Relation Prediction of Co-Morbid Diseases Using Knowledge Graph Completion

RETRACTED ARTICLE: DLMBHCO: design of an augmented bioinspired deep learning-based multidomain body parameter analysis via heterogeneous correlative body organ analysis

Progressive organ-level disorders in the human body are often correlated with diseases in other body parts. For instance, liver diseases can be linked with heart issues, while cancers can be linked with brain diseases (or psychological conditions). Defining such correlations is a complex task, and existing deep learning models that perform this task either showcase lower accuracy or are non-comprehensive when applied to real-time scenarios. To overcome these issues, this text proposes design of an augmented bioinspired deep learning-based multidomain body parameter analysis via heterogeneous correlative body organ analysis. The proposed model initially collects temporal and spatial data scans for different body parts and uses a multidomain feature extraction engine to convert these scans into vector sets. These vectors are processed by a Bacterial Foraging Optimizer (BFO), which assists in identification of highly variant feature sets, which are individually classified into different disease categories. A fusion of Inception Net, XCeption Net, and GoogLeNet Models is used to perform these classifications. The classified categories are linked with other disease types via temporal analysis of blood reports. The temporal analysis engine uses Modified Analytical Hierarchical Processing (MAHP) Model for calculating inter-organ disease dependency probabilities. Based on these probabilities, the model is able to generate a patient-level correlation map, which can be used by clinical experts to suggest remedial treatments, due to which the model was able to identify correlations between brain disorders and kidneys, heart diseases and lungs, heart diseases and liver, brain diseases and different types of cancers with high efficiency when evaluated under clinical scenarios. When validated on MITBIH, DEAP, CT Kidney, RIDER, and PLCO data samples, it was observed that the proposed model was capable of improving accuracy of correlation by 8.5%, while improving precision and recall by 3.2% when compared with existing correlation models under similar clinical scenarios.

Genetically and semantically aware homogeneous network for prediction and scoring of comorbidities

OBJECTIVE

Patients with comorbidities are highly prone to mortality risk than those suffering from a single disease. Therefore, quantification and prediction of disease comorbidities is necessary to stratify the mortality risk of the patients, predict the probability of their occurrence, design treatment strategies, and to prevent the progression of diseases. Enriching comorbidity disease relationships with rich semantics established by genetic components play a vital role in effectively quantifying and predicting comorbidities. However, the existing studies have not extensively explored the semantic richness conveyed by different types of genetic links connecting the comorbidity pairs.

METHODS

To solve this, a novel genetic-semantic aware weighted homogeneous network-based method, GSWHomoNet is proposed which first constructs the gene enriched comorbidity heterogeneous network, CoGHetNet with encoded genetic semantic aware weighted meta-path instance disease pair embedding to obtain an enhanced disease node embedding of the network. For enhanced comorbidity prediction and scoring, both direct and indirect semantically enriched comorbidity relationships of the disease nodes is preserved while transforming heterogeneous to homogeneous comorbidity network GSWHomoNet. The proposed GSWHomoNet not only helps discover comorbidity links transductively between known-known disease pairs but also improves the inductive link prediction between known-unknown disease pairs by supplying unknown disease nodes with semantically enriched heterogeneous structural knowledge.

RESULTS

The effectiveness of the proposed components is proved by AUC scores of 0.895 and 0.860, as well as AUPR scores of 0.903 and 0.873 for transductive and inductive link prediction respectively. In comorbidity scoring, GSWHomoNet outperformed other methods with a correlation result of 0.848. The effect of the improved association prediction ability of the genetic semantic aware weighted meta-path instance embedding based node embedding is proved on disease-microbe and bibliographic heterogeneous network datasets. For biological significance of GSWHomoNet-based comorbidity scoring, we compared it with gene, pathway, and protein-protein interaction (PPI) perspectives, revealing a stronger correlation with the PPI aspect. We identified a substantial number of predicted comorbidity disease pairs, with 77,456 and 48,972 pairs supported by literature evidence for transductive and inductive predictions, respectively. Additionally, we highlighted shared pathways and PPIs for these pairs, demonstrating the robustness of comorbidity predictions.

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 holistically and multi-dimensionally. 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.

In silico protein function prediction: the rise of machine learning-based approaches

Proteins function as integral actors in essential life processes, rendering the realm of protein research a fundamental domain that possesses the potential to propel advancements in pharmaceuticals and disease investigation. Within the context of protein research, an imperious demand arises to uncover protein functionalities and untangle intricate mechanistic underpinnings. Due to the exorbitant costs and limited throughput inherent in experimental investigations, computational models offer a promising alternative to accelerate protein function annotation. In recent years, protein pre-training models have exhibited noteworthy advancement across multiple prediction tasks. This advancement highlights a notable prospect for effectively tackling the intricate downstream task associated with protein function prediction. In this review, we elucidate the historical evolution and research paradigms of computational methods for predicting protein function. Subsequently, we summarize the progress in protein and molecule representation as well as feature extraction techniques. Furthermore, we assess the performance of machine learning-based algorithms across various objectives in protein function prediction, thereby offering a comprehensive perspective on the progress within this field.

Towards a knowledge graph for pre-/probiotics and microbiota-gut-brain axis diseases

Scientific publications present biological relationships but are structured for human reading, making it difficult to use this resource for semantic integration and querying. Existing databases, on the other hand, are well structured for automated analysis, but do not contain comprehensive biological knowledge. We devised an approach for constructing comprehensive knowledge graphs from these two types of resources and applied it to investigate relationships between pre-/probiotics and microbiota-gut-brain axis diseases. To this end, we created (i) a knowledge base, dubbed ppstatement, containing manually curated detailed annotations, and (ii) a knowledge base, called ppconcept, containing automatically annotated concepts. The resulting Pre-/Probiotics Knowledge Graph (PPKG) combines these two knowledge bases with three other public databases (i.e. MeSH, UMLS and SNOMED CT). To validate the performance of PPKG and to demonstrate the added value of integrating two knowledge bases, we created four biological query cases. The query cases demonstrate that we can retrieve co-occurring concepts of interest, and also that combining the two knowledge bases leads to more comprehensive query results than utilizing them separately. The PPKG enables users to pose research queries such as "which pre-/probiotics combinations may benefit depression?", potentially leading to novel biological insights.

Biomedical Relation Extraction with Knowledge Graph-based Recommendations

Biomedical Relation Extraction (RE) systems identify and classify relations between biomedical entities to enhance our knowledge of biological and medical processes. Most state-of-the-art systems use deep learning approaches, mainly to target relations between entities of the same type, such as proteins or pharmacological substances. However, these systems are mostly restricted to what they directly identify on the text and ignore specialized domain knowledge bases, such as ontologies, that formalize and integrate biomedical information typically structured as direct acyclic graphs. On the other hand, Knowledge Graph (KG)-based recommendation systems already showed the importance of integrating KGs to add additional features to items. Typical systems have users as people and items that can range from movies to books, which people saw or read and classified according to their satisfaction rate. This work proposes to integrate KGs into biomedical RE through a recommendation model to further improve their range of action. We developed a new RE system, named K-BiOnt, by integrating a baseline state-of-the-art deep biomedical RE system with an existing KG-based recommendation state-of-the-art system. Our results show that adding recommendations from KG-based recommendation improves the system's ability to identify true relations that the baseline deep RE model could not extract from the text. All the software and data supporting our work will be made publicly available upon acceptance of this manuscript.

Multitask Healthcare Management Recommendation System Leveraging Knowledge Graph

In this paper, a novel multitask healthcare management recommendation system leveraging the knowledge graph is proposed, which is based on deep neural network and 5G network, and it can be applied in mobile and terminal device to free up medical resources and provide treatment programs. The technique we applied is referred to as KG-based recommendation system. When several experiments have been carried out, it is demonstrated that it is more intelligent and precise in disease prediction and treatment recommendation, similar to the state of the art. Also, it works well in the accuracy and comprehension, which is much higher and highly consistent with the predictions of the theoretical model. The fact that our work involves studies of multitask healthcare management recommendation system, which can contribute to the smart healthcare development, proves to be promising and encouraging.

Application and evaluation of knowledge graph embeddings in biomedical data

Linked data and bio-ontologies enabling knowledge representation, standardization, and dissemination are an integral part of developing biological and biomedical databases. That is, linked data and bio-ontologies are employed in databases to maintain data integrity, data organization, and to empower search capabilities. However, linked data and bio-ontologies are more recently being used to represent information as multi-relational heterogeneous graphs, "knowledge graphs". The reason being, entities and relations in the knowledge graph can be represented as embedding vectors in semantic space, and these embedding vectors have been used to predict relationships between entities. Such knowledge graph embedding methods provide a practical approach to data analytics and increase chances of building machine learning models with high prediction accuracy that can enhance decision support systems. Here, we present a comparative assessment and a standard benchmark for knowledge graph-based representation learning methods focused on the link prediction task for biological relations. We systematically investigated and compared state-of-the-art embedding methods based on the design settings used for training and evaluation. We further tested various strategies aimed at controlling the amount of information related to each relation in the knowledge graph and its effects on the final performance. We also assessed the quality of the knowledge graph features through clustering and visualization and employed several evaluation metrics to examine their uses and differences. Based on this systematic comparison and assessments, we identify and discuss the limitations of knowledge graph-based representation learning methods and suggest some guidelines for the development of more improved methods.

Predicting the relationships between gut microbiota and mental disorders with knowledge graphs

Gut microbiota produce and modulate the production of neurotransmitters which have been implicated in mental disorders. Neurotransmitters may act as ‘matchmaker’ between gut microbiota imbalance and mental disorders. Most of the relevant research effort goes into the relationship between gut microbiota and neurotransmitters and the other between neurotransmitters and mental disorders, while few studies collect and analyze the dispersed research results in systematic ways. We therefore gather the dispersed results that in the existing studies into a structured knowledge base for identifying and predicting the potential relationships between gut microbiota and mental disorders. In this study, we propose to construct a gut microbiota knowledge graph for mental disorder, which named as MiKG4MD. It is extendable by linking to future ontologies by just adding new relationships between existing information and new entities. This extendibility is emphasized for the integration with existing popular ontologies/terminologies, e.g. UMLS, MeSH, and KEGG. We demonstrate the performance of MiKG4MD with three SPARQL query test cases. Results show that the MiKG4MD knowledge graph is an effective method to predict the relationships between gut microbiota and mental disorders.

Knowledge-Based Biomedical Data Science

Knowledge-based biomedical data science 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 recent progress in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as progress on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing to construct knowledge graphs, and the expansion of novel knowledge-based approaches to clinical and biological domains.