arXiv AI
OncoNoteBERT: A Foundation Representation Model for Natural Language Processing of Real-World Outpatient Oncology Notes
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arXiv Machine Learning
Sep 25
Language Specificity vs. Domain Diversity: Benchmarking Transformers for Bangla Medical NER
This study benchmarks transformer models for Bangla medical named entity recognition (NER), comparing BanglaBERT, multilingual BERT (mBERT), XLM‑RoBERTa, and GPT‑4o mini under zero‑shot and few‑shot prompting. Across a full test set of 3,179 samples, fine‑tuned XLM‑RoBERTa achieves a new state‑of‑the‑art F1‑score of 0.5959, while BanglaBERT lags with 0.4937, suggesting that domain diversity outweighs language specificity. The analysis shows high performance on Medicine and Specialist entities (F1 > 0.83) but lower accuracy on Symptoms (F1 0.4367), and demonstrates that fine‑tuned transformers outperform prompt‑only approaches by a factor of 3.76.
arXiv AI
Jun 2
KliniskVestBERT: BERT Model Specialised to Norwegian Clinical Texts
arXiv:2606. 01904v1 Announce Type: cross Abstract: The increasing application of Natural Language Processing (NLP) in healthcare demands language models specifically attuned to the complexities of clinical language.
arXiv Machine Learning
Jun 24
PORTER: Language-Grounded Event Representations for Portable Structured EHR Foundation Models
arXiv:2606. 24102v1 Announce Type: cross Abstract: Most electronic health record (EHR) foundation models encode clinical events as discrete event tokens from a fixed vocabulary and therefore cannot directly represent events containing unseen concepts or new combinations of concepts and attributes such as numeric values.
arXiv Machine Learning
Sep 10
Where Does the Signal Live? A Web Data Recipe for Medical Encoder Pretraining
The paper introduces a web‑data curation recipe for pretraining medical encoders, addressing the scarcity of large, diverse corpora in dense‑terminology domains like medicine. It proposes two complementary techniques: medical‑term density filtering to select documents rich in medical terminology, and signal‑amplifying rephrasing that uses an LLM to rewrite documents into denser variants with broader entity contexts. Applied to French medical NLP, the recipe produces the FineMed corpus and the DoctoBERT encoder family, achieving state‑of‑the‑art results on the DrBenchmark public benchmark and a proprietary clinical NER task.
arXiv AI
Sep 10
Semantic Context-aware mOdality fUsion Transformer (SCOUT): A Context-Aware Multimodal Transformer for Concept-Grounded Pathology Report Generation
SCOUT is a concept‑grounded multimodal transformer that generates whole‑slide pathology reports by integrating local histological patterns, whole‑slide context, and expert‑curated diagnostic concepts. It uses evolving visual representations and recursively updated slide‑ and concept‑conditioned representations, with separate attention pathways during decoding that are fused adaptively for each token. Evaluated on TCGA‑BRCA, HistAI, and REG‑2025, SCOUT outperformed existing methods, improving BLEU, METEOR, and ROUGE‑L scores and raising the Clinical Report Quality Score on REG‑2025.
arXiv AI
Aug 5
OncoTriad-QA: A Patient-Level Radiology-Pathology-Genomics Benchmark for Pan-Cancer Reasoning
arXiv:2608. 02615v1 Announce Type: cross Abstract: Cancer diagnosis and characterization require integrating complementary evidence from radiology, pathology, genomics, and clinical metadata.