Understanding components of mobility during the COVID-19 pandemic.

Travel restrictions have proven to be an effective strategy to control the spread of the COVID-19 epidemics, in part because they help delay disease propagation across territories. The question, however, as to how different types of travel behaviour, from commuting to holiday-related travel, contribute to the spread of infectious diseases remains open. Here, we address this issue by using factorization techniques to decompose the temporal network describing mobility flows throughout 2020 into interpretable components. Our results are based on two mobility datasets: the first is gathered from Danish mobile network operators; the second originates from the Facebook Data-For-Good project. We find that mobility patterns can be described as the aggregation of three mobility network components roughly corresponding to travel during workdays, weekends and holidays, respectively. We show that, across datasets, in periods of strict travel restrictions the component corresponding to workday travel decreases dramatically. Instead, the weekend component, increases. Finally, we study how each type of mobility (workday, weekend and holiday) contributes to epidemics spreading, by measuring how the effective distance, which quantifies how quickly a disease can travel between any two municipalities, changes across network components. This article is part of the theme issue 'Data science approaches to infectious disease surveillance'.

Multi-label Emotion Classification of COVID-19 Tweets with Deep Learning and Topic Modelling

The COVID-19 pandemic has become one of the severe diseases in recent years. As it majorly affects the common livelihood of people across the universe, it is essential for administrators and healthcare professionals to be aware of the views of the community so as to monitor the severity of the spread of the outbreak. The public opinions are been shared enormously in microblogging media like twitter and is considered as one of the popular sources to collect public opinions in any topic like politics, sports, entertainment etc., This work presents a combination of Intensity Based Emotion Classification Convolution Neural Network (IBEC-CNN) model and Non-negative Matrix Factorization (NMF) for detecting and analyzing the different topics discussed in the COVID-19 tweets as well the intensity of the emotional content of those tweets. The topics were identified using NMF and the emotions are classified using pretrained IBEC-CNN, based on predefined intensity scores. The research aimed at identifying the emotions in the Indian tweets related to COVID-19 and producing a list of topics discussed by the users during the COVID-19 pandemic. Using the Twitter Application Programming Interface (Twitter API), huge numbers of COVID-19 tweets are retrieved during January and July 2020. The extracted tweets are analyzed for emotions fear, joy, sadness and trust with proposed Intensity Based Emotion Classification Convolution Neural Network (IBEC-CNN) model which is pretrained. The classified tweets are given an intensity score varies from 1 to 3, with 1 being low intensity for the emotion, 2 being the moderate and 3 being the high intensity. To identify the topics in the tweets and the themes of those topics, Non-negative Matrix Factorization (NMF) has been employed. Analysis of emotions of COVID-19 tweets has identified, that the count of positive tweets is more than that of count of negative tweets during the period considered and the negative tweets related to COVID-19 is less than 5%. Also, more than 75% negative tweets expressed sadness, fear are of low intensity. A qualitative analysis has also been conducted and the topics detected are grouped into themes such as economic impacts, case reports, treatments, entertainment and vaccination. The results of analysis show that the issues related to the pandemic are expressed different emotions in twitter which helps in interpreting the public insights during the pandemic and these results are beneficial for planning the dissemination of factual health statistics to build the trust of the people. The performance comparison shows that the proposed IBEC-CNN model outperforms the conventional models and achieved 83.71% accuracy. The % of COVID-19 tweets that discussed the different topics vary from 7.45% to 26.43% on topics economy, Statistics on cases, Government/Politics, Entertainment, Lockdown, Treatments and Virtual Events. The least number of tweets discussed on politics/government on the other hand the tweets discussed most about treatments. © 2023 CRL Publishing. All rights reserved.

SmartTensors: Unsupervised and Physics-informed Machine Learning Framework for the Geoscience Applications

SmartTensors (https://github.com/SmartTensors) is a novel framework for unsupervised and physics-informed machine learning for geoscience applications. The methods in SmartTensors AI platform are developed using advanced matrix/tensor factorization constrained by penalties enforcing robustness and interpretability (e.g., nonnegativity, sparsity, physics, and mathematical constraints;etc.). This framework has been applied to analyze diverse datasets related to a wide range of problems: from COVID-19 to wildfires and climate. Here, we will focus on the analysis of geothermal prospectivity of the Great Basin, U.S. The basin covers a vast area that is yet to be thoroughly explored to discover new geothermal resources. The available regional geochemical data are expected to provide critical information about the geothermal reservoir properties in the basin, including temperature, fluid/heat flow, boundary conditions, and spatial extent. The geochemical data may also include hidden (latent) information that is a proxy for geothermal prospectivity. We processed the sparse geochemical dataset of 18 geochemical attributes observed at 14,341 locations. The data are analyzed using our GeoThermalCloud toolbox for geothermal exploration (https://github.com/SmartTensors/GeoThermalCloud.jl) whichis also a part of the SmartTensors framework. An unsupervised machine learning using non-negative matrix factorization with customized k-means clustering (NMFk) as implemented in SmartTensors identified three hidden geothermal signatures representing low-, medium-, and high-temperature reservoirs, respectively (Fig). NMFk also evaluated the probability of occurrence of these types of resources through the studied region. NMFk also reconstructed attributes from sparse into continuous over the study domain. Future work will add in the ML analyses other regional- and site-scale datasets including geological, geophysical, and geothermal attributes. © 2022 Society of Exploration Geophysicists and the American Association of Petroleum Geologists.

Adverse effect signature extraction and prediction for drugs treating COVID-19.

Given the considerable cost of drug discovery, drug repurposing is becoming attractive as it can effectively shorten the development timeline and reduce the development cost. However, most existing drug-repurposing methods omitted the heterogeneous health conditions of different COVID-19 patients. In this study, we evaluated the adverse effect (AE) profiles of 106 COVID-19 drugs. We extracted four AE signatures to characterize the AE distribution of 106 COVID-19 drugs by non-negative matrix factorization (NMF). By integrating the information from four distinct databases (AE, bioassay, chemical structure, and gene expression information), we predicted the AE profiles of 91 drugs with inadequate AE feedback. For each of the drug clusters, discriminant genes accounting for mechanisms of different AE signatures were identified by sparse linear discriminant analysis. Our findings can be divided into three parts. First, drugs abundant with AE-signature 1 (for example, remdesivir) should be taken with caution for patients with poor liver, renal, or cardiac functions, where the functional genes accumulate in the RHO GTPases Activate NADPH Oxidases pathway. Second, drugs featuring AE-signature 2 (for example, hydroxychloroquine) are unsuitable for patients with vascular disorders, with relevant genes enriched in signal transduction pathways. Third, drugs characterized by AE signatures 3 and 4 have relatively mild AEs. Our study showed that NMF and network-based frameworks contribute to more precise drug recommendations.

Approximating Sparse Semi-nonnegative Matrix Factorization for X-Ray Covid-19 Image Classification

Medical imaging has been intensively used to help the radiologists do the correct diagnosis for the COVID-19 disease. In particular, chest X-ray imaging is one of the prevalent information sources for COVID-19 diagnosis. The obtained images can be viewed as numerical data and processed by non-negative matrix factorization (NMF) algorithms, one of the available numerical data analysis tools. In this work, we propose a new sparse semi-NMF algorithm that can classify the patients into COVID-19 and normal patients, based on chest X-ray images. We show that the huge volume of data resulting from X-ray images can be significantly reduced without significant loss of classification accuracy. Then, we evaluate our algorithm by carrying out an experiment on a publicly available dataset, having a known chest X-ray image bi-partition. Experimental results demonstrate that the proposed sparse semi-NMF algorithm can predict COVID-19 patients with high accuracy,compared to state-of-the-art algorithms.

Characterizing Covid Waves via Spatio-Temporal Decomposition

In this paper we develop a framework for analyzing patterns of a disease or pandemic such as Covid. Given a dataset which records information about the spread of a disease over a set of locations, we consider the problem of identifying both the disease's intrinsic waves (temporal patterns) and their respective spatial epicenters. To do so we introduce a new method of spatio-temporal decomposition which we call diffusion NMF (D-NMF). Building upon classic matrix factorization methods, D-NMF takes into consideration a spatial structuring of locations (features) in the data and supports the idea that locations which are spatially close are more likely to experience the same set of waves. To illustrate the use of D-NMF, we analyze Covid case data at various spatial granularities. Our results demonstrate that D-NMF is very useful in separating the waves of an epidemic and identifying a few centers for each wave. © 2022 ACM.

Heterogeneity of technological structures between EU countries: An application of complex systems methods to Input-Output Tables

The identification of the channels through which a given shock spreads to the rest of the economy, determining its final impact, is essential to formulate effective policy interventions. Input-output tables (IOTs) are widely used to detect the network of intersectoral relations of a country - i.e., its sectoral technological structure or domestic supply chains - and the role of different sectors in the propagation of a shock. However, the heterogeneity that characterize the technological structures of different countries is inevitably a source of complexity for the development of supranational and timely coordinated policies because it requires to analyse and interpret a large amount of information. This paper proposes a unique problem setting that aims to deal with this complexity by facilitating the analysis and visualization of similarities and differences among the technological structures of countries, relying on the identification of a small number of archetypes and showing how their interpretation could be exploited to support the definition of coordinated policy interventions. Specifically, non-negative matrix factorization is used to extract the archetypal matrices of the technological structures of the 28 European countries from IOTs, revealing dense intersectoral relationships and a low degree of heterogeneity between them. Then, random walk indicators are applied to study shock propagation within these archetypes, uncovering sectoral centralities. Finally, COVID-19 lockdown restrictions are analysed to exemplify the use of the proposed approach for coordinated policy action.

Analysis of the impact of non-compulsory measures on human mobility in Japan during the COVID-19 pandemic.

To curb the spread of the COVID-19 pandemic, countries around the world have imposed restrictions on their population. This study quantitatively assessed the impact of non-compulsory measures on human mobility in Japan during the COVID-19 pandemic, through the analysis of large-scale anonymized mobile-phone data. The non-negative matrix factorization (NMF) method was used to analyze mobile statistics data from the Tokyo area. The results confirmed the suitability of the NMF method for extracting behavior patterns from aggregated mobile statistics data. Data analysis results indicated that although non-pharmaceutical interventions (NPIs) measures adopted by the Japanese government are non-compulsory and rely largely on requests for voluntary self-restriction, they are effective in reducing population mobility and motivating people to practice social distancing. In addition, the current study compared the mobility change in three cities (i.e., Tokyo, Osaka, and Hiroshima), and discussed their similarity and difference in behavior pattern changes during the pandemic. It is expected that the analytical tool proposed in this study can be used to monitor mobility changes in real-time during the pandemic, as well as the long-term evolution of population mobility patterns in the post-pandemic phase.

Intelligent Knowledge Understanding from Students Questionnaires: A Case Study

Learning Analytics techniques are widely used to improve students’ performance. Data collected from students’ assessments are helpful to predict their success and questionnaires are extensively adopted to assess students’ knowledge. Several mathematical models studying the correlation between students’ hidden skills and their performance to questionnaires’ items have been introduced. Among them, Non-negative matrix factorizations (NMFs) have been proven to be effective in automatically extracting hidden skills, a time-consuming activity that is usually tackled manually prone to subjective interpretations. In this paper, we present an intelligent data analysis approach based upon NMF. Data are collected from a competition, namely MathsChallenge, performed by the University of Foggia. In 2021 the competition has been held, for the first time, online due to the Covid-19 pandemic. © 2022, Springer Nature Switzerland AG.

Non-negative matrix factorization temporal topic models and clinical text data identify COVID-19 pandemic effects on primary healthcare and community health in Toronto, Canada.

OBJECTIVE: To demonstrate how non-negative matrix factorization can be used to learn a temporal topic model over a large collection of primary care clinical notes, characterizing diverse COVID-19 pandemic effects on the physical/mental/social health of residents of Toronto, Canada. MATERIALS AND METHODS: The study employs a retrospective open cohort design, consisting of 382,666 primary care progress notes from 44,828 patients, 54 physicians, and 12 clinics collected 01/01/2017 through 31/12/2020. Non-negative matrix factorization uncovers a meaningful latent topical structure permeating the corpus of primary care notes. The learned latent topical basis is transformed into a multivariate time series data structure. Time series methods and plots showcase the evolution/dynamics of learned topics over the study period and allow the identification of COVID-19 pandemic effects. We perform several post-hoc checks of model robustness to increase trust that descriptive/unsupervised inferences are stable over hyper-parameter configurations and/or data perturbations. RESULTS: Temporal topic modelling uncovers a myriad of pandemic-related effects from the expressive clinical text data. In terms of direct effects on patient-health, topics encoding respiratory disease symptoms display altered dynamics during the pandemic year. Further, the pandemic was associated with a multitude of indirect patient-level effects on topical domains representing mental health, sleep, social and familial dynamics, measurement of vitals/labs, uptake of prevention/screening maneuvers, and referrals to medical specialists. Finally, topic models capture changes in primary care practice patterns resulting from the pandemic, including changes in EMR documentation strategies and the uptake of telemedicine. CONCLUSION: Temporal topic modelling applied to a large corpus of rich primary care clinical text data, can identify a meaningful topical/thematic summarization which can provide policymakers and public health stakeholders a passive, cost-effective, technology for understanding holistic impacts of the COVID-19 pandemic on the primary healthcare system and community/public-health.

A recommender system approach for predicting effective antivirals

Emerging infectious diseases such as COVID-19, caused by the SARS-CoV-2 virus, require systematic strategies to assist in the discovery of effective treatments. Drug repositioning, the process of finding new therapeutic indications for commercialized drugs, is a promising alternative to the development of new drugs, with lower costs and shorter development times. In this paper, we propose a recommendation system called geometric confidence non-negative matrix factorization (GcNMF) to assist in the repositioning of 126 broad spectrum antiviral drugs for 80 viruses, including SARS-CoV-2. GcNMF models the non-Euclidean structure of the space using graphs, and produces a ranked list of drugs for each virus. Our experiments reveal that GcNMF significanlty outperforms other matrix decomposition methods at predicting missing drug-virus associations. Our analysis suggests that GcNMF could assist pharmacological experts in the search for effective drugs against viral diseases. ©2021 IEEE

Strategies to minimize heterogeneity and optimize clinical trials in Acute Respiratory Distress Syndrome (ARDS): Insights from mathematical modelling.

BACKGROUND: Mathematical modelling may aid in understanding the complex interactions between injury and immune response in critical illness. METHODS: We utilize a system biology model of COVID-19 to analyze the effect of altering baseline patient characteristics on the outcome of immunomodulatory therapies. We create example parameter sets meant to mimic diverse patient types. For each patient type, we define the optimal treatment, identify biologic programs responsible for clinical responses, and predict biomarkers of those programs. FINDINGS: Model states representing older and hyperinflamed patients respond better to immunomodulation than those representing obese and diabetic patients. The disparate clinical responses are driven by distinct biologic programs. Optimal treatment initiation time is determined by neutrophil recruitment, systemic cytokine expression, systemic microthrombosis and the renin-angiotensin system (RAS) in older patients, and by RAS, systemic microthrombosis and trans IL6 signalling for hyperinflamed patients. For older and hyperinflamed patients, IL6 modulating therapy is predicted to be optimal when initiated very early (<4th day of infection) and broad immunosuppression therapy (corticosteroids) is predicted to be optimally initiated later in the disease (7th - 9th day of infection). We show that markers of biologic programs identified by the model correspond to clinically identified markers of disease severity. INTERPRETATION: We demonstrate that modelling of COVID-19 pathobiology can suggest biomarkers that predict optimal response to a given immunomodulatory treatment. Mathematical modelling thus constitutes a novel adjunct to predictive enrichment and may aid in the reduction of heterogeneity in critical care trials. FUNDING: C.V. received a Marie Sklodowska Curie Actions Individual Fellowship (MSCA-IF-GF-2020-101028945). R.K.J.'s research is supported by R01-CA208205, and U01-CA 224348, R35-CA197743 and grants from the National Foundation for Cancer Research, Jane's Trust Foundation, Advanced Medical Research Foundation and Harvard Ludwig Cancer Center. No funder had a role in production or approval of this manuscript.

Machine learning and network medicine approaches for drug repositioning for COVID-19.

We present two machine learning approaches for drug repurposing. While we have developed them for COVID-19, they are disease-agnostic. The two methodologies are complementary, targeting SARS-CoV-2 and host factors, respectively. Our first approach consists of a matrix factorization algorithm to rank broad-spectrum antivirals. Our second approach, based on network medicine, uses graph kernels to rank drugs according to the perturbation they induce on a subnetwork of the human interactome that is crucial for SARS-CoV-2 infection/replication. Our experiments show that our top predicted broad-spectrum antivirals include drugs indicated for compassionate use in COVID-19 patients; and that the ranking obtained by our kernel-based approach aligns with experimental data. Finally, we present the COVID-19 repositioning explorer (CoREx), an interactive online tool to explore the interplay between drugs and SARS-CoV-2 host proteins in the context of biological networks, protein function, drug clinical use, and Connectivity Map. CoREx is freely available at: https://paccanarolab.org/corex/.

Indicator Regularized Non-Negative Matrix Factorization Method-Based Drug Repurposing for COVID-19.

A novel coronavirus, named COVID-19, has become one of the most prevalent and severe infectious diseases in human history. Currently, there are only very few vaccines and therapeutic drugs against COVID-19, and their efficacies are yet to be tested. Drug repurposing aims to explore new applications of approved drugs, which can significantly reduce time and cost compared with de novo drug discovery. In this study, we built a virus-drug dataset, which included 34 viruses, 210 drugs, and 437 confirmed related virus-drug pairs from existing literature. Besides, we developed an Indicator Regularized non-negative Matrix Factorization (IRNMF) method, which introduced the indicator matrix and Karush-Kuhn-Tucker condition into the non-negative matrix factorization algorithm. According to the 5-fold cross-validation on the virus-drug dataset, the performance of IRNMF was better than other methods, and its Area Under receiver operating characteristic Curve (AUC) value was 0.8127. Additionally, we analyzed the case on COVID-19 infection, and our results suggested that the IRNMF algorithm could prioritize unknown virus-drug associations.

Detection of Hate Speech in COVID-19-Related Tweets in the Arab Region: Deep Learning and Topic Modeling Approach.

BACKGROUND: The massive scale of social media platforms requires an automatic solution for detecting hate speech. These automatic solutions will help reduce the need for manual analysis of content. Most previous literature has cast the hate speech detection problem as a supervised text classification task using classical machine learning methods or, more recently, deep learning methods. However, work investigating this problem in Arabic cyberspace is still limited compared to the published work on English text. OBJECTIVE: This study aims to identify hate speech related to the COVID-19 pandemic posted by Twitter users in the Arab region and to discover the main issues discussed in tweets containing hate speech. METHODS: We used the ArCOV-19 dataset, an ongoing collection of Arabic tweets related to COVID-19, starting from January 27, 2020. Tweets were analyzed for hate speech using a pretrained convolutional neural network (CNN) model; each tweet was given a score between 0 and 1, with 1 being the most hateful text. We also used nonnegative matrix factorization to discover the main issues and topics discussed in hate tweets. RESULTS: The analysis of hate speech in Twitter data in the Arab region identified that the number of non-hate tweets greatly exceeded the number of hate tweets, where the percentage of hate tweets among COVID-19 related tweets was 3.2% (11,743/547,554). The analysis also revealed that the majority of hate tweets (8385/11,743, 71.4%) contained a low level of hate based on the score provided by the CNN. This study identified Saudi Arabia as the Arab country from which the most COVID-19 hate tweets originated during the pandemic. Furthermore, we showed that the largest number of hate tweets appeared during the time period of March 1-30, 2020, representing 51.9% of all hate tweets (6095/11,743). Contrary to what was anticipated, in the Arab region, it was found that the spread of COVID-19-related hate speech on Twitter was weakly related with the dissemination of the pandemic based on the Pearson correlation coefficient (r=0.1982, P=.50). The study also identified the commonly discussed topics in hate tweets during the pandemic. Analysis of the 7 extracted topics showed that 6 of the 7 identified topics were related to hate speech against China and Iran. Arab users also discussed topics related to political conflicts in the Arab region during the COVID-19 pandemic. CONCLUSIONS: The COVID-19 pandemic poses serious public health challenges to nations worldwide. During the COVID-19 pandemic, frequent use of social media can contribute to the spread of hate speech. Hate speech on the web can have a negative impact on society, and hate speech may have a direct correlation with real hate crimes, which increases the threat associated with being targeted by hate speech and abusive language. This study is the first to analyze hate speech in the context of Arabic COVID-19-related tweets in the Arab region.