Survival Predictions

High-risk non-muscle-invasive bladder cancer (HR-NMIBC) carries substantial risks of recurrence and progression, while current clinical risk stratification remains limited. CHIMERA was established as a multimodal AI challenge to benchmark prediction in HR-NMIBC under standardized evaluation. Task BRS predicts RNA-seq-defined BCG Response Subtypes from histopathology and structured clinicopathological data, whereas Task Progression models time-to-progression using histopathology, structured data, and RNA sequencing. A multimodal dataset of 368 patients was divided into public training and hidden validation and test sets. In total, 159 submissions were made, and 13 top-performing models were selected for benchmarking. The best models achieved a weighted F1 score of 0.73 for Task BRS and a C-index of 0.68 for Task Progression. Post-challenge analyses revealed task-dependent modality contributions, cohort-dependent performance degradation, and sensitivity to missing structured data. In Task BRS, histopathology partly compensated for pathology-derived structured variables, whereas progression models showed greater dependence on complementary inputs. Cross-model error analysis further identified patients that were consistently difficult across different architectures, with T1 substage associated with prediction difficulty. These findings highlight barriers to transportability and the importance of missingness-aware modeling and independent multi-institutional validation. CHIMERA provides a standardized multimodal benchmark for bladder cancer and a framework for studying not only model performance, but also robustness, information sufficiency, and patient-level prediction failure.

Multimodal learning has significantly advanced survival prediction by integrating pathology images with genomic data. However, clinical information, despite its critical role in reflecting a patient' s overall health, remains underutilized due to its discrete, sparse, and low-dimensional nature. Furthermore, the inherent heterogeneity across these modalities pose significant challenges in modeling cross-modal interactions. In this paper, we propose CIGTSurv, a Clinical Information Guided Tri-modal framework for Survival prediction. Specifically, we first design a holistic text template and use pretrained foundation models to transform clinical tabular data into high-dimensional tokenized embeddings. Using clinical information as an anchor, we then introduce a dual-level interaction mechanism: 1) a local prototype association (LPA) module based on cross-attention to explicitly learn token-level correspondences between different modalities, and 2) a global feature alignment (GFA) loss based on Maximum Mean Discrepancy (MMD) to implicitly enhance cross-modal distribution consistency. Extensive experiments on five TCGA cancer cohorts demonstrate that CIGTSurv achieves state-of-the-art (SOTA) survival prediction performance. Our source code is publicly available at https://github.com/Daijing-ai/CIGT-Surv.git.

There has been significant interest in using machine learning algorithms to predict kidney transplant outcomes, such as the number of years until a graft inevitably fails. These prediction algorithms could possibly be used for pre-transplant donor-recipient matching to identify more compatible donors and recipients and thus improve post-transplant outcomes. In this study, we explore the use of survival prediction models trained on deceased donor kidney transplant data from the Scientific Registry of Transplant Recipients (SRTR). We propose a novel paired recipient-based evaluation framework that compares graft outcomes between two recipients who received kidneys from the same deceased donor, allowing us to evaluate the counterfactual benefit of changing the recipient for a certain donor. We find that five different survival prediction models, ranging in complexity from linear to deep learning-based models, all result in ~60% paired recipient-based accuracy. We further translate this accuracy into an interpretable quantity of post-transplant years gained. We also highlight major limitations of the commonly used concordance index (C-index) metric for evaluating survival prediction accuracy in this setting and demonstrate that our proposed paired recipient-based accuracy metric is more clinically relevant and better reflects real-world allocation settings.

Attention-based multiple instance learning (ABMIL) is the predominant approach for slide-level prediction in computational pathology, yet its attention maps provide only local explanations: they indicate where a model focuses but not which histological features drive its predictions or how the model behaves across a patient cohort. We present Semantic Attention Global Explanations (SAGE), a post-hoc framework that extracts global, language-grounded explanations from a frozen ABMIL model. Using a pathology vision-language model, SAGE scores image patches against a dictionary of 25 histological concepts, aggregates these scores according to the model's learned attention, and quantifies how each concept relates to prediction risk across a cohort. Applied to survival prediction using seven TCGA cancer cohorts and three foundation models, SAGE recovered established prognostic features, such as the adverse association of necrosis, while revealing cancer-specific biology, including a favorable angiogenic signature in renal cell carcinoma consistent with known molecular subtypes. Ablation studies demonstrated that these associations depend on the model's learned attention rather than concept prevalence alone, and that the concept dictionary captures much of the prognostic information encoded by the foundation model features. Through semantically-grounded explanations, SAGE provides a scalable, model-agnostic framework for understanding what ABMIL survival models learn, enabling pathologists to interpret model behavior at the cohort level and offering the potential for biomarker identification.

In this work, we propose K-SurvMeans, a novel extension of K-Means for clustering survival data. The method explicitly uses the survival outcome in the clustering process to optimize cluster centers, thereby maximizing pairwise survival differences between clusters. The objective function encourages the clusters to be well-separated from the survival perspective. Since the resulting optimization problem is non-differentiable, we employ the Particle Swarm algorithm for the Optimization process. To further improve flexibility and mitigate the curse of dimensionality, we extend the framework to operate in a learned low-dimensional latent space obtained via a dimensionality reduction. This allows the method to capture better-separated clusters and enhance optimization efficiency by reducing the search space. Experiments on multiple publicly available benchmark survival datasets demonstrate that K-SurvMeans consistently yields clusters with improved separation in survival distributions compared to existing deep learning-based survival clustering methods.

Radiomic biomarkers derived from magnetic resonance imaging (MRI) have been widely investigated as non-invasive tools for tumor characterization and prognostic modeling in glioblastoma (GBM). However, their clinical translation remains limited, in part due to sensitivity to tumor segmentation variability. In this study, we systematically investigate the relationship between feature robustness and predictive utility in GBM survival modeling using the University of Pennsylvania Glioblastoma Imaging, Genomics, and Radiomics (UPENN-GBM) cohort. A total of 4,752 radiomic features were obtained from multiparametric MRI across three tumor subregions: enhancing tumor (ET), peritumoral edema (ED), and necrotic core (NC). Feature robustness was quantified using the intraclass correlation coefficient (ICC) based on the automatic and expert-refined segmentation versions. Among features with valid ICC estimates, 48.1% were classified as robust. Survival prediction was evaluated using cross-validation with Coxnet, Random Survival Forest, and Gradient Boosting Survival Analysis models. In this cohort, radiomic feature inclusion showed no consistent improvement over the clinical baseline, and robustness filtering produced no detectable performance gain. Model-selected features were less robust than the overall feature pool, indicating a lack of enrichment for robustness. These findings suggest that robustness alone is not a reliable criterion for feature selection in radiomics-based survival modelling.

Whole-slide survival models commonly provide risk rankings without calibrated statements about individual event times. We evaluate fixed-cutoff drcosarc, a post-hoc conformal wrapper for discrete-time multiple-instance learning survival heads using frozen UNI2-h representations, in an internal 18-configuration sweep across five TCGA cohorts and an external five-configuration evaluation across three CPTAC cohorts. We distinguish configuration--fold--split summaries of the inverse-probability-of-censoring-weighted (IPCW) estimate and median lower predictive bound (LPB) from a hierarchy-aware patient-ensemble estimand of the mean drcosarc--naive LPB difference. At $α=0.1$, the drcosarc IPCW estimate was nearest 0.90 in KIRC, LUAD, and STAD. Patient-ensemble drcosarc--naive intervals excluded zero in KIRC, KIRP, STAD, UCEC, and CPTAC-CCRCC, but included zero in internal LUAD, CPTAC-LUAD, CPTAC-UCEC, and the internal LUSC extension. In a 20-replicate low-censoring semi-synthetic setting with known event times, drcosarc empirical coverage was 0.9129 [0.9053, 0.9207]. An exploratory analysis supported a head-error-by-censoring interaction within that data-generating process. In a two-cohort ABMIL sensitivity analysis, increasing the hazard grid to $K=16$ raised localized marginal IPCW estimates above the prespecified 0.87 threshold and yielded positive paired LPB differences, although worst-group estimates remained below 0.87. Overall, performance was cohort dependent, and its interpretation changed with the patient-level unit, estimand, and censoring assumptions.

Predictive maintenance relies on accurate Remaining Useful Life estimation, often formulated using survival analysis over multivariate time-series data. While modern deep survival models achieve strong predictive performance, their black-box nature limits their use in safety-critical settings where actionable insight is required. In this work, we introduce \textit{SurvCF(t)}, the first framework for generating counterfactual explanations for survival models operating on time-series data. \textit{SurvCF(t)} identifies minimal, plausible, and temporally consistent changes to an asset's operational history that increase its predicted life time, framing explanation as a constrained optimization problem combining validity, proximity, sparsity, and plausibility. We evaluate the method on multiple benchmarks, including C-MAPSS, N-CMAPSS, and a real-world case study of the Scania Component_X dataset, demonstrating its ability to produce actionable and interpretable interventions. Our results show that \textit{SurvCF(t)} bridges the gap between survival prediction and prescriptive maintenance, enabling explainable and decision-oriented AI for maintenance strategies.

Deep survival models are evaluated almost exclusively by the concordance index (C-index), yet they are commonly trained using likelihood objectives such as the Cox partial likelihood, discrete-time negative log-likelihood, and DeepHit likelihood. This mismatch is usually considered acceptable because the C-index can be recomputed on validation data during training. However, for end-to-end training of high-capacity encoders on small, heavily censored oncology cohorts, frequent C-index evaluation is computationally expensive, making the loss value itself an important signal for monitoring, early stopping, and model selection. We show that likelihood losses are unreliable for this purpose and propose a value-monotone concordance loss. We prove that every strictly proper survival likelihood admits directions where the loss decreases while the C-index remains unchanged, causing the loss value to decouple from ranking performance. We then study a sigmoid concordance loss (SCL), whose value approximates one minus the C-index up to a temperature term, ensuring that lower loss corresponds to higher C-index during optimization. The loss is architecture agnostic and reduces to a convex survival ranking support vector machine for linear models. Across eighteen datasets from four modalities using a unified five-fold cross-validation protocol, SCL achieves discrimination comparable to standard likelihood losses and is the best or within one standard deviation of the best C-index. Unlike likelihood losses, SCL maintains a strong correlation between loss value and C-index during training, with rank correlations of 0.96 to 0.99 compared with -0.03 to 0.53 for likelihood losses. Calibration measured by the integrated Brier score is comparable. SCL provides a value-monotone optimization objective whose value can serve as a reliable surrogate for the C-index during expensive end-to-end training.

Survival models can model time-to-event outcomes using partially observed data. They are widely used in clinical prediction, including cancer risk, disease progression, treatment response, and mortality. Recent models often rely on rich inputs collected at a specific clinical encounter, such as medical images, laboratory tests, electronic health record snapshots, or sensor measurements. In large retrospective datasets, these inputs are usually collected over many calendar years. As a result, they may contain clues about when they were acquired through changes in devices, protocols, documentation, patient mix, or clinical practice. This creates a potential failure mode when outcomes are observed only up to a fixed study end date. More recent records necessarily have less potential follow-up than older records. A model that can infer the record date from the input may therefore learn to predict how much follow-up was available rather than the patient's true risk of experiencing the event. We call this failure mode administrative-cutoff leakage. In this paper, we characterize when this leakage can occur, distinguish it from classical informative censoring and genuine temporal changes in risk, and propose practical ways to detect it. In simulations, we show that administrative-cutoff leakage can inflate fixed-horizon AUC and can also affect Harrell's C-index under realistic follow-up patterns. We then demonstrate the same behavior in a real mammography cohort. These results motivate a simple design principle for survival prediction: for an n-year prediction task, the dataset should provide at least n years of potential follow-up after the latest input date. Otherwise, the models may be subject to bias induced by administrative-cutoff leakage.

Does every cancer patient truly need a complete diagnostic workup for accurate survival prediction? In multimodal clinical oncology, diagnostic modalities follow a clinically mandated order of escalating burden -- from demographics collected at intake to genomic profiling requiring specialized tissue analysis. Current multimodal survival methods either assume all modalities are available or passively handle missing data, but none actively reason about whether acquiring the next modality is justified for a given patient along this ordered workflow. We formulate this as a sequential decision problem and propose SAGEAgent (Sequential Acquisition Guided by Experience), a self-evolving LLM-based clinical agent that decides which diagnostic modalities to acquire for each patient, balancing predictive accuracy against clinical invasiveness. SAGEAgent reasons about each patient's evolving diagnostic state through clinical tools that translate numerical predictions into text, an episodic memory that retrieves similar past cases, and a semantic memory that accumulates reusable decision patterns from experience. Experiments on a glioma cohort combining TCGA-LGG, TCGA-GBM, and BraTS with four diagnostic modalities demonstrate that SAGEAgent achieves competitive survival prediction accuracy while reducing average acquisition burden by 55%.

Cardiovascular disease risk prediction models often rely on data from a single institution or centrally pooled datasets. Extending these models across institutions could be limited by privacy regulations and constraints on sharing patient-level data. Federated learning enables collaborative model development without transferring sensitive patient data, but its application in healthcare remains challenging because datasets often differ in size, population characteristics, and outcome definitions. In this study, we present a federated deep learning approach for privacy-preserving cardiovascular disease risk prediction that integrates two population-based cohorts with different characteristics: Lifelines, including 148,230 participants meeting the study inclusion criteria with self-reported outcomes, and the Rotterdam Study, including a smaller cohort of 10,155 participants with digitally linked clinical outcomes. Model performance was primarily evaluated on the Rotterdam Study because of its complete follow-up. Deep survival models trained using federated learning achieved higher predictive performance than models trained locally without federation. For the Rotterdam Study, the C-statistic increased from 0.728 (95% CI: 0.717-0.739) to 0.739 (95% CI: 0.728-0.749). For Lifelines, the C-statistic increased from 0.783 (95% CI: 0.775-0.791) to 0.787 (95% CI: 0.780-0.792). These findings suggest that federated deep learning across heterogeneous cohorts can improve cardiovascular disease risk prediction while preserving the privacy of individual-level patient data.

Accurate prognosis prediction is important for treatment planning in lung cancer, but deep learning-driven survival modelling is often limited by the scarcity of curated imaging cohorts with reliable outcome data. This study evaluates whether representations from a domain-specific foundation model can be used for multimodal survival prediction in data-constrained clinical settings. We assess the foundation model CT-CLIP as a feature extractor for pretreatment computed tomography images and clinical variables from 242 diagnosed lung cancer patients. The evaluation includes adaptation strategies based on frozen encoders, full fine-tuning, and low-rank adaptation, together with modality ablations and comparisons with clinical and multimodal baselines. The results show that a frozen CT-CLIP model combined with a trainable lightweight survival head outperforms the clinical baseline and achieves comparable or improved performance relative to other multimodal approaches, and separates patients into clinically meaningful high- and low-risk groups.

Genomic prediction models often fail to transfer across institutions because sequencing panels differ across sites, creating structural feature missingness at deployment. Existing approaches to this challenge typically restrict analysis to genes shared across cohorts, exclude patients with incomplete profiles, or rely on test-time imputation, all of which can reduce robustness and limit the use of multi-center data. We propose Survival prediction Handling Incomplete Features using Transformer (SHIFT), a missingness-aware survival model that directly predicts from incomplete genomic inputs without test-time imputation. SHIFT represents each genomic feature separately and uses masked self-attention, along with a feature-availability mask, so that predictions are based only on observed inputs. Further, we introduce variable-rate feature masking during training to improve robustness to heterogeneous missingness patterns. We evaluate the approach on glioblastoma and lung squamous cell carcinoma with external validation across multiple cohorts, including a challenging setting with severe cross-cohort panel mismatch. Across these settings, SHIFT shows strong generalization and compares favorably with standard survival baselines and imputation-based approaches, while using a single model across differing feature sets. We also find that incorporating patients from incomplete cohorts during development can improve performance on external data, suggesting that partially observed cohorts need not be excluded from model building. These results support missingness-aware modeling as a practical strategy for multi-center survival prediction in precision oncology.

Head and neck cancers (HNC) represent a significant global health burden, with accurate tumor delineation being essential for effective radiotherapy planning. The complexity of the oropharyngeal anatomy, combined with the heterogeneous appearance of tumors on imaging, makes manual segmentation time-intensive and subject to inter-observer variability. Beyond segmentation, predicting long-term clinical outcomes, such as recurrence-free survival (RFS), and determining human papillomavirus (HPV) status from noninvasive imaging, remain challenging yet clinically valuable goals. The HECKTOR 2025 challenge addresses these needs by establishing a comprehensive benchmark for automated HNC analysis using multimodal PET/CT imaging and electronic health records. Building on previous editions (2020-2022), this challenge features an expanded multi-institutional dataset comprising over 1,100 patients from 10 centers worldwide. Participants were tasked with three complementary objectives: (1) segmenting primary gross tumor volumes (GTVp) and metastatic lymph nodes (GTVn), (2) predicting recurrence-free survival, and (3) classifying HPV status. The challenge attracted 35 registered teams, with 15 final submissions evaluated on a held-out test set. Top-performing algorithms achieved a mean Dice similarity coefficient of 0.75 for segmentation, a concordance index of 0.66 for survival prediction, and a balanced accuracy of 0.56 for HPV classification. This paper presents a comprehensive analysis of the submitted methodologies, evaluates their performance across different lesion characteristics, and discusses their implications for clinical translation in automated oncology workflows and decision support systems.

Recent multimodal survival prediction models have demonstrated strong predictive performance by leveraging complementary information across modalities. However, such models generally assume data completeness and exhibit limited robustness toward missing modalities, which are frequently encountered in real-world clinical settings. We propose the Evidential Missing Modality Survival Fusion (EMMS) model for multimodal survival prediction under missing modalities. EMMS offers a straightforward, computationally effective approach to survival analysis without requiring a generative phase for missing data. By employing Dempster-Shafer theory and Gaussian Random Fuzzy Numbers for multimodal decision fusion, it considers both aleatoric and epistemic uncertainty alongside modality reliability for fusion. Moreover, the model treats missing modalities as vacuous evidence, preventing interference with available inputs and naturally reflecting increased uncertainty and calibrated predictions. Extensive experiments on four cancer datasets demonstrate state-of-the-art performance while providing calibrated and interpretable uncertainty estimates under incomplete multimodal observations, without introducing additional computational overhead.

Accurate survival prediction is essential for personalized treatment planning in head and neck cancer, yet remains challenging due to the heterogeneous and high-dimensional nature of multimodal clinical data. While deep survival models have improved predictive performance over classical statistical approaches, existing methods typically rely on static fusion strategies or temporally agnostic modeling, limiting their ability to capture structured clinical workflows. In this work, we propose ChronoSurv, a heterogeneous hierarchical directed graph framework for multimodal survival analysis. ChronoSurv represents patient care as a progression-aware clinical trajectory using directed graphs aligned with key diagnostic steps. A hierarchical topology incorporates fine-grained, coarse, and global representations, further supporting flexible adaptation to missing modalities, while heterogeneous message passing models complex and asymmetric relationships across modalities and clinical steps. Experimental results on two public datasets demonstrate that ChronoSurv achieves state-of-the-art discriminative performance while maintaining statistically reliable calibration. Comprehensive ablation studies further confirm the contribution of each architectural component, highlighting the potential of trajectory-aware graph modeling for multimodal survival prediction.

Alzheimer's Disease (AD) is a complex neurodegenerative disorder that continues to impact millions of people worldwide. Predicting AD conversion during the prodromal stage remains critical for disease understanding and patient care. As such, survival models are widely used for AD risk prediction, yet they are typically static predictors with limited interpretability and no capacity for natural language reasoning. In this work, we propose iLENS, an interpretable large language model (LLM) guided framework based on mixture-of-experts (MoE) for survival prediction in AD conversion. Our approach uses LLM to synthesize structured neuroimaging measurements and unstructured information to guide expert routing. Our framework demonstrates competitive predictive performance and capability in patient subtyping. Furthermore, our framework provides transparent, biologically grounded rationales for its routing decisions, bridging the gap between high-performance survival analysis and interpretable clinical decision support.

Survival prediction plays a central role for healthcare providers and clinical researchers. Accurate risk stratification enables early intervention and improved patient management. Most existing deep survival models learn one common feature representation for all patients, which may hide important differences between patient subgroups. In contrast, a Mixture-of-Experts (MoE) framework allows different parts of the model to focus on different patient patterns, leading to more individualized representations. Therefore, in this work, we propose a mixture-of-experts enhanced adaptive deep clustering survival framework (AdaCSM) for modeling such heterogeneous survival patterns. We introduce a routing-based expert mechanism that enables conditional specialization within a parametric survival modeling framework. The proposed architecture allocates patients to specialized risk predictors dynamically while preserving the patient survival and subtype clustering objectives. We compare our method with state-of-the-art survival and deep clustering models on multiple real-world longitudinal clinical cohorts spanning diverse disease domains. The proposed method demonstrates improved predictive performance and leads to interpretable results in survival analysis.

Accurate prediction of overall survival (OS) from positron emission tomography/computed tomography (PET/CT) can support personalized treatment and follow-up strategies in oncology. However, the impact of temporal modeling on imaging-based survival prediction remains insufficiently explored. We investigate how different temporal formulations influence survival prediction by developing two complementary approaches: Attention-guided Time-Conditioned Survival (ATCS) and Multi-Time Survival (MTS). We retrospectively analyzed pre-treatment PET/CT images from 848 patients with non-small cell lung cancer (NSCLC), including 556 for model development and 292 for held-out testing. A previously proposed Time-Conditioned Survival (TCS) model was used as a baseline. Models were trained using 5-fold cross-validation and evaluated on the test set using time-dependent area under the curve (AUC) at 6-month intervals from 0.5 to 5 years. Both ATCS and MTS outperformed the baseline TCS model, achieving mean AUCs of 0.794 and 0.793, respectively, compared to 0.767. ATCS performed better at earlier time points (0.5-3 years), whereas MTS performed better at later intervals (3.5-5 years). Combining tumor-specific and tissue-wise PET/CT features improved performance over either input alone. Finer temporal discretization improved short-term prediction, while coarser intervals provided more stable long-term estimates. These findings demonstrate that temporal modeling and input design influence PET/CT-based survival prediction. The proposed approaches enable time-specific survival estimation from pre-treatment imaging and may support improved risk stratification and clinical decision-making.

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.

We investigate whether information about time-to-event risk estimated by a Cox proportional hazards model can be transferred into a generative large language model. We propose a text-based survival modelling pipeline in which structured clinical covariates are converted into text prompts and a Qwen-based large language model is fine-tuned to generate patient-specific survival risk using Cox model predictions as a training target. Across GBSG2, ACTG320, and WHAS500, the model achieves competitive held-out discrimination and calibration despite being trained as a text-generation task rather than with a conventional survival-analysis loss. We further analyse the geometry of the model's hidden states, where t-SNE visualisations reveal smooth risk gradients in latent space, suggesting that the model represents survival risk as a continuous structure rather than isolated risk categories. Together, these findings suggest that large language models can internalise survival-risk structure while supporting calibrated prediction, providing a route towards time-to-event reasoning in language models.

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.

Quantization is a standard path to deploying large language models, and quantized models are typically judged acceptable when perplexity or downstream accuracy remains close to the full-precision original. But behavioral parity need not imply feature fidelity: the sparse-autoencoder (SAE) features used to interpret a full-precision model may change after weight rounding. We test this directly by using a frozen SAE as a fixed measurement basis, encoding full-precision and round-to-nearest (RTN) quantized activations on identical tokens, and measuring per-feature survival by Pearson correlation across bit-widths from INT8 to INT4 on Pythia-70M and Gemma-2-2B. Our central finding is that perplexity can miss feature damage: on Gemma-2-2B, INT7 improves perplexity while degrading 18.7% of active SAE features, and under sliding-window evaluation INT6 also improves perplexity while only 51.3% of active features survive. Feature survival is graded rather than cliff-like, with 62.4% of active Pythia features and 51.3% of active Gemma features surviving at INT6; most non-surviving features are blurred rather than fully damaged. Survival is also predictable from full-precision feature statistics alone, with cross-validated AUC 0.92--0.97 and peak activation as the strongest marginal predictor. Finally, RTN quantization and matched-perplexity magnitude pruning damage strongly overlapping feature sets, with Jaccard overlap 0.79--0.86 and damage-score Spearman correlation 0.98. These results show that behavioral metrics alone are insufficient evidence that full-precision interpretability findings transfer to quantized models, motivating feature-level audits of compression.

Machine learning predictors have become essential tools for guiding automated decision making. However, a major misalignment persists: predictive models are typically optimized in terms of standard statistical metrics in isolation from the algorithmic tasks they inform. We highlight this incongruity in the high-stakes domain of organ allocation by demonstrating that any algorithm relying on (even highly accurate) survival predictors optimized for standard metrics -- such as the Concordance index (C-index) -- can yield arbitrarily poor outcomes when used for allocation, failing to guarantee utility better than a uniform random selection. To bridge the gap between survival analysis and policy optimization, we introduce a decision-focused learning approach based on optimizing normalized discounted cumulative gain (NDCG), a mainstay metric in information retrieval. We establish the utility of NDCG in survival analysis by proving that it translates to guarantees on the performance of allocation. Empirically, we propose a bootstrapping approach to optimize the NDCG of existing survival models. Unlike prior work, we also address the challenge of right censorship when evaluating ranking. On historical heart transplant data from the US, our method dramatically boosts the NDCG of baseline models by 50-100%, which translates to tens of thousands of additional life years gained annually when deployed for transplant allocation. We anticipate that our framework will find broader applications in decision making with predictions.

The Charlson Comorbidities Index (CCI) is a weighted additive index widely used to estimate ten-year mortality risk, but its original weights may not reflect contemporary prognoses. This limitation is critical in Prostate Cancer (PCa), where radical treatment is recommended only for patients with a life expectancy of at least ten years. For candidates eligible for Radical Prostatectomy (RP), accurate estimation of ten-year other-cause mortality is essential to balance oncological benefit against competing risks and avoid overtreatment. We propose a data-driven framework to derive a comorbidity index tailored to PCa patients considered for RP. Using a retrospective single-institution cohort, we apply Population-Based Bio-Inspired Algorithms (PBBIAs) to recalibrate comorbidity weights and evolve alternative symbolic formulations optimized for ten-year survival discrimination. We compared six optimization strategies, including symbolic regression approaches based on Genetic Programming (GP), population-based metaheuristics, clinically validated baselines, and survival prediction models. Results show that GA, FST-PSO, and SLIM outperform both the original CCI and the PCCI, particularly when PCa-specific variables are included, improving the Concordance Index by up to 0.1. GPLearn yields compact and interpretable models with competitive performance. Overall, the proposed approach provides an updated and interpretable tool to improve patient selection for RP.

Objective: Survival analysis is central to medical prediction, yet large language models (LLMs) are rarely used as end-to-end survival models because censoring prevents straightforward supervised fine-tuning. Here we present LLMSurvival, a framework that enables censoring-aware survival analysis with unmodified LLMs operating directly on tabular clinical data. Materials and Methods: LLMSurvival reformulates time-to-event prediction as pairwise ranking among comparable subjects, and derives test-time risk by aggregating comparisons against anchor individuals from the training cohort. Results: Across two clinical tasks (ICU mortality prediction in MIMIC-IV and fragility fracture prediction in a NewYork-Presbyterian/Weill Cornell Medicine cohort), LLMSurvival improves overall concordance over Cox proportional hazards modeling by 3.1% for ICU mortality and 0.5% for fracture risk, 2.1% on average for ICU mortality and 2.8% for fracture risk over three established deep learning survival models. Discussion: The results show that survival modeling with censoring can be made compatible with LLM fine-tuning through comparison-based reformulation. The framework demonstrates high portability and superior performance over expert curated scores like SAPS-II and FRAX scores across diverse clinical context. Furthermore, the framework supports local deployment, as compact, publicly available base models provide sufficient performance. Conclusion: The LLMSurvival framework serves as a proof of concept for an integrated, censoring-conscious approach to survival analysis via LLMs.

Integrating multimodal datasets in clinical oncology is frequently hindered by high dimensionality and blockwise missingness, where entire data sources are unavailable for specific patient subsets. Standard survival models often struggle with these gaps, leading to biased results or patient exclusion. We introduce Multimodality Stacking with Blockwise missing values (MSB), a late-fusion framework for survival analysis that independently models modality-specific features before aggregating predictions via a cross-validated stacking meta-learner. MSB was validated on the PIONeeR study (n=443 patients, 378 biomarkers across eight heterogeneous sources) to predict progression-free survival in advanced non-small cell lung cancer patients receiving immunotherapy. MSB yielded higher predictive performance (C-index) than baseline algorithms. Improvements varied by baseline strength: linear models showed a 15.9% increase (p<0.001 for the Wilcoxon signed-rank test), random survival forests gained 5.4% (p=0.002), and gradient boosting methods improved by 2.1% (p=0.030). Beyond discrimination, MSB reduced the generalization gap (train-test difference in 5 folds cross-validation repeated 3 times: 0.055 vs 0.380 for linear models). Permutation importance analysis identified routine laboratory markers, clinical features, and PD-L1 expression as primary predictive drivers. Missing block indicators showed negligible importance, suggesting the model learned from biomarker values rather than data availability patterns. MSB provides a statistically validated framework for multimodal survival prediction with blockwise missingness. By enabling systematic biomarker evaluation without requiring complete data, MSB offers a practical tool for predictive modeling in biomedical research, pending external validation. Implementation is available at https://github.com/MohamedBoussena/MSB under Inria license.

Survival analysis aims to model how covariates and time jointly shape the time-to-event distribution under right censoring. Classical methods such as the Cox model and generalised additive models (GAMs) require interactions and time-varying effects to be manually specified, which is increasingly impractical on rich clinical datasets. We introduce KAPLAN-HR, a B-spline Kolmogorov-Arnold Network (KAN) for nonparametric estimation of the conditional hazard as a joint function of covariates and time. A single-layer KAPLAN-HR model recovers a GAM, while deeper architectures capture interactions and time-varying effects through composition. We establish a convergence rate for the nonparametric KAN hazard estimator that depends only on the smoothness of the underlying KAN representation and not on the covariate dimension, thereby mitigating the curse of dimensionality for KAN-representable targets. In evaluations over six clinical benchmark datasets, KAPLAN-HR matches or exceeds the predictive performance of established statistical and deep learning survival methods.

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).

We propose a novel multimodal deep learning framework for patient-level survival prediction, which integrates whole-slide histology features, RNA-seq expression profiles, and clinical variables. Our architecture combines an ABMIL module~\cite{ilse2018attention} for slide-level representation with feedforward encoders for RNA and clinical data. These embeddings are then integrated through low-rank bilinear cross-modal fusion~\cite{liu2018efficient} to model conditional interactions across modalities while controlling parameter growth. The model outputs continuous risk scores that are subsequently mapped to survival times using a nonparametric calibration procedure based on the Kaplan--Meier estimator~\cite{kaplan1958nonparametric}. By decomposing multimodal reasoning into independent pairwise interactions, the proposed fusion design promotes structural interpretability and parameter efficiency compared with full tensor and hierarchical fusion strategies. Experiments on the CHIMERA challenge dataset demonstrate improved predictive performance over concatenation-based baselines and competitive generalization on hidden evaluation cohorts. These results indicate that the proposed framework is a promising approach for multimodal survival prediction in HR-NMIBC. The implementation is publicly available at https://github.com/hassancpu/ChimeraChallenge2025_Task_3.

Protein sequence data from nature exhibits survivorship bias: we only observe data from those organisms that survive and reproduce, while non-functional protein mutations are eliminated by natural selection. Thus, predicting whether a protein sequence is functional often requires learning from positive examples alone. While positive-unlabeled (PU) learning frameworks offer a generic solution to this problem, existing PU methods ignore the evolutionary processes that shape sequence observability and cause survivorship bias. Consider a sequence that is one mutation away from a commonly-observed protein variant in a well-surveilled organism. If the sequence were functional, it would likely be observed. If it is not observed, this suggests non-functionality. In contrast, sequences that are unlikely to arise through mutation may be missing simply because they never arose. Thus, these two kinds of missing sequences should be treated differently when training models. In this work, we propose Evo-PU, a PU learning framework that uses a scientific understanding of nucleotide mutation to model survivorship bias for well-surveilled single-organism sequence data. On three prediction tasks using single-organism uniform-coverage surveillance data -- predicting results from held-out influenza and respiratory syncytial virus (RSV) mutagenesis studies, and predicting future SARS-CoV-2 variants -- Evo-PU outperforms standard PU learning, one-class classification (OCC), and protein language models (PLMs). On prediction tasks from multi-organism ProteinGym datasets with more heterogeneous surveillance coverage, we identify opportunities to generalize our approach.

``How long can I live and remain free of cancer?'' is often the first question a patient asks after receiving a cancer diagnosis and treatment. Accurate survival prediction helps alleviate psychological distress and supports risk stratification and personalized treatment planning. Recent survival prediction frameworks have shown strong performance using computed tomography (CT) images. However, variations in imaging acquisition introduce out-of-distribution (OOD) samples caused by covariate shifts that undermine model reliability. Despite this challenge, to our knowledge, no existing benchmark systematically studies OOD detection in cancer survival prediction. To address this gap, we introduce the Cancer sURvival bEnchmark for OOD Detection (CURE-OOD), the first benchmark for systematically evaluating OOD detection in survival prediction under controlled acquisition-induced distribution shifts. CURE-OOD defines scanner-parameter-based training, in-distribution (ID), and OOD test splits across four survival prediction tasks. Our experiments show that covariate shifts notably reduce survival prediction performance. It also shows that mainstream classification-oriented OOD detectors can fail in survival prediction. Finally, we include HazardDev as a simple survival-aware reference baseline for OOD detection. CURE-OOD enables systematic analysis of how distribution shifts affect both downstream survival performance and OOD detectability.

Pathology foundation models (PFMs) have recently emerged as powerful pretrained encoders for computational pathology, enabling transfer learning across a wide range of downstream tasks. However, systematic comparisons of these models for clinically meaningful prediction problems remain limited, especially in the context of survival prediction under external validation. In this study, we benchmark widely used and recently proposed PFMs for breast cancer survival prediction from whole-slide histopathology images. Using a standardized pipeline based on patch-level feature extraction and a unified survival modeling framework, we evaluate model representations across three independent clinical cohorts comprising more than 5,400 patients with long-term follow-up. Models are trained on one cohort and evaluated on two independent external cohorts, enabling a rigorous assessment of cross-dataset generalization. Overall, H-optimus-1 achieves the strongest survival prediction performance. More broadly, we observe consistent generational improvements across model families, with second-generation PFMs outperforming their first-generation counterparts. However, absolute performance differences between many recent PFMs remain modest, suggesting diminishing returns from further scaling of pretraining data or model size alone. Notably, the compact distilled model H0-mini slightly outperforms its larger teacher model H-optimus-0, despite using fewer than 8% of the parameters and enabling significantly faster feature extraction. Together, these results provide the first large-scale, externally validated benchmark of PFMs for breast cancer survival prediction, and offer practical guidance for efficient deployment of PFMs in clinical workflows.

Cancer survival prediction from multi-omics data remains challenging because prognostic signals are high-dimensional, heterogeneous, and distributed across interacting genes and pathways. We propose PathMoG, a pathway-centric modular graph neural network for multi-omics survival prediction. PathMoG reorganizes genome-scale inputs into 354 KEGG-informed pathway modules, introduces a Hierarchical Omics Modulation module to condition gene-expression representations on mutation, copy number variation, pathway, and clinical context, and uses dual-level attention to capture both intra-pathway driver signals and inter-pathway clinical relevance. We evaluated PathMoG on 5,650 patients across 10 TCGA cancer types and observed consistent improvements over representative survival baselines. The framework further provides gene-level, pathway-level, and patient-level interpretability, supporting biologically grounded and clinically relevant risk stratification.

Accurate prognostication and risk estimation are essential for guiding clinical decision-making and optimizing patient management. While radiologist-assessed features from CT scans provide valuable indicators of disease severity and outcomes, interpreting such images requires expert knowledge, and translating rich visual information into textual summaries inevitably leads to information loss. In this work, we propose a vision-language framework for 3D CT image understanding that leverages large-scale open-sourced CT images paired with radiology reports through visual instruction tuning. This pre-training enables the model to learn clinically meaningful visual-textual representations, which can then be adapted to downstream survival prediction tasks. By incorporating a survival prediction head on top of the pre-trained model, our approach improves survival prediction from CT images and clinical data while generating clinically meaningful language responses to predefined questions. Experimental results demonstrate that our method outperforms baseline methods in survival prediction, particularly, when clinical data alone is less predictive. The code will be released upon acceptance.

Standard approaches to goal-conditioned reinforcement learning (GCRL) that rely on temporal-difference learning can be unstable and sample-inefficient due to bootstrapping. While recent work has explored contrastive and supervised formulations to improve stability, we present a probabilistic alternative, called survival value learning (SVL), that reframes GCRL as a survival learning problem by modeling the time-to-goal from each state as a probability distribution. This structured distributional Monte Carlo perspective yields a closed-form identity that expresses the goal-conditioned value function as a discounted sum of survival probabilities, enabling value estimation via a hazard model trained via maximum likelihood on both event and right-censored trajectories. We introduce three practical value estimators, including finite-horizon truncation and two binned infinite-horizon approximations to capture long-horizon objectives. Experiments on offline GCRL benchmarks show that SVL combined with hierarchical actors matches or surpasses strong hierarchical TD and Monte Carlo baselines, excelling on complex, long-horizon tasks. Webpage and Code: https://simple-robotics.github.io/publications/survival-value-learning/

Multimodal survival analysis aims to improve cancer prognosis using heterogeneous biomedical data, such as histopathology images and genomic profiles. A common strategy is to align representations across modalities so that shared signals can be captured. However, strong cross-modal alignment can also remove modality-specific evidence that is critical for survival prediction. In this paper, we revisit multimodal survival learning from a simple observation: effective models should first discover shared patterns across modalities, and then preserve modality-specific signals. This motivates a representation learning principle that we refer to as Together Then Apart. Based on this idea, we propose TTA, a framework that balances cross-modal alignment and representation distinctiveness. TTA first performs prototype-based alignment to capture shared survival-related structures between modalities. It then encourages modality-specific distinctiveness through an anchor-guided contrastive objective. To further account for modality imbalance and noisy correspondences, we model cross-modal interactions using unbalanced optimal transport. We evaluate the proposed approach on multiple TCGA cancer cohorts with paired histopathology and genomic data. TTA consistently improves survival prediction over recent multimodal survival models. Moreover, the learned prototype structures reveal interpretable cross-modal patterns associated with clinical outcomes.

Survival analysis plays a vital role in making clinical decisions. However, the models currently in use are often difficult to interpret, which reduces their usefulness in clinical settings. Prototype learning presents a potential solution, yet traditional methods focus on local similarities and static matching, neglecting the broader tumor context and lacking strong semantic alignment with genomic data. To overcome these issues, we introduce an innovative prototype-based multimodal framework, FeatProto, aimed at enhancing cancer survival prediction by addressing significant limitations in current prototype learning methodologies within pathology. Our framework establishes a unified feature prototype space that integrates both global and local features of whole slide images (WSI) with genomic profiles. This integration facilitates traceable and interpretable decision-making processes. Our approach includes three main innovations: (1) A robust phenotype representation that merges critical patches with global context, harmonized with genomic data to minimize local bias. (2) An Exponential Prototype Update Strategy (EMA ProtoUp) that sustains stable cross-modal associations and employs a wandering mechanism to adapt prototypes flexibly to tumor heterogeneity. (3) A hierarchical prototype matching scheme designed to capture global centrality, local typicality, and cohort-level trends, thereby refining prototype inference. Comprehensive evaluations on four publicly available cancer datasets indicate that our method surpasses current leading unimodal and multimodal survival prediction techniques in both accuracy and interpretability, providing a new perspective on prototype learning for critical medical applications. Our source code is available at https://github.com/JSLiam94/FeatProto.

Cancer survival prediction from whole slide images (WSIs) is a challenging task in computational pathology due to the large size, irregular shape, and high granularity of the WSIs. These characteristics make it difficult to capture the full spectrum of patterns, from subtle cellular abnormalities to complex tissue interactions, which are crucial for accurate prognosis. To address this, we propose CrossFusion, a novel multi-scale feature integration framework that extracts and fuses information from patches across different magnification levels. By effectively modeling both scale-specific patterns and their interactions, CrossFusion generates a rich feature set that enhances survival prediction accuracy. We validate our approach across six cancer types from public datasets, demonstrating significant improvements over existing state-of-the-art methods. Moreover, when coupled with domain-specific feature extraction backbones, our method shows further gains in prognostic performance compared to general-purpose backbones. The source code is available at: https://github.com/RustinS/CrossFusion

Recent work has argued normatively, on synthetic data, that evaluating survival models by discrimination alone (concordance index) yields systematically misleading model comparisons, because the metric ignores calibration and time-dependent accuracy. Whether this matters for real, published, non-clinical models has not been tested. We reproduce three published survival-ML models across three structurally distinct domains -- hard-drive failure prediction, peer-to-peer credit default, and user disengagement on digital platforms -- validate our instrument against the anchor paper's own synthetic experiment, and test five pre-registered hypotheses under a Holm-corrected family-wise error rate. Three of five reject (though one pre-registered threshold clears by a narrow margin). A model reproducing the published literature's discrimination almost exactly (C = 0.9595 vs. 0.958 reported) fails a formal calibration test at p < 0.001; a broad feature-ablation search finds no single attribute responsible for its discrimination, so the calibration failure is not a trivial shortcut artifact. A lender's estimated default risk is biased upward by roughly two percentage points, growing to nearly four in the riskiest segment, when loan prepayment is treated as non-informative censoring rather than a competing risk. A platform's churn model shows probability estimates that degrade with the horizon even as global discrimination stays within the pre-registered C-index band. A direct test of whether metric choice inverts model preference does not reject, though with limited power given two to three models per domain; the failure mode we document is better characterized as misplaced confidence in a chosen model than as choosing the wrong one. We release a pre-registered evaluation harness with full code and an annotated notebook, so these results can be verified independently and the audit extended.