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.
By Rakib Abdullah, Md. Maruful Islam Maruf
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.
By Christian Autenried, Cosimo Persia
arXiv:2607. 18927v1 Announce Type: new Abstract: We present OntoBook, a method that converts medical ontology structure into pretraining signal for encoder language models.
By Rian Touchent (ALMAnaCH), \'Eric de la Clergerie (ALMAnaCH)
CardioLM introduces a multilingual suite of small language models tailored for cardiology, comprising CardioBERTa encoders and CardioNER NER models trained on the CardioCCC corpus of 508 cardiology case reports translated into seven languages. The study shows that specialty‑specific pretraining reduces pseudo‑perplexity significantly but only marginally improves strict span‑level F1, whereas joint multilingual training with XLM‑RoBERTa‑large yields the best F1 scores across languages and entity types. Clinicians rated CardioNER far superior to rule‑based baselines, indicating practical value for multi‑country clinical information extraction.
By Manuela-Daniela Danu, Miguel Rodr\'iguez-Ortega, Alberto Becerra-Tome, Pablo Arancibia, Fernando Gallego-Donoso, Lorenzo Pratesi, Xi Bai, Andrei-Damian Dinescu, Salvador Lima-L\'opez, Andrea Guala, Saskia Haitjema, Jonas Mack, Michele Miranda, Wesam Al Nabki, Jan Rodr\'iguez-Miret, Vasile George Marica, Vladim\'ir Kincl, Kate\v{r}ina Dost\'alov\'a, Michael Andrej, Alicia Ujil, Corinne Allaart, Machteld Boonstra, Malin Overmars, Anoop Shah, Giovanna Ceroni, Jonathan Kossoff, Domenico D'Amario, Renzo Laborante, Antonio Iaconelli, Isabella Fumarulo, Jacopo Lenkowicz, Livia Lilli, Emma Weiss, Alex Scafa, Felix Lindberg, Milou Gamage, Eul\`alia Farr\'e-Maduell, S\'ebastien Brati\`eres, Martin Krallinger, Bram van Es
arXiv:2608.29890v1 Announce Type: new
Abstract: Biomedical Named Entity Recognition (NER) is fundamental to healthcare AI applications, including clinical decision support and medical information ext...
By Nhu Vo, Phuong Nguyen, Nu Uyen Phuong Le, Inigo Jauregi Unanue, Dung D. Le, Massimo Piccardi, Wray Buntine
EHRAdapt is an adapter that maps electronic health record tuples directly into a frozen language model’s embedding space, using learned embeddings for modality, time gaps, and dedicated vectors for event codes. It represents each event vector as a sum of a frozen, ontology‑trained semantic prior and a low‑rank evidence residual, enabling robust learning even for rare clinical events. Experiments on four million patient records with three large language model backbones show that the full adapter outperforms all ablations in next‑event prediction and improves rare‑disease discrimination in classification tasks.
By Andre R Goncalves, Vincent Liu, Priyadip Ray
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.
By Lin Lawrence Guo, Adam Paul Yan, Emily Vettese, Lillian Sung
The paper introduces MITE, a method that transforms biomedical named entity recognition (BioNER) into a structure‑to‑structure generation task by encoding instructions and outputs in multiple programming languages (Python, C++, Java). This approach provides structurally diverse supervision without extra biomedical knowledge, and during inference it aggregates predictions via entity‑level voting to reduce language‑specific variance. Experiments on six BioNER datasets show that MITE outperforms BERT‑based and LLM‑based baselines and generalizes well across datasets.
By Songtao Li, Yijia Zhang, Jianyuan Yuan, Shidi Zhang, Fengyu Zhang, Hongfei Lin
The paper introduces CAST, a concept-guided artifact suppression tuning framework that uses sparse autoencoders to identify and suppress note-specific artifacts in clinical language models. CAST labels latent features with an LLM-assisted pipeline and ICD‑10 constraints, then fine‑tunes the model while providing post‑hoc per‑concept attributions for auditability. In experiments on MIMIC‑IV discharge‑note mortality prediction, CAST outperforms standard fine‑tuned encoders and competes with strong LLM baselines while offering a feature‑level audit trail of clinical concepts and suppressed artifacts.
By Jin Mu, Guanhua Chen
This thesis explores how to select and adapt NLP models for global health literature when annotated data and computational resources are scarce. It compares skip‑gram word2vec models trained on increasingly large specialized corpora with BioWordVec for semantic tag discovery, finding that larger coverage does not always yield more useful domain associations. The study also evaluates convolutional spaCy models versus a RoBERTa transformer for named entity recognition, noting a trade‑off between higher F1 scores and longer inference time, and investigates MiniLM few‑shot versus BART‑MNLI zero‑shot classification for multi‑label topic classification, highlighting practical constraints of inference cost.
"whyItMatters":"The work provides empirical guidance on balancing model accuracy and resource demands for building knowledge systems in low‑resource global health settings."
By Genis Skura, Antoine Geissb\"uhler, Jean-Luc Falcone
BioELX is a retrieve‑rerank framework for cross‑lingual biomedical entity linking that tackles two key problems: the English‑biased UMLS alias training data and the degradation caused by naïvely adding context. It fine‑tunes SapBERT_multi with Wikidata‑derived cross‑lingual alias supervision to create shared concept neighborhoods, and then reranks candidates using pretrained LLMs with mention‑anchored prompting to focus on the target mention. Experiments demonstrate state‑of‑the‑art performance on four benchmarks, improving Recall@1 by 4.8–18.2 percentage points without task‑specific annotations.
By Yi Wang, Corina Dima, Liangyu Zhong, Steffen Staab
The paper introduces Distilled Rapid Embedding Transfer (DRET), a parameter‑efficient method that injects biomedical domain knowledge from large specialized models into a smaller general‑purpose model without retraining on the original specialized corpora. DRET evolves through iterative strategies—tokenizer‑merge (DRET 1.x), hybrid embedding averaging (DRET 2.0), priority‑based embedding transfer (DRET 3.x), and further refinements (DRET 4.x)—and demonstrates that a 66‑million‑parameter DistilBERT can achieve competitive or superior performance on token‑level PICO classification compared to much larger models, while remaining lightweight. The authors validate the embedding‑level transfer with cosine similarity, semantic‑shift, and t‑SNE analyses, highlighting DRET’s potential for scalable, resource‑efficient biomedical text mining.
By Girish Sundaram, Daniel Berleant