Related papers: Comparison of biomedical relationship extraction m…

The graph of a Bayesian Network (BN) can be machine learned, determined by causal knowledge, or a combination of both. In disciplines like bioinformatics, applying BN structure learning algorithms can reveal new insights that would…

The rapid growth of research publications has placed great demands on digital libraries (DL) for advanced information management technologies. To cater to these demands, techniques relying on knowledge-graph structures are being advocated.…

Machine learning has been successfully used in critical domains, such as medicine. However, extracting meaningful insights from biomedical data is often constrained by the lack of their available disease labels. In this research, we…

Generative pre-trained transformer (GPT) models have shown promise in clinical entity and relation extraction tasks because of their precise extraction and contextual understanding capability. In this work, we further leverage the Unified…

Recently developed large pre-trained language models, e.g., BERT, have achieved remarkable performance in many downstream natural language processing applications. These pre-trained language models often contain hundreds of millions of…

To tackle the problem of domain-specific knowledge scarcity within large language models (LLMs), knowledge graph-retrievalaugmented method has been proven to be an effective and efficient technique for knowledge infusion. However, existing…

We hypothesize that large language models (LLMs) based on the transformer architecture can enable automated detection of clinical phenotype terms, including terms not documented in the HPO. In this study, we developed two types of models:…

Claims are a fundamental unit of scientific discourse. The exponential growth in the number of scientific publications makes automatic claim extraction an important problem for researchers who are overwhelmed by this information overload.…

Specialised transformers-based models (such as BioBERT and BioMegatron) are adapted for the biomedical domain based on publicly available biomedical corpora. As such, they have the potential to encode large-scale biological knowledge. We…

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 accurate extraction of clinical information from electronic medical records is particularly critical to clinical research but require much trained expertise and manual labor. In this study we developed a robust system for automated…

In the rapidly evolving landscape of enterprise natural language processing (NLP), the demand for efficient, lightweight models capable of handling multi-domain text automation tasks has intensified. This study conducts a comparative…

In the domain of semi-supervised learning, the current approaches insufficiently exploit the potential of considering inter-instance relationships among (un)labeled data. In this work, we address this limitation by providing an approach for…

This paper studies compressing pre-trained language models, like BERT (Devlin et al.,2019), via teacher-student knowledge distillation. Previous works usually force the student model to strictly mimic the smoothed labels predicted by the…

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet…

Knowledge-enhanced pre-trained models for language representation have been shown to be more effective in knowledge base construction tasks (i.e.,~relation extraction) than language models such as BERT. These knowledge-enhanced language…

Many real world systems need to operate on heterogeneous information networks that consist of numerous interacting components of different types. Examples include systems that perform data analysis on biological information networks; social…

Large language models (LLMs) are increasingly used in the mental health domain, yet it remains unclear how well they capture related biomedical knowledge and how reliably they apply it to clinically salient structured judgments. Here, we…

In this article, we present the BTransformer18 model, a deep learning architecture designed for multi-label relation extraction in French texts. Our approach combines the contextual representation capabilities of pre-trained language models…

The rapid expansion of medical literature presents growing challenges for structuring and integrating domain knowledge at scale. Knowledge Graphs (KGs) offer a promising solution by enabling efficient retrieval, automated reasoning, and…