation learning for drug-drug interaction prediction, MIRACLE for brevity, to capture inter-view molecule structure and intra-view interactions between molecules simultaneously. MIRACLE treats a DDI network as a multi-view graph where each node in the interaction graph itself is a drug molecular graph instance. We use GCNs and bond-aware attentive message passing networks to encode DDI relationships and drug molecular graphs in the MIRACLE learning stage, respectively. Also, we propose a novel unsupervised contrastive learning component to balance and integrate the multi-view information. Comprehensive experiments on multiple real datasets show that MIRACLE outperforms the state-of-the-art DDI prediction models consistently.
Drug-target interaction (DTI) prediction plays a crucial role in drug discovery, and deep learning approaches have achieved state-of-the-art performance in this field. We introduce an ensemble of deep learning models (EnsembleDLM) for DTI prediction. EnsembleDLM only uses the sequence information of chemical compounds and proteins, and it aggregates the predictions from multiple deep neural networks. This approach not only achieves state-of-the-art performance in Davis and KIBA datasets but also reaches cutting-edge performance in the cross-domain applications across different bio-activity types and different protein classes. We also demonstrate that EnsembleDLM achieves a good performance (Pearson correlation coefficient and concordance index > 0.8) in the new domain with approximately 50% transfer learning data, i.e., the training set has twice as much data as the test set.
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