Related papers: Building a Corpus for Biomedical Relation Extracti…
We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological…
The community of different types of microbes present in a biological niche plays a very important role in functioning of the system. The crosstalk or interactions among the different microbes contributes to the building blocks of such…
Biological relation networks contain rich information for understanding the biological mechanisms behind the relationship of entities such as genes, proteins, diseases, and chemicals. The vast growth of biomedical literature poses…
Text mining and information extraction for the medical domain has focused on scientific text generated by researchers. However, their direct access to individual patient experiences or patient-doctor interactions can be limited. Information…
This paper is devoted to the extraction of entities and semantic relations between them from scientific texts, where we consider scientific terms as entities. In this paper, we present a dataset that includes annotations for two tasks and…
We present a new corpus comprising annotations of medical entities in case reports, originating from PubMed Central's open access library. In the case reports, we annotate cases, conditions, findings, factors and negation modifiers.…
With the explosive growth of biomedical literature, designing automatic tools to extract information from the literature has great significance in biomedical research. Recently, transformer-based BERT models adapted to the biomedical domain…
This paper presents the formal release of MedMentions, a new manually annotated resource for the recognition of biomedical concepts. What distinguishes MedMentions from other annotated biomedical corpora is its size (over 4,000 abstracts…
This paper presents our participation in the AGAC Track from the 2019 BioNLP Open Shared Tasks. We provide a solution for Task 3, which aims to extract "gene - function change - disease" triples, where "gene" and "disease" are mentions of…
The delivery of appropriate targeted therapies to cancer patients requires the complete analysis of the molecular profiling of tumors and the patient's clinical characteristics in the context of existing knowledge and recent findings…
Knowledge base construction is crucial for summarising, understanding and inferring relationships between biomedical entities. However, for many practical applications such as drug discovery, the scarcity of relevant facts (e.g. gene X is…
Most work in relation extraction forms a prediction by looking at a short span of text within a single sentence containing a single entity pair mention. This approach often does not consider interactions across mentions, requires redundant…
Bioinformatics workflows are essential for complex biological data analyses and are often described in scientific articles with source code in public repositories. Extracting detailed workflow information from articles can improve…
We explore a generative relation extraction (RE) pipeline tailored to the study of interactions in the intestinal microbiome, a complex and low-resource biomedical domain. Our method leverages summarization with large language models (LLMs)…
Recognizing non-standard entity types and relations, such as B2B products, product classes and their producers, in news and forum texts is important in application areas such as supply chain monitoring and market research. However, there is…
A biomedical relation statement is commonly expressed in multiple sentences and consists of many concepts, including gene, disease, chemical, and mutation. To automatically extract information from biomedical literature, existing biomedical…
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations…
Causal relation extraction (CRE) is central to biomedical text mining, but current resources often conflate causal relations with broader associations, restrict annotation to sentence-level examples, or focus mainly on explicit causal cues.…
Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on…
Understanding causal narratives communicated in clinical notes can help make strides towards personalized healthcare. Extracted causal information from clinical notes can be combined with structured EHR data such as patients' demographics,…