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Electronic health records contain inconsistently structured or free-text data, requiring efficient preprocessing to enable predictive health care models. Although artificial intelligence-driven natural language processing tools show promise…
We study clinical Named Entity Recognition (NER) on the CADEC corpus and compare three families of approaches: (i) BERT-style encoders (BERT Base, BioClinicalBERT, RoBERTa-large), (ii) GPT-4o used with few-shot in-context learning (ICL)…
In this research, we explored the improvement in terms of multi-class disease classification via pre-trained language models over Medical-Abstracts-TC-Corpus that spans five medical conditions. We excluded non-cancer conditions and examined…
The escalating volume of collected healthcare textual data presents a unique challenge for automated Multi-Label Text Classification (MLTC), which is primarily due to the scarcity of annotated texts for training and their nuanced nature.…
Recognition of biomedical entities from literature is a challenging research focus, which is the foundation for extracting a large amount of biomedical knowledge existing in unstructured texts into structured formats. Using the sequence…
Clinical notes contain valuable unstructured information. Named entity recognition (NER) enables the automatic extraction of medical concepts; however, benchmarks for Portuguese remain scarce. In this study, we aimed to evaluate BERT-based…
Recent advances in natural language processing (NLP) have been driven bypretrained language models like BERT, RoBERTa, T5, and GPT. Thesemodels excel at understanding complex texts, but biomedical literature, withits domain-specific…
Biomedical named entity recognition (NER) is a fundamental task in text mining of medical documents and has many applications. Deep learning based approaches to this task have been gaining increasing attention in recent years as their…
The rapid growth of biomedical literature poses a significant challenge for curation and interpretation. This has become more evident during the COVID-19 pandemic. LitCovid, a literature database of COVID-19 related papers in PubMed, has…
Although supervised machine learning is popular for information extraction from clinical notes, creating large annotated datasets requires extensive domain expertise and is time-consuming. Meanwhile, large language models (LLMs) have…
The application of AI in oncology has been limited by its reliance on large, annotated datasets and the need for retraining models for domain-specific diagnostic tasks. Taking heed of these limitations, we investigated in-context learning…
This study evaluated the effect of BioBERT in medical text processing for the task of medical named entity recognition. Through comparative experiments with models such as BERT, ClinicalBERT, SciBERT, and BlueBERT, the results showed that…
Processing information locked within clinical health records is a challenging task that remains an active area of research in biomedical NLP. In this work, we evaluate a broad set of machine learning techniques ranging from simple RNNs to…
This paper presents a novel approach to accurately classify the hallmarks of cancer, which is a crucial task in cancer research. Our proposed method utilizes the Bidirectional Encoder Representations from Transformers (BERT) architecture,…
The practice of fine-tuning Pre-trained Language Models (PLMs) from general or domain-specific data to a specific task with limited resources, has gained popularity within the field of natural language processing (NLP). In this work, we…
The increasing availability of unstructured clinical narratives in electronic health records (EHRs) has created new opportunities for automated disease characterization, cohort identification, and clinical decision support. However,…
The global pandemic has made it more important than ever to quickly and accurately retrieve relevant scientific literature for effective consumption by researchers in a wide range of fields. We provide an analysis of several multi-label…
In this study, we compared the performance of four different methods for multi label text classification using a specific imbalanced business dataset. The four methods we evaluated were fine tuned BERT, Binary Relevance, Classifier Chains,…
We describe Bioformer team's participation in the multi-label topic classification task for COVID-19 literature (track 5 of BioCreative VII). Topic classification is performed using different BERT models (BioBERT, PubMedBERT, and…
The exponential growth of online textual content across diverse domains has necessitated advanced methods for automated text classification. Large Language Models (LLMs) based on transformer architectures have shown significant success in…