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Developing computational tools for integrative analysis across multiple types of omics data has been of immense importance in cancer molecular biology and precision medicine research. While recent advancements have yielded integrative…
This study presents a versatile ontology and a useful codification scheme for describing all kinds of engineered living materials (ELMs). The different components of the ontology, namely: families according to the taxonomy for ELMs,…
Clinical notes contain unstructured text provided by clinicians during patient encounters. These notes are usually accompanied by a sequence of diagnostic codes following the International Classification of Diseases (ICD). Correctly…
Artificial intelligence (AI) is reshaping modern healthcare by advancing disease diagnosis, treatment decision-making, and biomedical research. Among AI technologies, large language models (LLMs) have become especially impactful, enabling…
Organizing a large-scale knowledge graph into a typed property graph requires structural decisions -- which entities become nodes, which properties become edges, and what schema governs these choices. Existing approaches embed these…
Recognizing biomedical concepts in the text is vital for ontology refinement, knowledge graph construction, and concept relationship discovery. However, traditional concept recognition methods, relying on explicit mention identification,…
Biomedical knowledge graphs (BioMedKGs) are essential infrastructures for biomedical and healthcare big data and artificial intelligence (AI), facilitating natural language processing, model development, and data exchange. For decades,…
Automatic coding of International Classification of Diseases (ICD) is a multi-label text categorization task that involves extracting disease or procedure codes from clinical notes. Despite the application of state-of-the-art natural…
OTTR is a language for representing ontology modeling patterns, which enables to build ontologies or knowledge bases by instantiating templates. Thereby, particularities of the ontological representation language are hidden from the domain…
Large Language Models (LLMs) have become a pivotal research area, potentially making beneficial contributions in fields like healthcare where they can streamline automated billing and decision support. However, the frequent use of…
Algorithm design is crucial for effective problem-solving across various domains. The advent of Large Language Models (LLMs) has notably enhanced the automation and innovation within this field, offering new perspectives and promising…
Ontologies play a critical role in data exchange, information integration, and knowledge sharing across diverse smart building applications. Yet, semantic differences between the prevailing building ontologies hamper their purpose of…
Ever-expanding volumes of biomedical text require automated semantic annotation techniques to curate and put to best use. An established field of research seeks to link mentions in text to knowledge bases such as those included in the UMLS…
Mapping clinical documents to standardised clinical vocabularies is an important task, as it provides structured data for information retrieval and analysis, which is essential to clinical research, hospital administration and improving…
Reproducibility of computational results remains a challenge in materials science, as simulation workflows and parameters are often reported only in unstructured text and tables. While literature data are valuable for validation and reuse,…
Accurate tumor analysis is central to clinical radiology and precision oncology, where early detection, reliable lesion characterization, and pathology-level risk assessment guide diagnosis and treatment planning. Chain-of-Thought (CoT)…
Clinical coding is a critical task in healthcare, although traditional methods for automating clinical coding may not provide sufficient explicit evidence for coders in production environments. This evidence is crucial, as medical coders…
Motivation: Ontologies are widely used in biology for data annotation, integration, and analysis. In addition to formally structured axioms, ontologies contain meta-data in the form of annotation axioms which provide valuable pieces of…
Microbiology research has access to a very large amount of public information on the habitats of microorganisms. Many areas of microbiology research uses this information, primarily in biodiversity studies. However the habitat information…
International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned…