arXiv:2609.22734v1 Announce Type: cross
Abstract: Clinical domain classification plays an important role in organizing and analyzing large volumes of unstructured medical text. However, medical trans...
By Sravani Pottipati, Lakshmikar R. Polamreddy
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
arXiv:2606. 18703v1 Announce Type: new Abstract: Pretrained biological language models expose per-token probability distributions through masked-token prediction, providing the likelihood interface central to sequence design, variant scoring, and mechanistic interpretation.
By Yanjun Shao, Yundi Chen, Yashvi Patel, Aurelien Pelissier, Mar\'ia Rodr\'iguez Mart\'inez
arXiv:2607. 20465v1 Announce Type: new Abstract: The quality of training data fundamentally determines the capabilities of large language models (LLMs), yet no unified benchmark exists to measure how well LLMs, agents, and data-centric workflows actually prepare training data end to end.
By Hao Liang, Qifeng Cai, Yibo Lin, Jianzhuo Du, Qifeng Xia, Sizhe Qiu, Linzhuang Sun, Meiyi Qiang, Zhaoyang Han, Xiaochen Ma, Bohan Zeng, Ruichuan An, Conghui He, Wentao Zhang
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 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.
By Bofeng Huang, Jacques Sun, Diane Bouchacourt, Nicolas Barascud, Fajwel Fogel