相关论文: Supporting Workflow Reproducibility by Linking Bio…

In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…

This technical report introduces a Named Clinical Entity Recognition Benchmark for evaluating language models in healthcare, addressing the crucial natural language processing (NLP) task of extracting structured information from clinical…

The number of biomedical research articles published has doubled in the past 20 years. Search engine based systems naturally center around searching, but researchers may not have a clear goal in mind, or the goal may be expressed in a query…

Named Entity Recognition (NER) is a core natural language processing task in which pre-trained language models have shown remarkable performance. However, standard benchmarks like CoNLL 2003 do not address many of the challenges that…

Many research groups aspire to make data and code FAIR and reproducible, yet struggle because the data and code life cycles are disconnected, executable environments are often missing from published work, and technical skill requirements…

Disease name recognition and normalization, which is generally called biomedical entity linking, is a fundamental process in biomedical text mining. Recently, neural joint learning of both tasks has been proposed to utilize the mutual…

The Micropublications semantic model for scientific claims, evidence, argumentation and annotation in biomedical publications, is a metadata model of scientific argumentation, designed to support several key requirements for exchange and…

BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification…

Being able to duplicate published research results is an important process of conducting research whether to build upon these findings or to compare with them. This process is called "replicability" when using the original authors'…

Entity linking (EL) for biomedical text is typically benchmarked on English-only corpora with flat mentions, leaving the more realistic scenario of nested and multilingual mentions largely unexplored. We present our system for the BioNNE…

To reproduce eScience, several challenges need to be solved: scientific workflows need to be automated; the involved software versions need to be provided in an unambiguous way; input data needs to be easily accessible; High-Performance…

Background: Finding biomedical named entities is one of the most essential tasks in biomedical text mining. Recently, deep learning-based approaches have been applied to biomedical named entity recognition (BioNER) and showed promising…

The aim of this article is to introduce a reporting framework for reproducible, interactive research applied to Big Clinical Data, based on open source technologies. The framework is constituted by the following three axes: (i) data, (ii)…

The discoverability, attribution, and reusability of open research software are often hindered by its obscurity within academic manuscripts. To address this, the SoFAIR project (2024-2025) introduces a comprehensive workflow leveraging…

There are a few challenges related to the task of biomedical named entity recognition, which are: the existing methods consider a fewer number of biomedical entities (e.g., disease, symptom, proteins, genes); and these methods do not…

Extracting entities and relations for types of interest from text is important for understanding massive text corpora. Traditionally, systems of entity relation extraction have relied on human-annotated corpora for training and adopted an…

Operational rigor determines whether human-agent collaboration succeeds or fails. Scientific data pipelines need the equivalent of DevOps -- SciOps -- yet common approaches fragment provenance across disconnected systems without…

Reproducibility and sustainability present significant challenges in bioinformatics software development, where rapidly evolving tools and complex workflows often result in short-lived or difficult-to-adapt pipelines. This paper introduces…

Biomedical entity linking (BEL) is the task of grounding entity mentions to a knowledge base (KB). A popular approach to the task are name-based methods, i.e. those identifying the most appropriate name in the KB for a given mention, either…

Reproducibility should be a cornerstone of science as it enables validation and reuse. In recent years, the scientific community and the general public became increasingly aware of the reproducibility crisis, i.e. the wide-spread inability…