How some people's brains make an extraordinary recovery from stroke A well-known actor who had experienced a stroke was treated by stroke specialist Sandor Nardai. The actor had been left with aphasia, or an impaired ability to speak - brutal for anyone, but "probably the most devastating thing that could happen to an actor", says Nardai. After three months of recovery, though, the actor was able to say some words. After a year, he voiced a commercial. Remarkably, he eventually got well enough to return to live theatre, says Nardai, who is at Semmelweis University in Hungary.

Clinical reasoning in medicine is a hypothesis-driven process where physicians refine diagnoses from limited information through targeted history, physical examination, and diagnostic investigations. In contrast, current medical benchmarks for large language models (LLMs) primarily assess knowledge recall through single-turn questions, where complete clinical information is provided upfront. To address this gap, we introduce VivaBench, a multi-turn benchmark that evaluates sequential clinical reasoning in LLM agents. Our dataset comprises 1152 physiciancurated clinical vignettes structured as interactive scenarios that simulate a viva voce examination in medical training, requiring agents to actively probe for relevant findings, select appropriate investigations, and synthesize information across multiple steps to reach a diagnosis. We evaluated several state-of-the-art LLMs and found that while models demonstrate competence in diagnosing conditions within well-described clinical presentations, their performance degrades significantly when required to navigate diagnostic uncertainty. Our analysis identified several failure modes that mirror common issues in clinical practice, including: (1) fixation on initial hypotheses, (2) excessive investigation ordering, (3) premature diagnostic closure, and (4) missing critical conditions. These patterns reveal fundamental limitations in how current LLMs manage uncertainty and gather information sequentially. Through VivaBench, we provide a standardized benchmark for evaluating conversational medical AI systems for real-world clinical decision support. Beyond medical applications, we contribute to the larger corpus of research on agentic AI by demonstrating how sequential reasoning trajectories can diverge in complex decision-making environments.

Gene regulatory network (GRN) inference serves as a cornerstone for deciphering cellular decision-making processes. Early approaches rely exclusively on gene expression data, thus their predictive power remain fundamentally constrained by the vast combinatorial space of potential gene-gene interactions. Subsequent methods integrate prior knowledge to mitigate this challenge by restricting the solution space to biologically plausible interactions. However, we argue that the effectiveness of these approaches is contingent upon the precision of prior information and the reduction in the search space will circumscribe the models' potential for novel biological discoveries. To address these limitations, we introduce KINDLE, a three-stage framework that decouples GRN inference from prior knowledge dependencies.

Event sequences appear widely in domains such as medicine, finance, and remote sensing, yet modeling them is challenging due to their heterogeneity: sequences often contain multiple event types with diverse structures--for example, electronic health records that mix discrete events like medical procedures with continuous lab measurements. Existing approaches either tokenize all entries, violating natural inductive biases, or ignore parts of the data to enforce a consistent structure. In this work, we propose a simple yet powerful Marked Temporal Point Process (MTPP) framework for modeling event sequences with flexible structure, using a single unified model. Our approach employs a single autoregressive transformer with discrete and continuous prediction heads, capable of modeling variable-length, mixed-type event sequences. The continuous head leverages an expressive normalizing flow to model continuous event attributes, avoiding the numerical integration required for inter-event times in most competing methods.

There is growing interest in using machine learning (ML) to support clinical diagnosis, but most approaches rely on static, fully observed datasets and fail to reflect the sequential, resource-aware reasoning clinicians use in practice. Diagnosis remains complex and error prone, especially in high-pressure or resource-limited settings, underscoring the need for frameworks that help clinicians make timely and cost-effective decisions. We propose ACTMED(Adaptive Clinical Test selection via Model-based Experimental Design), a diagnostic framework that integrates Bayesian Experimental Design (BED) with large language models (LLMs) to better emulate real-world diagnostic reasoning. At each step, ACTMED selects the test expected to yield the greatest reduction in diagnostic uncertainty for a given patient. LLMs act as flexible simulators, generating plausible patient state distributions and supporting belief updates without requiring structured, task-specific training data. Clinicians can remain in the loop; reviewing test suggestions, interpreting intermediate outputs, and applying clinical judgment throughout. We evaluate ACTMEDon real-world datasets and show it can optimize test selection to improve diagnostic accuracy, interpretability, and resource use. This represents a step toward transparent, adaptive, and clinician-aligned diagnostic systems that generalize across settings with reduced reliance on domain-specific data.

Large language models (LLMs) have achieved significant performance progress in various natural language processing applications. However, LLMs still struggle to meet the strict requirements for accuracy and reliability in the medical field and face many challenges in clinical applications. Existing clinical diagnostic evaluation benchmarks for evaluating medical agents powered by LLMs have severe limitations. Firstly, most existing medical evaluation benchmarks face the risk of data leakage or contamination.

Background Childhood Anemia affects an estimated 40% of children aged 6-59 months globally and arises from heterogeneous nutritional, infectious, and socioeconomic factors that vary substantially across settings. This variability challenges the generalizability of predictive machine learning models, which often degrade under cross-population or temporal shifts. We investigated the utility a modern transformer-based tabular foundation model (TabPFN) as a complementatry framework with respect to supervised classical machine learning methods across diverse country contexts, with particular attention to data-scarce settings where surveillance capacity is most limited. Methods We conducted a multi-country prediction study using Demographic and Health Surveys (DHS) children's recode data from 16 countries spanning Africa, Asia, Latin America, the Caucasus, and the Middle East. The harmonized analytic cohort comprised of (n = 68,856)children aged 6-59 months with valid hemoglobin measurements. Anemia was defined using WHO age and altitude-adjusted thresholds and treated as a binary outcome. We trained Logistic Regression, XGBoost, and LightGBM models using standard supervised learning, and evaluated TabPFN v2.6 in an in-context learning setting. Performance was assessed using Area Under the Receiver Operating Characteristic Curve (AUC-ROC) and other standard classification metrics, with calibration evaluated via Brier score and expected calibration error (ECE). Uncertainty in performance estimates was quantified using bootstrap resampling to derive 95% confidence intervals. Robustness was assessed in a few-shot learning setting. Cross-population generalization was examined using leave-one-country-out (LOCO) validation and reverse-LOCO experiments to assess directional transferability. Subgroup analyses were conducted across five demographic strata: child age group, sex, maternal education, residence type, and household wealth quintile. Feature importance was assessed using standard linear and tree-based explainer SHAP values for the three supervised models and an adapted version of SHAP for TabPFN, aggregated across countries and examined at the country level. TabPFN also yielded the best probabilistic calibration across all 16 countries, achieving the lowest mean Brier score (0.203) and Expected Calibration Error (ECE = 0.042) of all models evaluated; LightGBM and Logistic Regression exhibited the greatest miscalibration, particularly at higher predicted probabilities. Under full-data conditions, within-country discrimination was moderate across all models (AUC-ROC 0.59-0.76) Under LOCO validation, performance declined modestly (AUC-ROC 0.58-0.69) Reverse-LOCO analyses revealed asymmetric and directional transferability, with epidemiologically diverse populations serving as more informative training sources and certain target populations remaining persistently difficult to predict regardless of model or training data.

In the era of precision medicine, genome-wide epigenetic modifications offer rich data that could inform risk prediction. However, these data are high-dimensional and exhibit complex dependence structures, which makes it difficult to jointly model them with low-dimensional covariates when the goal is to obtain interpretable effect estimates for covariate adjustment. Standard Bayesian additive regression trees (BART) provide strong predictive performance but treat all predictors uniformly within the tree ensemble, obscuring the contributions of significant covariates and complicating variable selection in high-dimensional settings. We propose a semi-parametric BART model (spBART) that addresses this limitation by modeling low-dimensional covariates through a parametric component with interpretable coefficients, while capturing complex nonlinear associations among high-dimensional predictors through the tree ensemble. To perform stable variable selection, we develop a cross-validation-based procedure that aggregates posterior inclusion probabilities across folds and applies Bayesian false discovery rate control. We apply the proposed method to a pooled case--control analysis of high-dimensional genome-wide 5-hydroxymethylcytosine profiles derived from circulating cell-free DNA in two multiple myeloma studies ($N = 869$). The approach identifies a parsimonious set of candidate loci and achieves strong out-of-sample discrimination (AUC $= 0.96$) in a held-out validation set. Overall, spBART provides a unified framework for combining interpretable covariate inference with flexible modeling and variable selection in high-dimensional biomedical studies.

Survival analysis provides a powerful statistical framework for modeling time-to-event outcomes in the presence of censoring. However, selecting an appropriate estimator from the many specialized survival approaches often requires substantial methodological and domain expertise. We introduce SurvivalPFN, a prior-data fitted network that amortizes Bayesian inference for censored observations through in-context learning. SurvivalPFN is pretrained on a diverse family of synthetic, identifiable, and right-censored data-generating processes, enabling it to amortize survival analysis in a single forward pass during inference. As a result, the model adapts to the effective complexity of each dataset without task-specific training or hyperparameter tuning, avoids restrictive parametric assumptions, and produces calibrated survival distributions. In a large-scale benchmark spanning 61 datasets, 21 methods, and 5 evaluation metrics, SurvivalPFN achieves strong predictive performance and often improves upon established survival models. These results suggest that SurvivalPFN offers a principled and practical foundation model for survival analysis, with potential applications in high-impact domains such as healthcare, finance, and engineering (https://github.com/rgklab/SurvivalPFN).

Tabular data underpins most high-value prediction problems in science and industry, and TabPFN has driven the foundation model revolution for this modality. Designed with feedback from our users, TabPFN-3 builds on this foundation to scale state-of-the-art performance to datasets with 1M training rows and substantially reduce training and inference time. Pretrained exclusively on synthetic data from our prior, TabPFN-3 dramatically pushes the frontier of tabular prediction and brings substantial gains on time series, relational, and tabular-text data. On the standard tabular benchmark TabArena, a forward pass of TabPFN-3 outperforms all other models, including tuned and ensembled baselines, by a significant margin, and pareto-dominates the speed/performance frontier. On more diverse datasets, TabPFN-3 ranks first on datasets with many classes, and beats 8-hour-tuned gradient-boosted-tree baselines on datasets up to 1M training rows and 200 features. TabPFN-3 introduces test-time compute scaling to tabular foundation models. Our API offering TabPFN-3-Plus (Thinking) exploits this to beat all non-TabPFN models by over 200 Elo on TabArena, rising to 420 Elo on the largest data subset, and outperforms AutoGluon 1.5 extreme while being 10x faster, without using LLMs, real data, internet search or any other model besides TabPFN. TabPFN-3 extends the capabilities of our models, enabling SOTA prediction on relational data (new SOTA foundation model on RelBenchV1) and tabular-text data (SOTA on TabSTAR via TabPFN-3-Plus); and improves existing integrations: a specialized checkpoint, TabPFN-TS-3, ranks 2nd on the time-series benchmark fev-bench, and SHAP-value computation is up to 120x faster. TabPFN-3 achieves this performance while being up to 20x faster than TabPFN-2.5. In addition, a reduced KV cache and row-chunking scale to 1M rows on one H100 with fast inference speed.