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We introduce Biomed-Enriched, a biomedical text dataset constructed from PubMed via a two-stage annotation process. In the first stage, a large language model annotates 400K paragraphs from PubMed scientific articles, assigning scores for…
This work presents biomedical and clinical language models for Spanish by experimenting with different pretraining choices, such as masking at word and subword level, varying the vocabulary size and testing with domain data, looking for…
The automation of text summarisation of biomedical publications is a pressing need due to the plethora of information available on-line. This paper explores the impact of several supervised machine learning approaches for extracting…
We present an overview of the TREC-COVID Challenge, an information retrieval (IR) shared task to evaluate search on scientific literature related to COVID-19. The goals of TREC-COVID include the construction of a pandemic search test…
We present the Neural Covidex, a search engine that exploits the latest neural ranking architectures to provide information access to the COVID-19 Open Research Dataset curated by the Allen Institute for AI. This web application exists as…
The volume of academic paper submissions and publications is growing at an ever increasing rate. While this flood of research promises progress in various fields, the sheer volume of output inherently increases the amount of noise. We…
The Precision Medicine Initiative states that treatments for a patient should take into account not only the patient's disease, but his/her specific genetic variation as well. The vast biomedical literature holds the potential for…
In many scientific fields, large language models (LLMs) have revolutionized the way text and other modalities of data (e.g., molecules and proteins) are handled, achieving superior performance in various applications and augmenting the…
Search engines play an essential role in our daily lives. Nonetheless, they are also very crucial in enterprise domain to access documents from various information sources. Since traditional search systems index the documents mainly by…
In this work, we propose a method for the automated refinement of subject annotations in biomedical literature at the level of concepts. Semantic indexing and search of biomedical articles in MEDLINE/PubMed are based on semantic subject…
The increasing rate at which scientific knowledge is discovered and health claims shared online has highlighted the importance of developing efficient fact-checking systems for scientific claims. The usual setting for this task in the…
The Query-By-Document (QBD) problem is an information retrieval problem where the query is a document, and the retrieved candidates are documents that match the query document, often in a domain or query specific manner. This can be crucial…
Here we proposed an approach to analyze text classification methods based on the presence or absence of task-specific terms (and their synonyms) in the text. We applied this approach to study six different transfer-learning and unsupervised…
The COVID-19 pandemic has driven ever-greater demand for tools which enable efficient exploration of biomedical literature. Although semi-structured information resulting from concept recognition and detection of the defining elements of…
In the scientific digital libraries, some papers from different research communities can be described by community-dependent keywords even if they share a semantically similar topic. Articles that are not tagged with enough keyword…
Biomedical research results are being published at a high rate, and with existing search engines, the vast amount of published work is usually easily accessible. However, reproducing published results, either experimental data or…
Domain-specific synonyms occur in many specialized search tasks, such as when searching medical documents, legal documents, and software engineering artifacts. We replicate prior work on ranking domain-specific synonyms in the consumer…
In the absence of sufficient medication for COVID patients due to the increased demand, disused drugs have been employed or the doses of those available were modified by hospital pharmacists. Some evidences for the use of alternative drugs…
The coronavirus disease (COVID-19) has claimed the lives of over 350,000 people and infected more than 6 million people worldwide. Several search engines have surfaced to provide researchers with additional tools to find and retrieve…
Understanding fine-grained links between documents is crucial for many applications, yet progress is limited by the lack of efficient methods for data curation. To address this limitation, we introduce a domain-agnostic framework for…