GeneICL: A Tabular Foundation Model for Bulk Transcriptomics

Predicting time-to-event outcomes such as mortality is a fundamental task in clinical decision-making, commonly addressed through survival analysis. While classical statistical and deep learning approaches have been widely studied, they typically require task-specific training and sufficient labeled data. Recent advances in tabular foundation models offer a new paradigm by learning general-purpose representations for structured data. However, their applicability to censored time-to-event prediction in clinical settings remains underexplored, as typical applications are restricted to discrete classification rather than survival analysis tasks. In this work, we propose a lightweight adaptation approach for applying tabular foundation models to clinical survival analysis by directly training a survival-aware head on top of the pretrained representations. We study representative architectures, including TabPFN, TabDPT, and TabICL, and adapt them using a multi-task logistic regression (MTLR) head to model right-censored time-to-event outcomes. We evaluate this approach on a diverse set of public survival benchmarks and two large-scale ICU cohorts, MIMIC-IV and eICU. Our results show that this transfer learning approach achieves competitive or superior performance compared to strong baselines. On MIMIC-IV, TabDPT-FT-MTLR reaches a C-index of 0.856, corresponding to a relative improvement of +1.4% over the best non-FM baseline (DeepSurv, 0.844) and +6.7% over the best zero-shot model (0.802). On eICU, TabICL-FT-MTLR achieves 0.797, yielding gains of +1.7% (DeepSurv, 0.784) and +6.4% (0.749), respectively. These findings highlight the importance of combining pretrained tabular representations with survival-aware objectives and suggest that tabular foundation models provide a practical and effective alternative for clinical survival prediction.

Tabular foundation models, such as TabPFNv2 and TabICL, have recently dethroned gradient-boosted trees at the top of predictive benchmarks, demonstrating the value of in-context learning for tabular data. We introduce TabICLv2, a new state-of-the-art foundation model for regression and classification built on three pillars: (1) a novel synthetic data generation engine designed for high pretraining diversity; (2) various architectural innovations, including a new scalable softmax in attention improving generalization to larger datasets without prohibitive long-sequence pretraining; and (3) optimized pretraining protocols, notably replacing AdamW with the Muon optimizer. On the TabArena and TALENT benchmarks, TabICLv2 without any tuning surpasses the performance of the current state of the art, RealTabPFN-2.5 (hyperparameter-tuned, ensembled, and fine-tuned on real data). With only moderate pretraining compute, TabICLv2 generalizes effectively to million-scale datasets under 50 GB GPU memory while being markedly faster than RealTabPFN-2.5. We provide extensive ablation studies to quantify these contributions and foster open research by releasing code for inference, pretraining, and synthetic data generation at https://github.com/soda-inria/tabicl.

Tabular foundation models (TFMs) have made rapid progress in standard classification and regression, but time-to-event survival prediction tasks have remained largely untouched. Unlike in standard regression tasks, survival prediction models must account for censored data. Standard TFMs cannot handle natively censored data, leading to biased and inaccurate predictions, making them unsuitable for real-world applications. To overcome this fundamental limitation, we propose \texttt{SurvPFN}, a prior-data fitted network (PFN), for survival prediction tasks. We pretrain \texttt{SurvPFN} on millions of synthetic survival prediction tasks to learn survival via distributional regression that accounts for censored data. \texttt{SurvPFN} works by (1) generating data with Weibull event times and a non-informative censoring mechanism; (2) integrating a censored event indicator; and (3) minimizing a censored negative log-likelihood. On SurvSet, a collection of real-world survival tasks, \texttt{SurvPFN} is highly competitive with classical and deep survival baselines without per-dataset fitting, a survival-specific architecture, or feature engineering. We show that survival can be treated as a continuous-time distributional regression problem with censored loss, unlocking the power of PFNs for time-to-event predictions.