Knowledge-based Biomedical Data Science 2019

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 table

Patient-Centric Knowledge Graphs: A Survey of Current Methods, Challenges, and Applications

Patient-Centric Knowledge Graphs (PCKGs) represent an important shift in healthcare that focuses on individualized patient care by mapping the patient's health information in a holistic and multi-dimensional way. PCKGs integrate various types of health data to provide healthcare professionals with a comprehensive understanding of a patient's health, enabling more personalized and effective care. This literature review explores the methodologies, challenges, and opportunities associated with PCKGs, focusing on their role in integrating disparate healthcare data and enhancing patient care through a unified health perspective. In addition, this review also discusses the complexities of PCKG development, including ontology design, data integration techniques, knowledge extraction, and structured representation of knowledge. It highlights advanced techniques such as reasoning, semantic search, and inference mechanisms essential in constructing and evaluating PCKGs for actionable healthcare insights. We further explore the practical applications of PCKGs in personalized medicine, emphasizing their significance in improving disease prediction and formulating effective treatment plans. Overall, this review provides a foundational perspective on the current state-of-the-art and best practices of PCKGs, guiding future research and applications in this dynamic field

Comparative Analysis of Contextual Relation Extraction based on Deep Learning Models

Contextual Relation Extraction (CRE) is mainly used for constructing a knowledge graph with a help of ontology. It performs various tasks such as semantic search, query answering, and textual entailment. Relation extraction identifies the entities from raw texts and the relations among them. An efficient and accurate CRE system is essential for creating domain knowledge in the biomedical industry. Existing Machine Learning and Natural Language Processing (NLP) techniques are not suitable to predict complex relations from sentences that consist of more than two relations and unspecified entities efficiently. In this work, deep learning techniques have been used to identify the appropriate semantic relation based on the context from multiple sentences. Even though various machine learning models have been used for relation extraction, they provide better results only for binary relations, i.e., relations occurred exactly between the two entities in a sentence. Machine learning models are not suited for complex sentences that consist of the words that have various meanings. To address these issues, hybrid deep learning models have been used to extract the relations from complex sentence effectively. This paper explores the analysis of various deep learning models that are used for relation extraction.Comment: This Paper Presented in the International Conference on FOSS Approaches towards Computational Intelligence and Language TTechnolog on February 2023, Thiruvananthapura