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Representation learning methods that transform encoded data (e.g., diagnosis and drug codes) into continuous vector spaces (i.e., vector embeddings) are critical for the application of deep learning in healthcare. Initial work in this area…

Retrieval over knowledge graphs is usually performed using dedicated, complex query languages like SPARQL. We propose a novel system, Ontology and Semantic Exploration Toolkit (OnSET) that allows non-expert users to easily build queries…

In computational biology, biological entities such as genes or proteins are usually annotated with terms extracted from Gene Ontology (GO). The functional similarity among terms of an ontology is evaluated by using Semantic Similarity…

There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types -- such as disease names, cell types or chemicals -- that are used in metadata associated with…

Mentions of new concepts appear regularly in texts and require automated approaches to harvest and place them into Knowledge Bases (KB), e.g., ontologies and taxonomies. Existing datasets suffer from three issues, (i) mostly assuming that a…

Because of the increasing number of electronic data, designing efficient tools to retrieve and exploit documents is a major challenge. Current search engines suffer from two main drawbacks: there is limited interaction with the list of…

We propose a knowledge engine called Sinoledge mainly for doctors, physicians, and researchers in medical field to organize thoughts, manage reasoning process, test and deploy to production environments effortlessly. Our proposal can be…

This work presents the architecture used in the ongoing OntologyNavigator project. It is a research tool to help advanced learners to find adapted IT papers to create scientific bibliographies. The purpose is the use of an IT representation…

Semantic Web is actually an extension of the current one in that it represents information more meaningfully for humans and computers alike. It enables the description of contents and services in machine-readable form, and enables…

Electronic health record (EHR) systems are used extensively throughout the healthcare domain. However, data interchangeability between EHR systems is limited due to the use of different coding standards across systems. Existing methods of…

The exchange of large and complex slide microscopy imaging data in biomedical research and pathology practice is impeded by a lack of data standardization and interoperability, which is detrimental to the reproducibility of scientific…

We present a system that uses a learned autocompletion mechanism to facilitate rapid creation of semi-structured clinical documentation. We dynamically suggest relevant clinical concepts as a doctor drafts a note by leveraging features from…

Today, we can find many search engines which provide us with information which is more operational in nature. None of the search engines provide domain specific information. This becomes very troublesome to a novice user who wishes to have…

The automated capturing and summarization of medical consultations has the potential to reduce the administrative burden in healthcare. Consultations are structured conversations that broadly follow a guideline with a systematic examination…

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…

Large sense-annotated datasets are increasingly necessary for training deep supervised systems in Word Sense Disambiguation. However, gathering high-quality sense-annotated data for as many instances as possible is a laborious and expensive…

We introduce the world's first clinical terminology for the Chinese healthcare community, namely MedCT, accompanied by a clinical foundation model MedBERT and an entity linking model MedLink. The MedCT system enables standardized and…

The way we analyse clinical texts has undergone major changes over the last years. The introduction of language models such as BERT led to adaptations for the (bio)medical domain like PubMedBERT and ClinicalBERT. These models rely on large…

Clinical text is rich in information, with mentions of treatment, medication and anatomy among many other clinical terms. Multiple terms can refer to the same core concepts which can be referred as a clinical entity. Ontologies like the…

Clinicians face several significant barriers to search and synthesize accurate, succinct, updated, and trustworthy medical information from several literature sources during the practice of medicine and patient care. In this talk, we will…