Knowledge graphs for covid-19: An exploratory review of the current landscape

Background: Searching through the COVID-19 research literature to gain actionable clinical insight is a formidable task, even for experts. The usefulness of this corpus in terms of improving patient care is tied to the ability to see the big picture that emerges when the studies are seen in conjunction rather than in isolation. When the answer to a search query requires linking together multiple pieces of information across documents, simple keyword searches are insufficient. To answer such complex information needs, an innovative artificial intelligence (AI) technology named a knowledge graph (KG) could prove to be effective. Methods: We conducted an exploratory literature review of KG applications in the context of COVID-19. The search term used was "covid-19 knowledge graph". In addition to PubMed, the first five pages of search results for Google Scholar and Google were considered for inclusion. Google Scholar was used to include non-peer-reviewed or non-indexed articles such as pre-prints and conference proceedings. Google was used to identify companies or consortiums active in this domain that have not published any literature, peer-reviewed or otherwise. Results: Our search yielded 34 results on PubMed and 50 results each on Google and Google Scholar. We found KGs being used for facilitating literature search, drug repurposing, clinical trial mapping, and risk factor analysis. Conclusions: Our synopses of these works make a compelling case for the utility of this nascent field of research

Navigating Healthcare Insights: A Birds Eye View of Explainability with Knowledge Graphs

Knowledge graphs (KGs) are gaining prominence in Healthcare AI, especially in drug discovery and pharmaceutical research as they provide a structured way to integrate diverse information sources, enhancing AI system interpretability. This interpretability is crucial in healthcare, where trust and transparency matter, and eXplainable AI (XAI) supports decision making for healthcare professionals. This overview summarizes recent literature on the impact of KGs in healthcare and their role in developing explainable AI models. We cover KG workflow, including construction, relationship extraction, reasoning, and their applications in areas like Drug-Drug Interactions (DDI), Drug Target Interactions (DTI), Drug Development (DD), Adverse Drug Reactions (ADR), and bioinformatics. We emphasize the importance of making KGs more interpretable through knowledge-infused learning in healthcare. Finally, we highlight research challenges and provide insights for future directions.Comment: IEEE AIKE 2023, 8 Page

KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response.

Integrated, up-to-date data about SARS-CoV-2 and COVID-19 is crucial for the ongoing response to the COVID-19 pandemic by the biomedical research community. While rich biological knowledge exists for SARS-CoV-2 and related viruses (SARS-CoV, MERS-CoV), integrating this knowledge is difficult and time-consuming, since much of it is in siloed databases or in textual format. Furthermore, the data required by the research community vary drastically for different tasks; the optimal data for a machine learning task, for example, is much different from the data used to populate a browsable user interface for clinicians. To address these challenges, we created KG-COVID-19, a flexible framework that ingests and integrates heterogeneous biomedical data to produce knowledge graphs (KGs), and applied it to create a KG for COVID-19 response. This KG framework also can be applied to other problems in which siloed biomedical data must be quickly integrated for different research applications, including future pandemics

Descriptive Knowledge Graph in Biomedical Domain

We present a novel system that automatically extracts and generates informative and descriptive sentences from the biomedical corpus and facilitates the efficient search for relational knowledge. Unlike previous search engines or exploration systems that retrieve unconnected passages, our system organizes descriptive sentences as a relational graph, enabling researchers to explore closely related biomedical entities (e.g., diseases treated by a chemical) or indirectly connected entities (e.g., potential drugs for treating a disease). Our system also uses ChatGPT and a fine-tuned relation synthesis model to generate concise and reliable descriptive sentences from retrieved information, reducing the need for extensive human reading effort. With our system, researchers can easily obtain both high-level knowledge and detailed references and interactively steer to the information of interest. We spotlight the application of our system in COVID-19 research, illustrating its utility in areas such as drug repurposing and literature curation.Comment: EMNLP 2023 Dem

CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations

Systemic analysis of available large-scale biological/biomedical data is critical for studying biological mechanisms, and developing novel and effective treatment approaches against diseases. However, different layers of the available data are produced using different technologies and scattered across individual computational resources without any explicit connections to each other, which hinders extensive and integrative multi-omics-based analysis. We aimed to address this issue by developing a new data integration/representation methodology and its application by constructing a biological data resource. CROssBAR is a comprehensive system that integrates large-scale biological/biomedical data from various resources and stores them in a NoSQL database. CROssBAR is enriched with the deep-learning-based prediction of relationships between numerous data entries, which is followed by the rigorous analysis of the enriched data to obtain biologically meaningful modules. These complex sets of entities and relationships are displayed to users via easy-tointerpret, interactive knowledge graphs within an open-access service. CROssBAR knowledge graphs incorporate relevant genes-proteins, molecular interactions, pathways, phenotypes, diseases, as well as known/predicted drugs and bioactive compounds, and they are constructed on-the-fly based on simple non-programmatic user queries. These intensely processed heterogeneous networks are expected to aid systems-level research, especially to infer biological mechanisms in relation to genes, proteins, their ligands, and diseases

Drug repurposing using biological networks

Drug repositioning is a strategy to identify new uses for existing, approved, or research drugs that are outside the scope of its original medical indication. Drug repurposing is based on the fact that one drug can act on multiple targets or that two diseases can have molecular similarities, among others. Currently, thanks to the rapid advancement of high-performance technologies, a massive amount of biological and biomedical data is being generated. This allows the use of computational methods and models based on biological networks to develop new possibilities for drug repurposing. Therefore, here, we provide an in-depth review of the main applications of drug repositioning that have been carried out using biological network models. The goal of this review is to show the usefulness of these computational methods to predict associations and to find candidate drugs for repositioning in new indications of certain diseases

Accelerating COVID-19 research with graph mining and transformer-based learning

In 2020, the White House released the, "Call to Action to the Tech Community on New Machine Readable COVID-19 Dataset," wherein artificial intelligence experts are asked to collect data and develop text mining techniques that can help the science community answer high-priority scientific questions related to COVID-19. The Allen Institute for AI and collaborators announced the availability of a rapidly growing open dataset of publications, the COVID-19 Open Research Dataset (CORD-19). As the pace of research accelerates, biomedical scientists struggle to stay current. To expedite their investigations, scientists leverage hypothesis generation systems, which can automatically inspect published papers to discover novel implicit connections. We present an automated general purpose hypothesis generation systems AGATHA-C and AGATHA-GP for COVID-19 research. The systems are based on graph-mining and the transformer model. The systems are massively validated using retrospective information rediscovery and proactive analysis involving human-in-the-loop expert analysis. Both systems achieve high-quality predictions across domains (in some domains up to 0.97% ROC AUC) in fast computational time and are released to the broad scientific community to accelerate biomedical research. In addition, by performing the domain expert curated study, we show that the systems are able to discover on-going research findings such as the relationship between COVID-19 and oxytocin hormone

Accelerating science with human-aware artificial intelligence

Artificial intelligence (AI) models trained on published scientific findings have been used to invent valuable materials and targeted therapies, but they typically ignore the human scientists who continually alter the landscape of discovery. Here we show that incorporating the distribution of human expertise by training unsupervised models on simulated inferences cognitively accessible to experts dramatically improves (up to 400%) AI prediction of future discoveries beyond those focused on research content alone, especially when relevant literature is sparse. These models succeed by predicting human predictions and the scientists who will make them. By tuning human-aware AI to avoid the crowd, we can generate scientifically promising "alien" hypotheses unlikely to be imagined or pursued without intervention until the distant future, which hold promise to punctuate scientific advance beyond questions currently pursued. Accelerating human discovery or probing its blind spots, human-aware AI enables us to move toward and beyond the contemporary scientific frontier