Background: Embedding models are critical components of Retrieval Augmented Generation (RAG) systems for retrieving and searching unstructured medical data. However, existing models are predominantly trained on publicly available English datasets, limiting their effectiveness in non-English health care settings. More importantly, these models lack training on real-world clinical documents, leading to inaccurate context retrieval when integrated into RAG systems for health care applications. This gap is particularly pronounced in specialized medical documentation containing domain-specific terminology, abbreviations, and nuanced clinical language. Objective: This retrospective study aimed to develop and validate embedding models specifically trained on real-world clinical documents from multiple medical specialties to improve medical information retrieval (IR) and RAG system performance in both German and English language contexts. Methods: We fine-tuned embedding models, so-called sentence transformers, using the multilingual-e5-large architecture as a foundation. Training data consisted of approximately 11 million question-answer pairs synthetically generated from 400,000 diverse clinical documents from a large German tertiary hospital, spanning 163,840 patients and 282,728 clinical cases between 2018 and 2023. The large language model generated medically relevant questions and corresponding answers for each document. The dataset was additionally pseudonymized and translated into English to aim for broader applicability. Models were evaluated in 2 distinct scenarios: IR using questions with multiple relevant passages, and RAG system performance in both cross-patient and patient-centered contexts. Results: In the IR evaluation, the fine-tuned miracle model achieved a mAP@100 of 0.27, outperforming the multilingual-e5-large baseline (0.14) and state-of-the-art models such as bge-m3 (0.11). In the RAG evaluation, the model demonstrated robust performance comparable with the baseline in the constrained patient-centered scenario (BERTScore F1 0.781 vs 0.778) and showed moderate improvements in the unconstrained cross-patient setting (BLEURT 0.56 vs 0.53). Notably, the model trained on pseudonymized data achieved comparable retrieval performance (mAP@100 0.25) and the highest scores for patient-centered contextual precision (0.93). Performance gains were robust in the German dataset, while the translated English model demonstrated promising results as a proof of concept for cross-lingual transfer. Conclusions: By leveraging a comprehensive real-world dataset spanning multiple medical specialties and using large language models for synthetic question generation, we successfully created and validated domain-specific embedding models. These models can improve medical IR in large-scale search spaces and perform competitively in constrained RAG applications. By publishing the models trained on pseudonymized data, other health care institutions can integrate or adapt these embedding models to their needs. This work establishes a reproducible framework for developing domain-specific clinical embedding models, with the potential to improve data retrieval in medical settings.

arXiv:2603.22705v2 Announce Type: new Abstract: Background: Autism spectrum disorder (ASD) is characterized by significant clinical and biological heterogeneity. Conventional group-mean analyses of eye movements often mask individual atypicalities, potentially overlooking critical pathological signatures. This study aimed to identify idiosyncratic oculomotor patterns in ASD using an "outlier analysis" of smooth pursuit eye movement (SPEM). Methods: We recorded SPEM during a slow Lissajous pursuit task in 18 adults with ASD and 39 typically developed (TD) individuals. To quantify individual deviations, we derived an "outlier score" based on the Mahalanobis distance. This score was calculated from a feature vector, optimized via Principal Component Analysis (PCA), comprising the temporal lag ($\Delta$t) and the spatial deviation ($\Delta$s). An outlier was statistically defined as a score exceeding $\sqrt{10}$ (approximately 3.16$\sigma$) relative to the TD normative distribution. Results: While the TD group exhibited a low outlier rate of 5.1%, the ASD group demonstrated a significantly higher prevalence of 38.9% (7/18) (binomial P = 0.0034). Furthermore, the mean outlier score was significantly elevated in the ASD group (3.00 $\pm$ 2.62) compared to the TD group (1.52 $\pm$ 0.80; P = 0.002). Notably, these extreme deviations were captured even when conventional mean-based comparisons showed limited sensitivity. Conclusions: Our outlier analysis successfully visualized the high degree of idiosyncratic atypicality in ASD oculomotor control. By shifting the focus from group averages to individual deviations, this approach provides a sensitive metric for capturing the inherent heterogeneity of ASD, offering a potential baseline for identifying clinical subtypes.

arXiv:2603.22871v1 Announce Type: new Abstract: Current large language models (LLMs) primarily rely on linear sequence generation and massive parameter counts, yet they severely struggle with complex algorithmic reasoning. While recent reasoning architectures, such as the Hierarchical Reasoning Model (HRM) and Tiny Recursive Model (TRM), demonstrate that compact recursive networks can tackle these tasks, their training dynamics often lack rigorous mathematical guarantees, leading to instability and representational collapse. We propose the Contraction Mapping Model (CMM), a novel architecture that reformulates discrete recursive reasoning into continuous Neural Ordinary and Stochastic Differential Equations (NODEs/NSDEs). By explicitly enforcing the convergence of the latent phase point to a stable equilibrium state and mitigating feature collapse with a hyperspherical repulsion loss, the CMM provides a mathematically grounded and highly stable reasoning engine. On the Sudoku-Extreme benchmark, a 5M-parameter CMM achieves a state-of-the-art accuracy of 93.7 %, outperforming the 27M-parameter HRM (55.0 %) and 5M-parameter TRM (87.4 %). Remarkably, even when aggressively compressed to an ultra-tiny footprint of just 0.26M parameters, the CMM retains robust predictive power, achieving 85.4 % on Sudoku-Extreme and 82.2 % on the Maze benchmark. These results establish a new frontier for extreme parameter efficiency, proving that mathematically rigorous latent dynamics can effectively replace brute-force scaling in artificial reasoning.

Nature, Published online: 25 March 2026; doi:10.1038/s41586-026-10112-7

Genome-wide analysis shows European dogs existed by 14,200 years ago, were already genetically distinct, received less Neolithic Southwest Asian admixture than humans did and contributed substantially to later European dogs.

Nature, Published online: 25 March 2026; doi:10.1038/s41586-026-10170-x

Analysis of nuclear and mitochondrial genomes from archaeological canid remains found across Europe and Anatolia shows that a genetically homogeneous dog population was already widely distributed across the region by 15,000 years ago.

npj Digital Medicine, Published online: 25 March 2026; doi:10.1038/s41746-026-02559-9

WiseMind: a knowledge-guided multi-agent framework for accurate and empathetic psychiatric diagnosis

Nature, Published online: 25 March 2026; doi:10.1038/d41586-026-00378-2

Two studies report the oldest dog genomes ever to be sequenced, representing leaps in scientists’ understanding of the animal’s origins.

Oncogenesis, Published online: 18 March 2026; doi:10.1038/s41389-026-00610-8

Correction: LXRα limits TGFβ-dependent hepatocellular carcinoma associated fibroblast differentiation