相关论文: Data Infrastructure and Approaches for Ontology-Ba…

The \textit{de facto} paradigm for applying dense retrieval (DR) to new tasks involves fine-tuning a pre-trained model for a specific task. However, this paradigm has two significant limitations: (1) It is difficult adapt the DR to a new…

The paper utilizes the graph embeddings generated for entities of a large biomedical database to perform link prediction to capture various new relationships among different entities. A novel node similarity measure is proposed that…

Information retrieval aims to find information that meets users' needs from the corpus. Different needs correspond to different IR tasks such as document retrieval, open-domain question answering, retrieval-based dialogue, etc., while they…

Deep learning-based approaches for generating novel drug molecules with specific properties have gained a lot of interest in the last few years. Recent studies have demonstrated promising performance for string-based generation of novel…

Starting from an unsolved problem of information retrieval this paper presents an ontology-based model for indexing and retrieval. The model combines the methods and experiences of cognitive-to-interpret indexing languages with the…

Drug discovery is a complex process with a large molecular space to be considered. By constraining the search space, the fragment-based drug design is an approach that can effectively sample the chemical space of interest. Here we propose a…

Information Retriever (IR) aims to find the relevant documents (e.g. snippets, passages, and articles) to a given query at large scale. IR plays an important role in many tasks such as open domain question answering and dialogue systems,…

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…

Designing a single molecule that modulates two targets is a promising strategy for polypharmacology, but it remains substantially harder than standard single-target generation because one candidate must satisfy two binding requirements…

Open-domain question answering requires retrieval systems able to cope with the diverse and varied nature of questions, providing accurate answers across a broad spectrum of query types and topics. To deal with such topic heterogeneity…

The objective of this research is to introduce a network specialized in predicting drugs that can be repurposed by investigating real-world evidence sources, such as clinical trials and biomedical literature. Specifically, it aims to…

One of the core problems in large-scale recommendations is to retrieve top relevant candidates accurately and efficiently, preferably in sub-linear time. Previous approaches are mostly based on a two-step procedure: first learn an…

Document retrieval has been an important research problem over many years in the information retrieval community. State-of-the-art techniques utilize various methods in matching documents to a given document including keywords, phrases, and…

The 2019 novel coronavirus (SARS-CoV-2) pandemic has resulted in more than a million deaths, high morbidities, and economic distress worldwide. There is an urgent need to identify medications that would treat and prevent novel diseases like…

The integration of artificial intelligence (AI) in early-stage drug discovery offers unprecedented opportunities for exploring chemical space and accelerating hit-to-lead optimization. However, docking optimization in generative approaches…

This article presents our steps to integrate complex and partly unstructured medical data into a clinical research database with subsequent decision support. Our main application is an integrated faceted search tool, accompanied by the…

Information retrieval (IR) for precision medicine (PM) often involves looking for multiple pieces of evidence that characterize a patient case. This typically includes at least the name of a condition and a genetic variation that applies to…

End users of recent biomedical information systems are often unaware of the storage structure and access mechanisms of the underlying data sources and can require simplified mechanisms for writing domain specific complex queries. This…

Identifying the secondary structure of an RNA is crucial for understanding its diverse regulatory functions. This paper focuses on how to enhance target identification in a Boltzmann ensemble of structures via chemical probing data. We…

The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph…