arXiv:2604. 15591v2 Announce Type: replace-cross Abstract: Effective biomedical information retrieval requires modeling domain semantics and hierarchical relationships among biomedical texts.
arXiv:2603.01690v3 Announce Type: replace-cross Abstract: While dense biomedical embeddings achieve strong performance, their opaque dimensions limit transparency in biomedical NLP. Recent question-b...
arXiv:2608. 04144v1 Announce Type: cross Abstract: Biomedical entity linking grounds mentions in clinical and scientific text to entities in a curated knowledge base (KB) with ontological structure, which supports downstream applications such as literature-scale information extraction and patient-record normalization.
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.
arXiv:2609.08174v1 Announce Type: new Abstract: We introduce OntologyBench, a tiered biomedical retrieval benchmark comprising 471,854 training and 125,744 evaluation query-document relevance pairs a...
arXiv:2608. 16005v1 Announce Type: new Abstract: This paper studies the problem of molecule-text alignment, which aims to project molecules and their textual descriptions into a joint latent space for downstream tasks including molecule search and molecular property prediction.
arXiv:2609.39975v1 Announce Type: cross Abstract: This paper presents an overview of the fourteenth edition of the BioASQ challenge, organized in the context of the Conference and Labs of the Evaluat...
MedFG-VQA is a lightweight medical visual question answering framework that uses a memory bank to enhance low‑frequency DCT features and graph‑enhanced cross‑attention for visual‑textual alignment. It introduces Frequency‑Memory Fusion to retrieve and fuse low‑frequency information from a learnable memory bank, and Graph‑Aware Cross‑Attention to refine cross‑modal features via graph convolution. The authors also create SynMed‑VQA, a synthetic dataset of over 2 million QA pairs across nine imaging modalities, and show that MedFG‑VQA matches or outperforms larger models on several biomedical VQA benchmarks while keeping computational costs low.
The paper proposes a method called Modular Expert Merging for Biomedical Retrieval, which combines independently trained domain‑specialized experts instead of large mixed‑domain training. Experiments across four decoder‑only LLM families (0.6B‑7B) and twelve retrieval tasks from MTEB show that merging experts consistently outperforms mixed‑domain training. The authors also introduce a Synthesize‑Train‑Merge (STM) framework that generates hard negatives with a top‑tier LLM, fine‑tunes experts via LoRA, and merges them, achieving strong biomedical retrieval performance while retaining competitive general‑domain results.
arXiv:2607. 08803v1 Announce Type: cross Abstract: The push toward large language models for biology (BioLM) has created a need for training corpora that can endow models with a genuine understanding of biology.
The paper introduces Hyperbolic Clinical Ontology Embeddings (HCOE), a method that transforms frozen BioBERT embeddings into a Poincaré ball to capture medical code hierarchies. HCOE employs ontology-guided contrastive learning and coarse‑to‑fine ontology‑path aggregation, leveraging ICD, CCS, and ATC hierarchies. Experiments on MIMIC‑IV demonstrate superior performance in clinical relation prediction, hierarchy transfer, and various predictive tasks such as mortality, readmission, medication recommendation, and rare drug prediction.
arXiv:2606. 06696v1 Announce Type: cross Abstract: Vision and language models (VLMs) hold immense promise to transform biomedical imaging workflows, from detecting lesions in chest X-rays to profiling cellular features in microscopy.
arXiv:2402. 01767v3 Announce Type: replace-cross Abstract: Retrieval-augmented generation (RAG) has rapidly advanced the language model field, particularly in question-answering (QA) systems.