Improving Health Literacy through Lay Summarization of Radiological Reports: An Evaluation of BioNER and Retrieval-Augmented Generation

Radiology reports are written primarily for clinicians, and their specialized terminology often makes them difficult for patients to interpret. As a result, many patients turn to publicly available Large Language Models (LLMs) to help explain their reports, despite well-documented risks of factual inaccuracies and hallucinations. Automated lay-summary generation has emerged as a promising alternative, yet the effectiveness of retrieval-enhanced and clinically informed approaches for radiology-specific communication remains underexplored. This study investigates the extent to which Retrieval-Augmented Generation (RAG) and Named Entity Recognition (NER) improve the quality, factual consistency, and readability of automatically generated lay summaries compared with standard LLM-based generation. We develop a framework combining NER-based extraction of clinically relevant findings with a RAG mechanism for contextual grounding, evaluated across few-shot and fine-tuned variants of two models (Qwen, BioBART). Results show that NER consistently improves readability and overall quality, while RAG alone offers no benefit and can introduce hallucinations from irrelevant retrieved terms. Combining RAG with NER degrades performance in few-shot settings but improves readability when fine-tuned. Fine-tuned BioBART with NER achieves the best overall performance, highlighting entity-aware extraction as the primary driver of improved patient-friendly summaries.

MiNER: Fine-Tuned Biomedical Natural Language Processing for Malaria Disease Entity Recognition in Clinical Texts

Malaria remains a significant global health burden, necessitating continuous research efforts to understand its complex molecular mechanisms, epidemiology, and potential therapeutic interventions. Extracting essential biomedical information from the vast and constantly growing malaria literature is a challenging task that demands innovative approaches. Recently, pre-trained language models have revolutionized natural language processing tasks, demonstrating remarkable capabilities in various domains. This paper proposes a fine-tuned pre-trained biomedical language model for biomedical information extraction from scientific literature on malaria disease. The proposed methodology selects and preprocesses a large corpus of scientific articles on malaria, and then annotates them with entities of clinical significance. It then leverages BioBERT, a state-of-the-art pre-trained language model, to encode the textual data into context-aware representations. We fine-tune the model using domain-specific annotations and supervised learning to enhance its ability to extract relevant biomedical named entities. Extensive experiments and comparisons with different encoding and machine learning algorithms show that the proposed approach significantly outperforms them in precision, recall, and accuracy. We also publish our human-labeled dataset for entity and relation extraction to enable other health informatics researchers to train advanced models for malaria information extraction.

Clinical Term Extraction using Open-Source Small Language Models

Clinical information for amyotrophic lateral sclerosis (ALS) care documented in unstructured clinical notes limits downstream analysis without extraction into structured formats. Open-source small language models with few-shot prompting for detecting the presence of ALS-relevant clinical terms in patient documentation were evaluated without task-specific training data. The detection task targeted 17 categories spanning functional scores, respiratory measures, medications, and related clinical and non-clinical attributes. Clinical note content was normalized from JSON-encoded discharge summaries and processed with a prompt template having structured JSON outputs. We compared 26 open-source models using aggregate, label-level, and manual-validation multilabel classification metrics. Manual validation showed that a regex rule baseline had higher overall micro-F1 and lower Hamming loss than any single SLM or TF-IDF baseline, while Qwen3-4B-Instruct-2507 was the highest-performing SLM by micro-F1. Model rankings varied by metric and label category, with the TF-IDF baseline showing high recall but low precision, some SLMs showing higher precision but lower recall, and Hammer2.1-7b showing strong performance for ALSFRS-R subscore detection. These findings support targeted hybrid extraction workflows rather than replacement of existing rule-based methods.

AAbAAC: An Annotated Corpus for Autoimmunity Information Extraction

Despite advances in information extraction driven by deep learning and large language models, performance gaps remain in highly specialized biomedical fields, where domainspecific complexity poses challenges for generalist models. In this work, we focus on the domain of autoimmunity, where the main entities of interest are autoimmune diseases, autoantibodies (i.e., molecules that may mark or cause these diseases), their molecular targets, their location in the body, and their associated clinical signs. Herein, we present AAbAAC (AutoAntibodies and Autoimmunity Annotated Corpus), a corpus of 115 abstracts selected from PubMed, where we manually annotated entities and their relationships. First, AAbAAC was used to evaluate several methods on the task of named entity recognition (NER), and secondly, to fine-tune NER models. Our study demonstrates the utility of AAbAAC for information extraction in the domain of autoimmunity, showing expected improvement in NER performance after finetuning. This illustrates the value of small-scale annotation efforts for specialized domains and contributes to the computational study of autoimmunity. The AAbAAC corpus is available at https://github.com/f-maury/AAbAAC.

Automatic bioinformatic software named entity recognition from literature

Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale. The lack of a comprehensive and up-to-date catalog of bioinformatics resources hinders efforts toward automated biomedical knowledge extraction and streamlined data analysis. Here we present SNAIL, a hybrid named entity recognition framework designed to automatically identify bioinformatics software and database (SW/DB) names from biomedical texts. SNAIL integrates complementary lexical and semantic modeling strategies. The lexical component captures orthographic patterns and contextual cues characteristic of SW/DB names, while the semantic component leverages contextual embeddings generated by transformer-based language models such as SciBERT, combined with an explicit token-masking strategy to enhance entity-focused representations. A large training corpus was constructed automatically through a hybrid pipeline that integrates citation-hinted extraction with large language model-assisted distillation. Evaluation on two independent benchmark datasets and real-world research articles demonstrates that SNAIL substantially outperforms existing approaches, including domain-specific methods such as bioNerDS2 and general-purpose large language models such as ChatGPT, Gemini, Grok and Claude. Applying SNAIL to large-scale literature analysis further reveals distinct journal-level preferences across bioinformatics subfields. These results demonstrate that SNAIL provides an accurate and scalable solution for identifying bioinformatics resources in scientific texts and enables systematic meta-analysis of tool usage and research trends.