Daily Papers

Models that can predict the occurrence of events ahead of time with low false-alarm rates are critical to the acceptance of decision support systems in the medical community. This challenging task is typically treated as a simple binary classification, ignoring temporal dependencies between samples, whereas we propose to exploit this structure. We first introduce a common theoretical framework unifying dynamic survival analysis and early event prediction. Following an analysis of objectives from both fields, we propose Temporal Label Smoothing (TLS), a simpler, yet best-performing method that preserves prediction monotonicity over time. By focusing the objective on areas with a stronger predictive signal, TLS improves performance over all baselines on two large-scale benchmark tasks. Gains are particularly notable along clinically relevant measures, such as event recall at low false-alarm rates. TLS reduces the number of missed events by up to a factor of two over previously used approaches in early event prediction.

This paper presents a differentially private approach to Kaplan-Meier estimation that achieves accurate survival probability estimates while safeguarding individual privacy. The Kaplan-Meier estimator is widely used in survival analysis to estimate survival functions over time, yet applying it to sensitive datasets, such as clinical records, risks revealing private information. To address this, we introduce a novel algorithm that applies time-indexed Laplace noise, dynamic clipping, and smoothing to produce a privacy-preserving survival curve while maintaining the cumulative structure of the Kaplan-Meier estimator. By scaling noise over time, the algorithm accounts for decreasing sensitivity as fewer individuals remain at risk, while dynamic clipping and smoothing prevent extreme values and reduce fluctuations, preserving the natural shape of the survival curve. Our results, evaluated on the NCCTG lung cancer dataset, show that the proposed method effectively lowers root mean squared error (RMSE) and enhances accuracy across privacy budgets (epsilon). At epsilon = 10, the algorithm achieves an RMSE as low as 0.04, closely approximating non-private estimates. Additionally, membership inference attacks reveal that higher epsilon values (e.g., epsilon geq 6) significantly reduce influential points, particularly at higher thresholds, lowering susceptibility to inference attacks. These findings confirm that our approach balances privacy and utility, advancing privacy-preserving survival analysis.

Estimating heterogeneous treatment effects (HTEs) from right-censored survival data is critical in high-stakes applications such as precision medicine and individualized policy-making. Yet, the survival analysis setting poses unique challenges for HTE estimation due to censoring, unobserved counterfactuals, and complex identification assumptions. Despite recent advances, from Causal Survival Forests to survival meta-learners and outcome imputation approaches, evaluation practices remain fragmented and inconsistent. We introduce SurvHTE-Bench, the first comprehensive benchmark for HTE estimation with censored outcomes. The benchmark spans (i) a modular suite of synthetic datasets with known ground truth, systematically varying causal assumptions and survival dynamics, (ii) semi-synthetic datasets that pair real-world covariates with simulated treatments and outcomes, and (iii) real-world datasets from a twin study (with known ground truth) and from an HIV clinical trial. Across synthetic, semi-synthetic, and real-world settings, we provide the first rigorous comparison of survival HTE methods under diverse conditions and realistic assumption violations. SurvHTE-Bench establishes a foundation for fair, reproducible, and extensible evaluation of causal survival methods. The data and code of our benchmark are available at: https://github.com/Shahriarnz14/SurvHTE-Bench .

Survival analysis, or time-to-event modelling, is a classical statistical problem that has garnered a lot of interest for its practical use in epidemiology, demographics or actuarial sciences. Recent advances on the subject from the point of view of machine learning have been concerned with precise per-individual predictions instead of population studies, driven by the rise of individualized medicine. We introduce here a conditional normalizing flow based estimate of the time-to-event density as a way to model highly flexible and individualized conditional survival distributions. We use a novel hierarchical formulation of normalizing flows to enable efficient fitting of flexible conditional distributions without overfitting and show how the normalizing flow formulation can be efficiently adapted to the censored setting. We experimentally validate the proposed approach on a synthetic dataset as well as four open medical datasets and an example of a common financial problem.

Providing effective treatment and making informed clinical decisions are essential goals of modern medicine and clinical care. We are interested in simulating disease dynamics for clinical decision-making, leveraging recent advances in large generative models. To this end, we introduce the Medical World Model (MeWM), the first world model in medicine that visually predicts future disease states based on clinical decisions. MeWM comprises (i) vision-language models to serve as policy models, and (ii) tumor generative models as dynamics models. The policy model generates action plans, such as clinical treatments, while the dynamics model simulates tumor progression or regression under given treatment conditions. Building on this, we propose the inverse dynamics model that applies survival analysis to the simulated post-treatment tumor, enabling the evaluation of treatment efficacy and the selection of the optimal clinical action plan. As a result, the proposed MeWM simulates disease dynamics by synthesizing post-treatment tumors, with state-of-the-art specificity in Turing tests evaluated by radiologists. Simultaneously, its inverse dynamics model outperforms medical-specialized GPTs in optimizing individualized treatment protocols across all metrics. Notably, MeWM improves clinical decision-making for interventional physicians, boosting F1-score in selecting the optimal TACE protocol by 13%, paving the way for future integration of medical world models as the second readers.

Dynamic treatment regimes (DTRs) are personalized, adaptive, multi-stage treatment plans that adapt treatment decisions both to an individual's initial features and to intermediate outcomes and features at each subsequent stage, which are affected by decisions in prior stages. Examples include personalized first- and second-line treatments of chronic conditions like diabetes, cancer, and depression, which adapt to patient response to first-line treatment, disease progression, and individual characteristics. While existing literature mostly focuses on estimating the optimal DTR from offline data such as from sequentially randomized trials, we study the problem of developing the optimal DTR in an online manner, where the interaction with each individual affect both our cumulative reward and our data collection for future learning. We term this the DTR bandit problem. We propose a novel algorithm that, by carefully balancing exploration and exploitation, is guaranteed to achieve rate-optimal regret when the transition and reward models are linear. We demonstrate our algorithm and its benefits both in synthetic experiments and in a case study of adaptive treatment of major depressive disorder using real-world data.

Analyzing outcomes in long-term cancer survivor studies can be complex. The effects of predictors on the failure process may be difficult to assess over longer periods of time, as the commonly used assumption of proportionality of hazards holding over an extended period is often questionable. In this manuscript, we compare seven different survival models that estimate the hazard rate and the effects of proportional and non-proportional covariates. In particular, we focus on an extension of the the multi-resolution hazard (MRH) estimator, combining a non-proportional hierarchical MRH approach with a data-driven pruning algorithm that allows for computational efficiency and produces robust estimates even in times of few observed failures. Using data from a large-scale randomized prostate cancer clinical trial, we examine patterns of biochemical failure and estimate the time-varying effects of androgen deprivation therapy treatment and other covariates. We compare the impact of different modeling strategies and smoothness assumptions on the estimated treatment effect. Our results show that the benefits of treatment diminish over time, possibly with implications for future treatment protocols.

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

Survival analysis is the problem of estimating probability distributions for future event times, which can be seen as a problem in uncertainty quantification. Although there are fundamental theories on strictly proper scoring rules for uncertainty quantification, little is known about those for survival analysis. In this paper, we investigate extensions of four major strictly proper scoring rules for survival analysis and we prove that these extensions are proper under certain conditions, which arise from the discretization of the estimation of probability distributions. We also compare the estimation performances of these extended scoring rules by using real datasets, and the extensions of the logarithmic score and the Brier score performed the best.

Clinical case reports encode temporal patient trajectories that are often underexploited by traditional machine learning methods relying on structured data. In this work, we introduce the forecasting problem from textual time series, where timestamped clinical findings -- extracted via an LLM-assisted annotation pipeline -- serve as the primary input for prediction. We systematically evaluate a diverse suite of models, including fine-tuned decoder-based large language models and encoder-based transformers, on tasks of event occurrence prediction, temporal ordering, and survival analysis. Our experiments reveal that encoder-based models consistently achieve higher F1 scores and superior temporal concordance for short- and long-horizon event forecasting, while fine-tuned masking approaches enhance ranking performance. In contrast, instruction-tuned decoder models demonstrate a relative advantage in survival analysis, especially in early prognosis settings. Our sensitivity analyses further demonstrate the importance of time ordering, which requires clinical time series construction, as compared to text ordering, the format of the text inputs that LLMs are classically trained on. This highlights the additional benefit that can be ascertained from time-ordered corpora, with implications for temporal tasks in the era of widespread LLM use.

The Cox proportional hazards model is widely used in survival analysis to model time-to-event data. However, it faces significant computational challenges in the era of large-scale data, particularly when dealing with time-dependent covariates. This paper proposes a moment-assisted subsampling method that is both statistically and computationally efficient for inference under the Cox model. This efficiency is achieved by integrating the computationally efficient uniform subsampling estimator and whole data sample moments that are easy to compute even for large datasets. The resulting estimator is asymptotically normal with a smaller variance than the uniform subsampling estimator. Additionally, we derive the optimal sample moment for the Cox model that minimizes the asymptotic variance in Loewner order. With the optimal moment, the proposed estimator can achieve the same estimation efficiency as the whole data-based partial likelihood estimator while maintaining the computational advantages of subsampling. Simulation studies and real data analyses demonstrate the promising finite sample performance of the proposed estimator in terms of both estimation and computational efficiency.

Purpose. Patients with advanced cancer may undergo multiple lines of treatment, switching therapies as their disease progresses. Motivated by a study of metastatic prostate cancer, we develop a microsimulation framework to study therapy sequence. Methods. We propose a discrete-time state transition model to study two lines of anti-cancer therapy. Based on digitized published progression-free survival (PFS) and overall survival (OS) curves, we infer event types (progression or death), and estimate transition probabilities using cumulative incidence functions with competing risks. Our model incorporates within-patient dependence over time, such that response to first-line therapy informs subsequent event probabilities. Parameters governing the degree of within-patient dependence can be used to calibrate the model-based results to those of a target trial. We demonstrate these methods in a study of two therapy sequences for metastatic prostate cancer, where Docetaxel (DCT) and Abiraterone Acetate (AA) are both appropriate for use in either first or second line treatment. We assess costs, Quality-Adjusted Life Years (QALYs) and Incremental Cost Effectiveness Ratio (ICER) for two treatment strategies: DCT then AA vs AA then DCT. Results. Using digitized survival curves from relevant clinical trials, we identified 8.6-13.9% of PFS times that should be categorized as deaths, allowing for estimation of cumulative incidence functions. Models assuming within-patient independence overestimated OS time, corrected with our calibration approach. Correction resulted in meaningful changes in the difference in QALYs between treatment strategies (0.07 vs 0.15) and the ICER (-\76,836/QALY vs -21,030/QALY). Conclusions. Microsimulation models can be successfully used to study cost-effectiveness of therapy sequences, taking care to account correctly for within-patient dependence.

Medical practitioners use survival models to explore and understand the relationships between patients' covariates (e.g. clinical and genetic features) and the effectiveness of various treatment options. Standard survival models like the linear Cox proportional hazards model require extensive feature engineering or prior medical knowledge to model treatment interaction at an individual level. While nonlinear survival methods, such as neural networks and survival forests, can inherently model these high-level interaction terms, they have yet to be shown as effective treatment recommender systems. We introduce DeepSurv, a Cox proportional hazards deep neural network and state-of-the-art survival method for modeling interactions between a patient's covariates and treatment effectiveness in order to provide personalized treatment recommendations. We perform a number of experiments training DeepSurv on simulated and real survival data. We demonstrate that DeepSurv performs as well as or better than other state-of-the-art survival models and validate that DeepSurv successfully models increasingly complex relationships between a patient's covariates and their risk of failure. We then show how DeepSurv models the relationship between a patient's features and effectiveness of different treatment options to show how DeepSurv can be used to provide individual treatment recommendations. Finally, we train DeepSurv on real clinical studies to demonstrate how it's personalized treatment recommendations would increase the survival time of a set of patients. The predictive and modeling capabilities of DeepSurv will enable medical researchers to use deep neural networks as a tool in their exploration, understanding, and prediction of the effects of a patient's characteristics on their risk of failure.

Survival analysis can sometimes involve individuals who will not experience the event of interest, forming what is known as the cured group. Identifying such individuals is not always possible beforehand, as they provide only right-censored data. Ignoring the presence of the cured group can introduce bias in the final model. This paper presents a method for estimating a semiparametric additive hazards model that accounts for the cured fraction. Unlike regression coefficients in a hazard ratio model, those in an additive hazard model measure hazard differences. The proposed method uses a primal-dual interior point algorithm to obtain constrained maximum penalized likelihood estimates of the model parameters, including the regression coefficients and the baseline hazard, subject to certain non-negativity constraints.

Clinical trials or studies oftentimes require long-term and/or costly follow-up of participants to evaluate a novel treatment/drug/vaccine. There has been increasing interest in the past few decades in using short-term surrogate outcomes as a replacement of the primary outcome i.e., in using the surrogate outcome, which can potentially be observed sooner, to make inference about the treatment effect on the long-term primary outcome. Very few of the available statistical methods to evaluate a surrogate are applicable to settings where both the surrogate and the primary outcome are time-to-event outcomes subject to censoring. Methods that can handle this setting tend to require parametric assumptions or be limited to assessing only the restricted mean survival time. In this paper, we propose a non-parametric approach to evaluate a censored surrogate outcome, such as time to progression, when the primary outcome is also a censored time-to-event outcome, such as time to death, and the treatment effect of interest is the difference in overall survival. Specifically, we define the proportion of the treatment effect on the primary outcome that is explained (PTE) by the censored surrogate outcome in this context, and estimate this proportion by defining and deriving an optimal transformation of the surrogate information. Our approach provides the added advantage of relaxed assumptions to guarantee that the true PTE is within (0,1), along with being model-free. Finite sample performance of our estimators are illustrated via extensive simulation studies and a real data application examining progression-free survival as a surrogate for overall survival for patients with metastatic colorectal cancer.

One straightforward metric to evaluate a survival prediction model is based on the Mean Absolute Error (MAE) -- the average of the absolute difference between the time predicted by the model and the true event time, over all subjects. Unfortunately, this is challenging because, in practice, the test set includes (right) censored individuals, meaning we do not know when a censored individual actually experienced the event. In this paper, we explore various metrics to estimate MAE for survival datasets that include (many) censored individuals. Moreover, we introduce a novel and effective approach for generating realistic semi-synthetic survival datasets to facilitate the evaluation of metrics. Our findings, based on the analysis of the semi-synthetic datasets, reveal that our proposed metric (MAE using pseudo-observations) is able to rank models accurately based on their performance, and often closely matches the true MAE -- in particular, is better than several alternative methods.

There has been increasing interest in modeling survival data using deep learning methods in medical research. In this paper, we proposed a Bayesian hierarchical deep neural networks model for modeling and prediction of survival data. Compared with previously studied methods, the new proposal can provide not only point estimate of survival probability but also quantification of the corresponding uncertainty, which can be of crucial importance in predictive modeling and subsequent decision making. The favorable statistical properties of point and uncertainty estimates were demonstrated by simulation studies and real data analysis. The Python code implementing the proposed approach was provided.

Causal structures for observational survival data provide crucial information regarding the relationships between covariates and time-to-event. We derive motivation from the information theoretic source coding argument, and show that incorporating the knowledge of the directed acyclic graph (DAG) can be beneficial if suitable source encoders are employed. As a possible source encoder in this context, we derive a variational inference based conditional variational autoencoder for causal structured survival prediction, which we refer to as DAGSurv. We illustrate the performance of DAGSurv on low and high-dimensional synthetic datasets, and real-world datasets such as METABRIC and GBSG. We demonstrate that the proposed method outperforms other survival analysis baselines such as Cox Proportional Hazards, DeepSurv and Deephit, which are oblivious to the underlying causal relationship between data entities.

Accurate prediction of major adverse cardiac events (MACE) remains a central challenge in cardiovascular prognosis. We present PRISM (Prompt-guided Representation Integration for Survival Modeling), a self-supervised framework that integrates visual representations from non-contrast cardiac cine magnetic resonance imaging with structured electronic health records (EHRs) for survival analysis. PRISM extracts temporally synchronized imaging features through motion-aware multi-view distillation and modulates them using medically informed textual prompts to enable fine-grained risk prediction. Across four independent clinical cohorts, PRISM consistently surpasses classical survival prediction models and state-of-the-art (SOTA) deep learning baselines under internal and external validation. Further clinical findings demonstrate that the combined imaging and EHR representations derived from PRISM provide valuable insights into cardiac risk across diverse cohorts. Three distinct imaging signatures associated with elevated MACE risk are uncovered, including lateral wall dyssynchrony, inferior wall hypersensitivity, and anterior elevated focus during diastole. Prompt-guided attribution further identifies hypertension, diabetes, and smoking as dominant contributors among clinical and physiological EHR factors.

We address the problem of learning the dynamics of an unknown non-parametric system linking a target and a feature time series. The feature time series is measured on a sparse and irregular grid, while we have access to only a few points of the target time series. Once learned, we can use these dynamics to predict values of the target from the previous values of the feature time series. We frame this task as learning the solution map of a controlled differential equation (CDE). By leveraging the rich theory of signatures, we are able to cast this non-linear problem as a high-dimensional linear regression. We provide an oracle bound on the prediction error which exhibits explicit dependencies on the individual-specific sampling schemes. Our theoretical results are illustrated by simulations which show that our method outperforms existing algorithms for recovering the full time series while being computationally cheap. We conclude by demonstrating its potential on real-world epidemiological data.

We investigate a new dynamical system that describes tumor-host interaction. The equation that describes the untreated tumor growth is based on non-extensive statistical mechanics. Recently, this model has been shown to fit successfully exponential, Gompertz, logistic, and power-law tumor growths. We have been able to include as many hallmarks of cancer as possible. We study also the dynamic response of cancer under therapy. Using our model, we can make predictions about the different outcomes when we change the parameters, and/or the initial conditions. We can determine the importance of different factors to influence tumor growth. We discover synergistic therapeutic effects of different treatments and drugs. Cancer is generally untreatable using conventional monotherapy. We consider conventional therapies, oncogene-targeted therapies, tumor-suppressors gene-targeted therapies, immunotherapies, anti-angiogenesis therapies, virotherapy, among others. We need therapies with the potential to target both tumor cells and the tumors' microenvironment. Drugs that target oncogenes and tumor-suppressor genes can be effective in the treatment of some cancers. However, most tumors do reoccur. We have found that the success of the new therapeutic agents can be seen when used in combination with other cancer-cell-killing therapies. Our results have allowed us to design a combinational therapy that can lead to the complete eradication of cancer.

Predicting the remaining useful life (RUL) of ball bearings is an active area of research, where novel machine learning techniques are continuously being applied to predict degradation trends and anticipate failures before they occur. However, few studies have explicitly addressed the challenge of handling censored data, where information about a specific event (\eg mechanical failure) is incomplete or only partially observed. To address this issue, we introduce a novel and flexible method for early fault detection using Kullback-Leibler (KL) divergence and RUL estimation using survival analysis that naturally supports censored data. We demonstrate our approach in the XJTU-SY dataset using a 5-fold cross-validation strategy across three different operating conditions. When predicting the time to failure for bearings under the highest load (C1, 12.0 kN and 2100 RPM) with 25% random censoring, our approach achieves a mean absolute error (MAE) of 14.7 minutes (95% CI = 13.6-15.8) using a linear CoxPH model, and an MAE of 12.6 minutes (95% CI = 11.8-13.4) using a nonlinear Random Survival Forests model, compared to an MAE of 18.5 minutes (95% CI = 17.4-19.6) using a linear LASSO model that does not support censoring. Moreover, our approach achieves a mean cumulative relative accuracy (CRA) of 0.7586 over 5 bearings under the highest load, which improves over several state-of-the-art baselines. Our work highlights the importance of considering censored data as part of the model design when building predictive models for early fault detection and RUL estimation.

As retailers around the world increase efforts in developing targeted marketing campaigns for different audiences, predicting accurately which customers are most likely to churn ahead of time is crucial for marketing teams in order to increase business profits. This work presents a deep survival framework to predict which customers are at risk of stopping to purchase with retail companies in non-contractual settings. By leveraging the survival model parameters to be learnt by recurrent neural networks, we are able to obtain individual level survival models for purchasing behaviour based only on individual customer behaviour and avoid time-consuming feature engineering processes usually done when training machine learning models.

We report DynaCLR, a self-supervised method for embedding cell and organelle Dynamics via Contrastive Learning of Representations of time-lapse images. DynaCLR integrates single-cell tracking and time-aware contrastive sampling to learn robust, temporally regularized representations of cell dynamics. DynaCLR embeddings generalize effectively to in-distribution and out-of-distribution datasets, and can be used for several downstream tasks with sparse human annotations. We demonstrate efficient annotations of cell states with a human-in-the-loop using fluorescence and label-free imaging channels. DynaCLR method enables diverse downstream biological analyses: classification of cell division and infection, clustering heterogeneous cell migration patterns, cross-modal distillation of cell states from fluorescence to label-free channel, alignment of asynchronous cellular responses and broken cell tracks, and discovering organelle response due to infection. DynaCLR is a flexible method for comparative analyses of dynamic cellular responses to pharmacological, microbial, and genetic perturbations. We provide PyTorch-based implementations of the model training and inference pipeline (https://github.com/mehta-lab/viscy) and a GUI (https://github.com/czbiohub-sf/napari-iohub) for the visualization and annotation of trajectories of cells in the real space and the embedding space.

This study quantifies the association between non-adherence to antipsychotic medications and adverse outcomes in individuals with schizophrenia. We frame the problem using survival analysis, focusing on the time to the earliest of several adverse events (early death, involuntary hospitalization, jail booking). We extend standard causal inference methods (T-learner, S-learner, nearest neighbor matching) to utilize various survival models to estimate individual and average treatment effects, where treatment corresponds to medication non-adherence. Analyses are repeated using different amounts of longitudinal information (3, 6, 9, and 12 months). Using data from Allegheny County in western Pennsylvania, we find strong evidence that non-adherence advances adverse outcomes by approximately 1 to 4 months. Ablation studies confirm that county-provided risk scores adjust for key confounders, as their removal amplifies the estimated effects. Subgroup analyses by medication formulation (injectable vs. oral) and medication type consistently show that non-adherence is associated with earlier adverse events. These findings highlight the clinical importance of adherence in delaying psychiatric crises and show that integrating survival analysis with causal inference tools can yield policy-relevant insights. We caution that although we apply causal inference, we only make associative claims and discuss assumptions needed for causal interpretation.

Complex, temporally evolving phenomena, from climate to brain activity, are governed by dynamical systems (DS). DS reconstruction (DSR) seeks to infer generative surrogate models of these from observed data, reproducing their long-term behavior. Existing DSR approaches require purpose-training for any new system observed, lacking the zero-shot and in-context inference capabilities known from LLMs. Here we introduce DynaMix, a novel multivariate ALRNN-based mixture-of-experts architecture pre-trained for DSR, the first DSR model able to generalize zero-shot to out-of-domain DS. Just from a provided context signal, without any re-training, DynaMix faithfully forecasts the long-term evolution of novel DS where existing time series (TS) foundation models, like Chronos, fail -- at a fraction of the number of parameters and orders of magnitude faster inference times. DynaMix outperforms TS foundation models in terms of long-term statistics, and often also short-term forecasts, even on real-world time series, like traffic or weather data, typically used for training and evaluating TS models, but not at all part of DynaMix' training corpus. We illustrate some of the failure modes of TS models for DSR problems, and conclude that models built on DS principles may bear a huge potential also for advancing the TS prediction field.

We develop a novel, general and computationally efficient framework, called Divide and Conquer Dynamic Programming (DCDP), for localizing change points in time series data with high-dimensional features. DCDP deploys a class of greedy algorithms that are applicable to a broad variety of high-dimensional statistical models and can enjoy almost linear computational complexity. We investigate the performance of DCDP in three commonly studied change point settings in high dimensions: the mean model, the Gaussian graphical model, and the linear regression model. In all three cases, we derive non-asymptotic bounds for the accuracy of the DCDP change point estimators. We demonstrate that the DCDP procedures consistently estimate the change points with sharp, and in some cases, optimal rates while incurring significantly smaller computational costs than the best available algorithms. Our findings are supported by extensive numerical experiments on both synthetic and real data.

We formulate the predicted-updates dynamic model, one of the first beyond-worst-case models for dynamic algorithms, which generalizes a large set of well-studied dynamic models including the offline dynamic, incremental, and decremental models to the fully dynamic setting when given predictions about the update times of the elements. In the most basic form of our model, we receive a set of predicted update times for all of the updates that occur over the event horizon. We give a novel framework that "lifts" offline divide-and-conquer algorithms into the fully dynamic setting with little overhead. Using this, we are able to interpolate between the offline and fully dynamic settings; when the ell_1 error of the prediction is linear in the number of updates, we achieve the offline runtime of the algorithm (up to poly log n factors). Provided a fully dynamic backstop algorithm, our algorithm will never do worse than the backstop algorithm regardless of the prediction error. Furthermore, our framework achieves a smooth linear trade-off between ell_1 error in the predictions and runtime. These correspond to the desiderata of consistency, robustness, and graceful degradation of the algorithms-with-predictions literature. We further extend our techniques to incremental and decremental settings, transforming algorithms in these settings when given predictions of only the deletion and insertion times, respectively. Our framework is general, and we apply it to obtain improved efficiency bounds over the state-of-the-art dynamic algorithms for a variety of problems including triconnectivity, planar digraph all pairs shortest paths, k-edge connectivity, and others, for prediction error of reasonable magnitude.

We revisit the structure learning problem for dynamic Bayesian networks and propose a method that simultaneously estimates contemporaneous (intra-slice) and time-lagged (inter-slice) relationships between variables in a time-series. Our approach is score-based, and revolves around minimizing a penalized loss subject to an acyclicity constraint. To solve this problem, we leverage a recent algebraic result characterizing the acyclicity constraint as a smooth equality constraint. The resulting algorithm, which we call DYNOTEARS, outperforms other methods on simulated data, especially in high-dimensions as the number of variables increases. We also apply this algorithm on real datasets from two different domains, finance and molecular biology, and analyze the resulting output. Compared to state-of-the-art methods for learning dynamic Bayesian networks, our method is both scalable and accurate on real data. The simple formulation and competitive performance of our method make it suitable for a variety of problems where one seeks to learn connections between variables across time.

Decisions about managing patients on the heart transplant waitlist are currently made by committees of doctors who consider multiple factors, but the process remains largely ad-hoc. With the growing volume of longitudinal patient, donor, and organ data collected by the United Network for Organ Sharing (UNOS) since 2018, there is increasing interest in analytical approaches to support clinical decision-making at the time of organ availability. In this study, we benchmark machine learning models that leverage longitudinal waitlist history data for time-dependent, time-to-event modeling of waitlist mortality. We train on 23,807 patient records with 77 variables and evaluate both survival prediction and discrimination at a 1-year horizon. Our best model achieves a C-Index of 0.94 and AUROC of 0.89, significantly outperforming previous models. Key predictors align with known risk factors while also revealing novel associations. Our findings can support urgency assessment and policy refinement in heart transplant decision making.

Mediation analysis learns the causal effect transmitted via mediator variables between treatments and outcomes and receives increasing attention in various scientific domains to elucidate causal relations. Most existing works focus on point-exposure studies where each subject only receives one treatment at a single time point. However, there are a number of applications (e.g., mobile health) where the treatments are sequentially assigned over time and the dynamic mediation effects are of primary interest. Proposing a reinforcement learning (RL) framework, we are the first to evaluate dynamic mediation effects in settings with infinite horizons. We decompose the average treatment effect into an immediate direct effect, an immediate mediation effect, a delayed direct effect, and a delayed mediation effect. Upon the identification of each effect component, we further develop robust and semi-parametrically efficient estimators under the RL framework to infer these causal effects. The superior performance of the proposed method is demonstrated through extensive numerical studies, theoretical results, and an analysis of a mobile health dataset.

As large language models (LLMs) advance in conversational and reasoning capabilities, their practical application in healthcare has become a critical research focus. However, there is a notable gap between the performance of medical LLMs on static benchmarks such as USMLE and their utility in real-world clinical decision-making. This discrepancy arises because traditional exams fail to capture the dynamic, interactive nature of medical consultations. To address this challenge, we introduce a novel dynamic verification framework that moves beyond static answer verifier, establishing a large-scale, high-fidelity interactive reinforcement learning system. Our framework comprises two key components: a Patient Simulator that creates realistic clinical environments using de-identified medical records, and a Clinical Rubrics Generator that dynamically produces multi-dimensional evaluation metrics. Building on this foundation, we develop Baichuan-M2, a 32B-parameter medical augmented reasoning model trained through a multi-stage reinforcement learning strategy with an improved Group Relative Policy Optimization (GRPO) algorithm. Evaluated on HealthBench, Baichuan-M2 outperforms all other open-source models and most advanced closed-source counterparts, achieving a score above 32 on the challenging HealthBench Hard benchmark-previously exceeded only by GPT-5. Our work demonstrates that robust dynamic verifier system is essential for aligning LLM capabilities with practical clinical applications, establishing a new Pareto front in the performance-parameter trade-off for medical AI deployment.

Physiological time series signals reflect complex, multi-scale dynamical processes of the human body. Existing modeling studies focus on static tasks such as classification, event forecasting, or short-horizon next step prediction, while long-horizon signal-level forecasting and predictive nature of physiological signals remain underexplored. We introduce NormWear-2, a world model that encodes both multivariate physiological signals and clinical intervention variables into a shared latent space and models their joint temporal evolution as a dynamical system. Our approach combines inference from prior pre-trained knowledge (intuition) with instant non-parametric latent state transition adaptation (insight), enabling coherent forecasting across multiple temporal scales, conditioned on heterogeneous clinical interventions. During the pretraining phase, we find that chaos-theoretic balancing of dynamical regime diversity yields more robust representations, with a smaller balanced corpus outperforming one twice its size and capturing bifurcation regimes. We evaluate the world model performance across diverse real-world physiological datasets spanning heterogeneous temporal resolutions and intervention regimes, covering daily life, point-of-care, and clinical settings, including fitness planning, hemodialysis, diabetes management, and surgical monitoring. These evaluation datasets comprise records from 8,026 subjects, spanning study durations from 3.2 hours for high-resolution signal data to 2.3 years for longitudinal clinical biomarker tracking. NormWear-2 achieves the best overall forecasting performance across time, frequency, and latent representation domains, with significant improvements over state-of-the-art time series foundation models, while maintaining competitive downstream representation quality, providing a step toward general-purpose world models for physiological signals.

The intricate dynamics of stock markets have led to extensive research on models that are able to effectively explain their inherent complexities. This study leverages the econometrics literature to explore the dynamic factor model as an interpretable model with sufficient predictive capabilities for capturing essential market phenomena. Although the model has been extensively applied for predictive purposes, this study focuses on analyzing the extracted loadings and common factors as an alternative framework for understanding stock price dynamics. The results reveal novel insights into traditional market theories when applied to the Philippine Stock Exchange using the Kalman method and maximum likelihood estimation, with subsequent validation against the capital asset pricing model. Notably, a one-factor model extracts a common factor representing systematic or market dynamics similar to the composite index, whereas a two-factor model extracts common factors representing market trends and volatility. Furthermore, an application of the model for nowcasting the growth rates of the Philippine gross domestic product highlights the potential of the extracted common factors as viable real-time market indicators, yielding over a 34% decrease in the out-of-sample prediction error. Overall, the results underscore the value of dynamic factor analysis in gaining a deeper understanding of market price movement dynamics.

Causal discovery for dynamical systems poses a major challenge in fields where active interventions are infeasible. Most methods used to investigate these systems and their associated benchmarks are tailored to deterministic, low-dimensional and weakly nonlinear time-series data. To address these limitations, we present CausalDynamics, a large-scale benchmark and extensible data generation framework to advance the structural discovery of dynamical causal models. Our benchmark consists of true causal graphs derived from thousands of coupled ordinary and stochastic differential equations as well as two idealized climate models. We perform a comprehensive evaluation of state-of-the-art causal discovery algorithms for graph reconstruction on systems with noisy, confounded, and lagged dynamics. CausalDynamics consists of a plug-and-play, build-your-own coupling workflow that enables the construction of a hierarchy of physical systems. We anticipate that our framework will facilitate the development of robust causal discovery algorithms that are broadly applicable across domains while addressing their unique challenges. We provide a user-friendly implementation and documentation on https://kausable.github.io/CausalDynamics.

Automating radiology report generation can significantly alleviate radiologists' workloads. Previous research has primarily focused on realizing highly concise observations while neglecting the precise attributes that determine the severity of diseases (e.g., small pleural effusion). Since incorrect attributes will lead to imprecise radiology reports, strengthening the generation process with precise attribute modeling becomes necessary. Additionally, the temporal information contained in the historical records, which is crucial in evaluating a patient's current condition (e.g., heart size is unchanged), has also been largely disregarded. To address these issues, we propose RECAP, which generates precise and accurate radiology reports via dynamic disease progression reasoning. Specifically, RECAP first predicts the observations and progressions (i.e., spatiotemporal information) given two consecutive radiographs. It then combines the historical records, spatiotemporal information, and radiographs for report generation, where a disease progression graph and dynamic progression reasoning mechanism are devised to accurately select the attributes of each observation and progression. Extensive experiments on two publicly available datasets demonstrate the effectiveness of our model.

This paper studies the problem of performing a sequence of optimal interventions in a causal dynamical system where both the target variable of interest and the inputs evolve over time. This problem arises in a variety of domains e.g. system biology and operational research. Dynamic Causal Bayesian Optimization (DCBO) brings together ideas from sequential decision making, causal inference and Gaussian process (GP) emulation. DCBO is useful in scenarios where all causal effects in a graph are changing over time. At every time step DCBO identifies a local optimal intervention by integrating both observational and past interventional data collected from the system. We give theoretical results detailing how one can transfer interventional information across time steps and define a dynamic causal GP model which can be used to quantify uncertainty and find optimal interventions in practice. We demonstrate how DCBO identifies optimal interventions faster than competing approaches in multiple settings and applications.

Breast cancer is a significant health concern affecting millions of women worldwide. Accurate survival risk stratification plays a crucial role in guiding personalised treatment decisions and improving patient outcomes. Here we present BioFusionNet, a deep learning framework that fuses image-derived features with genetic and clinical data to achieve a holistic patient profile and perform survival risk stratification of ER+ breast cancer patients. We employ multiple self-supervised feature extractors, namely DINO and MoCoV3, pretrained on histopathology patches to capture detailed histopathological image features. We then utilise a variational autoencoder (VAE) to fuse these features, and harness the latent space of the VAE to feed into a self-attention network, generating patient-level features. Next, we develop a co-dual-cross-attention mechanism to combine the histopathological features with genetic data, enabling the model to capture the interplay between them. Additionally, clinical data is incorporated using a feed-forward network (FFN), further enhancing predictive performance and achieving comprehensive multimodal feature integration. Furthermore, we introduce a weighted Cox loss function, specifically designed to handle imbalanced survival data, which is a common challenge in the field. The proposed model achieves a mean concordance index (C-index) of 0.77 and a time-dependent area under the curve (AUC) of 0.84, outperforming state-of-the-art methods. It predicts risk (high versus low) with prognostic significance for overall survival (OS) in univariate analysis (HR=2.99, 95% CI: 1.88--4.78, p<0.005), and maintains independent significance in multivariate analysis incorporating standard clinicopathological variables (HR=2.91, 95% CI: 1.80--4.68, p<0.005). The proposed method not only improves model performance but also addresses a critical gap in handling imbalanced data.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

This paper considers the problem of variable selection allowing for parameter instability. It distinguishes between signal and pseudo-signal variables that are correlated with the target variable, and noise variables that are not, and investigate the asymptotic properties of the One Covariate at a Time Multiple Testing (OCMT) method proposed by Chudik et al. (2018) under parameter insatiability. It is established that OCMT continues to asymptotically select an approximating model that includes all the signals and none of the noise variables. Properties of post selection regressions are also investigated, and in-sample fit of the selected regression is shown to have the oracle property. The theoretical results support the use of unweighted observations at the selection stage of OCMT, whilst applying down-weighting of observations only at the forecasting stage. Monte Carlo and empirical applications show that OCMT without down-weighting at the selection stage yields smaller mean squared forecast errors compared to Lasso, Adaptive Lasso, and boosting.

We present methodology for using dynamic evaluation to improve neural sequence models. Models are adapted to recent history via a gradient descent based mechanism, causing them to assign higher probabilities to re-occurring sequential patterns. Dynamic evaluation outperforms existing adaptation approaches in our comparisons. Dynamic evaluation improves the state-of-the-art word-level perplexities on the Penn Treebank and WikiText-2 datasets to 51.1 and 44.3 respectively, and the state-of-the-art character-level cross-entropies on the text8 and Hutter Prize datasets to 1.19 bits/char and 1.08 bits/char respectively.

Histopathological images contain rich phenotypic information that can be used to monitor underlying mechanisms contributing to diseases progression and patient survival outcomes. Recently, deep learning has become the mainstream methodological choice for analyzing and interpreting cancer histology images. In this paper, we present a comprehensive review of state-of-the-art deep learning approaches that have been used in the context of histopathological image analysis. From the survey of over 130 papers, we review the fields progress based on the methodological aspect of different machine learning strategies such as supervised, weakly supervised, unsupervised, transfer learning and various other sub-variants of these methods. We also provide an overview of deep learning based survival models that are applicable for disease-specific prognosis tasks. Finally, we summarize several existing open datasets and highlight critical challenges and limitations with current deep learning approaches, along with possible avenues for future research.

Dynamic feature selection, where we sequentially query features to make accurate predictions with a minimal budget, is a promising paradigm to reduce feature acquisition costs and provide transparency into a model's predictions. The problem is challenging, however, as it requires both predicting with arbitrary feature sets and learning a policy to identify valuable selections. Here, we take an information-theoretic perspective and prioritize features based on their mutual information with the response variable. The main challenge is implementing this policy, and we design a new approach that estimates the mutual information in a discriminative rather than generative fashion. Building on our approach, we then introduce several further improvements: allowing variable feature budgets across samples, enabling non-uniform feature costs, incorporating prior information, and exploring modern architectures to handle partial inputs. Our experiments show that our method provides consistent gains over recent methods across a variety of datasets.

Electronic Health Records (EHRs) contain rich temporal dynamics that conventional encoding approaches fail to adequately capture. While Large Language Models (LLMs) show promise for EHR modeling, they struggle to reason about sequential clinical events and temporal dependencies. We propose Next Event Prediction (NEP), a framework that enhances LLMs' temporal reasoning through autoregressive fine-tuning on clinical event sequences. By reformulating EHRs as timestamped event chains and predicting future medical events, NEP explicitly models disease progression patterns and causal relationships. Extensive evaluations across oncology survival prediction and clinical diagnosis tasks demonstrate NEP's superiority, outperforming specialized EHR models by 4.6% AUROC and general-purpose LLMs by 7.2% C-index in temporal reasoning tasks. Our analyses reveal dual benefits: state-of-the-art prediction accuracy combined with clinically interpretable attention patterns that align with known disease pathways.

[This paper was initially published in PHME conference in 2016, selected for further publication in International Journal of Prognostics and Health Management.] This paper describes an Autoregressive Partially-hidden Markov model (ARPHMM) for fault detection and prognostics of equipments based on sensors' data. It is a particular dynamic Bayesian network that allows to represent the dynamics of a system by means of a Hidden Markov Model (HMM) and an autoregressive (AR) process. The Markov chain assumes that the system is switching back and forth between internal states while the AR process ensures a temporal coherence on sensor measurements. A sound learning procedure of standard ARHMM based on maximum likelihood allows to iteratively estimate all parameters simultaneously. This paper suggests a modification of the learning procedure considering that one may have prior knowledge about the structure which becomes partially hidden. The integration of the prior is based on the Theory of Weighted Distributions which is compatible with the Expectation-Maximization algorithm in the sense that the convergence properties are still satisfied. We show how to apply this model to estimate the remaining useful life based on health indicators. The autoregressive parameters can indeed be used for prediction while the latent structure can be used to get information about the degradation level. The interest of the proposed method for prognostics and health assessment is demonstrated on CMAPSS datasets.

Accurate prediction of major adverse cardiovascular events recurrence risk in acute myocardial infarction patients based on postoperative cardiac MRI and associated clinical notes is crucial for precision treatment and personalized intervention. Existing methods primarily focus on risk stratification capability while overlooking the need for intermediate robust reasoning and model interpretability in clinical practice. Moreover, end-to-end risk prediction using LLM/VLM faces significant challenges due to data limitations and modeling complexity. To bridge this gap, we propose CardioCoT, a novel two-stage hierarchical reasoning-enhanced survival analysis framework designed to enhance both model interpretability and predictive performance. In the first stage, we employ an evidence-augmented self-refinement mechanism to guide LLM/VLMs in generating robust hierarchical reasoning trajectories based on associated radiological findings. In the second stage, we integrate the reasoning trajectories with imaging data for risk model training and prediction. CardioCoT demonstrates superior performance in MACE recurrence risk prediction while providing interpretable reasoning processes, offering valuable insights for clinical decision-making.

Dynamic Mode Decomposition (DMD) is an equation-free method that aims at reconstructing the best linear fit from temporal datasets. In this paper, we show that DMD does not provide accurate approximation for datasets describing oscillatory dynamics, like spiral waves and relaxation oscillations, or spatio-temporal Turing instability. Inspired from the classical "divide and conquer" approach, we propose a piecewise version of DMD (pDMD) to overcome this problem. The main idea is to split the original dataset in N submatrices and then apply the exact (randomized) DMD method in each subset of the obtained partition. We describe the pDMD algorithm in detail and we introduce some error indicators to evaluate its performance when N is increased. Numerical experiments show that very accurate reconstructions are obtained by pDMD for datasets arising from time snapshots of some reaction-diffusion PDE systems, like the FitzHugh-Nagumo model, the lambda-omega system and the DIB morpho-chemical system for battery modeling.

Deep-learning survival models for electronic health record (EHR) data are hard to compare across papers because the upstream preprocessing step, which includes cohort definition, time discretisation, missingness handling, and censoring rules, is typically undocumented and inconsistent. A reported difference in concordance between two mortality models can therefore reflect any of these choices rather than a modelling contribution. We present SurvBench, an open-source preprocessing pipeline that converts raw PhysioNet exports into model-ready tensors for survival analysis. SurvBench covers four critical-care databases (MIMIC-IV, eICU, MC-MED, HiRID) and four input modalities: time-series vitals and laboratory values, static demographics, International Classification of Diseases (ICD) codes, and radiology report embeddings. Every preprocessing decision is controlled through YAML configuration. Imputation, scaling, and feature filtering are fit on the training fold only. Missingness is recorded as a binary mask alongside each feature tensor. The pipeline handles single-risk endpoints (in-hospital and in-ICU mortality) and competing-risks endpoints (a three-way emergency-department admission pathway, with home discharge treated as administrative censoring). We also provide support for harmonised cross-dataset external validation between eICU and MIMIC-IV. SurvBench is publicly available at https://github.com/munibmesinovic/SurvBench, providing a robust platform that future deep-learning EHR survival work, especially nascent multi-modal approaches, can be measured against under matched preprocessing.

Mixture of Experts (MoE) models scale capacity but often suffer from representation collapse and gradient instability. We propose Dynamic Subspace Composition (DSC), a framework that approximates context-dependent weights via a state-dependent, sparse expansion of a shared basis bank. Formally, DSC models the weight update as a residual trajectory within a Star- Shaped Domain, employing a Magnitude-Gated Simplex Interpolation to ensure continuity at the identity. Unlike standard Mixture-of-LoRAs, which incurs O(M rd) parameter complexity by retrieving independent rank-r matrices, DSC constructs a compositional rank-K approximation from decoupled unit-norm basis vectors. This reduces parameter complexity to O(M d) and memory traffic to O(Kd), while Frame-Theoretic regularization and spectral constraints provide rigorous worst-case bounds on the dynamic update. The code is available at https://github. com/VladimerKhasia/DSC

We introduce DynaSent ('Dynamic Sentiment'), a new English-language benchmark task for ternary (positive/negative/neutral) sentiment analysis. DynaSent combines naturally occurring sentences with sentences created using the open-source Dynabench Platform, which facilities human-and-model-in-the-loop dataset creation. DynaSent has a total of 121,634 sentences, each validated by five crowdworkers, and its development and test splits are designed to produce chance performance for even the best models we have been able to develop; when future models solve this task, we will use them to create DynaSent version 2, continuing the dynamic evolution of this benchmark. Here, we report on the dataset creation effort, focusing on the steps we took to increase quality and reduce artifacts. We also present evidence that DynaSent's Neutral category is more coherent than the comparable category in other benchmarks, and we motivate training models from scratch for each round over successive fine-tuning.

Dynamic MRI is a technique of acquiring a series of images continuously to follow the physiological changes over time. However, such fast imaging results in low resolution images. In this work, abdominal deformation model computed from dynamic low resolution images have been applied to high resolution image, acquired previously, to generate dynamic high resolution MRI. Dynamic low resolution images were simulated into different breathing phases (inhale and exhale). Then, the image registration between breathing time points was performed using the B-spline SyN deformable model and using cross-correlation as a similarity metric. The deformation model between different breathing phases were estimated from highly undersampled data. This deformation model was then applied to the high resolution images to obtain high resolution images of different breathing phases. The results indicated that the deformation model could be computed from relatively very low resolution images.

Dynamic programming (DP) is a fundamental method in operations research, but formulating DP models has traditionally required expert knowledge of both the problem context and DP techniques. Large Language Models (LLMs) offer the potential to automate this process. However, DP problems pose unique challenges due to their inherently stochastic transitions and the limited availability of training data. These factors make it difficult to directly apply existing LLM-based models or frameworks developed for other optimization problems, such as linear or integer programming. We introduce DP-Bench, the first benchmark covering a wide range of textbook-level DP problems to enable systematic evaluation. We present Dynamic Programming Language Model (DPLM), a 7B-parameter specialized model that achieves performance comparable to state-of-the-art LLMs like OpenAI's o1 and DeepSeek-R1, and surpasses them on hard problems. Central to DPLM's effectiveness is DualReflect, our novel synthetic data generation pipeline, designed to scale up training data from a limited set of initial examples. DualReflect combines forward generation for diversity and backward generation for reliability. Our results reveal a key insight: backward generation is favored in low-data regimes for its strong correctness guarantees, while forward generation, though lacking such guarantees, becomes increasingly valuable at scale for introducing diverse formulations. This trade-off highlights the complementary strengths of both approaches and the importance of combining them.

The growing popularity of wearable sensors has generated large quantities of temporal physiological and activity data. Ability to analyze this data offers new opportunities for real-time health monitoring and forecasting. However, temporal physiological data presents many analytic challenges: the data is noisy, contains many missing values, and each series has a different length. Most methods proposed for time series analysis and classification do not handle datasets with these characteristics nor do they offer interpretability and explainability, a critical requirement in the health domain. We propose an unsupervised method for learning representations of time series based on common patterns identified within them. The patterns are, interpretable, variable in length, and extracted using Byte Pair Encoding compression technique. In this way the method can capture both long-term and short-term dependencies present in the data. We show that this method applies to both univariate and multivariate time series and beats state-of-the-art approaches on a real world dataset collected from wearable sensors.

We introduce Dynabench, an open-source platform for dynamic dataset creation and model benchmarking. Dynabench runs in a web browser and supports human-and-model-in-the-loop dataset creation: annotators seek to create examples that a target model will misclassify, but that another person will not. In this paper, we argue that Dynabench addresses a critical need in our community: contemporary models quickly achieve outstanding performance on benchmark tasks but nonetheless fail on simple challenge examples and falter in real-world scenarios. With Dynabench, dataset creation, model development, and model assessment can directly inform each other, leading to more robust and informative benchmarks. We report on four initial NLP tasks, illustrating these concepts and highlighting the promise of the platform, and address potential objections to dynamic benchmarking as a new standard for the field.

Longitudinal multimodal data, including electronic health records (EHR) and sequential chest X-rays (CXRs), is critical for modeling disease progression, yet remains underutilized due to two key challenges: (1) redundancy in consecutive CXR sequences, where static anatomical regions dominate over clinically-meaningful dynamics, and (2) temporal misalignment between sparse, irregular imaging and continuous EHR data. We introduce DiPro, a novel framework that addresses these challenges through region-aware disentanglement and multi-timescale alignment. First, we disentangle static (anatomy) and dynamic (pathology progression) features in sequential CXRs, prioritizing disease-relevant changes. Second, we hierarchically align these static and dynamic CXR features with asynchronous EHR data via local (pairwise interval-level) and global (full-sequence) synchronization to model coherent progression pathways. Extensive experiments on the MIMIC dataset demonstrate that DiPro could effectively extract temporal clinical dynamics and achieve state-of-the-art performance on both disease progression identification and general ICU prediction tasks.

Chest X-ray imaging (CXR) is an important diagnostic tool used in hospitals to assess patient conditions and monitor changes over time. Generative models, specifically diffusion-based models, have shown promise in generating realistic synthetic X-rays. However, these models mainly focus on conditional generation using single-time-point data, i.e., typically CXRs taken at a specific time with their corresponding reports, limiting their clinical utility, particularly for capturing temporal changes. To address this limitation, we propose a novel framework, EHRXDiff, which predicts future CXR images by integrating previous CXRs with subsequent medical events, e.g., prescriptions, lab measures, etc. Our framework dynamically tracks and predicts disease progression based on a latent diffusion model, conditioned on the previous CXR image and a history of medical events. We comprehensively evaluate the performance of our framework across three key aspects, including clinical consistency, demographic consistency, and visual realism. We demonstrate that our framework generates high-quality, realistic future images that capture potential temporal changes, suggesting its potential for further development as a clinical simulation tool. This could offer valuable insights for patient monitoring and treatment planning in the medical field.

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data. While large language models (LLMs) have shown strong performance in biomedical NLP, they often lack structured reasoning capabilities critical for high-stakes decision support. We present a unified, multi-task learning framework that aligns autoregressive LLMs with clinical reasoning for outcome prediction on the MSK-CHORD dataset. Our models are trained to jointly perform binary survival classification, continuous survival time regression, and natural language rationale generation. We evaluate three alignment strategies: (1) standard supervised fine-tuning (SFT), (2) SFT with Chain-of-Thought (CoT) prompting to elicit step-by-step reasoning, and (3) Group Relative Policy Optimization (GRPO), a reinforcement learning method that aligns model outputs to expert-derived reasoning trajectories. Experiments with LLaMa3-8B and Med42-8B backbones demonstrate that CoT prompting improves F1 by +6.0 and reduces MAE by 12%, while GRPO achieves state-of-the-art interpretability and predictive performance across BLEU, ROUGE, and BERTScore. We further show that existing biomedical LLMs often fail to produce valid reasoning traces due to architectural constraints. Our findings underscore the importance of reasoning-aware alignment in multi-task clinical modeling and set a new benchmark for interpretable, trustworthy LLMs in precision oncology.

This paper introduces a continuous-time stochastic dynamical framework for understanding how large language models (LLMs) may self-amplify latent biases or toxicity through their own chain-of-thought reasoning. The model posits an instantaneous "severity" variable x(t) in [0,1] evolving under a stochastic differential equation (SDE) with a drift term μ(x) and diffusion σ(x). Crucially, such a process can be consistently analyzed via the Fokker--Planck approach if each incremental step behaves nearly Markovian in severity space. The analysis investigates critical phenomena, showing that certain parameter regimes create phase transitions from subcritical (self-correcting) to supercritical (runaway severity). The paper derives stationary distributions, first-passage times to harmful thresholds, and scaling laws near critical points. Finally, it highlights implications for agents and extended LLM reasoning models: in principle, these equations might serve as a basis for formal verification of whether a model remains stable or propagates bias over repeated inferences.

Understanding how deep learning models predict oncology patient risk can provide critical insights into disease progression, support clinical decision-making, and pave the way for trustworthy and data-driven precision medicine. Building on recent advances in the spatial modeling of the tumor microenvironment using graph neural networks, we present an explainable cell graph (xCG) approach for survival prediction. We validate our model on a public cohort of imaging mass cytometry (IMC) data for 416 cases of lung adenocarcinoma. We explain survival predictions in terms of known phenotypes on the cell level by computing risk attributions over cell graphs, for which we propose an efficient grid-based layer-wise relevance propagation (LRP) method. Our ablation studies highlight the importance of incorporating the cancer stage and model ensembling to improve the quality of risk estimates. Our xCG method, together with the IMC data, is made publicly available to support further research.

Finetuning large language models (LLMs) enables user-specific customization but introduces critical safety risks: even a few harmful examples can compromise safety alignment. A common mitigation strategy is to update the model more strongly on examples deemed safe, while downweighting or excluding those flagged as unsafe. However, because safety context can shift within a single example, updating the model equally on both harmful and harmless parts of a response is suboptimal-a coarse treatment we term static safety shaping. In contrast, we propose dynamic safety shaping (DSS), a framework that uses fine-grained safety signals to reinforce learning from safe segments of a response while suppressing unsafe content. To enable such fine-grained control during finetuning, we introduce a key insight: guardrail models, traditionally used for filtering, can be repurposed to evaluate partial responses, tracking how safety risk evolves throughout the response, segment by segment. This leads to the Safety Trajectory Assessment of Response (STAR), a token-level signal that enables shaping to operate dynamically over the training sequence. Building on this, we present STAR-DSS, guided by STAR scores, that robustly mitigates finetuning risks and delivers substantial safety improvements across diverse threats, datasets, and model families-all without compromising capability on intended tasks. We encourage future safety research to build on dynamic shaping principles for stronger mitigation against evolving finetuning risks.

We study the problem of adaptively identifying patient subpopulations that benefit from a given treatment during a confirmatory clinical trial. This type of adaptive clinical trial has been thoroughly studied in biostatistics, but has been allowed only limited adaptivity so far. Here, we aim to relax classical restrictions on such designs and investigate how to incorporate ideas from the recent machine learning literature on adaptive and online experimentation to make trials more flexible and efficient. We find that the unique characteristics of the subpopulation selection problem -- most importantly that (i) one is usually interested in finding subpopulations with any treatment benefit (and not necessarily the single subgroup with largest effect) given a limited budget and that (ii) effectiveness only has to be demonstrated across the subpopulation on average -- give rise to interesting challenges and new desiderata when designing algorithmic solutions. Building on these findings, we propose AdaGGI and AdaGCPI, two meta-algorithms for subpopulation construction. We empirically investigate their performance across a range of simulation scenarios and derive insights into their (dis)advantages across different settings.

Magnetic resonance imaging (MRI) provides high spatial resolution and excellent soft-tissue contrast without using harmful ionising radiation. Dynamic MRI is an essential tool for interventions to visualise movements or changes of the target organ. However, such MRI acquisition with high temporal resolution suffers from limited spatial resolution - also known as the spatio-temporal trade-off of dynamic MRI. Several approaches, including deep learning based super-resolution approaches, have been proposed to mitigate this trade-off. Nevertheless, such an approach typically aims to super-resolve each time-point separately, treating them as individual volumes. This research addresses the problem by creating a deep learning model which attempts to learn both spatial and temporal relationships. A modified 3D UNet model, DDoS-UNet, is proposed - which takes the low-resolution volume of the current time-point along with a prior image volume. Initially, the network is supplied with a static high-resolution planning scan as the prior image along with the low-resolution input to super-resolve the first time-point. Then it continues step-wise by using the super-resolved time-points as the prior image while super-resolving the subsequent time-points. The model performance was tested with 3D dynamic data that was undersampled to different in-plane levels. The proposed network achieved an average SSIM value of 0.951pm0.017 while reconstructing the lowest resolution data (i.e. only 4\% of the k-space acquired) - which could result in a theoretical acceleration factor of 25. The proposed approach can be used to reduce the required scan-time while achieving high spatial resolution.

Estimating the impact of continuous treatment variables (e.g., dosage amount) on binary outcomes presents significant challenges in modeling and estimation because many existing approaches make strong assumptions that do not hold for certain continuous treatment variables. For instance, traditional logistic regression makes strong linearity assumptions that do not hold for continuous treatment variables like time of initiation. In this work, we propose a semiparametric regression framework that decomposes effects into two interpretable components: a prognostic score that captures baseline outcome risk based on a combination of clinical, genetic, and sociodemographic features, and a treatment-interaction score that flexibly models the optimal treatment level via a nonparametric link function. By connecting these two parametric scores with Nadaraya-Watson regression, our approach is both interpretable and flexible. The potential of our approach is demonstrated through numerical simulations that show empirical estimation convergence. We conclude by applying our approach to a real-world case study using the International Warfarin Pharmacogenomics Consortium (IWPC) dataset to show our approach's clinical utility by deriving personalized warfarin dosing recommendations that integrate both genetic and clinical data, providing insights towards enhancing patient safety and therapeutic efficacy in anticoagulation therapy.

Radiotherapy often involves a prolonged treatment period. During this time, patients may experience organ motion due to breathing and other physiological factors. Predicting and modeling this motion before treatment is crucial for ensuring precise radiation delivery. However, existing pre-treatment organ motion prediction methods primarily rely on deformation analysis using principal component analysis (PCA), which is highly dependent on registration quality and struggles to capture periodic temporal dynamics for motion modeling.In this paper, we observe that organ motion prediction closely resembles an autoregressive process, a technique widely used in natural language processing (NLP). Autoregressive models predict the next token based on previous inputs, naturally aligning with our objective of predicting future organ motion phases. Building on this insight, we reformulate organ motion prediction as an autoregressive process to better capture patient-specific motion patterns. Specifically, we acquire 4D CT scans for each patient before treatment, with each sequence comprising multiple 3D CT phases. These phases are fed into the autoregressive model to predict future phases based on prior phase motion patterns. We evaluate our method on a real-world test set of 4D CT scans from 50 patients who underwent radiotherapy at our institution and a public dataset containing 4D CT scans from 20 patients (some with multiple scans), totaling over 1,300 3D CT phases. The performance in predicting the motion of the lung and heart surpasses existing benchmarks, demonstrating its effectiveness in capturing motion dynamics from CT images. These results highlight the potential of our method to improve pre-treatment planning in radiotherapy, enabling more precise and adaptive radiation delivery.

Large language models (LLMs) trained with next-word-prediction have achieved success as clinical foundation models. Representations from these language backbones yield strong linear probe performance across biomedical tasks, suggesting that patient semantics emerge from next-token prediction at scale. However, this paradigm treats patients as a document to be summarized rather than a dynamical system to be simulated; a patient's trajectory emerges from their state evolving under interventions and time, requiring models that simulate dynamics rather than predict tokens. To address this, we introduce SMB-Structure, a world model for structured EHR that grounds a joint-embedding prediction architecture (JEPA) with next-token prediction (SFT). SFT grounds our model to reconstruct future patient states in token space, while JEPA predicts those futures in latent space from the initial patient representation alone, forcing trajectory dynamics to be encoded before the next state is observed. We validate across two large-scale cohorts: Memorial Sloan Kettering (23,319 oncology patients; 323,000+ patient-years) and INSPECT (19,402 pulmonary embolism patients). Using a linear probe evaluated at multiple points along the disease trajectory, we demonstrate that our training paradigm learns embeddings that capture disease dynamics not recoverable by autoregressive baselines, enabling SMB-Structure to achieve competitive performance on complex tasks characterized by high patient heterogeneity. Model weights are available at https://huggingface.co/standardmodelbio/SMB-v1-1.7B-Structure.

Clinical trials disruption has always represented a non negligible part of the ending of interventional studies. While the SARS-CoV-2 (COVID-19) pandemic has led to an impressive and unprecedented initiation of clinical research, it has also led to considerable disruption of clinical trials in other disease areas, with around 80% of non-COVID-19 trials stopped or interrupted during the pandemic. In many cases the disrupted trials will not have the planned statistical power necessary to yield interpretable results. This paper describes methods to compensate for the information loss arising from trial disruptions by incorporating additional information available from auxiliary data sources. The methods described include the use of auxiliary data on baseline and early outcome data available from the trial itself and frequentist and Bayesian approaches for the incorporation of information from external data sources. The methods are illustrated by application to the analysis of artificial data based on the Primary care pediatrics Learning Activity Nutrition (PLAN) study, a clinical trial assessing a diet and exercise intervention for overweight children, that was affected by the COVID-19 pandemic. We show how all of the methods proposed lead to an increase in precision relative to use of complete case data only.

Brain-to-image decoding has been recently propelled by the progress in generative AI models and the availability of large ultra-high field functional Magnetic Resonance Imaging (fMRI). However, current approaches depend on complicated multi-stage pipelines and preprocessing steps that typically collapse the temporal dimension of brain recordings, thereby limiting time-resolved brain decoders. Here, we introduce Dynadiff (Dynamic Neural Activity Diffusion for Image Reconstruction), a new single-stage diffusion model designed for reconstructing images from dynamically evolving fMRI recordings. Our approach offers three main contributions. First, Dynadiff simplifies training as compared to existing approaches. Second, our model outperforms state-of-the-art models on time-resolved fMRI signals, especially on high-level semantic image reconstruction metrics, while remaining competitive on preprocessed fMRI data that collapse time. Third, this approach allows a precise characterization of the evolution of image representations in brain activity. Overall, this work lays the foundation for time-resolved brain-to-image decoding.

A compartmental deterministic model that allows (1) immunity from two stages of infection and carriage, and (2) disease induced death, is used in studying the dynamics of meningitis epidemic process in a closed population. It allows for difference in the transmission rate of infection to a susceptible by a carrier and an infective. It is generalized to allow a proportion ({\phi}) of those susceptibles infected to progress directly to infectives in stage I. Both models are used in this study. The threshold conditions for the spread of carrier and infectives in stage I are derived for the two models. Sensitivity analysis is performed on the reproductive number derived from the next generation matrix. The case-carrier ratio profile for various parameters and threshold values are shown. So also are the graphs of the total number ever infected as influenced by {\epsilon} and {\phi}. The infection transmission rate (eta), the odds in favor of a carrier, over an infective, in transmitting an infection to a susceptible ({\epsilon}) and the carrier conversion rate ({\phi}) to an infective in stage I, are identified as key parameters that should be subject of attention for any control intervention strategy. The case-carrier ratio profiles provide evidence of a critical case-carrier ratio attained before the number of reported cases grows to an epidemic level. They also provide visual evidence of epidemiological context, in this case, epidemic incidence (in later part of dry season) and endemic incidence (during rainy season). Results from total proportion ever infected suggest that the model, in which {\phi}=0 obtained, can adequately represent, in essence, the generalized model for this study.

In many real-world sequential decision-making problems, an action does not immediately reflect on the feedback and spreads its effects over a long time frame. For instance, in online advertising, investing in a platform produces an instantaneous increase of awareness, but the actual reward, i.e., a conversion, might occur far in the future. Furthermore, whether a conversion takes place depends on: how fast the awareness grows, its vanishing effects, and the synergy or interference with other advertising platforms. Previous work has investigated the Multi-Armed Bandit framework with the possibility of delayed and aggregated feedback, without a particular structure on how an action propagates in the future, disregarding possible dynamical effects. In this paper, we introduce a novel setting, the Dynamical Linear Bandits (DLB), an extension of the linear bandits characterized by a hidden state. When an action is performed, the learner observes a noisy reward whose mean is a linear function of the hidden state and of the action. Then, the hidden state evolves according to linear dynamics, affected by the performed action too. We start by introducing the setting, discussing the notion of optimal policy, and deriving an expected regret lower bound. Then, we provide an optimistic regret minimization algorithm, Dynamical Linear Upper Confidence Bound (DynLin-UCB), that suffers an expected regret of order mathcal{O} Big( d sqrt{T}{(1-rho)^{3/2}} Big), where rho is a measure of the stability of the system, and d is the dimension of the action vector. Finally, we conduct a numerical validation on a synthetic environment and on real-world data to show the effectiveness of DynLin-UCB in comparison with several baselines.

Dynamic graph clustering aims to detect and track time-varying clusters in dynamic graphs, revealing the evolutionary mechanisms of complex real-world dynamic systems. Matrix factorization-based methods are promising approaches for this task; however, these methods often struggle with scalability and can be time-consuming when applied to large-scale dynamic graphs. Moreover, they tend to lack robustness and are vulnerable to real-world noisy data. To address these issues, we make three key contributions. First, to improve scalability, we propose temporal separated matrix factorization, where a single matrix is divided into multiple smaller matrices for independent factorization, resulting in faster computation. Second, to improve robustness, we introduce bi-clustering regularization, which jointly optimizes graph embedding and clustering, thereby filtering out noisy features from the graph embeddings. Third, to further enhance effectiveness and efficiency, we propose selective embedding updating, where we update only the embeddings of dynamic nodes while the embeddings of static nodes are fixed among different timestamps. Experimental results on six synthetic and five real-world benchmarks demonstrate the scalability, robustness and effectiveness of our proposed method. Source code is available at https://github.com/Clearloveyuan/DyG-MF.

In recent years, medical information technology has made it possible for electronic health record (EHR) to store fairly complete clinical data. This has brought health care into the era of "big data". However, medical data are often sparse and strongly correlated, which means that medical problems cannot be solved effectively. With the rapid development of deep learning in recent years, it has provided opportunities for the use of big data in healthcare. In this paper, we propose a temporal-saptial correlation attention network (TSCAN) to handle some clinical characteristic prediction problems, such as predicting death, predicting length of stay, detecting physiologic decline, and classifying phenotypes. Based on the design of the attention mechanism model, our approach can effectively remove irrelevant items in clinical data and irrelevant nodes in time according to different tasks, so as to obtain more accurate prediction results. Our method can also find key clinical indicators of important outcomes that can be used to improve treatment options. Our experiments use information from the Medical Information Mart for Intensive Care (MIMIC-IV) database, which is open to the public. Finally, we have achieved significant performance benefits of 2.0\% (metric) compared to other SOTA prediction methods. We achieved a staggering 90.7\% on mortality rate, 45.1\% on length of stay. The source code can be find: https://github.com/yuyuheintju/TSCAN.

Traditional benchmarks for large language models (LLMs) typically rely on static evaluations through storytelling or opinion expression, which fail to capture the dynamic requirements of real-time information processing in contemporary applications. To address this limitation, we present DynamicBench, a benchmark designed to evaluate the proficiency of LLMs in storing and processing up-to-the-minute data. DynamicBench utilizes a dual-path retrieval pipeline, integrating web searches with local report databases. It necessitates domain-specific knowledge, ensuring accurate responses report generation within specialized fields. By evaluating models in scenarios that either provide or withhold external documents, DynamicBench effectively measures their capability to independently process recent information or leverage contextual enhancements. Additionally, we introduce an advanced report generation system adept at managing dynamic information synthesis. Our experimental results confirm the efficacy of our approach, with our method achieving state-of-the-art performance, surpassing GPT4o in document-free and document-assisted scenarios by 7.0% and 5.8%, respectively. The code and data will be made publicly available.

Dynamic analysis enables detecting Windows malware by executing programs in a controlled environment and logging their actions. Previous work has proposed training machine learning models, i.e., convolutional and long short-term memory networks, on homogeneous input features like runtime APIs to either detect or classify malware, neglecting other relevant information coming from heterogeneous data like network and file operations. To overcome these issues, we introduce Nebula, a versatile, self-attention Transformer-based neural architecture that generalizes across different behavioral representations and formats, combining diverse information from dynamic log reports. Nebula is composed by several components needed to tokenize, filter, normalize and encode data to feed the transformer architecture. We firstly perform a comprehensive ablation study to evaluate their impact on the performance of the whole system, highlighting which components can be used as-is, and which must be enriched with specific domain knowledge. We perform extensive experiments on both malware detection and classification tasks, using three datasets acquired from different dynamic analyses platforms, show that, on average, Nebula outperforms state-of-the-art models at low false positive rates, with a peak of 12% improvement. Moreover, we showcase how self-supervised learning pre-training matches the performance of fully-supervised models with only 20% of training data, and we inspect the output of Nebula through explainable AI techniques, pinpointing how attention is focusing on specific tokens correlated to malicious activities of malware families. To foster reproducibility, we open-source our findings and models at https://github.com/dtrizna/nebula.

We consider the classic supervised learning problem, where a continuous non-negative random label Y (i.e. a random duration) is to be predicted based upon observing a random vector X valued in R^d with dgeq 1 by means of a regression rule with minimum least square error. In various applications, ranging from industrial quality control to public health through credit risk analysis for instance, training observations can be right censored, meaning that, rather than on independent copies of (X,Y), statistical learning relies on a collection of ngeq 1 independent realizations of the triplet (X, ; min{Y,; C},; δ), where C is a nonnegative r.v. with unknown distribution, modeling censorship and δ=I{Yleq C} indicates whether the duration is right censored or not. As ignoring censorship in the risk computation may clearly lead to a severe underestimation of the target duration and jeopardize prediction, we propose to consider a plug-in estimate of the true risk based on a Kaplan-Meier estimator of the conditional survival function of the censorship C given X, referred to as Kaplan-Meier risk, in order to perform empirical risk minimization. It is established, under mild conditions, that the learning rate of minimizers of this biased/weighted empirical risk functional is of order O_{P}(log(n)/n) when ignoring model bias issues inherent to plug-in estimation, as can be attained in absence of censorship. Beyond theoretical results, numerical experiments are presented in order to illustrate the relevance of the approach developed.

Understanding the dynamic behavior of computer programs during normal working conditions is an important task, which has multiple security benefits such as the development of behavior-based anomaly detection, vulnerability discovery, and patching. Existing works achieved this goal by collecting and analyzing various data including network traffic, system calls, instruction traces, etc. In this paper, we explore the use of a new type of data, performance counters, to analyze the dynamic behavior of programs. Using existing primitives, we develop a tool named perfextract to capture data from different performance counters for a program during its startup time, thus forming multiple time series to represent the dynamic behavior of the program. We analyze the collected data and develop a semi-supervised clustering algorithm that allows us to classify each program using its performance counter time series into a specific group and to identify the intrinsic behavior of that group. We carry out extensive experiments with 18 real-world programs that belong to 4 groups including web browsers, text editors, image viewers, and audio players. The experimental results show that the examined programs can be accurately differentiated based on their performance counter data regardless of whether programs are run in physical or virtual environments.

We introduce Dynaboard, an evaluation-as-a-service framework for hosting benchmarks and conducting holistic model comparison, integrated with the Dynabench platform. Our platform evaluates NLP models directly instead of relying on self-reported metrics or predictions on a single dataset. Under this paradigm, models are submitted to be evaluated in the cloud, circumventing the issues of reproducibility, accessibility, and backwards compatibility that often hinder benchmarking in NLP. This allows users to interact with uploaded models in real time to assess their quality, and permits the collection of additional metrics such as memory use, throughput, and robustness, which -- despite their importance to practitioners -- have traditionally been absent from leaderboards. On each task, models are ranked according to the Dynascore, a novel utility-based aggregation of these statistics, which users can customize to better reflect their preferences, placing more/less weight on a particular axis of evaluation or dataset. As state-of-the-art NLP models push the limits of traditional benchmarks, Dynaboard offers a standardized solution for a more diverse and comprehensive evaluation of model quality.

We provide an optimization-based framework to perform counterfactual analysis in a dynamic model with hidden states. Our framework is grounded in the ``abduction, action, and prediction'' approach to answer counterfactual queries and handles two key challenges where (1) the states are hidden and (2) the model is dynamic. Recognizing the lack of knowledge on the underlying causal mechanism and the possibility of infinitely many such mechanisms, we optimize over this space and compute upper and lower bounds on the counterfactual quantity of interest. Our work brings together ideas from causality, state-space models, simulation, and optimization, and we apply it on a breast cancer case study. To the best of our knowledge, we are the first to compute lower and upper bounds on a counterfactual query in a dynamic latent-state model.

Longitudinal analysis has great potential to reveal developmental trajectories and monitor disease progression in medical imaging. This process relies on consistent and robust joint 4D segmentation. Traditional techniques are dependent on the similarity of images over time and the use of subject-specific priors to reduce random variation and improve the robustness and sensitivity of the overall longitudinal analysis. This is however slow and computationally intensive as subject-specific templates need to be rebuilt every time. The focus of this work to accelerate this analysis with the use of deep learning. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The proposed approach is based on deep CNNs and incorporates semantic segmentation and provides a longitudinal relationship for the same subject. The state of art using 3D patches as inputs to modified Unet provides results around {0.91 pm 0.5} Dice and using multi-view atlas in CNNs provide around the same results. In this work, different models are explored, each offers better accuracy and fast results while increasing the segmentation quality. These methods are evaluated on 135 scans from the EADC-ADNI Harmonized Hippocampus Protocol. Proposed CNN based segmentation approaches demonstrate how 2D segmentation using prior slices can provide similar results to 3D segmentation while maintaining good continuity in the 3D dimension and improved speed. Just using 2D modified sagittal slices provide us a better Dice and longitudinal analysis for a given subject. For the ADNI dataset, using the simple UNet CNN technique gives us {0.84 pm 0.5} and while using modified CNN techniques on the same input yields {0.89 pm 0.5}. Rate of atrophy and RMS error are calculated for several test cases using various methods and analyzed.

Practitioners frequently aim to infer an unobserved population trajectory using sample snapshots at multiple time points. For instance, in single-cell sequencing, scientists would like to learn how gene expression evolves over time. But sequencing any cell destroys that cell. So we cannot access any cell's full trajectory, but we can access snapshot samples from many cells. Stochastic differential equations are commonly used to analyze systems with full individual-trajectory access; since here we have only sample snapshots, these methods are inapplicable. The deep learning community has recently explored using Schr\"odinger bridges (SBs) and their extensions to estimate these dynamics. However, these methods either (1) interpolate between just two time points or (2) require a single fixed reference dynamic within the SB, which is often just set to be Brownian motion. But learning piecewise from adjacent time points can fail to capture long-term dependencies. And practitioners are typically able to specify a model class for the reference dynamic but not the exact values of the parameters within it. So we propose a new method that (1) learns the unobserved trajectories from sample snapshots across multiple time points and (2) requires specification only of a class of reference dynamics, not a single fixed one. In particular, we suggest an iterative projection method inspired by Schr\"odinger bridges; we alternate between learning a piecewise SB on the unobserved trajectories and using the learned SB to refine our best guess for the dynamics within the reference class. We demonstrate the advantages of our method via a well-known simulated parametric model from ecology, simulated and real data from systems biology, and real motion-capture data.

Clinical trials are pivotal for developing new medical treatments but typically carry risks such as patient mortality and enrollment failure that waste immense efforts spanning over a decade. Applying artificial intelligence (AI) to predict key events in clinical trials holds great potential for providing insights to guide trial designs. However, complex data collection and question definition requiring medical expertise have hindered the involvement of AI thus far. This paper tackles these challenges by presenting a comprehensive suite of 23 meticulously curated AI-ready datasets covering multi-modal input features and 8 crucial prediction challenges in clinical trial design, encompassing prediction of trial duration, patient dropout rate, serious adverse event, mortality rate, trial approval outcome, trial failure reason, drug dose finding, design of eligibility criteria. Furthermore, we provide basic validation methods for each task to ensure the datasets' usability and reliability. We anticipate that the availability of such open-access datasets will catalyze the development of advanced AI approaches for clinical trial design, ultimately advancing clinical trial research and accelerating medical solution development.

Longitudinal treatment decisions require predicting potential outcomes under future treatment sequences in the presence of time-varying confounding, heterogeneous patient dynamics, and limited domain-specific data. Existing longitudinal causal estimators typically train a new model for each cohort or simulator. We introduce Causal Longitudinal Prior-Fitted Networks (CausalLongPFN), a prior-fitted in-context predictor for longitudinal causal prediction. The model is pretrained entirely on synthetic episodes sampled from a broad prior over temporal structural causal models, exposing it to treatment-confounder feedback, latent heterogeneity, nonlinear state evolution, delayed effects, and cumulative treatment responses. At test time, CausalLongPFN is frozen: it conditions on support trajectories, a query history, and a proposed future treatment sequence, and returns a predictive distribution over future outcomes without gradient updates or propensity-model fitting. Multi-step predictions are obtained by recursively applying the one-step predictor under the specified treatment sequence. We evaluate on branchable cancer, HIV, and warfarin benchmarks with ground-truth counterfactual labels, and on factual-only rolling-origin prediction in MIMIC-III ICU trajectories. CausalLongPFN is competitive with domain-trained longitudinal baselines on counterfactual benchmarks and performs strongly on factual MIMIC-III prediction, suggesting that broad synthetic causal pretraining can provide a useful frozen alternative when repeated domain-specific training is costly or impractical.

We introduce ProtoPathway, an interpretable-by-design multimodal framework for cancer survival prediction that unifies whole slide imaging and transcriptomics through encoders producing biologically grounded representations on both sides of the fusion. On the histopathology side, K learnable morphological prototypes, trained end-to-end with the survival objective, serve as the slide representation itself: patches flow into prototype tokens via soft assignment, compressing variable-length patch sets into fixed task-adaptive tokens. On the genomic side, a bipartite graph neural network encodes gene expression within the Reactome pathway hierarchy, producing pathway embeddings that reflect both constituent genes and their broader biological context through bidirectional message passing over a shared gene--pathway graph. Cross-modal attention then operates over a compact prototype times pathway matrix in which prototypes query pathways, modeling the biological direction in which molecular programs give rise to tissue morphology. Because both axes carry stable task-learned identity, the attention matrix is itself an interpretability output, yielding native inference-time attribution across the full biological hierarchy, from genes through pathways and prototypes to spatial tissue maps. We evaluate on five TCGA cancer cohorts, demonstrating competitive or superior survival prediction with substantially improved biological interpretability and reduced computational cost, with interpretability claims validated through fold-stratified rank-based population-level analysis. Our source code, model weights, and Reactome pathways, together with a unified codebase reimplementing all multimodal survival baselines under identical preprocessing and evaluation, are available at: https://github.com/AmayaGS/ProtoPathway.

Conventional medical cancer screening methods are costly, labor-intensive, and extremely difficult to scale. Although AI can improve cancer detection, most systems rely on complex or specialized medical data, making them impractical for large-scale screening. We introduce Can-SAVE, a lightweight AI system that ranks population-wide cancer risks solely based on medical history events. By integrating survival model outputs into a gradient-boosting framework, our approach detects subtle, long-term patient risk patterns - often well before clinical symptoms manifest. Can-SAVE was rigorously evaluated on a real-world dataset of 2.5 million adults spanning five Russian regions, marking the study as one of the largest and most comprehensive deployments of AI-driven cancer risk assessment. In a retrospective oncologist-supervised study over 1.9M patients, Can-SAVE achieves a 4-10x higher detection rate at identical screening volumes and an Average Precision (AP) of 0.228 vs. 0.193 for the best baseline (LoRA-tuned Qwen3-Embeddings via DeepSeek-R1 summarization). In a year-long prospective pilot (426K patients), our method almost doubled the cancer detection rate (+91%) and increased population coverage by 36% over the national screening protocol. The system demonstrates practical scalability: a city-wide population of 1 million patients can be processed in under three hours using standard hardware, enabling seamless clinical integration. This work proves that Can-SAVE achieves nationally significant cancer detection improvements while adhering to real-world public healthcare constraints, offering immediate clinical utility and a replicable framework for population-wide screening. Code for training and feature engineering is available at https://github.com/sb-ai-lab/Can-SAVE.

Tokenization strategies shape how models process electronic health records, yet fair comparisons of their effectiveness remain limited. We present a systematic evaluation of tokenization approaches for clinical time series modeling using transformer-based architectures, revealing task-dependent and sometimes counterintuitive findings about temporal and value feature importance. Through controlled ablations across four clinical prediction tasks on MIMIC-IV, we demonstrate that explicit time encodings provide no consistent statistically significant benefit for the evaluated downstream tasks. Value features show task-dependent importance, affecting mortality prediction but not readmission, suggesting code sequences alone can carry sufficient predictive signal. We further show that frozen pretrained code encoders dramatically outperform their trainable counterparts while requiring dramatically fewer parameters. Larger clinical encoders provide consistent improvements across tasks, benefiting from frozen embeddings that eliminate computational overhead. Our controlled evaluation enables fairer tokenization comparisons and demonstrates that simpler, parameter-efficient approaches can, in many cases, achieve strong performance, though the optimal tokenization strategy remains task-dependent.

Missing values, irregularly collected samples, and multi-resolution signals commonly occur in multivariate time series data, making predictive tasks difficult. These challenges are especially prevalent in the healthcare domain, where patients' vital signs and electronic records are collected at different frequencies and have occasionally missing information due to the imperfections in equipment or patient circumstances. Researchers have handled each of these issues differently, often handling missing data through mean value imputation and then using sequence models over the multivariate signals while ignoring the different resolution of signals. We propose a unified model named Multi-resolution Flexible Irregular Time series Network (Multi-FIT). The building block for Multi-FIT is the FIT network. The FIT network creates an informative dense representation at each time step using signal information such as last observed value, time difference since the last observed time stamp and overall mean for the signal. Vertical FIT (FIT-V) is a variant of FIT which also models the relationship between different temporal signals while creating the informative dense representations for the signal. The multi-FIT model uses multiple FIT networks for sets of signals with different resolutions, further facilitating the construction of flexible representations. Our model has three main contributions: a.) it does not impute values but rather creates informative representations to provide flexibility to the model for creating task-specific representations b.) it models the relationship between different signals in the form of support signals c.) it models different resolutions in parallel before merging them for the final prediction task. The FIT, FIT-V and Multi-FIT networks improve upon the state-of-the-art models for three predictive tasks, including the forecasting of patient survival.

Dynamic adaptation has become an essential technique in accelerating distributed machine learning (ML) training. Recent studies have shown that dynamically adjusting model structure (e.g., lottery ticket hypothesis) or hyperparameters (e.g., batch size) can significantly accelerate training without sacrificing accuracy. However, existing ML cluster schedulers are not designed to handle dynamic adaptation. We show that existing schemes fail to provide fairness and degrade system efficiency when the training throughput changes over time under dynamic adaptation. We design Shockwave, a scheduler with future planning that builds on two key ideas. First, Shockwave extends classic market theory from static settings to dynamic settings to co-optimize efficiency and fairness. Second, Shockwave utilizes stochastic dynamic programming to handle dynamic changes. We build a system for Shockwave and validate its performance with both trace-driven simulation and cluster experiments. Results show that for traces of ML jobs with dynamic adaptation, Shockwave improves makespan by 1.3X and fairness by 2X when compared with existing fair scheduling schemes.

Many natural dynamic processes -- such as in vivo cellular differentiation or disease progression -- can only be observed through the lens of static sample snapshots. While challenging, reconstructing their temporal evolution to decipher underlying dynamic properties is of major interest to scientific research. Existing approaches enable data transport along a temporal axis but are poorly scalable in high dimension and require restrictive assumptions to be met. To address these issues, we propose \textbf{Multi-Marginal temporal Schr\"odinger Bridge Matching} (MMtSBM) for video generation from unpaired data, extending the theoretical guarantees and empirical efficiency of Diffusion Schr\"odinger Bridge Matching (arXiv:archive/2303.16852) by deriving the Iterative Markovian Fitting algorithm to multiple marginals in a novel factorized fashion. Experiments show that MMtSBM retains theoretical properties on toy examples, achieves state-of-the-art performance on real world datasets such as transcriptomic trajectory inference in 100 dimensions, and for the first time recovers couplings and dynamics in very high dimensional image settings. Our work establishes multi-marginal Schr\"odinger bridges as a practical and principled approach for recovering hidden dynamics from static data.

A ubiquitous feature of data of our era is their extra-large sizes and dimensions. Analyzing such high-dimensional data poses significant challenges, since the feature dimension is often much larger than the sample size. This thesis introduces robust and computationally efficient methods to address several common challenges associated with high-dimensional data. In my first manuscript, I propose a coherent approach to variable screening that accommodates nonlinear associations. I develop a novel variable screening method that transcends traditional linear assumptions by leveraging mutual information, with an intended application in neuroimaging data. This approach allows for accurate identification of important variables by capturing nonlinear as well as linear relationships between the outcome and covariates. Building on this foundation, I develop new optimization methods for sparse estimation using nonconvex penalties in my second manuscript. These methods address notable challenges in current statistical computing practices, facilitating computationally efficient and robust analyses of complex datasets. The proposed method can be applied to a general class of optimization problems. In my third manuscript, I contribute to robust modeling of high-dimensional correlated observations by developing a mixed-effects model based on Tsallis power-law entropy maximization and discussed the theoretical properties of such distribution. This model surpasses the constraints of conventional Gaussian models by accommodating a broader class of distributions with enhanced robustness to outliers. Additionally, I develop a proximal nonlinear conjugate gradient algorithm that accelerates convergence while maintaining numerical stability, along with rigorous statistical properties for the proposed framework.

Real-world deployment of machine learning models is challenging because data evolves over time. While no model can work when data evolves in an arbitrary fashion, if there is some pattern to these changes, we might be able to design methods to address it. This paper addresses situations when data evolves gradually. We introduce a time-varying propensity score that can detect gradual shifts in the distribution of data which allows us to selectively sample past data to update the model -- not just similar data from the past like that of a standard propensity score but also data that evolved in a similar fashion in the past. The time-varying propensity score is quite general: we demonstrate different ways of implementing it and evaluate it on a variety of problems ranging from supervised learning (e.g., image classification problems) where data undergoes a sequence of gradual shifts, to reinforcement learning tasks (e.g., robotic manipulation and continuous control) where data shifts as the policy or the task changes.

Survival risk stratification is an important step in clinical decision making for breast cancer management. We propose a novel deep learning approach for this purpose by integrating histopathological imaging, genetic and clinical data. It employs vision transformers, specifically the MaxViT model, for image feature extraction, and self-attention to capture intricate image relationships at the patient level. A dual cross-attention mechanism fuses these features with genetic data, while clinical data is incorporated at the final layer to enhance predictive accuracy. Experiments on the public TCGA-BRCA dataset show that our model, trained using the negative log likelihood loss function, can achieve superior performance with a mean C-index of 0.64, surpassing existing methods. This advancement facilitates tailored treatment strategies, potentially leading to improved patient outcomes.

With the increasing availability of wearable devices, photoplethysmography (PPG) has emerged as a promising non-invasive tool for monitoring human hemodynamics. We propose a deep learning framework to estimate vascular age (AI-vascular age) from PPG signals, incorporating a distribution-aware loss to address biases caused by imbalanced data. The model was developed using data from the UK Biobank (UKB), with 98,672 participants in the development cohort and 113,559 participants (144,683 data pairs) for clinical evaluation. After adjusting for key confounders, individuals with a vascular age gap (AI-vascular age minus calendar age) exceeding 9 years had a significantly higher risk of major adverse cardiovascular and cerebrovascular events (MACCE) (HR = 2.37, p < 0.005) and secondary outcomes, including diabetes (HR = 2.69, p < 0.005), hypertension (HR = 2.88, p < 0.005), coronary heart disease (HR = 2.20, p < 0.005), heart failure (HR = 2.15, p < 0.005), myocardial infarction (HR = 2.51, p < 0.005), stroke (HR = 2.55, p < 0.005), and all-cause mortality (HR = 2.51, p < 0.005). Conversely, participants with a vascular age gap below -9 years exhibited a significantly lower incidence of these outcomes. We further evaluated the longitudinal applicability of AI-vascular age using serial PPG data from the UKB, demonstrating its value in risk stratification by leveraging AI-vascular age at two distinct time points to predict future MACCE incidence. External validation was performed on a MIMIC-III-derived cohort (n = 2,343), where each one-year increase in vascular age gap was significantly associated with elevated in-hospital mortality risk (OR = 1.02, p < 0.005). In conclusion, our study establishes AI-vascular age as a novel, non-invasive digital biomarker for cardiovascular health assessment.

Large language models (LLMs) have emerged as powerful tools for analyzing complex datasets. Recent studies demonstrate their potential to generate useful, personalized responses when provided with patient-specific health information that encompasses lifestyle, biomarkers, and context. As LLM-driven health applications are increasingly adopted, rigorous and efficient one-sided evaluation methodologies are crucial to ensure response quality across multiple dimensions, including accuracy, personalization and safety. Current evaluation practices for open-ended text responses heavily rely on human experts. This approach introduces human factors and is often cost-prohibitive, labor-intensive, and hinders scalability, especially in complex domains like healthcare where response assessment necessitates domain expertise and considers multifaceted patient data. In this work, we introduce Adaptive Precise Boolean rubrics: an evaluation framework that streamlines human and automated evaluation of open-ended questions by identifying gaps in model responses using a minimal set of targeted rubrics questions. Our approach is based on recent work in more general evaluation settings that contrasts a smaller set of complex evaluation targets with a larger set of more precise, granular targets answerable with simple boolean responses. We validate this approach in metabolic health, a domain encompassing diabetes, cardiovascular disease, and obesity. Our results demonstrate that Adaptive Precise Boolean rubrics yield higher inter-rater agreement among expert and non-expert human evaluators, and in automated assessments, compared to traditional Likert scales, while requiring approximately half the evaluation time of Likert-based methods. This enhanced efficiency, particularly in automated evaluation and non-expert contributions, paves the way for more extensive and cost-effective evaluation of LLMs in health.

A Mamba state-space model trained only for next-step prediction appears to recover Granger-causal structure through a simple readout S = |W_{out} W_{in}|, with early experiments suggesting the phenomenon generalized across architectures and benefited from interventional data at p < 10^{-5}. We package the protocol used to test that claim -- standardized synthetic generators (VAR/Lorenz/CauseMe-style), three intervention semantics (do(X=c), soft-noise, random-forcing), edge-provenance cards on three real datasets, and size-matched control arms -- as a reusable falsification benchmark, and walk the claim through it in five stages. The method-level claim does not survive: (i) a plain linear bottleneck does as well or better; (ii) tuned Lasso beats the bottleneck on synthetic CauseMe-style benchmarks, and on Lorenz-96 (the only real benchmark with unambiguous ground truth) classical PCMCI and Granger lead a tight cluster in which the bottleneck trails; (iii) the headline intervention advantage is roughly 60% a sample-size confound, and the residual disappears under standard do(X=c) interventions, surviving only under a non-standard random-forcing scheme; (iv) even that residual reproduces, with a larger effect, in classical bivariate Granger -- the effect is method-agnostic. What survives is a narrow characterization result; the benchmark is the lasting artifact, and each stage above is one of its control arms.

Predicting mortality-related outcomes from images offers the prospect of accessible, noninvasive, and scalable health screening. We present a method that leverages pretrained vision transformer foundation models to estimate remaining lifespan from facial and whole-body images, alongside robust uncertainty quantification. We show that predictive uncertainty varies systematically with the true remaining lifespan, and that this uncertainty can be effectively modeled by learning a Gaussian distribution for each sample. Our approach achieves state-of-the-art mean absolute error (MAE) of 7.48 years on an established Dataset, and further improves to 4.79 and 5.07 years MAE on two new, higher-quality datasets curated and published in this work. Importantly, our models provide well-calibrated uncertainty estimates, as demonstrated by a bucketed expected calibration error of 0.62 years. While not intended for clinical deployment, these results highlight the potential of extracting medically relevant signals from images. We make all code and datasets available to facilitate further research.

The rise of large language models (LLMs) has shifted time series analysis from narrow analytics to general-purpose reasoning. Yet, existing benchmarks cover only a small set of health time series modalities and tasks, failing to reflect the diverse domains and extensive temporal dependencies inherent in real-world physiological modeling. To bridge these gaps, we introduce HEARTS (Health Reasoning over Time Series), a unified benchmark for evaluating hierarchical reasoning capabilities of LLMs over general health time series. HEARTS integrates 16 real-world datasets across 12 health domains and 20 signal modalities, and defines a comprehensive taxonomy of 110 tasks grouped into four core capabilities: Perception, Inference, Generation, and Deduction. Evaluating 14 state-of-the-art LLMs on more than 20K test samples reveals intriguing findings. First, LLMs substantially underperform specialized models, and their performance is only weakly related to general reasoning scores. Moreover, LLMs often rely on simple heuristics and struggle with multi-step temporal reasoning. Finally, performance declines with increasing temporal complexity, with similar failure modes within model families, indicating that scaling alone is insufficient. By making these gaps measurable, HEARTS provides a standardized testbed and living benchmark for developing next-generation LLM agents capable of reasoning over diverse health signals.

The rapid proliferation of Large Language Models (LLMs) and diverse specialized benchmarks necessitates a shift from fragmented, task-specific metrics to a holistic, competitive ranking system that effectively aggregates performance across multiple ability dimensions. Primarily using static scoring, current evaluation methods are fundamentally limited. They struggle to determine the proper mix ratio across diverse benchmarks, and critically, they fail to capture a model's dynamic competitive fitness or its vulnerability when confronted with sequential, high-stakes tasks. To address this, we introduce the novel Competitive Swiss-System Dynamics (CSD) framework. CSD simulates a multi-round, sequential contest where models are dynamically paired across a curated sequence of benchmarks based on their accumulated win-loss record. And Monte Carlo Simulation (N=100,000 iterations) is used to approximate the statistically robust Expected Win Score (E[S_m]), which eliminates the noise of random pairing and early-round luck. Furthermore, we implement a Failure Sensitivity Analysis by parameterizing the per-round elimination quantity (T_k), which allows us to profile models based on their risk appetite--distinguishing between robust generalists and aggressive specialists. We demonstrate that CSD provides a more nuanced and context-aware ranking than traditional aggregate scoring and static pairwise models, representing a vital step towards risk-informed, next-generation LLM evaluation.

Personalized treatment effect estimates are often of interest in high-stakes applications -- thus, before deploying a model estimating such effects in practice, one needs to be sure that the best candidate from the ever-growing machine learning toolbox for this task was chosen. Unfortunately, due to the absence of counterfactual information in practice, it is usually not possible to rely on standard validation metrics for doing so, leading to a well-known model selection dilemma in the treatment effect estimation literature. While some solutions have recently been investigated, systematic understanding of the strengths and weaknesses of different model selection criteria is still lacking. In this paper, instead of attempting to declare a global `winner', we therefore empirically investigate success- and failure modes of different selection criteria. We highlight that there is a complex interplay between selection strategies, candidate estimators and the data used for comparing them, and provide interesting insights into the relative (dis)advantages of different criteria alongside desiderata for the design of further illuminating empirical studies in this context.

We consider offline reinforcement learning (RL) methods in possibly nonstationary environments. Many existing RL algorithms in the literature rely on the stationarity assumption that requires the system transition and the reward function to be constant over time. However, the stationarity assumption is restrictive in practice and is likely to be violated in a number of applications, including traffic signal control, robotics and mobile health. In this paper, we develop a consistent procedure to test the nonstationarity of the optimal Q-function based on pre-collected historical data, without additional online data collection. Based on the proposed test, we further develop a sequential change point detection method that can be naturally coupled with existing state-of-the-art RL methods for policy optimization in nonstationary environments. The usefulness of our method is illustrated by theoretical results, simulation studies, and a real data example from the 2018 Intern Health Study. A Python implementation of the proposed procedure is available at https://github.com/limengbinggz/CUSUM-RL.

Feature selection helps reduce data acquisition costs in ML, but the standard approach is to train models with static feature subsets. Here, we consider the dynamic feature selection (DFS) problem where a model sequentially queries features based on the presently available information. DFS is often addressed with reinforcement learning, but we explore a simpler approach of greedily selecting features based on their conditional mutual information. This method is theoretically appealing but requires oracle access to the data distribution, so we develop a learning approach based on amortized optimization. The proposed method is shown to recover the greedy policy when trained to optimality, and it outperforms numerous existing feature selection methods in our experiments, thus validating it as a simple but powerful approach for this problem.

Dynamic imaging addresses the recovery of a time-varying 2D or 3D object at each time instant using its undersampled measurements. In particular, in the case of dynamic tomography, only a single projection at a single view angle may be available at a time, making the problem severely ill-posed. In this work, we propose an approach, RED-PSM, which combines for the first time two powerful techniques to address this challenging imaging problem. The first, are partially separable models, which have been used to efficiently introduce a low-rank prior for the spatio-temporal object. The second is the recent Regularization by Denoising (RED), which provides a flexible framework to exploit the impressive performance of state-of-the-art image denoising algorithms, for various inverse problems. We propose a partially separable objective with RED and a computationally efficient and scalable optimization scheme with variable splitting and ADMM. Theoretical analysis proves the convergence of our objective to a value corresponding to a stationary point satisfying the first-order optimality conditions. Convergence is accelerated by a particular projection-domain-based initialization. We demonstrate the performance and computational improvements of our proposed RED-PSM with a learned image denoiser by comparing it to a recent deep-prior-based method known as TD-DIP. Although the main focus is on dynamic tomography, we also show the performance advantages of RED-PSM in a cardiac dynamic MRI setting.

As machine intelligence evolves, the need to test and compare the problem-solving abilities of different AI models grows. However, current benchmarks are often overly simplistic, allowing models to perform uniformly well, making it difficult to distinguish their capabilities. Additionally, benchmarks typically rely on static question-answer pairs, which models might memorize or guess. To address these limitations, we introduce the Dynamic Intelligence Assessment (DIA), a novel methodology for testing AI models using dynamic question templates and improved metrics across multiple disciplines such as mathematics, cryptography, cybersecurity, and computer science. The accompanying DIA-Bench dataset, which includes 150 diverse and challenging task templates with mutable parameters, is presented in various formats such as text, PDFs, compiled binaries, and visual puzzles. Our framework introduces four new metrics to assess a model's reliability and confidence across multiple attempts. These metrics revealed that even simple questions are frequently answered incorrectly when posed in varying forms, highlighting significant gaps in models' reliability. Notably, models like GPT-4o tended to overestimate their mathematical abilities, while ChatGPT-4o demonstrated better decision-making and performance through effective tool usage. We evaluated eight state-of-the-art large language models (LLMs) using DIA-Bench, showing that current models struggle with complex tasks and often display unexpectedly low confidence, even with simpler questions. The DIA framework sets a new standard for assessing not only problem-solving but also a model's adaptive intelligence and ability to assess its own limitations. The dataset is publicly available on our project's website.

Learning accurate predictive models of real-world dynamic phenomena (e.g., climate, biological) remains a challenging task. One key issue is that the data generated by both natural and artificial processes often comprise time series that are irregularly sampled and/or contain missing observations. In this work, we propose the Neural Continuous-Discrete State Space Model (NCDSSM) for continuous-time modeling of time series through discrete-time observations. NCDSSM employs auxiliary variables to disentangle recognition from dynamics, thus requiring amortized inference only for the auxiliary variables. Leveraging techniques from continuous-discrete filtering theory, we demonstrate how to perform accurate Bayesian inference for the dynamic states. We propose three flexible parameterizations of the latent dynamics and an efficient training objective that marginalizes the dynamic states during inference. Empirical results on multiple benchmark datasets across various domains show improved imputation and forecasting performance of NCDSSM over existing models.

Motivation: Emerging drug-drug interaction (DDI) prediction is crucial for new drugs but is hindered by distribution changes between known and new drugs in real-world scenarios. Current evaluation often neglects these changes, relying on unrealistic i.i.d. split due to the absence of drug approval data. Results: We propose DDI-Ben, a benchmarking framework for emerging DDI prediction under distribution changes. DDI-Ben introduces a distribution change simulation framework that leverages distribution changes between drug sets as a surrogate for real-world distribution changes of DDIs, and is compatible with various drug split strategies. Through extensive benchmarking on ten representative methods, we show that most existing approaches suffer substantial performance degradation under distribution changes. Our analysis further indicates that large language model (LLM) based methods and the integration of drug-related textual information offer promising robustness against such degradation. To support future research, we release the benchmark datasets with simulated distribution changes. Overall, DDI-Ben highlights the importance of explicitly addressing distribution changes and provides a foundation for developing more resilient methods for emerging DDI prediction. Availability and implementation: Our code and data are available at https://github.com/LARS-research/DDI-Bench.

Alzheimer's Disease (AD) is marked by significant inter-individual variability in its progression, complicating accurate prognosis and personalized care planning. This heterogeneity underscores the critical need for predictive models capable of forecasting patient-specific disease trajectories. Artificial Intelligence (AI) offers powerful tools to address this challenge by analyzing complex, multi-modal, and longitudinal patient data. This paper provides a comprehensive survey of AI methodologies applied to personalized AD progression prediction. We review key approaches including state-space models for capturing temporal dynamics, deep learning techniques like Recurrent Neural Networks for sequence modeling, Graph Neural Networks (GNNs) for leveraging network structures, and the emerging concept of AI-driven digital twins for individualized simulation. Recognizing that data limitations often impede progress, we examine common challenges such as high dimensionality, missing data, and dataset imbalance. We further discuss AI-driven mitigation strategies, with a specific focus on synthetic data generation using Variational Autoencoders (VAEs) and Generative Adversarial Networks (GANs) to augment and balance datasets. The survey synthesizes the strengths and limitations of current approaches, emphasizing the trend towards multimodal integration and the persistent need for model interpretability and generalizability. Finally, we identify critical open challenges, including robust external validation, clinical integration, and ethical considerations, and outline promising future research directions such as hybrid models, causal inference, and federated learning. This review aims to consolidate current knowledge and guide future efforts in developing clinically relevant AI tools for personalized AD prognostication.

In lung radiotherapy, infrared cameras can track reflective objects on the chest to estimate tumor motion due to breathing, but treatment system latencies hinder radiation beam precision. Real-time recurrent learning (RTRL) is a potential solution that can learn patterns within non-stationary respiratory data but has high complexity. This study assesses the capabilities of resource-efficient online RNN algorithms, namely unbiased online recurrent optimization (UORO), sparse-1 step approximation (SnAp-1), and decoupled neural interfaces (DNI) to forecast respiratory motion during radiotherapy treatment accurately. We use time series containing the 3D positions of external markers on the chest of healthy subjects. We propose efficient implementations for SnAp-1 and DNI that compress the influence and immediate Jacobian matrices and accurately update the linear coefficients used in credit assignment estimation, respectively. Data was originally sampled at 10Hz; we resampled it at 3.33Hz and 30Hz to analyze the effect of the sampling rate on performance. We use UORO, SnAp-1, and DNI to forecast each marker's 3D position with horizons h<=2.1s (the time interval in advance for which the prediction is made) and compare them with RTRL, least mean squares, kernel support vector regression, and linear regression. RNNs trained online achieved similar or better accuracy than most previous works using larger training databases and deep learning, even though we used only the first minute of each sequence to predict motion within that exact sequence. SnAp-1 had the lowest normalized root mean square errors (nRMSEs) averaged over the horizon values considered, equal to 0.335 and 0.157, at 3.33Hz and 10.0Hz, respectively. Similarly, UORO had the lowest nRMSE at 30Hz, equal to 0.086. DNI's inference time (6.8ms per time step at 30Hz, Intel Core i7-13700 CPU) was the lowest among the RNN methods.

Dynamic Algorithm Configuration (DAC) aims to dynamically control a target algorithm's hyperparameters in order to improve its performance. Several theoretical and empirical results have demonstrated the benefits of dynamically controlling hyperparameters in domains like evolutionary computation, AI Planning or deep learning. Replicating these results, as well as studying new methods for DAC, however, is difficult since existing benchmarks are often specialized and incompatible with the same interfaces. To facilitate benchmarking and thus research on DAC, we propose DACBench, a benchmark library that seeks to collect and standardize existing DAC benchmarks from different AI domains, as well as provide a template for new ones. For the design of DACBench, we focused on important desiderata, such as (i) flexibility, (ii) reproducibility, (iii) extensibility and (iv) automatic documentation and visualization. To show the potential, broad applicability and challenges of DAC, we explore how a set of six initial benchmarks compare in several dimensions of difficulty.

Reinforcement learning (RL) tasks are typically framed as Markov Decision Processes (MDPs), assuming that decisions are made at fixed time intervals. However, many applications of great importance, including healthcare, do not satisfy this assumption, yet they are commonly modelled as MDPs after an artificial reshaping of the data. In addition, most healthcare (and similar) problems are offline by nature, allowing for only retrospective studies. To address both challenges, we begin by discussing the Semi-MDP (SMDP) framework, which formally handles actions of variable timings. We next present a formal way to apply SMDP modifications to nearly any given value-based offline RL method. We use this theory to introduce three SMDP-based offline RL algorithms, namely, SDQN, SDDQN, and SBCQ. We then experimentally demonstrate that only these SMDP-based algorithms learn the optimal policy in variable-time environments, whereas their MDP counterparts do not. Finally, we apply our new algorithms to a real-world offline dataset pertaining to warfarin dosing for stroke prevention and demonstrate similar results.

Throughout the different phases of a drug development program, randomized trials are used to establish the tolerability, safety, and efficacy of a candidate drug. At each stage one aims to optimize the design of future studies by extrapolation from the available evidence at the time. This includes collected trial data and relevant external data. However, relevant external data are typically available as averages only, for example from trials on alternative treatments reported in the literature. Here we report on such an example from a drug development for wet age-related macular degeneration. This disease is the leading cause of severe vision loss in the elderly. While current treatment options are efficacious, they are also a substantial burden for the patient. Hence, new treatments are under development which need to be compared against existing treatments. The general statistical problem this leads to is meta-analysis, which addresses the question of how we can combine datasets collected under different conditions. Bayesian methods have long been used to achieve partial pooling. Here we consider the challenge when the model of interest is complex (hierarchical and nonlinear) and one dataset is given as raw data while the second dataset is given as averages only. In such a situation, common meta-analytic methods can only be applied when the model is sufficiently simple for analytic approaches. When the model is too complex, for example nonlinear, an analytic approach is not possible. We provide a Bayesian solution by using simulation to approximately reconstruct the likelihood of the external summary and allowing the parameters in the model to vary under the different conditions. We first evaluate our approach using fake-data simulations and then report results for the drug development program that motivated this research.

Significant work has been recently dedicated to the stochastic delayed bandit setting because of its relevance in applications. The applicability of existing algorithms is however restricted by the fact that strong assumptions are often made on the delay distributions, such as full observability, restrictive shape constraints, or uniformity over arms. In this work, we weaken them significantly and only assume that there is a bound on the tail of the delay. In particular, we cover the important case where the delay distributions vary across arms, and the case where the delays are heavy-tailed. Addressing these difficulties, we propose a simple but efficient UCB-based algorithm called the PatientBandits. We provide both problems-dependent and problems-independent bounds on the regret as well as performance lower bounds.

Extracting causal relationships from observed correlations is a growing area in probabilistic reasoning, originating with the seminal work of Pearl and others from the early 1990s. This paper develops a new, categorically oriented view based on a clear distinction between syntax (string diagrams) and semantics (stochastic matrices), connected via interpretations as structure-preserving functors. A key notion in the identification of causal effects is that of an intervention, whereby a variable is forcefully set to a particular value independent of any prior propensities. We represent the effect of such an intervention as an endofunctor which performs `string diagram surgery' within the syntactic category of string diagrams. This diagram surgery in turn yields a new, interventional distribution via the interpretation functor. While in general there is no way to compute interventional distributions purely from observed data, we show that this is possible in certain special cases using a calculational tool called comb disintegration. We demonstrate the use of this technique on a well-known toy example, where we predict the causal effect of smoking on cancer in the presence of a confounding common cause. After developing this specific example, we show this technique provides simple sufficient conditions for computing interventions which apply to a wide variety of situations considered in the causal inference literature.

Time series research has gathered lots of interests in the last decade, especially for Time Series Classification (TSC) and Time Series Forecasting (TSF). Research in TSC has greatly benefited from the University of California Riverside and University of East Anglia (UCR/UEA) Time Series Archives. On the other hand, the advancement in Time Series Forecasting relies on time series forecasting competitions such as the Makridakis competitions, NN3 and NN5 Neural Network competitions, and a few Kaggle competitions. Each year, thousands of papers proposing new algorithms for TSC and TSF have utilized these benchmarking archives. These algorithms are designed for these specific problems, but may not be useful for tasks such as predicting the heart rate of a person using photoplethysmogram (PPG) and accelerometer data. We refer to this problem as Time Series Extrinsic Regression (TSER), where we are interested in a more general methodology of predicting a single continuous value, from univariate or multivariate time series. This prediction can be from the same time series or not directly related to the predictor time series and does not necessarily need to be a future value or depend heavily on recent values. To the best of our knowledge, research into TSER has received much less attention in the time series research community and there are no models developed for general time series extrinsic regression problems. Most models are developed for a specific problem. Therefore, we aim to motivate and support the research into TSER by introducing the first TSER benchmarking archive. This archive contains 19 datasets from different domains, with varying number of dimensions, unequal length dimensions, and missing values. In this paper, we introduce the datasets in this archive and did an initial benchmark on existing models.

Covariates provide valuable information on external factors that influence time series and are critical in many real-world time series forecasting tasks. For example, in retail, covariates may indicate promotions or peak dates such as holiday seasons that heavily influence demand forecasts. Recent advances in pretraining large language model architectures for time series forecasting have led to highly accurate forecasters. However, the majority of these models do not readily use covariates as they are often specific to a certain task or domain. This paper introduces a new method to incorporate covariates into pretrained time series forecasting models. Our proposed approach incorporates covariate information into pretrained forecasting models through modular blocks that inject past and future covariate information, without necessarily modifying the pretrained model in consideration. In order to evaluate our approach, we introduce a benchmark composed of 32 different synthetic datasets with varying dynamics to evaluate the effectivity of forecasting models with covariates. Extensive evaluations on both synthetic and real datasets show that our approach effectively incorporates covariate information into pretrained models, outperforming existing baselines.

The face is a rich source of information that can be utilized to infer a person's biological age, sex, phenotype, genetic defects, and health status. All of these factors are relevant for predicting an individual's remaining lifespan. In this study, we collected a dataset of over 24,000 images (from Wikidata/Wikipedia) of individuals who died of natural causes, along with the number of years between when the image was taken and when the person passed away. We made this dataset publicly available. We fine-tuned multiple Convolutional Neural Network (CNN) models on this data, at best achieving a mean absolute error of 8.3 years in the validation data using VGGFace. However, the model's performance diminishes when the person was younger at the time of the image. To demonstrate the potential applications of our remaining lifespan model, we present examples of using it to estimate the average loss of life (in years) due to the COVID-19 pandemic and to predict the increase in life expectancy that might result from a health intervention such as weight loss. Additionally, we discuss the ethical considerations associated with such models.

The acute phase of the Covid-19 pandemic has made apparent the need for decision support based upon accurate epidemic modeling. This process is substantially hampered by under-reporting of cases and related data incompleteness issues. In this article we adopt the Bayesian paradigm and synthesize publicly available data via a discrete-time stochastic epidemic modeling framework. The models allow for estimating the total number of infections while accounting for the endemic phase of the pandemic. We assess the prediction of the infection rate utilizing mobility information, notably the principal components of the mobility data. We evaluate variational Bayes in this context and find that Hamiltonian Monte Carlo offers a robust inference alternative for such models. We elaborate upon vector analysis of the epidemic dynamics, thus enriching the traditional tools used for decision making. In particular, we show how certain 2-dimensional plots on the phase plane may yield intuitive information regarding the speed and the type of transmission dynamics. We investigate the potential of a two-stage analysis as a consequence of cutting feedback, for inference on certain functionals of the model parameters. Finally, we show that a point mass on critical parameters is overly restrictive and investigate informative priors as a suitable alternative.

Survival prediction using whole slide images (WSIs) can be formulated as a multiple instance learning (MIL) problem. However, existing MIL methods often fail to explicitly capture pathological heterogeneity within WSIs, both globally -- through long-tailed morphological distributions, and locally through -- tile-level prediction uncertainty. Optimal transport (OT) provides a principled way of modeling such heterogeneity by incorporating marginal distribution constraints. Building on this insight, we propose OTSurv, a novel MIL framework from an optimal transport perspective. Specifically, OTSurv formulates survival predictions as a heterogeneity-aware OT problem with two constraints: (1) global long-tail constraint that models prior morphological distributions to avert both mode collapse and excessive uniformity by regulating transport mass allocation, and (2) local uncertainty-aware constraint that prioritizes high-confidence patches while suppressing noise by progressively raising the total transport mass. We then recast the initial OT problem, augmented by these constraints, into an unbalanced OT formulation that can be solved with an efficient, hardware-friendly matrix scaling algorithm. Empirically, OTSurv sets new state-of-the-art results across six popular benchmarks, achieving an absolute 3.6% improvement in average C-index. In addition, OTSurv achieves statistical significance in log-rank tests and offers high interpretability, making it a powerful tool for survival prediction in digital pathology. Our codes are available at https://github.com/Y-Research-SBU/OTSurv.

With significant advancements in diffusion models, addressing the potential risks of dataset bias becomes increasingly important. Since generated outputs directly suffer from dataset bias, mitigating latent bias becomes a key factor in improving sample quality and proportion. This paper proposes time-dependent importance reweighting to mitigate the bias for the diffusion models. We demonstrate that the time-dependent density ratio becomes more precise than previous approaches, thereby minimizing error propagation in generative learning. While directly applying it to score-matching is intractable, we discover that using the time-dependent density ratio both for reweighting and score correction can lead to a tractable form of the objective function to regenerate the unbiased data density. Furthermore, we theoretically establish a connection with traditional score-matching, and we demonstrate its convergence to an unbiased distribution. The experimental evidence supports the usefulness of the proposed method, which outperforms baselines including time-independent importance reweighting on CIFAR-10, CIFAR-100, FFHQ, and CelebA with various bias settings. Our code is available at https://github.com/alsdudrla10/TIW-DSM.

Background: Cancer remains one of the leading causes of morbidity and mortality worldwide. Comprehensive datasets that combine histopathological images with genetic and survival data across various tumour sites are essential for advancing computational pathology and personalised medicine. Results: We present SurGen, a dataset comprising 1,020 H&E-stained whole slide images (WSIs) from 843 colorectal cancer cases. The dataset includes detailed annotations for key genetic mutations (KRAS, NRAS, BRAF) and mismatch repair status, as well as survival data for 426 cases. To demonstrate SurGen's practical utility, we conducted a proof-of-concept machine learning experiment predicting mismatch repair status from the WSIs, achieving a test AUROC of 0.8316. These preliminary results underscore the dataset's potential to facilitate research in biomarker discovery, prognostic modelling, and advanced machine learning applications in colorectal cancer. Conclusions: SurGen offers a valuable resource for the scientific community, enabling studies that require high-quality WSIs linked with comprehensive clinical and genetic information on colorectal cancer. Our initial findings affirm the dataset's capacity to advance diagnostic precision and foster the development of personalised treatment strategies in colorectal oncology. Data available online at https://doi.org/10.6019/S-BIAD1285.

Integrating multi-modal clinical data, such as electronic health records (EHR) and chest X-ray images (CXR), is particularly beneficial for clinical prediction tasks. However, in a temporal setting, multi-modal data are often inherently asynchronous. EHR can be continuously collected but CXR is generally taken with a much longer interval due to its high cost and radiation dose. When clinical prediction is needed, the last available CXR image might have been outdated, leading to suboptimal predictions. To address this challenge, we propose DDL-CXR, a method that dynamically generates an up-to-date latent representation of the individualized CXR images. Our approach leverages latent diffusion models for patient-specific generation strategically conditioned on a previous CXR image and EHR time series, providing information regarding anatomical structures and disease progressions, respectively. In this way, the interaction across modalities could be better captured by the latent CXR generation process, ultimately improving the prediction performance. Experiments using MIMIC datasets show that the proposed model could effectively address asynchronicity in multimodal fusion and consistently outperform existing methods.

To effectively optimize and personalize treatments, it is necessary to investigate the heterogeneity of treatment effects. With the wide range of users being treated over many online controlled experiments, the typical approach of manually investigating each dimension of heterogeneity becomes overly cumbersome and prone to subjective human biases. We need an efficient way to search through thousands of experiments with hundreds of target covariates and hundreds of breakdown dimensions. In this paper, we propose a systematic paradigm for detecting, surfacing and characterizing heterogeneous treatment effects. First, we detect if treatment effect variation is present in an experiment, prior to specifying any breakdowns. Second, we surface the most relevant dimensions for heterogeneity. Finally, we characterize the heterogeneity beyond just the conditional average treatment effects (CATE) by studying the conditional distributions of the estimated individual treatment effects. We show the effectiveness of our methods using simulated data and empirical studies.