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Register a new userSpatial Graph Attention and Curiosity-driven Policy for Antiviral Drug Discovery
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Added by
Yulun Wu
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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We developed Distilled Graph Attention Policy Networks (DGAPNs), a curiosity-driven reinforcement learning model to generate novel graph-structured chemical representations that optimize user-defined objectives by efficiently navigating a physically constrained domain. The framework is examined on the task of generating molecules that are designed to bind, noncovalently, to functional sites of SARS-CoV-2 proteins. We present a spatial Graph Attention Network (sGAT) that leverages self-attention over both node and edge attributes as well as encoding spatial structure -- this capability is of considerable interest in areas such as molecular and synthetic biology and drug discovery. An attentional policy network is then introduced to learn decision rules for a dynamic, fragment-based chemical environment, and state-of-the-art policy gradient techniques are employed to train the network with enhanced stability. Exploration is efficiently encouraged by incorporating innovation reward bonuses learned and proposed by random network distillation. In experiments, our framework achieved outstanding results compared to state-of-the-art algorithms, while increasing the diversity of proposed molecules and reducing the complexity of paths to chemical synthesis.
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Ride-hailing demand prediction is an essential task in spatial-temporal data mining. Accurate Ride-hailing demand prediction can help to pre-allocate resources, improve vehicle utilization and user experiences. Graph Convolutional Networks (GCN) is commonly used to model the complicated irregular non-Euclidean spatial correlations. However, existing GCN-based ride-hailing demand prediction methods only assign the same importance to different neighbor regions, and maintain a fixed graph structure with static spatial relationships throughout the timeline when extracting the irregular non-Euclidean spatial correlations. In this paper, we propose the Spatial-Temporal Dynamic Graph Attention Network (STDGAT), a novel ride-hailing demand prediction method. Based on the attention mechanism of GAT, STDGAT extracts different pair-wise correlations to achieve the adaptive importance allocation for different neighbor regions. Moreover, in STDGAT, we design a novel time-specific commuting-based graph attention mode to construct a dynamic graph structure for capturing the dynamic time-specific spatial relationships throughout the timeline. Extensive experiments are conducted on a real-world ride-hailing demand dataset, and the experimental results demonstrate the significant improvement of our method on three evaluation metrics RMSE, MAPE and MAE over state-of-the-art baselines.
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.
In many real-world scenarios where extrinsic rewards to the agent are extremely sparse, curiosity has emerged as a useful concept providing intrinsic rewards that enable the agent to explore its environment and acquire information to achieve its goals. Despite their strong performance on many sparse-reward tasks, existing curiosity approaches rely on an overly holistic view of state transitions, and do not allow for a structured understanding of specific aspects of the environment. In this paper, we formulate curiosity based on grounded question answering by encouraging the agent to ask questions about the environment and be curious when the answers to these questions change. We show that natural language questions encourage the agent to uncover specific knowledge about their environment such as the physical properties of objects as well as their spatial relationships with other objects, which serve as valuable curiosity rewards to solve sparse-reward tasks more efficiently.
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
In the past several months, COVID-19 has spread over the globe and caused severe damage to the people and the society. In the context of this severe situation, an effective drug discovery method to generate potential drugs is extremely meaningful. In this paper, we provide a methodology of discovering potential drugs for the treatment of Severe Acute Respiratory Syndrome Corona-Virus 2 (commonly known as SARS-CoV-2). We proposed a new model called Genetic Constrained Graph Variational Autoencoder (GCGVAE) to solve this problem. We trained our model based on the data of various viruses protein structure, including that of the SARS, HIV, Hep3, and MERS, and used it to generate possible drugs for SARS-CoV-2. Several optimization algorithms, including valency masking and genetic algorithm, are deployed to fine tune our model. According to the simulation, our generated molecules have great effectiveness in inhibiting SARS-CoV-2. We quantitatively calculated the scores of our generated molecules and compared it with the scores of existing drugs, and the result shows our generated molecules scores much better than those existing drugs. Moreover, our model can be also applied to generate effective drugs for treating other viruses given their protein structure, which could be used to generate drugs for future viruses.
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