COVID-19 Literature Knowledge Graph Construction and Drug Repurposing Report Generation
University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Columbia University（哥伦比亚大学）；Brandeis University（布兰迪斯大学）；University of Washington（华盛顿大学）；University of California, Los Angeles（加利福尼亚大学洛杉矶分校）；Colorado University（科罗拉多大学）；Army Research Lab（陆军研究实验室）；QS2；Department of Defense（国防部）
To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.
We report development of a data infrastructure for drug repurposing that takes advantage of two currently available chemical ontologies. The data infrastructure includes a database of compound- target associations augmented with molecular ontological labels. It also contains two computational tools for prediction of new associations. We describe two drug-repurposing systems: one, Nascent Ontological Information Retrieval for Drug Repurposing (NOIR-DR), based on an information retrieval strategy, and another, based on non-negative matrix factorization together with compound similarity, that was…
Drug repurposing is more relevant than ever due to drug development's rising costs and the need to respond to emerging diseases quickly. Knowledge graph embedding enables drug repurposing using heterogeneous data sources combined with state-of-the-art machine learning models to predict new drug-disease links in the knowledge graph. As in many machine learning applications, significant work is still required to understand the predictive models' behavior. We propose a structured methodology to understand better machine learning models' results for drug repurposing, suggesting key elements of the…
University of Texas Health Science Center at Houston（休斯顿德克萨斯大学健康科学中心）；University of Minnesota（明尼苏达大学）；University of Pennsylvania（宾夕法尼亚大学）；University of Maryland School of Medicine（马里兰大学医学院）
To date, there are no effective treatments for most neurodegenerative diseases. Knowledge graphs can provide comprehensive and semantic representation for heterogeneous data, and have been successfully leveraged in many biomedical applications including drug repurposing. Our objective is to construct a knowledge graph from literature to study relations between Alzheimer's disease (AD) and chemicals, drugs and dietary supplements in order to identify opportunities to prevent or delay neurodegenerative progression. We collected biomedical annotations and extracted their relations using SemRep vi…
Knowledge graph (KG) is used to represent data in terms of entities and structural relations between the entities. This representation can be used to solve complex problems such as recommendation systems and question answering. In this study, a set of candidate drugs for COVID-19 are proposed by using Drug repurposing knowledge graph (DRKG). DRKG is a biological knowledge graph constructed using a vast amount of open source biomedical knowledge to understand the mechanism of compounds and the related biological functions. Node and relation embeddings are learned using knowledge graph embedding…
DrugReason: Dynamic Multi-View Reasoning over Knowledge Graph and Language Evidence for Drug Repurposing
University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）；Stevens Institute of Technology（史蒂文斯理工学院）；Emory University（埃默里大学）；Massachusetts Institute of Technology（麻省理工学院）
IBM Research（IBM研究院）；University of Melbourne（墨尔本大学）；Cures Within Reach for Cancer（癌症可及疗法组织）；Massachusetts Institute of Technology（麻省理工学院）；Harvard Medical School（哈佛医学院）
More than 200 generic drugs approved by the U.S. Food and Drug Administration for non-cancer indications have shown promise for treating cancer. Due to their long history of safe patient use, low cost, and widespread availability, repurposing of generic drugs represents a major opportunity to rapidly improve outcomes for cancer patients and reduce healthcare costs worldwide. Evidence on the efficacy of non-cancer generic drugs being tested for cancer exists in scientific publications, but trying to manually identify and extract such evidence is intractable. In this paper, we introduce a system…
In the absence of sufficient medication for COVID patients due to the increased demand, disused drugs have been employed or the doses of those available were modified by hospital pharmacists. Some evidences for the use of alternative drugs can be found in the existing scientific literature that could assist in such decisions. However, exploiting large corpus of documents in an efficient manner is not easy, since drugs may not appear explicitly related in the texts and could be mentioned under different brand names. Drugs4Covid combines word embedding techniques and semantic web technologies to…
UniD$^3$: A Knowledge Graph-Enhanced RAG Framework for Drug-Disease Discovery and Reasoning
Department of Health Outcomes and Biomedical Informatics, University of Florida（佛罗里达大学健康成果与生物医学信息学系）；Department of Hematology, H. Lee Moffitt Cancer Center and Research Institute（血液科，H. Lee Moffitt癌症中心与研究院）；Center for Bioinformatics and Computational Biology, Houston Methodist Research Institute（生物信息学与计算生物学中心，休斯顿方法主义研究学院）；Department of Cardiothoracic Surgery, Weill Cornell Medicine, Cornell University（心胸外科，Weill Cornell医学，康奈尔大学）；Department of Biostatistics and Health Data Science, Indiana University School of Medicine（生物统计学与健康数据科学系，印第安纳大学医学院）
Wuhan University（武汉大学）；Hainan University（海南大学）；Shanghai University of Engineering Science（上海工程技术大学）；Institute of Scientific and Technical Information of China（中国科学技术信息研究所）
Knowledge graphs (KGs) on COVID-19 have been constructed to accelerate the research process of COVID-19. However, KGs are always incomplete, especially the new constructed COVID-19 KGs. Link prediction task aims to predict missing entities for (e, r, t) or (h, r, e), where h and t are certain entities, e is an entity that needs to be predicted and r is a relation. This task also has the potential to solve COVID-19 related KGs' incomplete problem. Although various knowledge graph embedding (KGE) approaches have been proposed to the link prediction task, these existing methods suffer from the li…
AstraZeneca（阿斯利康）；University of Cambridge（剑桥大学）；Harvard Medical School（哈佛医学院）；McGill University（麦吉尔大学）；Mila - Quebec AI Institute（米拉-魁北克人工智能研究所）
Drug discovery and development is a complex and costly process. Machine learning approaches are being investigated to help improve the effectiveness and speed of multiple stages of the drug discovery pipeline. Of these, those that use Knowledge Graphs (KG) have promise in many tasks, including drug repurposing, drug toxicity prediction and target gene-disease prioritisation. In a drug discovery KG, crucial elements including genes, diseases and drugs are represented as entities, whilst relationships between them indicate an interaction. However, to construct high-quality KGs, suitable data is …
University of Minnesota（明尼苏达大学）；University of Ljubljana（卢布尔雅那大学）；Pontifical Catholic University of Rio de Janeiro（里约热内卢天主教大学）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
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 both PubMed and COVID-19-focused research literature. Our approach relies on semantic triples extracted using SemRep (via SemMedDB). We identified an informative subset of semantic triples using filtering rules and an accuracy classifier developed on a BERT variant, and used this subset to construct a knowledge graph…
The novel coronavirus disease 2019 (COVID-19) began in Wuhan, China in late 2019 and to date has infected over 14M people worldwide, resulting in over 750,000 deaths. On March 10, 2020 the World Health Organization (WHO) declared the outbreak a global pandemic. Many academics and researchers, not restricted to the medical domain, began publishing papers describing new discoveries. However, with the large influx of publications, it was hard for these individuals to sift through the large amount of data and make sense of the findings. The White House and a group of industry research labs, lead b…
Being a global pandemic, the COVID-19 outbreak received global media attention. In this study, we analyze news publications from CNN and The Guardian - two of the world's most influential media organizations. The dataset includes more than 36,000 articles, analyzed using the clinical and biomedical Natural Language Processing (NLP) models from the Spark NLP for Healthcare library, which enables a deeper analysis of medical concepts than previously achieved. The analysis covers key entities and phrases, observed biases, and change over time in news coverage by correlating mined medical symptoms…
Stanford University（斯坦福大学）；Robert Gordon University（罗伯特戈登大学）
The COVID-19 pandemic created a deluge of questionable and contradictory scientific claims about drug efficacy -- an "infodemic" with lasting consequences for science and society. In this work, we argue that NLP models can help domain experts distill and understand the literature in this complex, high-stakes area. Our task is to automatically identify contradictory claims about COVID-19 drug efficacy. We frame this as a natural language inference problem and offer a new NLI dataset created by domain experts. The NLI framing allows us to create curricula combining existing datasets and our own.…
Since the classification of COVID-19 as a global pandemic, there have been many attempts to treat and contain the virus. Although there is no specific antiviral treatment recommended for COVID-19, there are several drugs that can potentially help with symptoms. In this work, we mined a large twitter dataset of 424 million tweets of COVID-19 chatter to identify discourse around drug mentions. While seemingly a straightforward task, due to the informal nature of language use in Twitter, we demonstrate the need of machine learning alongside traditional automated methods to aid in this task. By ap…
In this research, we present our work participation for the DrugProt task of BioCreative VII challenge. Drug-target interactions (DTIs) are critical for drug discovery and repurposing, which are often manually extracted from the experimental articles. There are >32M biomedical articles on PubMed and manually extracting DTIs from such a huge knowledge base is challenging. To solve this issue, we provide a solution for Track 1, which aims to extract 10 types of interactions between drug and protein entities. We applied an Ensemble Classifier model that combines BioMed-RoBERTa, a state of art lan…
Scientific literature tends to grow as a function of funding and interest in a given field. Mining such literature can reveal trends that may not be immediately apparent. The CORD-19 corpus represents a growing corpus of scientific literature associated with COVID-19. We examined the intersection of a set of candidate therapeutics identified in a drug-repurposing study with temporal instances of the CORD-19 corpus to determine if it was possible to find and measure changes associated with them over time. We propose that the techniques we used could form the basis of a tool to pre-screen new ca…
Bangladesh University of Engineering and Technology（孟加拉国工程技术大学）；Hamad Bin Khalifa University（哈马德·本·哈利法大学）
We are presenting COVID-19Base, a knowledgebase highlighting the biomedical entities related to COVID-19 disease based on literature mining. To develop COVID-19Base, we mine the information from publicly available scientific literature and related public resources. We considered seven topic-specific dictionaries, including human genes, human miRNAs, human lncRNAs, diseases, Protein Databank, drugs, and drug side effects, are integrated to mine all scientific evidence related to COVID-19. We have employed an automated literature mining and labeling system through a novel approach to measure the…
Previous work established skip-gram word2vec models could be used to mine knowledge in the materials science literature for the discovery of thermoelectrics. Recent transformer architectures have shown great progress in language modeling and associated fine-tuned tasks, but they have yet to be adapted for drug discovery. We present a RoBERTa transformer-based method that extends the masked language token prediction using query-target conditioning to treat the specificity challenge. The transformer discovery method entails several benefits over the word2vec method including domain-specific (ant…
