The paper introduces WaterBERT, a domain‑adapted encoder model trained on a 2.97‑billion‑token water treatment corpus to capture domain‑specific semantics for literature mining. Fine‑tuned versions of WaterBERT outperform general‑purpose and other domain BERT models on tasks such as treatment process classification, named entity recognition, and relation extraction. The authors also demonstrate WaterBERT’s utility in large‑scale processing, generating coherent research topics, building a structured knowledge graph from 693,211 abstracts, and creating a Water Knowledge‑Enhanced Retrieval System that surpasses text‑based baselines.
arXiv:2608. 19201v1 Announce Type: cross Abstract: 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.
SciNLP is a new benchmark dataset for full‑text entity and relation extraction in the NLP domain, comprising 60 manually annotated papers with 6,429 entities and 1,649 relations. It is the first dataset to provide full‑text annotations of entities and their relationships specifically for NLP literature. Experiments show that models trained on SciNLP outperform baselines on certain tasks, and the dataset enabled the automatic construction of a fine‑grained knowledge graph with an average node degree of 3.3.
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."
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.
arXiv:2608. 08636v1 Announce Type: cross Abstract: Scientific named entity recognition (SciNER) plays a crucial role in information extraction and knowledge discovery from scientific texts.
BELXTR is a new biomedical entity linking model that uses a multi‑vector (late interaction) architecture to preserve token‑level matching information, unlike traditional embedding‑based approaches that compress mentions into a single vector. By extending the XTR model with a task‑specific training objective and active query expansion, BELXTR achieves state‑of‑the‑art performance on half of ten evaluated corpora, with an average 5‑percentage‑point gain in recall@1. The model shows especially strong results on cross‑species gene disambiguation, outperforming an LLM‑powered retrieve‑and‑rerank pipeline and approaching a specialized rule‑based system.
arXiv:2609.00228v1 Announce Type: new Abstract: Scientific domain entity linking (EL) differs from general domain EL because mentions and entity names often lack lexical overlap. Another challenge is...
The paper introduces a weakly supervised framework for extracting dataset mentions from forced displacement and Fragile, Conflict, and Violence (FCV) documents. It uses a lightweight model trained on general research literature to generate candidate mentions, which are then refined by a large language model that validates or rejects them and corrects boundaries. The refined annotations are augmented with synthetic and contrastive examples to fine‑tune the model, achieving 74.1% precision and 70.5% recall on a benchmark of 1,706 passages, with higher precision (89.5%) on passages that contain dataset references.
RATIO (Retrieval Across Typed Ideation Operations) is a large-scale benchmark designed to evaluate how well retrieval systems can support scientific inspiration. It defines relevance through three ideation moves—Address, Broaden, and Specify—each targeting different levels of abstraction in literature retrieval. The benchmark is built from millions of full-text CS papers using a novel discourse-marker distant supervision method, and includes extensive LLM and human vetting to ensure quality.
arXiv:2510. 16152v2 Announce Type: replace-cross Abstract: Scientific literature is increasingly fragmented by disciplinary boundaries, specialized terminology, and potentially sparse keyword systems, making it difficult to capture the evolving structure of modern science.
arXiv:2608. 03855v1 Announce Type: new Abstract: Transformer models have revolutionized natural language processing (NLP), and text-based molecular representations like SMILES have successfully extended these architectures to chemistry.
EvidenceNet is a disease‑specific dataset that transforms full‑text biomedical literature into structured evidence records and graph representations, preserving study design, provenance, and quantitative support. Using an LLM‑assisted pipeline, it extracts experimentally grounded findings, normalizes entities, scores evidence quality, and links related records via typed semantic relations. The released subsets—EvidenceNet‑HCC and EvidenceNet‑CRC—contain thousands of evidence records and richly connected graphs, with high extraction and relation‑type accuracy, enabling retrieval‑augmented question answering and graph‑based tasks such as link prediction and target prioritization.