Dmitrii Seletkov, Paul Hager, Georgios Kaissis, Rickmer Braren, Daniel Rueckert, Raphael Rehms
Survival analysis is crucial for many medical applications, but remains challenging for modern machine learning due to limited data, censoring, and the heterogeneity of tabular covariates. While the prior-fitted paradigm, which relies on pretraining models on large collections of synthetic datasets, has recently facilitated tabular foundation models for classification and regression, its suitability for time-to-event modeling remains unclear. We propose a flexible survival data generation framework that defines a rich survival prior with explicit control over covariates and time-event distributions. Building on this prior, we introduce Survival In-Context (SIC), a prior-fitted in-context learning model for survival analysis that is pretrained exclusively on synthetic data. SIC is trained to approximate Bayesian posterior predictive inference under the synthetic survival prior, enabling individualized survival prediction in a single forward pass, requiring no task-specific training or hyperparameter tuning. Across a broad evaluation on real-world survival datasets, SIC achieves competitive or superior performance compared to classical and deep survival models, particularly in small and medium-sized data regimes, highlighting the promise of a prior-fitted paradigm for survival analysis. The code and pretrained models are available at https://github.com/yayapa/sic
Moritz Schlager, Friederike Jungmann, Samuel Schmidgall, Philipp Raffler, Franziska Hartl, Eva Wende, Paula Roßm"uller, Conrad Ketzer 等 18 位作者
Realistic patient simulation is a key requirement for developing and testing clinical LLMs at scale without costly user studies. Existing simulators lack realism and controllability: they overshare information and miss the variability of real patient behavior. Here, we introduce PatientsWithPersonality (PWP), a patient simulation framework that generates realistic yet diverse patient responses through explicit personality parametrization over a latent patient state. Grounded in the six-dimensional HEXACO personality model, it gives fine-grained control over conversational style, cooperativeness, and information disclosure. We evaluate PWP in the first direct comparison of different patient simulators under a shared protocol, anchored in transcripts of real physician-patient encounters. Clinicians judge PWP conversations as realistic at least as often as the recorded encounters themselves and far more often than prior simulators, and almost never flag them as "too informative". Our simulator also reproduces the disclosure pacing of real patients, and its HEXACO-conditioned personality traits can be recovered by clinicians and an autorater. PWP further shows a substantially wider behavioral range than the closest baseline. In a downstream benchmark, LLMs interviewing patients simulated by PWP perform closest to how they perform on the real encounters, whereas prior simulators make the task easier. PWP thus provides a realistic, steerable, and diverse patient population for improving and benchmarking clinical LLMs.
Kristian Schwethelm, Jonas Kuntzer, Conrad Ketzer, Eva Wende, Moritz Schlager, Daniel Rueckert, Georgios Kaissis, Friederike Jungmann 等 9 位作者
MIMIC is one of the most widely used public hospital datasets for machine learning on electronic health records, yet clinically important information, such as past medical history, allergies, and diagnostic findings, remains confined to free-text discharge summaries. Studies requiring this information must therefore build their own extraction pipelines, duplicating substantial effort across projects. We release MIMIC-Note-Extract (MNE), a large-scale dataset that uses a hybrid extraction pipeline combining deterministic parsing with schema-guided large language model generation to transform 16 sections from 300,720 discharge summaries into structured tables. MNE adds information that has no structured MIMIC counterpart and enriches related tables with broader coverage and greater clinical detail, including 10 times more patient-history entries and medication histories for more than twice as many admissions. Validation by medical doctors confirms extraction accuracy above 92% across sections. Using MNE, we construct a clinical decision-making benchmark for LLM agents, demonstrating how reusable structured representations of clinical narratives reduce data curation effort.
Hendrik Möller, Hanna Schoen, Robert Graf, Matan Atad, Nathan Molinier, Anjany Sekuboyina, Bettina K. Budai, Fabian Bamberg 等 17 位作者
The human spine commonly consists of seven cervical, twelve thoracic, and five lumbar vertebrae. However, enumeration anomalies may result in individuals having eleven or thirteen thoracic vertebrae and four or six lumbar vertebrae. Although the identification of enumeration anomalies has potential clinical implications for chronic back pain and operation planning, the thoracolumbar junction is often poorly assessed and rarely described in clinical reports. Additionally, even though multiple deep-learning-based vertebra labeling algorithms exist, there is a lack of methods to automatically label enumeration anomalies. Our work closes that gap by introducing "Vertebra Identification with Anomaly Handling" (VERIDAH), a novel vertebra labeling algorithm based on multiple classification heads combined with a weighted vertebra sequence prediction algorithm. We show that our approach surpasses existing models on T2w TSE sagittal (98.30% vs. 94.24% of subjects with all vertebrae correctly labeled, p < 0.001) and CT imaging (99.18% vs. 77.26% of subjects with all vertebrae correctly labeled, p < 0.001) and works in arbitrary field-of-view images. VERIDAH correctly labeled the presence 2 Möller et al. of thoracic enumeration anomalies in 87.80% and 96.30% of T2w and CT images, respectively, and lumbar enumeration anomalies in 94.48% and 97.22% for T2w and CT, respectively. Our code and models are available at: https://github.com/Hendrik-code/spineps.
Kristian Schwethelm, Daniel Rueckert, Georgios Kaissis
We measure how much one recurrence is worth to a looped transformer in equivalent unique parameters. From an iso-depth pretraining sweep across recurrence counts $r \in \{1, 2, 4, 8\}$ spanning ${\sim}50\times$ in training compute, we fit a joint scaling law $L = E + A\,(N_\text{once} + r^{\varphi} N_\text{rec})^{-α} + B\,D^{-β}$ and measure a recurrence-equivalence exponent $\varphi = 0.46$. Intuitively, $\varphi$ tells us whether looping a block $r$ times is equivalent in validation loss to $r$ unique blocks of a non-looped model (full equivalence, $\varphi{=}1$) or to a single block run repeatedly with no capacity gain ($\varphi{=}0$). Our $\varphi = 0.46$ sits in between, so replacing unique blocks with shared recurrences increases validation loss at matched training compute. For example, at $r{=}4$ a 410M looped model performs on par with a 580M non-looped model, but incurs the training cost of a 1B non-looped one. We demonstrate the utility of $\varphi$ as a diagnostic tool on two case studies: commonly used truncated backpropagation lowers $\varphi$ to $0.38$, indicating that the loop mechanism is poorly trained under truncation, even though validation loss decreases. Conversely, hyperconnections raise $\varphi$ to $0.65$, a genuine capacity gain. Our method separates true loop improvements from training-side gains, a distinction raw validation loss cannot make. Code is available at https://github.com/kschwethelm/looped-lm-scaling.