A Strategy Transfer and Decision Support Approach for Epidemic Control in Experience Shortage Scenarios

Epidemic outbreaks can cause critical health concerns and severe global economic crises. For countries or regions with new infectious disease outbreaks, it is essential to generate preventive strategies by learning lessons from others with similar risk profiles. A Strategy Transfer and Decision Support Approach (STDSA) is proposed based on the profile similarity evaluation. There are four steps in this method: (1) The similarity evaluation indicators are determined from three dimensions, i.e., the Basis of National Epidemic Prevention & Control, Social Resilience, and Infection Situation. (2) The data related to the indicators are collected and preprocessed. (3) The first round of screening on the preprocessed dataset is conducted through an improved collaborative filtering algorithm to calculate the preliminary similarity result from the perspective of the infection situation. (4) Finally, the K-Means model is used for the second round of screening to obtain the final similarity values. The approach will be applied to decision-making support in the context of COVID-19. Our results demonstrate that the recommendations generated by the STDSA model are more accurate and aligned better with the actual situation than those produced by pure K-means models. This study will provide new insights into preventing and controlling epidemics in regions that lack experience.

DeepDDS: deep graph neural network with attention mechanism to predict synergistic drug combinations

Drug combination therapy has become a increasingly promising method in the treatment of cancer. However, the number of possible drug combinations is so huge that it is hard to screen synergistic drug combinations through wet-lab experiments. Therefore, computational screening has become an important way to prioritize drug combinations. Graph neural network have recently shown remarkable performance in the prediction of compound-protein interactions, but it has not been applied to the screening of drug combinations. In this paper, we proposed a deep learning model based on graph neural networks and attention mechanism to identify drug combinations that can effectively inhibit the viability of specific cancer cells. The feature embeddings of drug molecule structure and gene expression profiles were taken as input to multi-layer feedforward neural network to identify the synergistic drug combinations. We compared DeepDDS with classical machine learning methods and other deep learning-based methods on benchmark data set, and the leave-one-out experimental results showed that DeepDDS achieved better performance than competitive methods. Also, on an independent test set released by well-known pharmaceutical enterprise AstraZeneca, DeepDDS was superior to competitive methods by more than 16\% predictive precision. Furthermore, we explored the interpretability of the graph attention network, and found the correlation matrix of atomic features revealed important chemical substructures of drugs. We believed that DeepDDS is an effective tool that prioritized synergistic drug combinations for further wet-lab experiment validation.