An End-to-End Knowledge Graph Based Question Answering Approach for COVID-19

Question Answering based on Knowledge Graph (KG) has emerged as a popular research area in general domain. However, few works focus on the COVID-19 kg-based question answering, which is very valuable for biomedical domain. In addition, existing question answering methods rely on knowledge embedding models to represent knowledge (i.e., entities and questions), but the relations between entities are neglected. In this paper, we construct a COVID-19 knowledge graph and propose an end-to-end knowledge graph question answering approach that can utilize relation information to improve the performance. Experimental result shows that the effectiveness of our approach on the COVID-19 knowledge graph question answering. Our code and data are available at https://github.com/CHNcreater/COVID-19-KGQA. © 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

STORM-GAN: Spatio-Temporal Meta-GAN for Cross-City Estimation of Human Mobility Responses to COVID-19

Human mobility estimation is crucial during the COVID-19 pandemic due to its significant guidance for policymakers to make non-pharmaceutical interventions. While deep learning approaches outperform conventional estimation techniques on tasks with abundant training data, the continuously evolving pandemic poses a significant challenge to solving this problem due to data non-stationarity, limited observations, and complex social contexts. Prior works on mobility estimation either focus on a single city or lack the ability to model the spatio-temporal dependencies across cities and time periods. To address these issues, we make the first attempt to tackle the cross-city human mobility estimation problem through a deep meta-generative framework. We propose a Spatio-Temporal Meta-Generative Adversarial Network (STORM-GAN) model that estimates dynamic human mobility responses under a set of social and policy conditions related to COVID-19. Facilitated by a novel spatio-temporal task-based graph (STTG) embedding, STORM-GAN is capable of learning shared knowledge from a spatio-temporal distribution of estimation tasks and quickly adapting to new cities and time periods with limited training samples. The STTG embedding component is designed to capture the similarities among cities to mitigate cross-task heterogeneity. Experimental results on real-world data show that the proposed approach can greatly improve estimation performance and outperform baselines. © 2022 IEEE.

Human Trajectory Completion with Transformers

With outbreak of the COVID-19 pandemic, contact tracing has become an important problem. It has been proven that maintaining social distance and isolating affected people are highly beneficial for curbing the spread of COVID-19, which all depend on identifying people's trajectories. However, the current interview-based approach is costly, and the existing mobile app-based schemes rely on complete and accurate data. In this paper, we propose a transformer encoder-based approach with spatial position embedding extracted using a graph Combinatorial Laplacian matrix to interpolate incomplete human trajectories. To model human trajectory, we propose a graphical embedded module to extract spatial features based on predefined location clusters. The incomplete trajectory sequences are first preprocessed into matrices and then used to train a deep transformer encoder network for trajectory completion. Our experiments using a real world Bluetooth Low Energy (BLE) dataset validate the efficacy of our proposed approach, which outperforms several baseline methods. © 2022 IEEE.

Characterizing Disease Spreading via Visibility Graph Embedding

Gaining timely insights on real-world emergency events, such as infectious disease outbreaks, is critical for developing appropriate response strategies. In this work, we propose a data-driven approach to study the spreading dynamics of the global Covid-19 pandemic. Specifically, we aim to identify a set of most 'similar' geographic regions as proxies for making predictions on a targeted location. Example predictions include the number of new cases, number of hospitalizations, and number of deaths. Such predictions can be made at different levels of regional granularities, including city, county, and state levels. Our approach starts by transforming regional time series into graph representations using the natural visibility graph (NVG) model in order to capture their intrinsic trends and properties. These graphs are then projected onto a common embedding space using graph-level network embedding techniques. Essentially, each time series is converted as a data point in a feature embedding space, where spatial proximity indicates similarity among time series. Given a targeted region, our approach can identify the most 'relevant' geographic regions by finding its k-nearest neighbors in the embedding space. Subsequently, appropriate response strategies and policies (e.g., school shutdown, indoor dining restriction) can be adapted based on the success or failure experiences from relevant regions. Our approach will potentially provide valuable insights in mitigating the spreading of infectious disease. © 2021 IEEE.

An Analysis of COVID-19 Knowledge Graph Construction and Applications

The construction and application of knowledge graphs have seen a rapid increase across many disciplines in re-cent years. Additionally, the problem of uncovering relationships between developments in the COVID-19 pandemic and social me-dia behavior is of great interest to researchers hoping to curb the spread of the disease. In this paper we present a knowledge graph constructed from COVID-19 related tweets in the Los Angeles area, supplemented with federal and state policy announcements and disease spread statistics. By incorporating dates, topics, and events as entities, we construct a knowledge graph that describes the connections between these useful information. We use natural language processing and change point analysis to extract tweet-topic, tweet-date, and event-date relations. Further analysis on the constructed knowledge graph provides insight into how tweets reflect public sentiments towards COVID-19 related topics and how changes in these sentiments correlate with real-world events. © 2021 IEEE.

Automatic detection of COVID-19 vaccine misinformation with graph link prediction.

Enormous hope in the efficacy of vaccines became recently a successful reality in the fight against the COVID-19 pandemic. However, vaccine hesitancy, fueled by exposure to social media misinformation about COVID-19 vaccines became a major hurdle. Therefore, it is essential to automatically detect where misinformation about COVID-19 vaccines on social media is spread and what kind of misinformation is discussed, such that inoculation interventions can be delivered at the right time and in the right place, in addition to interventions designed to address vaccine hesitancy. This paper is addressing the first step in tackling hesitancy against COVID-19 vaccines, namely the automatic detection of known misinformation about the vaccines on Twitter, the social media platform that has the highest volume of conversations about COVID-19 and its vaccines. We present CoVaxLies, a new dataset of tweets judged relevant to several misinformation targets about COVID-19 vaccines on which a novel method of detecting misinformation was developed. Our method organizes CoVaxLies in a Misinformation Knowledge Graph as it casts misinformation detection as a graph link prediction problem. The misinformation detection method detailed in this paper takes advantage of the link scoring functions provided by several knowledge embedding methods. The experimental results demonstrate the superiority of this method when compared with classification-based methods, widely used currently.

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.