arXiv:2607. 00147v1 Announce Type: new Abstract: Rare disease differential diagnosis is a critical yet arduous clinical task, requiring physicians to identify precise phenotypes from complex, unstructured patient symptoms and execute intricate reasoning within a vast search space.
arXiv:2606.22419v3 Announce Type: replace Abstract: A recent Nature Medicine study reports that general-purpose frontier LLMs outperform specialized retrieval-augmented clinical tools on medical benc...
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:2606. 16149v1 Announce Type: new Abstract: Most medical AI systems improve by scaling additional machinery: more fine-tuning data, more agents, and/or larger retrieval databases.
The paper proposes a behavior-based fusion model that combines large language models (LLMs) with ontology rankers to improve rare-disease diagnosis. By examining ranked lists, agreement, and ontology support, the model learns how much to rely on each system per case, achieving significant recall gains on Phenopacket Store and RAMEDIS benchmarks. Importantly, the fused diagnoses retain candidate-level ontology evidence for inspection.
arXiv:2607. 23290v1 Announce Type: new Abstract: Rare diseases collectively affect an estimated 3.
arXiv:2604. 09737v2 Announce Type: replace-cross Abstract: Structured prediction with large language models requires outputs that are label-accurate, ontology-constrained, structurally valid, and evidence-grounded under label imbalance and heterogeneous group difficulty.
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.
arXiv:2607. 22555v1 Announce Type: new Abstract: Medical diagnosis is a multi-stage process: extract facts, consult knowledge, generate a differential analysis, and select the best diagnosis with explanations.
arXiv:2608.21948v1 Announce Type: new Abstract: Complex clinical reasoning requires models to update diagnostic hypotheses as new evidence emerges and to coordinate different medical specialities und...
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:2606.16149v5 Announce Type: replace Abstract: Rare disease diagnosis depends on expert reasoning that is scarce and difficult to transfer. Large language models rank the correct disease first i...