Graph Neural Network Models for Chemical Compound Activeness Prediction For COVID-19 Drugs Discovery using Lipinski's Descriptors

In this study, we implemented graph neural network (GNN) methods to forecast in vitro inhibitory bioactivity or pharmacological concentration of chemical compounds against severe acute respiratory syndrome (SARS) coronaviruses from the graph representation amongst the compounds (i.e., nodes) and their respective features(i.e., node features) obtained by RDKit tool from their respectively SMILES (Simplified MolecularInput Line-Entry System), and we compared GNN models by experiments with our graph data of 375 nodes with 44,475 edges or links. This was done in response to the severe and significant consequences of the ongoing Coronavirus disease 2019 (COVID-19) disease. As a result, we discovered that implemented models, simple graph convolution (SGC), and graph convolution network (GCN) performed significantly well with comparable performance. © 2022 IEEE.

How Severe is Your COVID-19? Predicting SARS-CoV-2 Infection with Graph Attention Capsule Networks

Recent studies in machine learning have demonstrated the effectiveness of applying graph neural networks (GNNs) to single-cell RNA sequencing (scRNA-seq) data to predict COVID-19 disease states. In this study, we propose a graph attention capsule network (GACapNet) which extracts and fuses Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) transcriptomic patterns to improve node classification performance on cells and genes. Significantly different from the existing GNN approaches, we innovatively incorporate a capsule layer with dynamic routing into our model architecture to combine and fuse gene features effectively and to allow those more prominent gene features present in the output. We evaluate our GACapNet model on two scRNA-seq datasets, and the experimental results show that our GACapNet model significantly outperforms state-of-the-art baseline models. Therefore, our study demonstrates the capability of advanced machine learning models to generate predictive features and evolutionary patterns of the SARS-CoV-2 pathogen, and the applicability of closing knowledge gaps in the pathogenesis and recovery of COVID-19. © 2022 IEEE.

Identifying the Superspreader in Proactive Backward Contact Tracing by Deep Learning

The goal of proactive contact tracing is to diminish the spread of an epidemic by means of contact tracing mobile apps and big data analysis. Finding superspreaders as has been used in Japan and Australia during the early days of the COVID-19 pandemic has proven effective as backward contact tracing can pick up infections that might otherwise be missed. In this paper, we formulate a proactive contact tracing problem to identify the superspreaders using maximum-likelihood estimation, graph traversal and deep learning algorithms. This problem is challenging due to its sheer combinatorial complexity, problem scale and the fact that the underlying infection network topology is rarely known. We propose a deep learning-based framework using Graph Neural Networks to iteratively refine the supervised learning of proactive contact tracing networks using smaller infection networks and to identify the superspreader. By optimizing the graph traversal and topological features for deep learning, proactive contact tracing strategies can be developed to contain superspreading in an epidemic outbreak.

Fusing hybrid attentive network with self-supervised dual-channel heterogeneous graph for knowledge tracing

Recently the large-scale influence of Covid-19 promoted the fast development of intelligent tutoring systems (ITS). As a major task of ITS, Knowledge Tracing (KT) aims to capture a student's dynamic knowledge state based on his historical response sequences and provide personalized learning assistance to him. However, most existing KT methods have encountered the data sparsity problem. In real scenarios, an online tutoring system usually has an extensive collection of questions while each student can only interact with a limited number of questions. As a result, the records of some questions could be extremely sparse, which degrades the performance of traditional KT models. To resolve this issue, we propose a Dual-channel Heterogeneous Graph Network (DHGN) to learn informative representations of questions from students' records by capturing both the high-order heterogeneous and local relations. As the supervised learning manner applied in previous methods is incapable of exploiting unobserved relations between questions, we innovatively integrate a self-supervised framework into the KT task and employ contrastive learning via the two channels of DHGN, supplementing as an auxiliary task to improve the KT performance. Moreover, we adopt the attention mechanism, which has achieved impressive performance in natural language processing tasks, to effectively capture students' knowledge state. But the standard attention network is inapplicable to the KT task because the current knowledge state of a student usually shows strong dependency on his recently interactive questions, unlike the situation of language processing tasks, which focus more on the long-term dependency. To avoid the inefficiency of standard attention networks in the KT task, we further devise a novel Hybrid Attentive Network (HAN), which produces both the global attention and the hierarchical local attention to model the long-term and short-term intents, respectively. Then, by the gating network, a student's long-term and short-term intents are combined for efficient prediction. We conduct extensive experiments on several real-world datasets. Experimental results demonstrate that our proposed methods achieve significant performance improvement compared to existing state-of-the-art baselines, which validates the effectiveness of the proposed dual-channel heterogeneous graph framework and hybrid attentive network. © 2023 Elsevier Ltd

Quarantine in Motion: A Graph Learning Framework to Reduce Disease Transmission Without Lockdown

Exposure notification applications are developed to increase the scale and speed of disease contact tracing. Indeed, by taking advantage of Bluetooth technology, they track the infected population's mobility and then inform close contacts to get tested. In this paper, we ask whether these applications can extend from reactive to preemptive risk management tools? To this end, we propose a new framework that utilizes graph neural networks (GNN) and real-world Foursquare mobility data to predict high risk locations on an hourly basis. As a proof of concept, we then simulate a risk-informed Foursquare population of over 36,000 people in Austin TX after the peak of an outbreak. We find that even after 50% of the population has been infected with COVID-19, they can still maintain their mobility, while reducing the new infections by 13%. Consequently, these results are a first step towards achieving what we call Quarantine in Motion. © 2022 IEEE.

Contact Tracing and Epidemic Intervention via Deep Reinforcement Learning

The recent outbreak of COVID-19 poses a serious threat to people's lives. Epidemic control strategies have also caused damage to the economy by cutting off humans' daily commute. In this article, we develop an Individual-based Reinforcement Learning Epidemic Control Agent (IDRLECA) to search for smart epidemic control strategies that can simultaneously minimize infections and the cost of mobility intervention. IDRLECA first hires an infection probability model to calculate the current infection probability of each individual. Then, the infection probabilities together with individuals' health status and movement information are fed to a novel GNN to estimate the spread of the virus through human contacts. The estimated risks are used to further support an RL agent to select individual-level epidemic-control actions. The training of IDRLECA is guided by a specially designed reward function considering both the cost of mobility intervention and the effectiveness of epidemic control. Moreover, we design a constraint for control-action selection that eases its difficulty and further improve exploring efficiency. Extensive experimental results demonstrate that IDRLECA can suppress infections at a very low level and retain more than 95% of human mobility. © 2023 Copyright held by the owner/author(s). Publication rights licensed to ACM.

Learning on Health Fairness and Environmental Justice via Interactive Visualization

This paper introduces an interactive visualization interface with a machine learning consensus analysis that enables the researchers to explore the impact of atmospheric and socioeconomic factors on COVID-19 clinical severity by employing multiple Recurrent Graph Neural Networks. We designed and implemented a visualization interface that leverages coordinated multi-views to support exploratory and predictive analysis of hospitalizations and other socio-geographic variables at multiple dimensions, simultaneously. By harnessing the strength of geometric deep learning, we build a consensus machine learning model to include knowledge from county-level records and investigate the complex interrelationships between global infectious disease, environment, and social justice. Additionally, we make use of unique NASA satellite-based observations which are not broadly used in the context of climate justice applications. Our current interactive interface focus on three US states (California, Pennsylvania, and Texas) to demonstrate its scientific value and presented three case studies to make qualitative evaluations. © 2022 IEEE.

International Workshop on Learning with Knowledge Graphs: Construction, Embedding, and Reasoning

A knowledge graph (KG) consists of numerous triples, in which each triple, i.e., (head entity, relation, tail entity), denotes a real-world assertion. Many large-scale KGs have been developed, e.g., general-purpose KGs Freebase and YAGO. Also, lots of domain-specific KGs are emerging, e.g., COVID-19 KGs, biomedical KGs, and agricultural KGs. By embedding KGs into low-dimensional vectors, i.e., representations of entities and relations, we could integrate KGs into machine learning models and enhance the performance of many prediction tasks, including search, recommendations, and question answering. During the construction, refinement, embedding, and application of KGs, a variety of KG learning algorithms have been developed to handle challenges in various real-world scenarios. Moreover, graph neural networks have also brought new opportunities to KG learning. This workshop aims to engage with active researchers from KG communities, recommendation communities, natural language processing communities, and other communities, and deliver state-of-the-art research insights into the core challenges in KG learning. © 2023 Owner/Author.

Few-Shot Semantic Relation Prediction Across Heterogeneous Graphs

Semantic relation prediction aims to mine the implicit relationships between objects in heterogeneous graphs, which consist of different types of objects and different types of links. In real-world scenarios, new semantic relations constantly emerge and they typically appear with only a few labeled data. Since a variety of semantic relations exist in multiple heterogeneous graphs, the transferable knowledge can be mined from some existing semantic relations to help predict the new semantic relations with few labeled data. This inspires a novel problem of few-shot semantic relation prediction across heterogeneous graphs. However, the existing methods cannot solve this problem because they not only require a large number of labeled samples as input, but also focus on a single graph with a fixed heterogeneity. Targeting this novel and challenging problem, in this paper, we propose a Meta-learning based Graph neural network for Semantic relation prediction, named MetaGS. Firstly, MetaGS decomposes the graph structure between objects into multiple normalized subgraphs, then adopts a two-view graph neural network to capture local heterogeneous information and global structure information of these subgraphs. Secondly, MetaGS aggregates the information of these subgraphs with a hyper-prototypical network, which can learn from existing semantic relations and adapt to new semantic relations. Thirdly, using the well-initialized two-view graph neural network and hyper-prototypical network, MetaGS can effectively learn new semantic relations from different graphs while overcoming the limitation of few labeled data. Extensive experiments on three real-world datasets have demonstrated the superior performance of MetaGS over the state-of-the-art methods. IEEE

MepoGNN: Metapopulation Epidemic Forecasting with Graph Neural Networks

Epidemic prediction is a fundamental task for epidemic control and prevention. Many mechanistic models and deep learning models are built for this task. However, most mechanistic models have difficulty estimating the time/region-varying epidemiological parameters, while most deep learning models lack the guidance of epidemiological domain knowledge and interpretability of prediction results. In this study, we propose a novel hybrid model called MepoGNN for multi-step multi-region epidemic forecasting by incorporating Graph Neural Networks (GNNs) and graph learning mechanisms into Metapopulation SIR model. Our model can not only predict the number of confirmed cases but also explicitly learn the epidemiological parameters and the underlying epidemic propagation graph from heterogeneous data in an end-to-end manner. Experiment results demonstrate our model outperforms the existing mechanistic models and deep learning models by a large margin. Furthermore, the analysis on the learned parameters demonstrates the high reliability and interpretability of our model and helps better understanding of epidemic spread. Our model and data have already been public on GitHub https://github.com/deepkashiwa20/MepoGNN.git. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Deep Graph Networks for Drug Repurposing with Multi-Protein Targets

In the early phases of the COVID-19 pandemic, repurposing of drugs approved for use in other diseases helped counteract the aggressiveness of the virus. Therefore, the availability of effective and flexible methodologies to speed up and prioritize the repurposing process is fundamental to tackle present and future challenges to worldwide health. This work addresses the problem of drug repurposing through the lens of deep learning for graphs, by designing an architecture that exploits both structural and biological information to propose a reduced set of drugs that may be effective against an unknown disease. Our main contribution is a method to repurpose a drug against multiple proteins, rather than the most common single-drug/single-protein setting. The method leverages graph embeddings to encode the relevant proteins'and drugs'information based on gene ontology data and structural similarities. Finally, we publicly release a comprehensive and unified data repository for graph-based analysis to foster further studies on COVID-19 and drug repurposing. We empirically validate the proposed approach in a general drug repurposing setting, showing that it generalizes better than single protein repurposing schemes. We conclude the manuscript with an exemplified application of our method to the COVID-19 use case. All source code is publicly available. IEEE

Who's Next: Rising Star Prediction via Diffusion of User Interest in Social Networks

Finding items with potential to increase sales is of great importance in online market. In this paper, we propose to study this novel and practical problem: rising star prediction. We call these potential items Rising Star , which implies their ability to rise from low-turnover items to best-sellers in the future. Rising stars can be used to help with unfair recommendation in e-commerce platform, balance supply and demand to benefit the retailers and allocate marketing resources rationally. Although the study of rising star can bring great benefits, it also poses challenges to us. The sales trend of rising star fluctuates sharply in the short-term and exhibits more contingency caused by some external events (e.g., COVID-19 caused increasing purchase of the face mask) than other items, which cannot be solved by existing sales prediction methods. To address above challenges, in this paper, we observe that the presence of rising stars is closely correlated with the early diffusion of user interest in social networks, which is validated in the case of Taocode (an intermediary that diffuses user interest in Taobao). Thus, we propose a novel framework, RiseNet, to incorporate the user interest diffusion process with the item dynamic features to effectively predict rising stars. Specifically, we adopt a coupled mechanism to capture the dynamic interplay between items and user interest, and a special designed GNN based framework to quantify user interest. Our experimental results on large-scale real-world datasets provided by Taobao demonstrate the effectiveness of our proposed framework.

EpiGNN: Exploring Spatial Transmission with Graph Neural Network for Regional Epidemic Forecasting

Epidemic forecasting is the key to effective control of epidemic transmission and helps the world mitigate the crisis that threatens public health. To better understand the transmission and evolution of epidemics, we propose EpiGNN, a graph neural network-based model for epidemic forecasting. Specifically, we design a transmission risk encoding module to characterize local and global spatial effects of regions in epidemic processes and incorporate them into the model. Meanwhile, we develop a Region-Aware Graph Learner (RAGL) that takes transmission risk, geographical dependencies, and temporal information into account to better explore spatial-temporal dependencies and makes regions aware of related regions' epidemic situations. The RAGL can also combine with external resources, such as human mobility, to further improve prediction performance. Comprehensive experiments on five real-world epidemic-related datasets (including influenza and COVID-19) demonstrate the effectiveness of our proposed method and show that EpiGNN outperforms state-of-the-art baselines by 9.48% in RMSE. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Collaborative Filtering Model of Graph Neural Network Based on Random Walk

This paper proposes a novel graph neural network recommendation method to alleviate the user cold-start problem caused by too few relevant items in personalized recommendation collaborative filtering. A deep feedforward neural network is constructed to transform the bipartite graph of user–item interactions into the spectral domain, using a random wandering method to discover potential correlation information between users and items. Then, a finite-order polynomial is used to optimize the convolution process and accelerate the convergence of the convolutional network, so that deep connections between users and items in the spectral domain can be discovered quickly. We conducted experiments on the classic dataset MovieLens-1M. The recall and precision were improved, and the results show that the method can improve the accuracy of recommendation results, tap the association information between users and items more effectively, and significantly alleviate the user cold-start problem.

Explainable Prediction of the Severity of COVID-19 Outbreak for US Counties

Ever since the COVID-19 outbreak, various works have focused on using multitude of different static and dynamic features to aid the prediction of disease forecasting models. However, in the absence of historical pandemic data these models will not be able to give any meaningful insight about the areas which are most likely to be affected based on preexisting conditions. Furthermore, the black box nature of neural networks often becomes an impediment for the concerned authorities to derive any meaning from. In this paper, we propose a novel explainable Graph Neural Network (GNN) framework called Graph-COVID-19-Explainer (GC-Explainer) that gives explainable prediction for the severity of the spread during initial outbreak. We utilize a comprehensive set of static population characteristics to use as node features of Graph where each node corresponds to a geographical region. Unlike post-hoc methods of GNN explanations, we propose a framework for learning important features during the training of the model. We further apply our model on real-world early pandemic data to show the validity of our approach. Through GC-Explainer, we show that static features along with spatial dependency among regions can be used to explain the varied degree of severity in outbreak during the early part of the pandemic and provide a framework to identify the at-risk areas for any infectious disease outbreak, especially when historical data is not available. © 2022 IEEE.

Graph and Capsule Convolutional Neural Network Based Classification of Lung Cancer, Pneumonia, COVID-19 using Lung CT and Ultrasound Radiography Imaging

Pulmonary / Lung nodules are a sign of lung cancer. Pneumonia, Lung nodules show up on imaging scans like X-rays, CT or ultrasound scans. The healthcare team may refer to the growth as a spot on the lung, coin lesion, or shadow. Coronavirus (COVID-19) has been identified as a worldwide epidemic, affecting individuals all over the nation. It is vital to identify COVID-19-affected persons to limit the virus's spread. According to the latest study, radiographic approaches can be used to diagnose contamination utilizing deep learning (DL) methods. Considering that DL is a valuable approach and methodology for image analysis, various studies on COVID-19 case detection utilizing radiographs to train DL networks have been conducted. Although just a handful of studies presume to have excellent prediction results, their proposed systems may suffer from a restricted amount of data. Employing graph and capsule, Convolutional Neural Network (CNN) can overcome the shortcomings by predicting multiple disorders using a single network implemented in a hospital. We present a novel comparative method that has paved the way for an open-source COVID-19 case classification approach based on graph and capsule images with CT and ultrasound. Experimental results show that the Capsule network attained the best 98.93% AUC, 99.2% accuracy, 98.4% Fl-score, 98.40% sensitivity, 98.40% specificity, 9S.4l% precision using CT labels. Whereas the ultrasound test set the graph network performed well with 96.93% AUC, 97.26% accuracy, 95.92% Fl-score, 95.90% sensitivity, 97.94% specificity, 96.08% precision. © 2022 IEEE.

Towards De Novo Drug Design for the Coronavirus: A Drug-Target Interaction Prediction Approach using Atom-enhanced Graph Neural Network with Multi-hop Gating Mechanism

For humans, the COVID-19 pandemic and Coronavirus have undeniably been a nightmare. Although there are effective vaccines, specific drugs are still urgent. Normally, to identify potential drugs, one needs to design and then test interactions between the drug and the virus in an in silico manner for determining candidates. This Drug-Target Interaction (DTI) process, can be done by molecular docking, which is too complicated and time-consuming for manual works. Therefore, it opens room for applying Artificial Intelligence (AI) techniques. In particular, Graph Neural Network (GNN) attracts recent attention since its high suitability for the nature of drug compounds and virus proteins. However, to introduce such a representation well-reflecting biological structures of biological compounds is not a trivial task. Moreover, since available datasets of Coronavirus are still not highly popular, the recently developed GNNs have been suffering from overfitting on them. We then address those issues by proposing a novel model known as Atom-enhanced Graph Neural Network with Multi-hop Gating Mechanism. On one hand, our model can learn more precise features of compounds and proteins. On the other hand, we introduce a new gating mechanism to create better atom representation from non-neighbor information. Once applying transfer learning from very large databanks, our model enjoys promising performance, especially when experimenting with Coronavirus. © 2022 IEEE.

Research on COVID-19 document fine-grained classification based on graph neural network

Since the outbreak of COVID-19, academia has published tens of thousands of new papers. Facing so much literature knowledge, how to realize the fine-grained classification of covid-19 literature and help researchers carry out research? This is an urgent problem to be solved. This paper makes COVID-19 text classification graph data set, designs covid-19 scientific literature fine-grained classification model LC-GAT based on graph attention network, adds attention mechanism at word level, sentence level and graph level, effectively retains the classification information contained in article title and key words, and significantly improves the performance of covid-19 scientific literature fine-grained classification. This paper has positive significance for the classification of COVID-19 scientific literature. © 2022 IEEE.

Reviving the economy while saving lives: a deep reinforcement learning approach for smart POI reopening

With the gradual improvements in COVID-19 metrics and the accelerated immunization progress, countries around the world have began to focus on reviving the economy while continuously strengthening epidemic control. POInt-of-Interest (POI) reopening, as a necessity for restoring human mobilities, has become a crucial step to recouple economic recovery and public health management. In contrast to the lock-down policy, POI reopening demands a dynamic trade-off between epidemic interventions and economic costs. In the urban scenario, there exist three key challenges in developing effective POI reopening strategies as follows. (1) During the POI reopening process, there are multiple urban factors affecting the epidemic transmission, which are difficult to simultaneously incorporate and balance in a single reopening strategy;(2) the effects of POI reopening on both economic recovery and epidemic control are long-term, which are hard to capture by static models;and (3) the dual objectives of minimizing infections and maintaining POIs' visits are conflicting, making it difficult to achieve a flexible and scalable trade-off. To tackle the above challenges, we propose Reopener, a deep reinforcement learning (RL) framework for smart POI reopening. First, we utilize a bipartite graph neural network to automatically encode all urban factors that would affect the epidemic prevention and POI visit restriction. Second, we employ a RL-based deep policy network to enable flexible updates in restrictions on POIs along with the trend of epidemic. Third, we design a novel reward function to guide the RL agent to learn smartly, thus comprehensively trading off infections and visit sustainability of POIs. Extensive experimental results demonstrate that Reopener outperforms all baseline methods with remarkable improvements, by reducing the overall economic cost by at least 6.42%. Reopener can effectively suppress infections and support a phase-based POI reopening process, which provides valuable insights for strategy design in post-COVID-19 economic recovery. © 2022 Owner/Author.

Reinforcement Learning and Graph Neural Networks for Designing Novel Drugs with Optimized Affinity: Application to SARS-CoV-2

Drugs are generally designed for a specific target protein. Recent studies have demonstrated the capability of deep learning-based models to accelerate and cheapen the drug development process. The proposed deep learning models can generate novel molecules with optimized drug-like properties. However, the properties addressed are often limited and may be misleading. This is because they do not reflect the complete information about the binding affinity of the designed drug and the target protein. In this work, we exploit the state-of-The-Art progress made in drug-Target-Affinity (DTA) prediction to assess the binding affinity of drugs generated by a developed molecular generator against the corona-virus main protease (SARS-CoV-2 Mpro). The molecular generator is a recurrent neural network-based model, while the DTA predictor is a graph neural network (GNN), famously known as GraphDTA. We train the molecular generator using reinforcement learning (RL) to optimize the GraphDTA-predicted score. As this is the first benchmark of this kind (to the best of our knowledge), we report our benchmarking results;of 1.79% desirability;with the hope of motivating future improvements in this regard. © 2022 IEEE.