A novel framework based on network embedding for the simulation and analysis of disease progression

Modelling infectious disease spreading is crucial for planning effective containment measures, as shown in the COVID-19 pandemic. The effectiveness of planned measures can also be measured regarding saved lives and economic resources. Therefore, introducing methods able to model the evolution and the impact of measures, as well as planning tailored and updated measures, is a crucial step. Existing models for spreading modelling belong to two main classes: (i) compartmental models based on ordinary differential equations and (ii) contact-based models based on a contact structure using an underlining layer to simulate diffusion. Nevertheless, none of these methods can leverage the high computational power of artificial intelligence and deep learning. We propose a novel framework for simulating and analysing disease progression for these methods. The framework is based on the multiscale simulation of the spreading based on using a multiscale contact model built on top of a diffusion model customised by the user. The evolution of the spreading, modelled as a graph with attributed nodes, is then mapped into a latent space through graph embedding. Finally, deep learning models are used in the latent space to analyse and forecast methods without running expensive computational simulations of the contact-based model. © 2022 IEEE.

Annotating Protein Structures for Understanding SARS-CoV-2 Interactome

Protein Contact Network (PCN) is an emerging paradigm for modelling protein structure. A common approach to interpreting such data is through network-based analyses. It has been shown that clustering analysis may discover allostery in PCN. Nevertheless Network Embedding has shown good performances in discovering hidden communities and structures in network. SARS-CoV-2 proteins, and in particular S protein, have a modular structure that need to be annotated to understand complex mechanism of infections. Such annotations, and in particular the highlighting of regions participating in the binding of human ACE2 and TMPRSS, may help the design of tailored strategy for preventing and blocking infection. In this work, we compare some approaches for graph embedding with respect to some classical clustering approaches for annotating protein structures. Results shows that embedding may reveal interesting structure that constitute the starting point for further analysis. © 2022 CEUR-WS. All rights reserved.

Masked Face Recognition from Synthesis to Reality

As we have been seriously hit by the COVID-19 pandemic, wearing a facial mask is a crucial action that we can take for our protection. This paper reports a comprehensive study on the recognition of masked faces. By using facial landmarks, we synthesize the facial mask for each face in several benchmark databases with different challenging factors. The IJB-B and IJB-C databases are selected for evaluating the performance against the variation across pose, illumination and expression (PIE). The FG-Net database is selected for evaluating the performance across age. The SCface is chosen for evaluating the performance on low-resolution images. The MS-1MV2 is exploited as the base training set. We use the ResNet-100 as the feature embedding network connected to state-of-the-art loss functions designed for tackling face recognition. The loss functions considered include the Center Loss, the Marginal Loss, the Angular Softmax Loss, the Large Margin Cosine Loss and the Additive Angular Margin Loss. Both verification and identification are conducted in our evaluation. The performances for recognizing faces with and without the synthetic masks are all evaluated for a complete comparison. The network with the best loss function for recognizing synthetic masked faces is then assessed on a real masked face database, the cleaned RMFRD (c-RMFRD) dataset. Compared with a human user test on the c-RMFRD, the network trained on the synthetic masked faces outperforms human vision for a large gap. Our contributions are fourfold. The first is a comprehensive study for tackling masked face recognition by using state-of-the-art loss functions against various compounding factors. For comparison purpose, the second is another comprehensive study on the recognition of faces without masks by using the same loss functions against the same challenging factors. The third is the verification of the network trained on synthetic masked faces for tackling the real masked face recognition with performance better than human inspectors. The fourth is the highlight on the challenges of masked face recognition and the directions for future research. Our code, trained models and dataset are available via the project GitHub site. Author

When Sketch Face Recognition Meets Mask Obfuscation: Database and Benchmark

During this unprecedented time of the COVID19 pandemic, wearing face masks has become a necessity. While these masks aim to secure an individual from getting infected by any kind of viruses including COVID-19;they significantly obfuscate the identity. The situation becomes even worse when an attacker performs a crime and the place does not have any surveillance cameras. The identification of criminals in such conditions highly depends on the witnesses and generation of sketches based on their description. To the best of our knowledge, in the literature, no work has been performed for matching sketch images with masks. In this research, we have first created the mask sketch face database using more than 50 identities. The sketch images are generated using a different variant of pencils, which can be seen as different sketch artists. The recognition experiments are performed using state-of-the-art face embedding networks including ArcFace and DeepID which show that the recognition performance degrades significantly when the sketch mask images are used for identification. In another set of experiments, it is observed that the recognition algorithm is robust in handling the digital face mask images. However, the ineffectiveness in handling the variations that occurred due to sketches is a serious concern and needs attention. © 2021 IEEE.

Knowledge graphs and their applications in drug discovery.

INTRODUCTION: Knowledge graphs have proven to be promising systems of information storage and retrieval. Due to the recent explosion of heterogeneous multimodal data sources generated in the biomedical domain, and an industry shift toward a systems biology approach, knowledge graphs have emerged as attractive methods of data storage and hypothesis generation. AREAS COVERED: In this review, the author summarizes the applications of knowledge graphs in drug discovery. They evaluate their utility; differentiating between academic exercises in graph theory, and useful tools to derive novel insights, highlighting target identification and drug repurposing as two areas showing particular promise. They provide a case study on COVID-19, summarizing the research that used knowledge graphs to identify repurposable drug candidates. They describe the dangers of degree and literature bias, and discuss mitigation strategies. EXPERT OPINION: Whilst knowledge graphs and graph-based machine learning have certainly shown promise, they remain relatively immature technologies. Many popular link prediction algorithms fail to address strong biases in biomedical data, and only highlight biological associations, failing to model causal relationships in complex dynamic biological systems. These problems need to be addressed before knowledge graphs reach their true potential in drug discovery.

Constructing co-occurrence network embeddings to assist association extraction for COVID-19 and other coronavirus infectious diseases.

OBJECTIVE: As coronavirus disease 2019 (COVID-19) started its rapid emergence and gradually transformed into an unprecedented pandemic, the need for having a knowledge repository for the disease became crucial. To address this issue, a new COVID-19 machine-readable dataset known as the COVID-19 Open Research Dataset (CORD-19) has been released. Based on this, our objective was to build a computable co-occurrence network embeddings to assist association detection among COVID-19-related biomedical entities. MATERIALS AND METHODS: Leveraging a Linked Data version of CORD-19 (ie, CORD-19-on-FHIR), we first utilized SPARQL to extract co-occurrences among chemicals, diseases, genes, and mutations and build a co-occurrence network. We then trained the representation of the derived co-occurrence network using node2vec with 4 edge embeddings operations (L1, L2, Average, and Hadamard). Six algorithms (decision tree, logistic regression, support vector machine, random forest, naïve Bayes, and multilayer perceptron) were applied to evaluate performance on link prediction. An unsupervised learning strategy was also developed incorporating the t-SNE (t-distributed stochastic neighbor embedding) and DBSCAN (density-based spatial clustering of applications with noise) algorithms for case studies. RESULTS: The random forest classifier showed the best performance on link prediction across different network embeddings. For edge embeddings generated using the Average operation, random forest achieved the optimal average precision of 0.97 along with a F1 score of 0.90. For unsupervised learning, 63 clusters were formed with silhouette score of 0.128. Significant associations were detected for 5 coronavirus infectious diseases in their corresponding subgroups. CONCLUSIONS: In this study, we constructed COVID-19-centered co-occurrence network embeddings. Results indicated that the generated embeddings were able to extract significant associations for COVID-19 and coronavirus infectious diseases.