Novel approach by natural language processing for COVID-19 knowledge discovery.

BACKGROUND: The impact of COVID-19 on public health has mandated an 'all hands on deck' scientific response. The current clinical study and basic research on COVID-19 are mainly based on existing publications or our knowledge of coronavirus. However, efficiently retrieval of accurate, relevant knowledge on COVID-19 can pose significant challenges for researchers. METHODS: To improve quality in accessing important literature findings, we developed a novel natural language processing (NLP) method to automatically recognize the associations among potential targeted host organ systems, associated clinical manifestations, and pathways. We further validated these associations through clinician experts' evaluations and prioritize candidate drug targets through bioinformatics network analysis. RESULTS: We found that the angiotensin-converting enzyme 2 (ACE2), a receptor that SARS-CoV-2 required for cell entry, is associated with cardiovascular and endocrine organ system and diseases. Furthermore, we found SARS-CoV-2 is associated with some important pathways such as IL-6, TNF-alpha, and IL-1 beta-induced dyslipidemia, which are related to inflammation, lipogenesis, and oxidative stress mechanisms, suggesting potential drug candidates. CONCLUSION: We prioritized the list of therapeutic targets involved in antiviral and immune modulating drugs for experimental validation, rendering it valuable during public health crises marked by stresses on clinical and research capacity. Our automatic intelligence pipeline also contributes to other novel and emerging disease management and treatments in the future.

OmicLoupe: facilitating biological discovery by interactive exploration of multiple omic datasets and statistical comparisons.

BACKGROUND: Visual exploration of gene product behavior across multiple omic datasets can pinpoint technical limitations in data and reveal biological trends. Still, such exploration is challenging as there is a need for visualizations that are tailored for the purpose. RESULTS: The OmicLoupe software was developed to facilitate visual data exploration and provides more than 15 interactive cross-dataset visualizations for omics data. It expands visualizations to multiple datasets for quality control, statistical comparisons and overlap and correlation analyses, while allowing for rapid inspection and downloading of selected features. The usage of OmicLoupe is demonstrated in three different studies, where it allowed for detection of both technical data limitations and biological trends across different omic layers. An example is an analysis of SARS-CoV-2 infection based on two previously published studies, where OmicLoupe facilitated the identification of gene products with consistent expression changes across datasets at both the transcript and protein levels. CONCLUSIONS: OmicLoupe provides fast exploration of omics data with tailored visualizations for comparisons within and across data layers. The interactive visualizations are highly informative and are expected to be useful in various analyses of both newly generated and previously published data. OmicLoupe is available at quantitativeproteomics.org/omicloupe.

Artificial Intelligence in Action: Addressing the COVID-19 Pandemic with Natural Language Processing.

The COVID-19 (coronavirus disease 2019) pandemic has had a significant impact on society, both because of the serious health effects of COVID-19 and because of public health measures implemented to slow its spread. Many of these difficulties are fundamentally information needs; attempts to address these needs have caused an information overload for both researchers and the public. Natural language processing (NLP)-the branch of artificial intelligence that interprets human language-can be applied to address many of the information needs made urgent by the COVID-19 pandemic. This review surveys approximately 150 NLP studies and more than 50 systems and datasets addressing the COVID-19 pandemic. We detail work on four core NLP tasks: information retrieval, named entity recognition, literature-based discovery, and question answering. We also describe work that directly addresses aspects of the pandemic through four additional tasks: topic modeling, sentiment and emotion analysis, caseload forecasting, and misinformation detection. We conclude by discussing observable trends and remaining challenges.

Examining the concept of equity in community psychology with natural language processing.

Large amounts of text-based data, like study abstracts, often go unanalyzed because the task is laborious. Natural language processing (NLP) uses computer-based algorithms not traditionally implemented in community psychology to effectively and efficiently process text. These methods include examining the frequency of words and phrases, the clustering of topics, and the interrelationships of words. This article applied NLP to explore the concept of equity in community psychology. The COVID-19 crisis has made pre-existing health equity gaps even more salient. Community psychology has a specific interest in working with organizations, systems, and communities to address social determinants that perpetuate inequities by refocusing interventions around achieving health and wellness for all. This article examines how community psychology has discussed equity thus far to identify strengths and gaps for future research and practice. The results showed the prominence of community-based participatory research and the diversity of settings researchers work in. However, the total number of abstracts with equity concepts was lower than expected, which suggests there is a need for a continued focus on equity.

Knowledge discovery from emergency ambulance dispatch during COVID-19: A case study of Nagoya City, Japan.

Accurate forecasting of medical service requirements is an important big data problem that is crucial for resource management in critical times such as natural disasters and pandemics. With the global spread of coronavirus disease 2019 (COVID-19), several concerns have been raised regarding the ability of medical systems to handle sudden changes in the daily routines of healthcare providers. One significant problem is the management of ambulance dispatch and control during a pandemic. To help address this problem, we first analyze ambulance dispatch data records from April 2014 to August 2020 for Nagoya City, Japan. Significant changes were observed in the data during the pandemic, including the state of emergency (SoE) declared across Japan. In this study, we propose a deep learning framework based on recurrent neural networks to estimate the number of emergency ambulance dispatches (EADs) during a SoE. The fusion of data includes environmental factors, the localization data of mobile phone users, and the past history of EADs, thereby providing a general framework for knowledge discovery and better resource management. The results indicate that the proposed blend of training data can be used efficiently in a real-world estimation of EAD requirements during periods of high uncertainties such as pandemics.

Drug repurposing for COVID-19 via knowledge graph completion.

OBJECTIVE: To discover candidate drugs to repurpose for COVID-19 using literature-derived knowledge and knowledge graph completion methods. METHODS: We propose a novel, integrative, and neural network-based literature-based discovery (LBD) approach to identify drug candidates from PubMed and other COVID-19-focused research literature. Our approach relies on semantic triples extracted using SemRep (via SemMedDB). We identified an informative and accurate subset of semantic triples using filtering rules and an accuracy classifier developed on a BERT variant. We used this subset to construct a knowledge graph, and applied five state-of-the-art, neural knowledge graph completion algorithms (i.e., TransE, RotatE, DistMult, ComplEx, and STELP) to predict drug repurposing candidates. The models were trained and assessed using a time slicing approach and the predicted drugs were compared with a list of drugs reported in the literature and evaluated in clinical trials. These models were complemented by a discovery pattern-based approach. RESULTS: Accuracy classifier based on PubMedBERT achieved the best performance (F1 = 0.854) in identifying accurate semantic predications. Among five knowledge graph completion models, TransE outperformed others (MR = 0.923, Hits@1 = 0.417). Some known drugs linked to COVID-19 in the literature were identified, as well as others that have not yet been studied. Discovery patterns enabled identification of additional candidate drugs and generation of plausible hypotheses regarding the links between the candidate drugs and COVID-19. Among them, five highly ranked and novel drugs (i.e., paclitaxel, SB 203580, alpha 2-antiplasmin, metoclopramide, and oxymatrine) and the mechanistic explanations for their potential use are further discussed. CONCLUSION: We showed that a LBD approach can be feasible not only for discovering drug candidates for COVID-19, but also for generating mechanistic explanations. Our approach can be generalized to other diseases as well as to other clinical questions. Source code and data are available at https://github.com/kilicogluh/lbd-covid.

Network graph representation of COVID-19 scientific publications to aid knowledge discovery.

INTRODUCTION: Numerous scientific journal articles related to COVID-19 have been rapidly published, making navigation and understanding of relationships difficult. METHODS: A graph network was constructed from the publicly available COVID-19 Open Research Dataset (CORD-19) of COVID-19-related publications using an engine leveraging medical knowledge bases to identify discrete medical concepts and an open-source tool (Gephi) to visualise the network. RESULTS: The network shows connections between diseases, medications and procedures identified from the title and abstract of 195 958 COVID-19-related publications (CORD-19 Dataset). Connections between terms with few publications, those unconnected to the main network and those irrelevant were not displayed. Nodes were coloured by knowledge base and the size of the node related to the number of publications containing the term. The data set and visualisations were made publicly accessible via a webtool. CONCLUSION: Knowledge management approaches (text mining and graph networks) can effectively allow rapid navigation and exploration of entity inter-relationships to improve understanding of diseases such as COVID-19.

Science as collaborative knowledge generation.

The COVID-19 pandemic points to the need for scientists to pool their efforts in order to understand this disease and respond to the ensuing crisis. Other global challenges also require such scientific cooperation. Yet in academic institutions, reward structures and incentives are based on systems that primarily fuel the competition between (groups of) scientific researchers. Competition between individual researchers, research groups, research approaches, and scientific disciplines is seen as an important selection mechanism and driver of academic excellence. These expected benefits of competition have come to define the organizational culture in academia. There are clear indications that the overreliance on competitive models undermines cooperative exchanges that might lead to higher quality insights. This damages the well-being and productivity of individual researchers and impedes efforts towards collaborative knowledge generation. Insights from social and organizational psychology on the side effects of relying on performance targets, prioritizing the achievement of success over the avoidance of failure, and emphasizing self-interest and efficiency, clarify implicit mechanisms that may spoil valid attempts at transformation. The analysis presented here elucidates that a broader change in the academic culture is needed to truly benefit from current attempts to create more open and collaborative practices for cumulative knowledge generation.

Knowledge synthesis of 100 million biomedical documents augments the deep expression profiling of coronavirus receptors.

The COVID-19 pandemic demands assimilation of all biomedical knowledge to decode mechanisms of pathogenesis. Despite the recent renaissance in neural networks, a platform for the real-time synthesis of the exponentially growing biomedical literature and deep omics insights is unavailable. Here, we present the nferX platform for dynamic inference from over 45 quadrillion possible conceptual associations from unstructured text, and triangulation with insights from single-cell RNA-sequencing, bulk RNA-seq and proteomics from diverse tissue types. A hypothesis-free profiling of ACE2 suggests tongue keratinocytes, olfactory epithelial cells, airway club cells and respiratory ciliated cells as potential reservoirs of the SARS-CoV-2 receptor. We find the gut as the putative hotspot of COVID-19, where a maturation correlated transcriptional signature is shared in small intestine enterocytes among coronavirus receptors (ACE2, DPP4, ANPEP). A holistic data science platform triangulating insights from structured and unstructured data holds potential for accelerating the generation of impactful biological insights and hypotheses.