Daily Papers

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.

In longitudinal clinical practice, every chest X-ray is read in the context of the patients prior exam, and much of what the radiologist communicates is the change from one visit to the next. To the best of our knowledge, we present the first training-free best-of-N sampling scheme for pre-trained chest X-ray report generators that is explicitly aware of this longitudinal prior to current transition. We call it transition-aware best-of-N sampling, each report is split into sentences and embedded into an unordered set in Rd; each (prior, current) pair is reduced to a fixed-dim directional vector via a set-to-set distance designed to encode the change between the two sets; and candidates are scored by cosine distance from their candidate transition vector to a cached bank of ground-truth training transition vectors, aggregated as min or kNN. We instantiate the framework with four directional set distances (mean-shift, novelty residual, directed-Hausdorff anchor, and cost-weighted optimal transport) and evaluate on a multi-visit AP-PA cohort, running inference under three prompts on three vision-language generators. Transition-aware best-of-N outperforms random selection across the board, with the largest relative gains on the Impression section.

Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, predictive modeling of such data remains challenging due to high dimensionality, irregular sampling, and data sparsity. To address these issues, we propose ImageFlowNet, a novel model designed to forecast disease trajectories from initial images while preserving spatial details. ImageFlowNet first learns multiscale joint representation spaces across patients and time points, then optimizes deterministic or stochastic flow fields within these spaces using a position-parameterized neural ODE/SDE framework. The model leverages a UNet architecture to create robust multiscale representations and mitigates data scarcity by combining knowledge from all patients. We provide theoretical insights that support our formulation of ODEs, and motivate our regularizations involving high-level visual features, latent space organization, and trajectory smoothness. We validate ImageFlowNet on three longitudinal medical image datasets depicting progression in geographic atrophy, multiple sclerosis, and glioblastoma, demonstrating its ability to effectively forecast disease progression and outperform existing methods. Our contributions include the development of ImageFlowNet, its theoretical underpinnings, and empirical validation on real-world datasets. The official implementation is available at https://github.com/KrishnaswamyLab/ImageFlowNet.

Machine learning (ML)-based malware detection systems often fail to account for the dynamic nature of real-world training and test data distributions. In practice, these distributions evolve due to frequent changes in the Android ecosystem, adversarial development of new malware families, and the continuous emergence of both benign and malicious applications. Prior studies have shown that such concept drift -- distributional shifts in benign and malicious samples, leads to significant degradation in detection performance over time. Despite the practical importance of this issue, existing datasets are often outdated and limited in temporal scope, diversity of malware families, and sample scale, making them insufficient for the systematic evaluation of concept drift in malware detection. To address this gap, we present LAMDA, the largest and most temporally diverse Android malware benchmark to date, designed specifically for concept drift analysis. LAMDA spans 12 years (2013-2025, excluding 2015), includes over 1 million samples (approximately 37% labeled as malware), and covers 1,380 malware families and 150,000 singleton samples, reflecting the natural distribution and evolution of real-world Android applications. We empirically demonstrate LAMDA's utility by quantifying the performance degradation of standard ML models over time and analyzing feature stability across years. As the most comprehensive Android malware dataset to date, LAMDA enables in-depth research into temporal drift, generalization, explainability, and evolving detection challenges. The dataset and code are available at: https://iqsec-lab.github.io/LAMDA/.

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

Tracking tumor lesions across serial CT scans is essential for oncological response assessment. Existing automated methods face a fundamental trade-off: end-to-end trackers achieve high automation but offer no opportunity to correct silent tracking failures, while decoupled registration-segmentation pipelines permit user verification yet discard the lesion's prior appearance, limiting accuracy in ambiguous cases. In this work, we propose a Verified Tracking paradigm: a clinician verifies a registration-proposed prompt, which the model leverages alongside the baseline lesion appearance to resolve segmentation ambiguities. We present a unified framework combining early spatial prompt fusion with latent temporal difference weighting for longitudinally-informed segmentation. To address data scarcity, we leverage large-scale synthetic pretraining, proving essential for exploiting longitudinal context, improving performance by up to 4.5 Dice points over training from scratch. Our approach secured first place in the MICCAI autoPET IV challenge. We further curate and release PanTrack, a new longitudinal pancreatic cancer benchmark, to assess out-of-distribution generalization. Experiments show that our model outperforms prior work in both fully automatic and the proposed verified tracking setting offering a clinically safe middle ground between automation and control. Code, model and dataset will be released at https://github.com/MIC-DKFZ/LongiSeg

Synthetic data is increasingly used to enable the development and evaluation of AI systems in domains where access to real-world data is restricted. In healthcare, clinical documentation presents particular challenges due to its sensitivity. This work introduces a synthetic clinical notes pipeline and dataset designed to support the development of clinical AI tools while avoiding the privacy risks associated with real patient data. The dataset is generated using a modular pipeline that combines structured patient generation, semi-structured patient journey simulation, and unstructured clinical note generation using large language models. The pipeline is designed to prioritise internal consistency across longitudinal patient records, while also capturing variation in writing style, note structure, and clinical detail. Additional mechanisms, including LLM-based validation and augmentation steps, are used to improve faithfulness, realism, and diversity of the generated notes. We release a dataset of 70 synthetic patients, each associated with 20-50 clinical notes spanning a full hospital journey. The dataset is provided at multiple levels of validation, enabling users to balance realism and scalability depending on their use case. This dataset supports the development, testing, and evaluation of clinical AI systems, including summarisation tools, coding models, and decision support systems, without reliance on real patient data.

We present Agent-to-Sim (ATS), a framework for learning interactive behavior models of 3D agents from casual longitudinal video collections. Different from prior works that rely on marker-based tracking and multiview cameras, ATS learns natural behaviors of animal and human agents non-invasively through video observations recorded over a long time-span (e.g., a month) in a single environment. Modeling 3D behavior of an agent requires persistent 3D tracking (e.g., knowing which point corresponds to which) over a long time period. To obtain such data, we develop a coarse-to-fine registration method that tracks the agent and the camera over time through a canonical 3D space, resulting in a complete and persistent spacetime 4D representation. We then train a generative model of agent behaviors using paired data of perception and motion of an agent queried from the 4D reconstruction. ATS enables real-to-sim transfer from video recordings of an agent to an interactive behavior simulator. We demonstrate results on pets (e.g., cat, dog, bunny) and human given monocular RGBD videos captured by a smartphone.

Recent research has demonstrated the capability of behavior signals captured by smartphones and wearables for longitudinal behavior modeling. However, there is a lack of a comprehensive public dataset that serves as an open testbed for fair comparison among algorithms. Moreover, prior studies mainly evaluate algorithms using data from a single population within a short period, without measuring the cross-dataset generalizability of these algorithms. We present the first multi-year passive sensing datasets, containing over 700 user-years and 497 unique users' data collected from mobile and wearable sensors, together with a wide range of well-being metrics. Our datasets can support multiple cross-dataset evaluations of behavior modeling algorithms' generalizability across different users and years. As a starting point, we provide the benchmark results of 18 algorithms on the task of depression detection. Our results indicate that both prior depression detection algorithms and domain generalization techniques show potential but need further research to achieve adequate cross-dataset generalizability. We envision our multi-year datasets can support the ML community in developing generalizable longitudinal behavior modeling algorithms.

We present a large longitudinal dataset of tweets from two sets of users that are suspected to be affiliated with ISIS. These sets of users are identified based on a prior study and a campaign aimed at shutting down ISIS Twitter accounts. These users have engaged with known ISIS accounts at least once during 2014-2015 and are still active as of 2021. Some of them have directly supported the ISIS users and their tweets by retweeting them, and some of the users that have quoted tweets of ISIS, have uncertain connections to ISIS seed accounts. This study and the dataset represent a unique approach to analyzing ISIS data. Although much research exists on ISIS online activities, few studies have focused on individual accounts. Our approach to validating accounts as well as developing a framework for differentiating accounts' functionality (e.g., propaganda versus operational planning) offers a foundation for future research. We perform some descriptive statistics and preliminary analyses on our collected data to provide deeper insight and highlight the significance and practicality of such analyses. We further discuss several cross-disciplinary potential use cases and research directions.

Cancer screening is a reasoning task. A radiologist observes findings, compares them to prior scans, integrates clinical context, and reaches a diagnostic conclusion confirmed by pathology. We present RadThinking, a Visual Question Answering (VQA) dataset that makes this reasoning explicit and trainable. RadThinking releases VQA pairs at three difficulty tiers. Foundation VQAs are atomic perception questions. Single-step reasoning VQAs apply one clinical rule. Compositional VQAs require multi-step chain-of-thought to reach a guideline category such as LI-RADS-5. For every compositional VQA, we release the chain of foundation VQAs that solves it. The chain follows the rules of the governing clinical reporting standard. The dataset spans 20,362 CT scans from 9,131 patients across 43 cancer groups, plus 2,077 verified healthy controls with >1-year follow-up. To our knowledge, RadThinking is the first cancer-screening VQA corpus that stratifies questions by reasoning depth and grounds compositions in clinical reporting standards. The foundation tier supplies atomic perception supervision. The compositional tier supplies chain-of-thought data and verifiable rewards for reinforcement-learning recipes such as DeepSeek-R1 and OpenAI o1. RadThinking enables systematic training and evaluation of whether AI systems can reason about cancer, not merely detect it.

Automated radiology report generation offers an effective solution to alleviate radiologists' workload. However, most existing methods focus primarily on single or fixed-view images to model current disease conditions, which limits diagnostic accuracy and overlooks disease progression. Although some approaches utilize longitudinal data to track disease progression, they still rely on single images to analyze current visits. To address these issues, we propose enhanced contrastive learning with Multi-view Longitudinal data to facilitate chest X-ray Report Generation, named MLRG. Specifically, we introduce a multi-view longitudinal contrastive learning method that integrates spatial information from current multi-view images and temporal information from longitudinal data. This method also utilizes the inherent spatiotemporal information of radiology reports to supervise the pre-training of visual and textual representations. Subsequently, we present a tokenized absence encoding technique to flexibly handle missing patient-specific prior knowledge, allowing the model to produce more accurate radiology reports based on available prior knowledge. Extensive experiments on MIMIC-CXR, MIMIC-ABN, and Two-view CXR datasets demonstrate that our MLRG outperforms recent state-of-the-art methods, achieving a 2.3% BLEU-4 improvement on MIMIC-CXR, a 5.5% F1 score improvement on MIMIC-ABN, and a 2.7% F1 RadGraph improvement on Two-view CXR.

In this work, we introduce Brain Latent Progression (BrLP), a novel spatiotemporal disease progression model based on latent diffusion. BrLP is designed to predict the evolution of diseases at the individual level on 3D brain MRIs. Existing deep generative models developed for this task are primarily data-driven and face challenges in learning disease progressions. BrLP addresses these challenges by incorporating prior knowledge from disease models to enhance the accuracy of predictions. To implement this, we propose to integrate an auxiliary model that infers volumetric changes in various brain regions. Additionally, we introduce Latent Average Stabilization (LAS), a novel technique to improve spatiotemporal consistency of the predicted progression. BrLP is trained and evaluated on a large dataset comprising 11,730 T1-weighted brain MRIs from 2,805 subjects, collected from three publicly available, longitudinal Alzheimer's Disease (AD) studies. In our experiments, we compare the MRI scans generated by BrLP with the actual follow-up MRIs available from the subjects, in both cross-sectional and longitudinal settings. BrLP demonstrates significant improvements over existing methods, with an increase of 22% in volumetric accuracy across AD-related brain regions and 43% in image similarity to the ground-truth scans. The ability of BrLP to generate conditioned 3D scans at the subject level, along with the novelty of integrating prior knowledge to enhance accuracy, represents a significant advancement in disease progression modeling, opening new avenues for precision medicine. The code of BrLP is available at the following link: https://github.com/LemuelPuglisi/BrLP.

Climate-vulnerable road networks require a paradigm shift from reactive, fix-on-failure repairs to predictive, decision-ready maintenance. This paper introduces ST-ResGAT, a novel Spatio-Temporal Residual Graph Attention Network that fuses residual graph-attention encoding with GRU temporal aggregation to forecast pavement deterioration. Engineered for resource-constrained deployment, the framework translates continuous Pavement Condition Index (PCI) forecasts directly into the American Society for Testing and Materials (ASTM)-compliant maintenance priorities. Using a real-world inspection dataset of 750 segments in Sylhet, Bangladesh (2021-2024), ST-ResGAT significantly outperforms traditional non-spatial machine learning baselines, achieving exceptional predictive fidelity (R2 = 0.93, RMSE = 2.72). Crucially, ablation testing confirmed the mathematical necessity of modeling topological neighbor effects, proving that structural decay acts as a spatial contagion. Uniquely, we integrate GNNExplainer to unbox the model, demonstrating that its learned priorities align perfectly with established physical engineering theory. Furthermore, we quantify classification safety: achieving 85.5% exact ASTM class agreement and 100% adjacent-class containment, ensuring bounded, engineer-safe predictions. To connect model outputs to policy, we generate localized longitudinal maintenance profiles, perform climate stress-testing, and derive Pareto sustainability frontiers. ST-ResGAT therefore offers a practical, explainable, and sustainable blueprint for intelligent infrastructure management in high-risk, low-resource geological settings.

Large Language Models (LLMs) have led to significant improvements in many tasks across various domains, such as code interpretation, response generation, and ambiguity handling. These LLMs, however, when upgrading, primarily prioritize enhancing user experience while neglecting security, privacy, and safety implications. Consequently, unintended vulnerabilities or biases can be introduced. Previous studies have predominantly focused on specific versions of the models and disregard the potential emergence of new attack vectors targeting the updated versions. Through the lens of adversarial examples within the in-context learning framework, this longitudinal study addresses this gap by conducting a comprehensive assessment of the robustness of successive versions of LLMs, vis-\`a-vis GPT-3.5. We conduct extensive experiments to analyze and understand the impact of the robustness in two distinct learning categories: zero-shot learning and few-shot learning. Our findings indicate that, in comparison to earlier versions of LLMs, the updated versions do not exhibit the anticipated level of robustness against adversarial attacks. In addition, our study emphasizes the increased effectiveness of synergized adversarial queries in most zero-shot learning and few-shot learning cases. We hope that our study can lead to a more refined assessment of the robustness of LLMs over time and provide valuable insights of these models for both developers and users.

There has been a surge of interest in assistive wearable agents: agents embodied in wearable form factors (e.g., smart glasses) who take assistive actions toward a user's goal/query (e.g. "Where did I leave my keys?"). In this work, we consider the important complementary problem of inferring that goal from multi-modal contextual observations. Solving this "goal inference" problem holds the promise of eliminating the effort needed to interact with such an agent. This work focuses on creating WAGIBench, a strong benchmark to measure progress in solving this problem using vision-language models (VLMs). Given the limited prior work in this area, we collected a novel dataset comprising 29 hours of multimodal data from 348 participants across 3,477 recordings, featuring ground-truth goals alongside accompanying visual, audio, digital, and longitudinal contextual observations. We validate that human performance exceeds model performance, achieving 93% multiple-choice accuracy compared with 84% for the best-performing VLM. Generative benchmark results that evaluate several families of modern vision-language models show that larger models perform significantly better on the task, yet remain far from practical usefulness, as they produce relevant goals only 55% of the time. Through a modality ablation, we show that models benefit from extra information in relevant modalities with minimal performance degradation from irrelevant modalities.

Large Language Models (LLMs) have shown strong promise for mining Electronic Health Records (EHRs) by reasoning over longitudinal clinical information to capture context-rich patient trajectories. However, leveraging LLMs for structured EHRs (e.g., standardized diagnosis and medication codes) presents two key challenges. First, translating time-stamped EHR sequences into plain text can obscure both temporal structure and code identities, weakening the ability to capture code co-occurrence and longitudinal regularities. Second, unlike cohort-trained predictive models that learn a shared, task-aligned representation space across patients, LLMs are often applied in a case-isolated inference setting where each patient is processed independently without leveraging population-level patterns. To address these challenges, we introduce RePrompT, a time-aware LLM framework that integrates structured EHR encoders through prompt tuning, without modifying underlying architectures. Specifically, RePrompT recurrently incorporates latent states from prior visits to preserve longitudinal information, and injects population-level information through trainable prompt tokens derived from a cohort-trained, task-aligned EHR encoder. Experiments on MIMIC-III and MIMIC-IV demonstrate that RePrompT consistently outperforms both EHR-based and LLM-based baselines across multiple clinical prediction tasks.

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.

The growing availability of longitudinal Magnetic Resonance Imaging (MRI) datasets has facilitated Artificial Intelligence (AI)-driven modeling of disease progression, making it possible to predict future medical scans for individual patients. However, despite significant advancements in AI, current methods continue to face challenges including achieving patient-specific individualization, ensuring spatiotemporal consistency, efficiently utilizing longitudinal data, and managing the substantial memory demands of 3D scans. To address these challenges, we propose Brain Latent Progression (BrLP), a novel spatiotemporal model designed to predict individual-level disease progression in 3D brain MRIs. The key contributions in BrLP are fourfold: (i) it operates in a small latent space, mitigating the computational challenges posed by high-dimensional imaging data; (ii) it explicitly integrates subject metadata to enhance the individualization of predictions; (iii) it incorporates prior knowledge of disease dynamics through an auxiliary model, facilitating the integration of longitudinal data; and (iv) it introduces the Latent Average Stabilization (LAS) algorithm, which (a) enforces spatiotemporal consistency in the predicted progression at inference time and (b) allows us to derive a measure of the uncertainty for the prediction at the global and voxel level. We train and evaluate BrLP on 11,730 T1-weighted (T1w) brain MRIs from 2,805 subjects and validate its generalizability on an external test set comprising 2,257 MRIs from 962 subjects. Our experiments compare BrLP-generated MRI scans with real follow-up MRIs, demonstrating state-of-the-art accuracy compared to existing methods. The code is publicly available at: https://github.com/LemuelPuglisi/BrLP.

Researchers are usually interested in examining the impact of covariates when separating heterogeneous samples into latent classes that are more homogeneous. The majority of theoretical and empirical studies with such aims have focused on identifying covariates as predictors of class membership in the structural equation modeling framework. In other words, the covariates only indirectly affect the sample heterogeneity. However, the covariates' influence on between-individual differences can also be direct. This article presents a mixture model that investigates covariates to explain within-cluster and between-cluster heterogeneity simultaneously, known as a mixture-of-experts (MoE) model. This study aims to extend the MoE framework to investigate heterogeneity in nonlinear trajectories: to identify latent classes, covariates as predictors to clusters, and covariates that explain within-cluster differences in change patterns over time. Our simulation studies demonstrate that the proposed model generally estimates the parameters unbiasedly, precisely and exhibits appropriate empirical coverage for a nominal 95% confidence interval. This study also proposes implementing structural equation model forests to shrink the covariate space of the proposed mixture model. We illustrate how to select covariates and construct the proposed model with longitudinal mathematics achievement data. Additionally, we demonstrate that the proposed mixture model can be further extended in the structural equation modeling framework by allowing the covariates that have direct effects to be time-varying.

Longitudinal modelling of Alzheimer's disease progression is clinically useful only if it can describe not just the most likely next diagnosis, but how a patient may evolve over time and how reliable that forecast is. Most deep learning approaches reduce this problem to single-step classification, treating cognitively normal, mild cognitive impairment, and dementia as flat categories while providing limited insight into how uncertainty accumulates across future visits. We propose a probabilistic framework that combines ordinal diagnosis prediction, multi-horizon trajectory generation, and decomposed uncertainty estimation. A Temporal Fusion Transformer encoder is adapted with a CORAL ordinal output layer, asymmetric loss weighting, and converter oversampling to respect disease-stage ordering and improve sensitivity to MCI-to-dementia transitions. Conditioned on the learned patient-context representation, an autoregressive Mixture Density Network generates five-year probabilistic trajectories for diagnosis state, CDR Sum of Boxes, MMSE orientation, and hippocampal volume. On ADNI, the model outperforms linear, recurrent, and transformer baselines for next-visit diagnosis prediction, with the strongest gains on MCI-versus-dementia discrimination. Generated trajectories achieve near-nominal 90% credible interval coverage, widening uncertainty across the forecast horizon, and biomarker dynamics consistent with expected Alzheimer's disease progression. We further separate aleatoric from epistemic uncertainty using analytic mixture variance and a five-member bootstrap ensemble, which provides the strongest encoder diversity and output-level epistemic signal. Epistemic uncertainty is higher for rare progression archetypes, MCI and dementia patients, and under external evaluation on OASIS-3, where it increases alongside prediction error.

We propose a computationally efficient inferential procedure for longitudinal function-on-function regression. The method follows a marginal three-step approach: (1) fit massive pointwise longitudinal scalar-on-function regression models, (2) smooth the resulting estimates along the bivariate functional domain, and (3) compute confidence bands using either an analytic approach for Gaussian data or a cluster bootstrap for Gaussian or non-Gaussian data. Simulation studies demonstrate that the proposed method achieves accurate estimation and valid inference, while substantially reducing computational burden compared to existing approaches. Methods are motivated by a physical activity intervention trial in older adults where high-dimensional wearable data were collected longitudinally across multiple visits. Our applications reveal significant increases in physical activity in the morning using interpersonal intervention strategies, but not intrapersonal strategies. The proposed methods are implemented in an R package.

Prior-data fitted networks (PFNs) have emerged as powerful foundation models for tabular causal inference, yet their extension to time series remains limited by the absence of synthetic data generators that provide interventional targets. Existing time series benchmarks generate observational data with ground-truth causal graphs but lack the interventional data required for training causal foundation models. To address this, we propose CausalTimePrior, a principled framework for generating synthetic temporal structural causal models (TSCMs) with paired observational and interventional time series. Our prior supports configurable causal graph structures, nonlinear autoregressive mechanisms, regime-switching dynamics, and multiple intervention types (hard, soft, time-varying). We demonstrate that PFNs trained on CausalTimePrior can perform in-context causal effect estimation on held-out TSCMs, establishing a pathway toward foundation models for time series causal inference.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Epidemiologists often wish to estimate quantities that are easy to communicate and correspond to the results of realistic public health scenarios. Methods from causal inference can answer these questions. We adopt the language of potential outcomes under Rubin's original Bayesian framework and show that the parametric g-formula is easily amenable to a Bayesian approach. We show that the frequentist properties of the Bayesian g-formula suggest it improves the accuracy of estimates of causal effects in small samples or when data may be sparse. We demonstrate our approach to estimate the effect of environmental tobacco smoke on body mass index z-scores among children aged 4-9 years who were enrolled in a longitudinal birth cohort in New York, USA. We give a general algorithm and supply SAS and Stan code that can be adopted to implement our computational approach in both time-fixed and longitudinal data.

Sequential Bayesian inference can be used for continual learning to prevent catastrophic forgetting of past tasks and provide an informative prior when learning new tasks. We revisit sequential Bayesian inference and test whether having access to the true posterior is guaranteed to prevent catastrophic forgetting in Bayesian neural networks. To do this we perform sequential Bayesian inference using Hamiltonian Monte Carlo. We propagate the posterior as a prior for new tasks by fitting a density estimator on Hamiltonian Monte Carlo samples. We find that this approach fails to prevent catastrophic forgetting demonstrating the difficulty in performing sequential Bayesian inference in neural networks. From there we study simple analytical examples of sequential Bayesian inference and CL and highlight the issue of model misspecification which can lead to sub-optimal continual learning performance despite exact inference. Furthermore, we discuss how task data imbalances can cause forgetting. From these limitations, we argue that we need probabilistic models of the continual learning generative process rather than relying on sequential Bayesian inference over Bayesian neural network weights. In this vein, we also propose a simple baseline called Prototypical Bayesian Continual Learning, which is competitive with state-of-the-art Bayesian continual learning methods on class incremental continual learning vision benchmarks.

Priors are essential for reconstructing images from noisy and/or incomplete measurements. The choice of the prior determines both the quality and uncertainty of recovered images. We propose turning score-based diffusion models into principled image priors ("score-based priors") for analyzing a posterior of images given measurements. Previously, probabilistic priors were limited to handcrafted regularizers and simple distributions. In this work, we empirically validate the theoretically-proven probability function of a score-based diffusion model. We show how to sample from resulting posteriors by using this probability function for variational inference. Our results, including experiments on denoising, deblurring, and interferometric imaging, suggest that score-based priors enable principled inference with a sophisticated, data-driven image prior.

Brain tissue segmentation is essential for neuroscience and clinical studies. However, segmentation on longitudinal data is challenging due to dynamic brain changes across the lifespan. Previous researches mainly focus on self-supervision with regularizations and will lose longitudinal generalization when fine-tuning on a specific age group. In this paper, we propose a dual meta-learning paradigm to learn longitudinally consistent representations and persist when fine-tuning. Specifically, we learn a plug-and-play feature extractor to extract longitudinal-consistent anatomical representations by meta-feature learning and a well-initialized task head for fine-tuning by meta-initialization learning. Besides, two class-aware regularizations are proposed to encourage longitudinal consistency. Experimental results on the iSeg2019 and ADNI datasets demonstrate the effectiveness of our method. Our code is available at https://github.com/ladderlab-xjtu/DuMeta.

Powerful priors allow us to perform inference with insufficient information. In this paper, we propose an autoregressive prior for 3D shapes to solve multimodal 3D tasks such as shape completion, reconstruction, and generation. We model the distribution over 3D shapes as a non-sequential autoregressive distribution over a discretized, low-dimensional, symbolic grid-like latent representation of 3D shapes. This enables us to represent distributions over 3D shapes conditioned on information from an arbitrary set of spatially anchored query locations and thus perform shape completion in such arbitrary settings (e.g., generating a complete chair given only a view of the back leg). We also show that the learned autoregressive prior can be leveraged for conditional tasks such as single-view reconstruction and language-based generation. This is achieved by learning task-specific naive conditionals which can be approximated by light-weight models trained on minimal paired data. We validate the effectiveness of the proposed method using both quantitative and qualitative evaluation and show that the proposed method outperforms the specialized state-of-the-art methods trained for individual tasks. The project page with code and video visualizations can be found at https://yccyenchicheng.github.io/AutoSDF/.

Clinicians trace cephalometric radiographs following a structured anatomical workflow, yet no prior system encodes this into computation. We present a five-phase anatomy-guided pipeline producing confidence-weighted spatial priors that shape HRNet-W32 training, achieving 1.04 mm mean radial error on 25 landmarks across 1,502 radiographs from 7+ imaging devices. A training x inference prior matrix isolates the mechanism: anatomical priors maintain a 1% validation-to-test gap versus 88% without priors (1.94 mm), despite identical validation convergence. The matrix establishes that all trained models are inference-independent, the expanded architecture alone provides no benefit, random priors yield partial but unstable improvement (1.72 mm), and only image-specific anatomically correct priors produce the 1.04 mm result -- functioning as a training-time regularizer requiring no automated prior generation at deployment. Five-fold cross-validation (p=0.0015), patient-level permutation testing (p<0.0001, n=151), quantified Grad-CAM analysis (88% vs. 74% in-zone activation, p<0.001), and clinical measurement validation (skeletal classification kappa=0.79-0.84, zero Class II<->III reversals, ICC>0.95) provide converging evidence. Cross-domain experiments on echocardiography, cervical spine, and hand radiography support the hypothesis that prior effectiveness scales with the spatial entropy of the landmark distribution.

Structured variational autoencoders (SVAEs) combine probabilistic graphical model priors on latent variables, deep neural networks to link latent variables to observed data, and structure-exploiting algorithms for approximate posterior inference. These models are particularly appealing for sequential data, where the prior can capture temporal dependencies. However, despite their conceptual elegance, SVAEs have proven difficult to implement, and more general approaches have been favored in practice. Here, we revisit SVAEs using modern machine learning tools and demonstrate their advantages over more general alternatives in terms of both accuracy and efficiency. First, we develop a modern implementation for hardware acceleration, parallelization, and automatic differentiation of the message passing algorithms at the core of the SVAE. Second, we show that by exploiting structure in the prior, the SVAE learns more accurate models and posterior distributions, which translate into improved performance on prediction tasks. Third, we show how the SVAE can naturally handle missing data, and we leverage this ability to develop a novel, self-supervised training approach. Altogether, these results show that the time is ripe to revisit structured variational autoencoders.

Most bandit algorithms assume that the reward variances or their upper bounds are known, and that they are the same for all arms. This naturally leads to suboptimal performance and higher regret due to variance overestimation. On the other hand, underestimated reward variances may lead to linear regret due to committing early to a suboptimal arm. This motivated prior works on variance-adaptive frequentist algorithms, which have strong instance-dependent regret bounds but cannot incorporate prior knowledge on reward variances. We lay foundations for the Bayesian setting, which incorporates prior knowledge. This results in lower regret in practice, due to using the prior in the algorithm design, and also improved regret guarantees. Specifically, we study Gaussian bandits with {unknown heterogeneous reward variances}, and develop a Thompson sampling algorithm with prior-dependent Bayes regret bounds. We achieve lower regret with lower reward variances and more informative priors on them, which is precisely why we pay only for what is uncertain. This is the first result of its kind. Finally, we corroborate our theory with extensive experiments, which show the superiority of our variance-adaptive Bayesian algorithm over prior frequentist approaches. We also show that our approach is robust to model misspecification and can be applied with estimated priors.

Denoising diffusion probabilistic models have been recently proposed to generate high-quality samples by estimating the gradient of the data density. The framework defines the prior noise as a standard Gaussian distribution, whereas the corresponding data distribution may be more complicated than the standard Gaussian distribution, which potentially introduces inefficiency in denoising the prior noise into the data sample because of the discrepancy between the data and the prior. In this paper, we propose PriorGrad to improve the efficiency of the conditional diffusion model for speech synthesis (for example, a vocoder using a mel-spectrogram as the condition) by applying an adaptive prior derived from the data statistics based on the conditional information. We formulate the training and sampling procedures of PriorGrad and demonstrate the advantages of an adaptive prior through a theoretical analysis. Focusing on the speech synthesis domain, we consider the recently proposed diffusion-based speech generative models based on both the spectral and time domains and show that PriorGrad achieves faster convergence and inference with superior performance, leading to an improved perceptual quality and robustness to a smaller network capacity, and thereby demonstrating the efficiency of a data-dependent adaptive prior.

Posterior sampling allows the exploitation of prior knowledge of the environment's transition dynamics to improve the sample efficiency of reinforcement learning. The prior is typically specified as a class of parametric distributions, a task that can be cumbersome in practice, often resulting in the choice of uninformative priors. In this work, we propose a novel posterior sampling approach in which the prior is given as a (partial) causal graph over the environment's variables. The latter is often more natural to design, such as listing known causal dependencies between biometric features in a medical treatment study. Specifically, we propose a hierarchical Bayesian procedure, called C-PSRL, simultaneously learning the full causal graph at the higher level and the parameters of the resulting factored dynamics at the lower level. For this procedure, we provide an analysis of its Bayesian regret, which explicitly connects the regret rate with the degree of prior knowledge. Our numerical evaluation conducted in illustrative domains confirms that C-PSRL strongly improves the efficiency of posterior sampling with an uninformative prior while performing close to posterior sampling with the full causal graph.

In this paper we develop a dynamic form of Bayesian optimization for machine learning models with the goal of rapidly finding good hyperparameter settings. Our method uses the partial information gained during the training of a machine learning model in order to decide whether to pause training and start a new model, or resume the training of a previously-considered model. We specifically tailor our method to machine learning problems by developing a novel positive-definite covariance kernel to capture a variety of training curves. Furthermore, we develop a Gaussian process prior that scales gracefully with additional temporal observations. Finally, we provide an information-theoretic framework to automate the decision process. Experiments on several common machine learning models show that our approach is extremely effective in practice.

Chest Xray imaging is a widely used diagnostic tool in modern medicine, and its high utilization creates substantial workloads for radiologists. To alleviate this burden, vision language models are increasingly applied to automate Chest Xray radiology report generation (CXRRRG), aiming for clinically accurate descriptions while reducing manual effort. Conventional approaches, however, typically rely on single images, failing to capture the longitudinal context necessary for producing clinically faithful comparison statements. Recently, growing attention has been directed toward incorporating longitudinal data into CXR RRG, enabling models to leverage historical studies in ways that mirror radiologists diagnostic workflows. Nevertheless, existing surveys primarily address single image CXRRRG and offer limited guidance for longitudinal settings, leaving researchers without a systematic framework for model design. To address this gap, this survey provides the first comprehensive review of longitudinal radiology report generation (LRRG). Specifically, we examine dataset construction strategies, report generation architectures alongside longitudinally tailored designs, and evaluation protocols encompassing both longitudinal specific measures and widely used benchmarks. We further summarize LRRG methods performance, alongside analyses of different ablation studies, which collectively highlight the critical role of longitudinal information and architectural design choices in improving model performance. Finally, we summarize five major limitations of current research and outline promising directions for future development, aiming to lay a foundation for advancing this emerging field.

Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine learning framework based on multi-mean Gaussian processes (GPs), accounting for individual and gene correlations across time. This method provides future predictions of DNA methylation status at different individual ages while accounting for uncertainty. Our model is trained on a birth cohort of children with methylation profiled at ages 0-4, and we demonstrated that the status of methylation sites for each child can be accurately predicted at ages 5-7. We show that methylation profiles predicted by multi-mean GPs can be used to estimate other phenotypes, such as epigenetic age, and enable comparison to other health measures of interest. This approach encourages epigenetic studies to move towards longitudinal design for investigating epigenetic changes during development, ageing and disease progression.

Accurate segmentation of Multiple Sclerosis (MS) lesions in longitudinal MRI scans is crucial for monitoring disease progression and treatment efficacy. Although changes across time are taken into account when assessing images in clinical practice, most existing deep learning methods treat scans from different timepoints separately. Among studies utilizing longitudinal images, a simple channel-wise concatenation is the primary albeit suboptimal method employed to integrate timepoints. We introduce a novel approach that explicitly incorporates temporal differences between baseline and follow-up scans through a unique architectural inductive bias called Difference Weighting Block. It merges features from two timepoints, emphasizing changes between scans. We achieve superior scores in lesion segmentation (Dice Score, Hausdorff distance) as well as lesion detection (lesion-level F_1 score) as compared to state-of-the-art longitudinal and single timepoint models across two datasets. Our code is made publicly available at www.github.com/MIC-DKFZ/Longitudinal-Difference-Weighting.

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.

Sequential learning with Gaussian processes (GPs) is challenging when access to past data is limited, for example, in continual and active learning. In such cases, errors can accumulate over time due to inaccuracies in the posterior, hyperparameters, and inducing points, making accurate learning challenging. Here, we present a method to keep all such errors in check using the recently proposed dual sparse variational GP. Our method enables accurate inference for generic likelihoods and improves learning by actively building and updating a memory of past data. We demonstrate its effectiveness in several applications involving Bayesian optimization, active learning, and continual learning.

The Bayesian treatment of neural networks dictates that a prior distribution is specified over their weight and bias parameters. This poses a challenge because modern neural networks are characterized by a large number of parameters, and the choice of these priors has an uncontrolled effect on the induced functional prior, which is the distribution of the functions obtained by sampling the parameters from their prior distribution. We argue that this is a hugely limiting aspect of Bayesian deep learning, and this work tackles this limitation in a practical and effective way. Our proposal is to reason in terms of functional priors, which are easier to elicit, and to "tune" the priors of neural network parameters in a way that they reflect such functional priors. Gaussian processes offer a rigorous framework to define prior distributions over functions, and we propose a novel and robust framework to match their prior with the functional prior of neural networks based on the minimization of their Wasserstein distance. We provide vast experimental evidence that coupling these priors with scalable Markov chain Monte Carlo sampling offers systematically large performance improvements over alternative choices of priors and state-of-the-art approximate Bayesian deep learning approaches. We consider this work a considerable step in the direction of making the long-standing challenge of carrying out a fully Bayesian treatment of neural networks, including convolutional neural networks, a concrete possibility.

Longitudinal health agents must reason across multi-source trajectories that combine continuous device streams, sparse clinical exams, and episodic life events - yet evaluating them is hard: real-world data cannot be released at scale, and temporally grounded attribution questions seldom admit definitive answers without structured ground truth. We present ESL-Bench, an event-driven synthesis framework and benchmark providing 100 synthetic users, each with a 1-5 year trajectory comprising a health profile, a multi-phase narrative plan, daily device measurements, periodic exam records, and an event log with explicit per-indicator impact parameters. Each indicator follows a baseline stochastic process driven by discrete events with sigmoid-onset, exponential-decay kernels under saturation and projection constraints; a hybrid pipeline delegates sparse semantic artifacts to LLM-based planning and dense indicator dynamics to algorithmic simulation with hard physiological bounds. Users are each paired with 100 evaluation queries across five dimensions - Lookup, Trend, Comparison, Anomaly, Explanation - stratified into Easy, Medium, and Hard tiers, with all ground-truth answers programmatically computable from the recorded event-indicator relationships. Evaluating 13 methods spanning LLMs with tools, DB-native agents, and memory-augmented RAG, we find that DB agents (48-58%) substantially outperform memory RAG baselines (30-38%), with the gap concentrated on Comparison and Explanation queries where multi-hop reasoning and evidence attribution are required.

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.

Many applications involve estimating the mean of multiple binomial outcomes as a common problem -- assessing intergenerational mobility of census tracts, estimating prevalence of infectious diseases across countries, and measuring click-through rates for different demographic groups. The most standard approach is to report the plain average of each outcome. Despite simplicity, the estimates are noisy when the sample sizes or mean parameters are small. In contrast, the Empirical Bayes (EB) methods are able to boost the average accuracy by borrowing information across tasks. Nevertheless, the EB methods require a Bayesian model where the parameters are sampled from a prior distribution which, unlike the commonly-studied Gaussian case, is unidentified due to discreteness of binomial measurements. Even if the prior distribution is known, the computation is difficult when the sample sizes are heterogeneous as there is no simple joint conjugate prior for the sample size and mean parameter. In this paper, we consider the compound decision framework which treats the sample size and mean parameters as fixed quantities. We develop an approximate Stein's Unbiased Risk Estimator (SURE) for the average mean squared error given any class of estimators. For a class of machine learning-assisted linear shrinkage estimators, we establish asymptotic optimality, regret bounds, and valid inference. Unlike existing work, we work with the binomials directly without resorting to Gaussian approximations. This allows us to work with small sample sizes and/or mean parameters in both one-sample and two-sample settings. We demonstrate our approach using three datasets on firm discrimination, education outcomes, and innovation rates.

Causal inference, estimating causal effects from observational data, is a fundamental tool in many disciplines. Of particular importance across a variety of domains is the continuous treatment setting, where the variable of intervention has a continuous range. This setting is far less explored and represents a substantial shift from the binary treatment setting, with models needing to represent effects across a continuum of treatment values. In this paper, we present the first causal foundation model for the continuous treatment setting. Our model meta-learns the ability to predict causal effects across a wide variety of unseen tasks without additional training or fine-tuning. First, we design a novel prior over data-generating processes with continuous treatment variables in order to generate a rich causal training corpus. We then train a transformer to reconstruct individual treatment-response curves given only observational data, leveraging in-context learning to amortize expensive Bayesian posterior inference. Our model achieves state-of-the-art performance on individual treatment-response curve reconstruction tasks compared to causal models which are trained specifically for those tasks.

Children learn powerful internal models of the world around them from a few years of egocentric visual experience. Can such internal models be learned from a child's visual experience with highly generic learning algorithms or do they require strong inductive biases? Recent advances in collecting large-scale, longitudinal, developmentally realistic video datasets and generic self-supervised learning (SSL) algorithms are allowing us to begin to tackle this nature vs. nurture question. However, existing work typically focuses on image-based SSL algorithms and visual capabilities that can be learned from static images (e.g. object recognition), thus ignoring temporal aspects of the world. To close this gap, here we train self-supervised video models on longitudinal, egocentric headcam recordings collected from a child over a two year period in their early development (6-31 months). The resulting models are highly effective at facilitating the learning of action concepts from a small number of labeled examples; they have favorable data size scaling properties; and they display emergent video interpolation capabilities. Video models also learn more robust object representations than image-based models trained with the exact same data. These results suggest that important temporal aspects of a child's internal model of the world may be learnable from their visual experience using highly generic learning algorithms and without strong inductive biases.

Extending discrete-time causal Prior-data Fitted Networks for time series to continuous time invites writing the mechanism as a stochastic differential equation (SDE) -- but if the SDE is integrated once per observation gap, the trajectory law depends on when it is observed, and the prior remains a discrete-time Markov model in SDE clothing. We propose a precise continuity criterion -- trajectory-law invariance to the observation schedule -- together with a three-tier taxonomy (discrete; naive observation-grid integration; fine-grid integration with decoupled observation) and a construction realising the top tier on a random DAG with OU or small-MLP nonlinear drifts, irregular observation schedules, and hard / soft / time-varying interventions. A 2 times 2 encoder times integrator ablation, run independently on a linear and a nonlinear prior, finds fine-grid integration beats naive on 8/8 cells (sign-consistency p < 1/256) with the gap growing as the eval grid refines; the encoder axis is null with fine integration but time-aware-leading with naive. We release the prior and a preliminary zero-shot protocol on pharmacokinetic and physical-system data.

This study introduces PV-RNN, a novel variational RNN inspired by the predictive-coding ideas. The model learns to extract the probabilistic structures hidden in fluctuating temporal patterns by dynamically changing the stochasticity of its latent states. Its architecture attempts to address two major concerns of variational Bayes RNNs: how can latent variables learn meaningful representations and how can the inference model transfer future observations to the latent variables. PV-RNN does both by introducing adaptive vectors mirroring the training data, whose values can then be adapted differently during evaluation. Moreover, prediction errors during backpropagation, rather than external inputs during the forward computation, are used to convey information to the network about the external data. For testing, we introduce error regression for predicting unseen sequences as inspired by predictive coding that leverages those mechanisms. The model introduces a weighting parameter, the meta-prior, to balance the optimization pressure placed on two terms of a lower bound on the marginal likelihood of the sequential data. We test the model on two datasets with probabilistic structures and show that with high values of the meta-prior the network develops deterministic chaos through which the data's randomness is imitated. For low values, the model behaves as a random process. The network performs best on intermediate values, and is able to capture the latent probabilistic structure with good generalization. Analyzing the meta-prior's impact on the network allows to precisely study the theoretical value and practical benefits of incorporating stochastic dynamics in our model. We demonstrate better prediction performance on a robot imitation task with our model using error regression compared to a standard variational Bayes model lacking such a procedure.

MRI is an indispensable clinical tool, offering a rich variety of tissue contrasts to support broad diagnostic and research applications. Clinical exams routinely acquire multiple structural sequences that provide complementary information for differential diagnosis, while research protocols often incorporate advanced functional, diffusion, spectroscopic, and relaxometry sequences to capture multidimensional insights into tissue structure and composition. However, these capabilities come at the cost of prolonged scan times, which reduce patient throughput, increase susceptibility to motion artifacts, and may require trade-offs in image quality or diagnostic scope. Over the last two decades, advances in image reconstruction algorithms--alongside improvements in hardware and pulse sequence design--have made it possible to accelerate acquisitions while preserving diagnostic quality. Central to this progress is the ability to incorporate prior information to regularize the solutions to the reconstruction problem. In this tutorial, we overview the basics of MRI reconstruction and highlight state-of-the-art approaches, beginning with classical methods that rely on explicit hand-crafted priors, and then turning to deep learning methods that leverage a combination of learned and crafted priors to further push the performance envelope. We also explore the translational aspects and eventual clinical implications of these methods. We conclude by discussing future directions to address remaining challenges in MRI reconstruction. The tutorial is accompanied by a Python toolbox (https://github.com/tutorial-MRI-recon/tutorial) to demonstrate select methods discussed in the article.

Longitudinal clinical notes contain rich evidence of how patients evolve over time, but converting this signal into training supervision for clinical prediction remains challenging. We extend Foresight Learning to clinical prediction by converting time-ordered MIMIC-III notes into examples consisting of past patient context, a natural-language question about a possible future event, and a label resolved from later documentation. This process yields 6,900 prediction examples from 702 admissions across medications, procedures, organ support, microbiology, and mortality. A small LoRA adapter trained on these examples improves over the prompted base model, reducing expected calibration error from 0.1269 to 0.0398 and Brier score from 0.199 to 0.145, while slightly outperforming GPT-5 point estimates on held-out questions. The approach enables reusable clinical prediction supervision from longitudinal notes without hand-engineered structured features or endpoint-specific classifiers.

Autoencoders and their variants are among the most widely used models in representation learning and generative modeling. However, autoencoder-based models usually assume that the learned representations are i.i.d. and fail to capture the correlations between the data samples. To address this issue, we propose a novel Sparse Gaussian Process Bayesian Autoencoder (SGPBAE) model in which we impose fully Bayesian sparse Gaussian Process priors on the latent space of a Bayesian Autoencoder. We perform posterior estimation for this model via stochastic gradient Hamiltonian Monte Carlo. We evaluate our approach qualitatively and quantitatively on a wide range of representation learning and generative modeling tasks and show that our approach consistently outperforms multiple alternatives relying on Variational Autoencoders.

Can a diffusion model trained on bedrooms recover human faces? Diffusion models are widely used as priors for inverse problems, but standard approaches usually assume a high-fidelity model trained on data that closely match the unknown signal. In practice, one often must use a mismatched or low-fidelity diffusion prior. Surprisingly, these weak priors often perform nearly as well as full-strength, in-domain baselines. We study when and why inverse solvers are robust to weak diffusion priors. Through extensive experiments, we find that weak priors succeed when measurements are highly informative (e.g., many observed pixels), and we identify regimes where they fail. Our theory, based on Bayesian consistency, gives conditions under which high-dimensional measurements make the posterior concentrate near the true signal. These results provide a principled justification on when weak diffusion priors can be used reliably.

Masked autoencoders (MAEs) are increasingly applied to electronic health records (EHR) for learning general-purpose representations that support diverse clinical tasks. However, existing approaches typically rely on uniform random masking, implicitly assuming all features are equally predictable. In reality, laboratory tests exhibit substantial heterogeneity in volatility: some biomarkers (e.g., sodium) remain stable, while others (e.g., lactate) fluctuate considerably and are more difficult to model. Clinically, volatile biomarkers often signal acute pathophysiology and require more sophisticated modeling to capture their complex temporal patterns. We propose a volatility-aware pretraining strategy, Coefficient of Variation Masking (CV-Masking), that adaptively adjusts masking probabilities according to the intrinsic variability of each feature. Combined with a value-only masking objective aligned with clinical workflows, CV-Masking yields systematic improvements over random and variance-based strategies. Experiments on a large panel of laboratory tests show that CV-Masking enhances reconstruction, improves downstream predictive performance, and accelerates convergence, producing more robust and clinically meaningful EHR representations.

Combined electric power system and High-Altitude Electromagnetic Pulse (HEMP) models are being developed to determine the effect of a HEMP on the US power grid. The work relies primarily on deterministic methods; however, it is computationally untenable to evaluate the E1 HEMP response of large numbers of grid components distributed across a large interconnection. Further, the deterministic assessment of these components' failures are largely unachievable. E1 HEMP laboratory testing of the components is accomplished, but is expensive, leaving few data points to construct failure models of grid components exposed to E1 HEMP. The use of Bayesian priors, developed using the subject matter expertise, combined with the minimal test data in a Bayesian inference process, provides the basis for the development of more robust and cost-effective statistical component failure models. These can be used with minimal computational burden in a simulation environment such as sampling of Cumulative Distribution Functions (CDFs).

Uncertainty quantification is essential when dealing with ill-conditioned inverse problems due to the inherent nonuniqueness of the solution. Bayesian approaches allow us to determine how likely an estimation of the unknown parameters is via formulating the posterior distribution. Unfortunately, it is often not possible to formulate a prior distribution that precisely encodes our prior knowledge about the unknown. Furthermore, adherence to handcrafted priors may greatly bias the outcome of the Bayesian analysis. To address this issue, we propose to use the functional form of a randomly initialized convolutional neural network as an implicit structured prior, which is shown to promote natural images and excludes images with unnatural noise. In order to incorporate the model uncertainty into the final estimate, we sample the posterior distribution using stochastic gradient Langevin dynamics and perform Bayesian model averaging on the obtained samples. Our synthetic numerical experiment verifies that deep priors combined with Bayesian model averaging are able to partially circumvent imaging artifacts and reduce the risk of overfitting in the presence of extreme noise. Finally, we present pointwise variance of the estimates as a measure of uncertainty, which coincides with regions that are more difficult to image.

While Large Language Models (LLMs) have shown strong performance on clinical text understanding, they struggle with longitudinal prediction tasks such as dementia prognosis, which require reasoning over complex, non-monotonic symptom trajectories across multiple visits. Standard supervised training lacks explicit annotations for symptom evolution, while direct Reinforcement Learning (RL) is hindered by sparse binary rewards. To address this challenge, we introduce Dementia-R1, an RL-based framework for longitudinal dementia prognosis from unstructured clinical notes. Our approach adopts a Cold-Start RL strategy that pre-trains the model to predict verifiable clinical indices extracted from patient histories, enhancing the capability to reason about disease progression before determining the final clinical status. Extensive experiments demonstrate that Dementia-R1 achieves an F1 score of 77.03% on real-world unstructured clinical datasets. Notably, on the ADNI benchmark, our 7B model rivals GPT-4o, effectively capturing fluctuating cognitive trajectories. Code is available at https://anonymous.4open.science/r/dementiar1-CDB5

We present a new distribution-free conformal prediction algorithm for sequential data (e.g., time series), called the sequential predictive conformal inference (SPCI). We specifically account for the nature that time series data are non-exchangeable, and thus many existing conformal prediction algorithms are not applicable. The main idea is to adaptively re-estimate the conditional quantile of non-conformity scores (e.g., prediction residuals), upon exploiting the temporal dependence among them. More precisely, we cast the problem of conformal prediction interval as predicting the quantile of a future residual, given a user-specified point prediction algorithm. Theoretically, we establish asymptotic valid conditional coverage upon extending consistency analyses in quantile regression. Using simulation and real-data experiments, we demonstrate a significant reduction in interval width of SPCI compared to other existing methods under the desired empirical coverage.

The prior drift is crucial in Continual Test-Time Adaptation (CTTA) methods that only use unlabeled test data, as it can cause significant error propagation. In this paper, we introduce VCoTTA, a variational Bayesian approach to measure uncertainties in CTTA. At the source stage, we transform a pre-trained deterministic model into a Bayesian Neural Network (BNN) via a variational warm-up strategy, injecting uncertainties into the model. During the testing time, we employ a mean-teacher update strategy using variational inference for the student model and exponential moving average for the teacher model. Our novel approach updates the student model by combining priors from both the source and teacher models. The evidence lower bound is formulated as the cross-entropy between the student and teacher models, along with the Kullback-Leibler (KL) divergence of the prior mixture. Experimental results on three datasets demonstrate the method's effectiveness in mitigating prior drift within the CTTA framework.

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.

This paper presents a Bayesian nonparametric latent feature model specially suitable for exploratory analysis of high-dimensional count data. We perform a non-negative doubly sparse matrix factorization that has two main advantages: not only we are able to better approximate the row input distributions, but the inferred topics are also easier to interpret. By combining the three-parameter and restricted Indian buffet processes into a single prior, we increase the model flexibility, allowing for a full spectrum of sparse solutions in the latent space. We demonstrate the usefulness of our approach in the analysis of countries' economic structure. Compared to other approaches, empirical results show our model's ability to give easy-to-interpret information and better capture the underlying sparsity structure of data.

[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.

Generating realistic time series data is important for many engineering and scientific applications. Existing work tackles this problem using generative adversarial networks (GANs). However, GANs are often unstable during training, and they can suffer from mode collapse. While variational autoencoders (VAEs) are known to be more robust to these issues, they are (surprisingly) less often considered for time series generation. In this work, we introduce Koopman VAE (KVAE), a new generative framework that is based on a novel design for the model prior, and that can be optimized for either regular and irregular training data. Inspired by Koopman theory, we represent the latent conditional prior dynamics using a linear map. Our approach enhances generative modeling with two desired features: (i) incorporating domain knowledge can be achieved by leverageing spectral tools that prescribe constraints on the eigenvalues of the linear map; and (ii) studying the qualitative behavior and stablity of the system can be performed using tools from dynamical systems theory. Our results show that KVAE outperforms state-of-the-art GAN and VAE methods across several challenging synthetic and real-world time series generation benchmarks. Whether trained on regular or irregular data, KVAE generates time series that improve both discriminative and predictive metrics. We also present visual evidence suggesting that KVAE learns probability density functions that better approximate empirical ground truth distributions.

We present an approach to modeling an image-space prior on scene dynamics. Our prior is learned from a collection of motion trajectories extracted from real video sequences containing natural, oscillating motion such as trees, flowers, candles, and clothes blowing in the wind. Given a single image, our trained model uses a frequency-coordinated diffusion sampling process to predict a per-pixel long-term motion representation in the Fourier domain, which we call a neural stochastic motion texture. This representation can be converted into dense motion trajectories that span an entire video. Along with an image-based rendering module, these trajectories can be used for a number of downstream applications, such as turning still images into seamlessly looping dynamic videos, or allowing users to realistically interact with objects in real pictures.

Chest X-Ray (CXR) report generation is a promising approach to improving the efficiency of CXR interpretation. However, a significant increase in diagnostic accuracy is required before that can be realised. Motivated by this, we propose a framework that is more inline with a radiologist's workflow by considering longitudinal data. Here, the decoder is additionally conditioned on the report from the subject's previous imaging study via a prompt. We also propose a new reward for reinforcement learning based on CXR-BERT, which computes the similarity between reports. We conduct experiments on the MIMIC-CXR dataset. The results indicate that longitudinal data improves CXR report generation. CXR-BERT is also shown to be a promising alternative to the current state-of-the-art reward based on RadGraph. This investigation indicates that longitudinal CXR report generation can offer a substantial increase in diagnostic accuracy. Our Hugging Face model is available at: https://huggingface.co/aehrc/cxrmate and code is available at: https://github.com/aehrc/cxrmate.

We incorporate discrete and continuous time Markov processes as building blocks into probabilistic graphical models with latent and observed variables. We introduce the automatic Backward Filtering Forward Guiding (BFFG) paradigm (Mider et al., 2021) for programmable inference on latent states and model parameters. Our starting point is a generative model, a forward description of the probabilistic process dynamics. We backpropagate the information provided by observations through the model to transform the generative (forward) model into a pre-conditional model guided by the data. It approximates the actual conditional model with known likelihood-ratio between the two. The backward filter and the forward change of measure are suitable to be incorporated into a probabilistic programming context because they can be formulated as a set of transformation rules. The guided generative model can be incorporated in different approaches to efficiently sample latent states and parameters conditional on observations. We show applicability in a variety of settings, including Markov chains with discrete state space, interacting particle systems, state space models, branching diffusions and Gamma processes.

Recent studies on inverse problems have proposed posterior samplers that leverage the pre-trained diffusion models as powerful priors. These attempts have paved the way for using diffusion models in a wide range of inverse problems. However, the existing methods entail computationally demanding iterative sampling procedures and optimize a separate solution for each measurement, which leads to limited scalability and lack of generalization capability across unseen samples. To address these limitations, we propose a novel approach, Diffusion prior-based Amortized Variational Inference (DAVI) that solves inverse problems with a diffusion prior from an amortized variational inference perspective. Specifically, instead of separate measurement-wise optimization, our amortized inference learns a function that directly maps measurements to the implicit posterior distributions of corresponding clean data, enabling a single-step posterior sampling even for unseen measurements. Extensive experiments on image restoration tasks, e.g., Gaussian deblur, 4times super-resolution, and box inpainting with two benchmark datasets, demonstrate our approach's superior performance over strong baselines. Code is available at https://github.com/mlvlab/DAVI.

A new prior is proposed for learning representations of high-level concepts of the kind we manipulate with language. This prior can be combined with other priors in order to help disentangling abstract factors from each other. It is inspired by cognitive neuroscience theories of consciousness, seen as a bottleneck through which just a few elements, after having been selected by attention from a broader pool, are then broadcast and condition further processing, both in perception and decision-making. The set of recently selected elements one becomes aware of is seen as forming a low-dimensional conscious state. This conscious state is combining the few concepts constituting a conscious thought, i.e., what one is immediately conscious of at a particular moment. We claim that this architectural and information-processing constraint corresponds to assumptions about the joint distribution between high-level concepts. To the extent that these assumptions are generally true (and the form of natural language seems consistent with them), they can form a useful prior for representation learning. A low-dimensional thought or conscious state is analogous to a sentence: it involves only a few variables and yet can make a statement with very high probability of being true. This is consistent with a joint distribution (over high-level concepts) which has the form of a sparse factor graph, i.e., where the dependencies captured by each factor of the factor graph involve only very few variables while creating a strong dip in the overall energy function. The consciousness prior also makes it natural to map conscious states to natural language utterances or to express classical AI knowledge in a form similar to facts and rules, albeit capturing uncertainty as well as efficient search mechanisms implemented by attention mechanisms.

Modeling latent variables with priors and hyperpriors is an essential problem in variational image compression. Formally, trade-off between rate and distortion is handled well if priors and hyperpriors precisely describe latent variables. Current practices only adopt univariate priors and process each variable individually. However, we find inter-correlations and intra-correlations exist when observing latent variables in a vectorized perspective. These findings reveal visual redundancies to improve rate-distortion performance and parallel processing ability to speed up compression. This encourages us to propose a novel vectorized prior. Specifically, a multivariate Gaussian mixture is proposed with means and covariances to be estimated. Then, a novel probabilistic vector quantization is utilized to effectively approximate means, and remaining covariances are further induced to a unified mixture and solved by cascaded estimation without context models involved. Furthermore, codebooks involved in quantization are extended to multi-codebooks for complexity reduction, which formulates an efficient compression procedure. Extensive experiments on benchmark datasets against state-of-the-art indicate our model has better rate-distortion performance and an impressive 3.18times compression speed up, giving us the ability to perform real-time, high-quality variational image compression in practice. Our source code is publicly available at https://github.com/xiaosu-zhu/McQuic.

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.

Inferring unbiased treatment effects has received widespread attention in the machine learning community. In recent years, our community has proposed numerous solutions in standard settings, high-dimensional treatment settings, and even longitudinal settings. While very diverse, the solution has mostly relied on neural networks for inference and simultaneous correction of assignment bias. New approaches typically build on top of previous approaches by proposing new (or refined) architectures and learning algorithms. However, the end result -- a neural-network-based inference machine -- remains unchallenged. In this paper, we introduce a different type of solution in the longitudinal setting: a closed-form ordinary differential equation (ODE). While we still rely on continuous optimization to learn an ODE, the resulting inference machine is no longer a neural network. Doing so yields several advantages such as interpretability, irregular sampling, and a different set of identification assumptions. Above all, we consider the introduction of a completely new type of solution to be our most important contribution as it may spark entirely new innovations in treatment effects in general. We facilitate this by formulating our contribution as a framework that can transform any ODE discovery method into a treatment effects method.

Autoregressive models have achieved impressive results over a wide range of domains in terms of generation quality and downstream task performance. In the continuous domain, a key factor behind this success is the usage of quantized latent spaces (e.g., obtained via VQ-VAE autoencoders), which allow for dimensionality reduction and faster inference times. However, using existing pre-trained models to perform new non-trivial tasks is difficult since it requires additional fine-tuning or extensive training to elicit prompting. This paper introduces LASS as a way to perform vector-quantized Latent Autoregressive Source Separation (i.e., de-mixing an input signal into its constituent sources) without requiring additional gradient-based optimization or modifications of existing models. Our separation method relies on the Bayesian formulation in which the autoregressive models are the priors, and a discrete (non-parametric) likelihood function is constructed by performing frequency counts over latent sums of addend tokens. We test our method on images and audio with several sampling strategies (e.g., ancestral, beam search) showing competitive results with existing approaches in terms of separation quality while offering at the same time significant speedups in terms of inference time and scalability to higher dimensional data.

Continuous Glucose Monitoring (CGM) can detect early metabolic subphenotypes (insulin resistance, IR; β-cell dysfunction), but population-scale deployment faces two coupled problems. First, the same physiological state appears through multiple views (CGM time series, venous OGTT, Glucodensity summaries), so single-view representations fail to transfer when deployment shifts the modality or setting. Second, baselines perform inconsistently across these shifts. Both problems point to one remedy: representations that abstract away from any single view to capture higher-level temporal and distributional structure. We propose CGM-JEPA, a self-supervised pretraining framework which predicts masked latent representations rather than raw values, yielding abstraction that transfers across modalities. X-CGM-JEPA adds a masked Glucodensity cross-view objective for complementary distributional information. We pretrain on sim389k unlabeled CGM readings from 228 subjects and evaluate on two clinical cohorts (N=27 and N=17 public-release subsets) across three regimes (cohort generalization, venous-to-CGM transfer, home CGM) under 20-iteration times 2-fold cross-validation. X-CGM-JEPA ranks first or second on AUROC for both endpoints across all three regimes while no baseline does, exceeding the strongest baseline by up to +6.5 pp in cohort generalization and +3.6 pp in venous-to-CGM transfer (paired Wilcoxon, p<0.001). Under modality shift, it matches mean AUROC while redistributing toward weaker subgroups (ethnicity AUROC gap shrinks 25-54%); on sparse in-domain venous data, the distributional view lifts label-aware clustering (ARI +39%, NMI +40%). Code and weights: https://github.com/cruiseresearchgroup/CGM-JEPA

Latent Gaussian process (GP) models are widely used in neuroscience to uncover hidden state evolutions from sequential observations, mainly in neural activity recordings. While latent GP models provide a principled and powerful solution in theory, the intractable posterior in non-conjugate settings necessitates approximate inference schemes, which may lack scalability. In this work, we propose cvHM, a general inference framework for latent GP models leveraging Hida-Mat\'ern kernels and conjugate computation variational inference (CVI). With cvHM, we are able to perform variational inference of latent neural trajectories with linear time complexity for arbitrary likelihoods. The reparameterization of stationary kernels using Hida-Mat\'ern GPs helps us connect the latent variable models that encode prior assumptions through dynamical systems to those that encode trajectory assumptions through GPs. In contrast to previous work, we use bidirectional information filtering, leading to a more concise implementation. Furthermore, we employ the Whittle approximate likelihood to achieve highly efficient hyperparameter learning.

Recent works have revealed that infinitely-wide feed-forward or recurrent neural networks of any architecture correspond to Gaussian processes referred to as Neural Network Gaussian Processes (NNGPs). While these works have extended the class of neural networks converging to Gaussian processes significantly, however, there has been little focus on broadening the class of stochastic processes that such neural networks converge to. In this work, inspired by the scale mixture of Gaussian random variables, we propose the scale mixture of NNGPs for which we introduce a prior distribution on the scale of the last-layer parameters. We show that simply introducing a scale prior on the last-layer parameters can turn infinitely-wide neural networks of any architecture into a richer class of stochastic processes. With certain scale priors, we obtain heavy-tailed stochastic processes, and in the case of inverse gamma priors, we recover Student's t processes. We further analyze the distributions of the neural networks initialized with our prior setting and trained with gradient descents and obtain similar results as for NNGPs. We present a practical posterior-inference algorithm for the scale mixture of NNGPs and empirically demonstrate its usefulness on regression and classification tasks. In particular, we show that in both tasks, the heavy-tailed stochastic processes obtained from our framework are robust to out-of-distribution data.

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.

Changepoints are abrupt variations in the generative parameters of a data sequence. Online detection of changepoints is useful in modelling and prediction of time series in application areas such as finance, biometrics, and robotics. While frequentist methods have yielded online filtering and prediction techniques, most Bayesian papers have focused on the retrospective segmentation problem. Here we examine the case where the model parameters before and after the changepoint are independent and we derive an online algorithm for exact inference of the most recent changepoint. We compute the probability distribution of the length of the current ``run,'' or time since the last changepoint, using a simple message-passing algorithm. Our implementation is highly modular so that the algorithm may be applied to a variety of types of data. We illustrate this modularity by demonstrating the algorithm on three different real-world data sets.

Unsupervised pretraining has been transformative in many supervised domains. However, applying such ideas to reinforcement learning (RL) presents a unique challenge in that fine-tuning does not involve mimicking task-specific data, but rather exploring and locating the solution through iterative self-improvement. In this work, we study how unlabeled prior trajectory data can be leveraged to learn efficient exploration strategies. While prior data can be used to pretrain a set of low-level skills, or as additional off-policy data for online RL, it has been unclear how to combine these ideas effectively for online exploration. Our method SUPE (Skills from Unlabeled Prior data for Exploration) demonstrates that a careful combination of these ideas compounds their benefits. Our method first extracts low-level skills using a variational autoencoder (VAE), and then pseudo-relabels unlabeled trajectories using an optimistic reward model, transforming prior data into high-level, task-relevant examples. Finally, SUPE uses these transformed examples as additional off-policy data for online RL to learn a high-level policy that composes pretrained low-level skills to explore efficiently. We empirically show that SUPE reliably outperforms prior strategies, successfully solving a suite of long-horizon, sparse-reward tasks. Code: https://github.com/rail-berkeley/supe.

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.

We propose a monocular depth estimation method based on visual autoregressive (VAR) priors, offering an alternative to diffusion-based approaches. Our method adapts a large-scale text-to-image VAR model and introduces a scale-wise conditional upsampling mechanism with classifier-free guidance. Our approach performs inference in ten fixed autoregressive stages, requiring only 74K synthetic samples for fine-tuning, and achieves competitive results. We report state-of-the-art performance in indoor benchmarks under constrained training conditions, and strong performance when applied to outdoor datasets. This work establishes autoregressive priors as a complementary family of geometry-aware generative models for depth estimation, highlighting advantages in data scalability, and adaptability to 3D vision tasks. Code available at "https://github.com/AmirMaEl/VAR-Depth".

Large language models (LLMs) sometimes fail to respond appropriately to deterministic tasks -- such as counting or forming acronyms -- because the implicit prior distribution they have learned over sequences of tokens influences their responses. In this work, we show that, in at least some cases, LLMs actually compute the information needed to perform these tasks correctly, and we identify some interventions that can allow them to access this information to improve their performance. First, we show that simply prompting the language model to not rely on its prior knowledge leads to dramatic improvements in prior-dominated tasks. We then use mechanistic interpretability techniques to localize the prior within the LLM and manipulate the extent to which that prior influences its responses. Specifically, we show that it is possible to identify layers of the underlying neural network that correlate with the prior probability of a response and that lightweight finetuning of these layers with basic prompts on prior-dominated tasks achieves high performance on held-out answers. These results suggest that the information required to produce a correct response is contained within the representations of the problems formed by the models. Furthermore, we show that this finetuning is significantly more effective for prior-dominated tasks, and that the error after finetuning is no longer correlated with the prior. Our results suggest that it may be possible to define effective methods for manipulating the extent to which LLMs rely upon their priors in solving problems, potentially increasing their performance in settings where LLMs hallucinate for reasons related to the prior probability of token sequences.

The variational autoencoder (VAE) is a popular, deep, latent-variable model (DLVM) due to its simple yet effective formulation for modeling the data distribution. Moreover, optimizing the VAE objective function is more manageable than other DLVMs. The bottleneck dimension of the VAE is a crucial design choice, and it has strong ramifications for the model's performance, such as finding the hidden explanatory factors of a dataset using the representations learned by the VAE. However, the size of the latent dimension of the VAE is often treated as a hyperparameter estimated empirically through trial and error. To this end, we propose a statistical formulation to discover the relevant latent factors required for modeling a dataset. In this work, we use a hierarchical prior in the latent space that estimates the variance of the latent axes using the encoded data, which identifies the relevant latent dimensions. For this, we replace the fixed prior in the VAE objective function with a hierarchical prior, keeping the remainder of the formulation unchanged. We call the proposed method the automatic relevancy detection in the variational autoencoder (ARD-VAE). We demonstrate the efficacy of the ARD-VAE on multiple benchmark datasets in finding the relevant latent dimensions and their effect on different evaluation metrics, such as FID score and disentanglement analysis.

Longitudinal brain analysis is essential for understanding healthy aging and identifying pathological deviations. Longitudinal registration of sequential brain MRI underpins such analyses. However, existing methods are limited by reliance on densely sampled time series, a trade-off between accuracy and temporal smoothness, and an inability to prospectively forecast future brain states. To overcome these challenges, we introduce TimeFlow, a learning-based framework for longitudinal brain MRI registration. TimeFlow uses a U-Net backbone with temporal conditioning to model neuroanatomy as a continuous function of age. Given only two scans from an individual, TimeFlow estimates accurate and temporally coherent deformation fields, enabling non-linear extrapolation to predict future brain states. This is achieved by our proposed inter-/extra-polation consistency constraints applied to both the deformation fields and deformed images. Remarkably, these constraints preserve temporal consistency and continuity without requiring explicit smoothness regularizers or densely sampled sequential data. Extensive experiments demonstrate that TimeFlow outperforms state-of-the-art methods in terms of both future timepoint forecasting and registration accuracy. Moreover, TimeFlow supports novel biological brain aging analyses by differentiating neurodegenerative trajectories from normal aging without requiring segmentation, thereby eliminating the need for labor-intensive annotations and mitigating segmentation inconsistency. TimeFlow offers an accurate, data-efficient, and annotation-free framework for longitudinal analysis of brain aging and chronic diseases, capable of forecasting brain changes beyond the observed study period.

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.

Pretrained Vision-Language-Action (VLA) policies have achieved strong single-step manipulation, but their inference remains largely memoryless, which is brittle in non-Markovian long-horizon settings with occlusion, state aliasing, and subtle post-action changes. Prior approaches inject history either by stacking frames, which scales visual tokens and latency while adding near-duplicate pixels, or by learning additional temporal interfaces that require (re-)training and may break the original single-frame inference graph. We present TempoFit, a training-free temporal retrofit that upgrades frozen VLAs through state-level memory. Our key insight is that prefix attention K/V already form a model-native, content-addressable runtime state; reusing them across timesteps introduces history without new tokens or trainable modules. TempoFit stores layer-wise FIFO prefix K/V at selected intermediate layers, performs parameter-free K-to-K retrieval with Frame-Gap Temporal Bias (FGTB), a fixed recency bias inspired by positional biases in NLP, to keep decisions present-dominant, and injects the retrieved context via pre-attention residual loading with norm-preserving rescaling to avoid distribution shift under frozen weights. On LIBERO-LONG, TempoFit improves strong pretrained backbones by up to +4.0% average success rate while maintaining near-real-time latency, and it transfers consistently to CALVIN and real-robot long-horizon tasks.

Identifying patient cohorts is fundamental to numerous healthcare tasks, including clinical trial recruitment and retrospective studies. Current cohort retrieval methods in healthcare organizations rely on automated queries of structured data combined with manual curation, which are time-consuming, labor-intensive, and often yield low-quality results. Recent advancements in large language models (LLMs) and information retrieval (IR) offer promising avenues to revolutionize these systems. Major challenges include managing extensive eligibility criteria and handling the longitudinal nature of unstructured Electronic Medical Records (EMRs) while ensuring that the solution remains cost-effective for real-world application. This paper introduces a new task, Automatic Cohort Retrieval (ACR), and evaluates the performance of LLMs and commercial, domain-specific neuro-symbolic approaches. We provide a benchmark task, a query dataset, an EMR dataset, and an evaluation framework. Our findings underscore the necessity for efficient, high-quality ACR systems capable of longitudinal reasoning across extensive patient databases.

Diffusion models have emerged as the new state-of-the-art generative model with high quality samples, with intriguing properties such as mode coverage and high flexibility. They have also been shown to be effective inverse problem solvers, acting as the prior of the distribution, while the information of the forward model can be granted at the sampling stage. Nonetheless, as the generative process remains in the same high dimensional (i.e. identical to data dimension) space, the models have not been extended to 3D inverse problems due to the extremely high memory and computational cost. In this paper, we combine the ideas from the conventional model-based iterative reconstruction with the modern diffusion models, which leads to a highly effective method for solving 3D medical image reconstruction tasks such as sparse-view tomography, limited angle tomography, compressed sensing MRI from pre-trained 2D diffusion models. In essence, we propose to augment the 2D diffusion prior with a model-based prior in the remaining direction at test time, such that one can achieve coherent reconstructions across all dimensions. Our method can be run in a single commodity GPU, and establishes the new state-of-the-art, showing that the proposed method can perform reconstructions of high fidelity and accuracy even in the most extreme cases (e.g. 2-view 3D tomography). We further reveal that the generalization capacity of the proposed method is surprisingly high, and can be used to reconstruct volumes that are entirely different from the training dataset.

Temporally dense single-person "small data" have become widely available thanks to mobile apps and wearable sensors. Many caregivers and self-trackers want to use these data to help a specific person change their behavior to achieve desired health outcomes. Ideally, this involves discerning possible causes from correlations using that person's own observational time series data. In this paper, we estimate within-individual average treatment effects of physical activity on sleep duration, and vice-versa. We introduce the model twin randomization (MoTR; "motor") method for analyzing an individual's intensive longitudinal data. Formally, MoTR is an application of the g-formula (i.e., standardization, back-door adjustment) under serial interference. It estimates stable recurring effects, as is done in n-of-1 trials and single case experimental designs. We compare our approach to standard methods (with possible confounding) to show how to use causal inference to make better personalized recommendations for health behavior change, and analyze 222 days of Fitbit sleep and steps data for one of the authors.

Sequential VAEs have been successfully considered for many high-dimensional time series modelling problems, with many variant models relying on discrete-time mechanisms such as recurrent neural networks (RNNs). On the other hand, continuous-time methods have recently gained attraction, especially in the context of irregularly-sampled time series, where they can better handle the data than discrete-time methods. One such class are Gaussian process variational autoencoders (GPVAEs), where the VAE prior is set as a Gaussian process (GP). However, a major limitation of GPVAEs is that it inherits the cubic computational cost as GPs, making it unattractive to practioners. In this work, we leverage the equivalent discrete state space representation of Markovian GPs to enable linear time GPVAE training via Kalman filtering and smoothing. We show on a variety of high-dimensional temporal and spatiotemporal tasks that our method performs favourably compared to existing approaches whilst being computationally highly scalable.

Respiratory viral infections pose a global health burden, yet the cellular immune responses driving protection or pathology remain unclear. Natural infection cohorts often lack pre-exposure baseline data and structured temporal sampling. In contrast, inoculation and vaccination trials generate insightful longitudinal transcriptomic data. However, the scattering of these datasets across platforms, along with inconsistent metadata and preprocessing procedure, hinders AI-driven discovery. To address these challenges, we developed the Human Respiratory Viral Immunization LongitudinAl Gene Expression (HR-VILAGE-3K3M) repository: an AI-ready, rigorously curated dataset that integrates 14,136 RNA-seq profiles from 3,178 subjects across 66 studies encompassing over 2.56 million cells. Spanning vaccination, inoculation, and mixed exposures, the dataset includes microarray, bulk RNA-seq, and single-cell RNA-seq from whole blood, PBMCs, and nasal swabs, sourced from GEO, ImmPort, and ArrayExpress. We harmonized subject-level metadata, standardized outcome measures, applied unified preprocessing pipelines with rigorous quality control, and aligned all data to official gene symbols. To demonstrate the utility of HR-VILAGE-3K3M, we performed predictive modeling of vaccine responders and evaluated batch-effect correction methods. Beyond these initial demonstrations, it supports diverse systems immunology applications and benchmarking of feature selection and transfer learning algorithms. Its scale and heterogeneity also make it ideal for pretraining foundation models of the human immune response and for advancing multimodal learning frameworks. As the largest longitudinal transcriptomic resource for human respiratory viral immunization, it provides an accessible platform for reproducible AI-driven research, accelerating systems immunology and vaccine development against emerging viral threats.

Heterogeneity and comorbidity are two interwoven challenges associated with various healthcare problems that greatly hampered research on developing effective treatment and understanding of the underlying neurobiological mechanism. Very few studies have been conducted to investigate heterogeneous causal effects (HCEs) in graphical contexts due to the lack of statistical methods. To characterize this heterogeneity, we first conceptualize heterogeneous causal graphs (HCGs) by generalizing the causal graphical model with confounder-based interactions and multiple mediators. Such confounders with an interaction with the treatment are known as moderators. This allows us to flexibly produce HCGs given different moderators and explicitly characterize HCEs from the treatment or potential mediators on the outcome. We establish the theoretical forms of HCEs and derive their properties at the individual level in both linear and nonlinear models. An interactive structural learning is developed to estimate the complex HCGs and HCEs with confidence intervals provided. Our method is empirically justified by extensive simulations and its practical usefulness is illustrated by exploring causality among psychiatric disorders for trauma survivors.

We study adaptive querying for learning user-dependent quantities of interest, such as responses to held-out items and psychometric indicators, within tight question budgets. Classical Bayesian design and computerized adaptive testing typically rely on restrictive parametric assumptions or expensive posterior approximations, limiting their use in heterogeneous, high-dimensional, and cold-start settings. We introduce a persona-induced latent variable model that represents a user's state through membership in a finite dictionary of AI personas, each offering response distributions produced by a large language model. This yields expressive priors with closed-form posterior updates and efficient finite-mixture predictions, enabling scalable Bayesian design for sequential item selection. Experiments on synthetic data and WorldValuesBench demonstrate that persona-based posteriors deliver accurate probabilistic predictions and an interpretable adaptive elicitation pipeline.

Diffusion models recently proved to be remarkable priors for Bayesian inverse problems. However, training these models typically requires access to large amounts of clean data, which could prove difficult in some settings. In this work, we present a novel method based on the expectation-maximization algorithm for training diffusion models from incomplete and noisy observations only. Unlike previous works, our method leads to proper diffusion models, which is crucial for downstream tasks. As part of our method, we propose and motivate an improved posterior sampling scheme for unconditional diffusion models. We present empirical evidence supporting the effectiveness of our method.

Markov jump processes are continuous-time stochastic processes with a wide range of applications in both natural and social sciences. Despite their widespread use, inference in these models is highly non-trivial and typically proceeds via either Monte Carlo or expectation-maximization methods. In this work we introduce an alternative, variational inference algorithm for Markov jump processes which relies on neural ordinary differential equations, and is trainable via back-propagation. Our methodology learns neural, continuous-time representations of the observed data, that are used to approximate the initial distribution and time-dependent transition probability rates of the posterior Markov jump process. The time-independent rates of the prior process are in contrast trained akin to generative adversarial networks. We test our approach on synthetic data sampled from ground-truth Markov jump processes, experimental switching ion channel data and molecular dynamics simulations. Source code to reproduce our experiments is available online.

Longitudinal chest X-ray (CXR) interpretation requires reasoning over disease evolution across multiple patient visits, yet most existing medical VQA benchmarks focus on single images or short-horizon image pairs. We introduce MI-CXR, a benchmark for standardized evaluation of Multi-Interval longitudinal reasoning over multi-visit CXR sequences, without requiring free-form report generation or additional clinical context. MI-CXR comprises five-way multiple-choice questions over five-visit patient timelines and instantiates three complementary task families: Temporal Event Localization, Interval-wise Change Reasoning, and Global Trajectory Summarization, which assess clinically grounded visual reasoning over time. Evaluating 14 state-of-the-art vision-language models (VLMs) shows low overall performance, with an average accuracy of 29.3%, only modestly above random guessing. Using stage-wise diagnostic probing, we find that models often produce locally plausible interval descriptions but fail to enforce temporal constraints or compose evidence into globally consistent decisions over the full timeline. These findings reveal key limitations of current VLMs and establish MI-CXR as a principled benchmark for longitudinal medical reasoning. The benchmark is available at https://github.com/AIDASLab/MI-CXR

Approximations to Gaussian processes based on inducing variables, combined with variational inference techniques, enable state-of-the-art sparse approaches to infer GPs at scale through mini batch-based learning. In this work, we address one limitation of sparse GPs, which is due to the challenge in dealing with a large number of inducing variables without imposing a special structure on the inducing inputs. In particular, we introduce a novel hierarchical prior, which imposes sparsity on the set of inducing variables. We treat our model variationally, and we experimentally show considerable computational gains compared to standard sparse GPs when sparsity on the inducing variables is realized considering the nearest inducing inputs of a random mini-batch of the data. We perform an extensive experimental validation that demonstrates the effectiveness of our approach compared to the state-of-the-art. Our approach enables the possibility to use sparse GPs using a large number of inducing points without incurring a prohibitive computational cost.

We present TabPFN, a trained Transformer that can do supervised classification for small tabular datasets in less than a second, needs no hyperparameter tuning and is competitive with state-of-the-art classification methods. TabPFN performs in-context learning (ICL), it learns to make predictions using sequences of labeled examples (x, f(x)) given in the input, without requiring further parameter updates. TabPFN is fully entailed in the weights of our network, which accepts training and test samples as a set-valued input and yields predictions for the entire test set in a single forward pass. TabPFN is a Prior-Data Fitted Network (PFN) and is trained offline once, to approximate Bayesian inference on synthetic datasets drawn from our prior. This prior incorporates ideas from causal reasoning: It entails a large space of structural causal models with a preference for simple structures. On the 18 datasets in the OpenML-CC18 suite that contain up to 1 000 training data points, up to 100 purely numerical features without missing values, and up to 10 classes, we show that our method clearly outperforms boosted trees and performs on par with complex state-of-the-art AutoML systems with up to 230times speedup. This increases to a 5 700times speedup when using a GPU. We also validate these results on an additional 67 small numerical datasets from OpenML. We provide all our code, the trained TabPFN, an interactive browser demo and a Colab notebook at https://github.com/automl/TabPFN.

Background: Electronic Health Records hold detailed longitudinal information about each patient's health status and general clinical history, a large portion of which is stored within the unstructured text. Existing approaches focus mostly on structured data and a subset of single-domain outcomes. We explore how temporal modelling of patients from free text and structured data, using deep generative transformers can be used to forecast a wide range of future disorders, substances, procedures or findings. Methods: We present Foresight, a novel transformer-based pipeline that uses named entity recognition and linking tools to convert document text into structured, coded concepts, followed by providing probabilistic forecasts for future medical events such as disorders, substances, procedures and findings. We processed the entire free-text portion from three different hospital datasets totalling 811336 patients covering both physical and mental health. Findings: On tests in two UK hospitals (King's College Hospital, South London and Maudsley) and the US MIMIC-III dataset precision@10 0.68, 0.76 and 0.88 was achieved for forecasting the next disorder in a patient timeline, while precision@10 of 0.80, 0.81 and 0.91 was achieved for forecasting the next biomedical concept. Foresight was also validated on 34 synthetic patient timelines by five clinicians and achieved relevancy of 97% for the top forecasted candidate disorder. As a generative model, it can forecast follow-on biomedical concepts for as many steps as required. Interpretation: Foresight is a general-purpose model for biomedical concept modelling that can be used for real-world risk forecasting, virtual trials and clinical research to study the progression of disorders, simulate interventions and counterfactuals, and educational purposes.

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.

This paper investigates the use of prior computation to estimate the value function to improve sample efficiency in on-policy policy gradient methods in reinforcement learning. Our approach is to estimate the value function from prior computations, such as from the Q-network learned in DQN or the value function trained for different but related environments. In particular, we learn a new value function for the target task while combining it with a value estimate from the prior computation. Finally, the resulting value function is used as a baseline in the policy gradient method. This use of a baseline has the theoretical property of reducing variance in gradient computation and thus improving sample efficiency. The experiments show the successful use of prior value estimates in various settings and improved sample efficiency in several tasks.

As machine learning has moved towards leveraging large models as priors for downstream tasks, the community has debated the right form of prior for solving reinforcement learning (RL) problems. If one were to try to prefetch as much computation as possible, they would attempt to learn a prior over the policies for some yet-to-be-determined reward function. Recent work (forward-backward (FB) representation learning) has tried this, arguing that an unsupervised representation learning procedure can enable optimal control over arbitrary rewards without further fine-tuning. However, FB's training objective and learning behavior remain mysterious. In this paper, we demystify FB by clarifying when such representations can exist, what its objective optimizes, and how it converges in practice. We draw connections with rank matching, fitted Q-evaluation, and contraction mapping. Our analysis suggests a simplified unsupervised pre-training method for RL that, instead of enabling optimal control, performs one step of policy improvement. We call our proposed method one-step forward-backward representation learning (one-step FB). Experiments in didactic settings, as well as in 10 state-based and image-based continuous control domains, demonstrate that one-step FB converges to errors 10^5 smaller and improves zero-shot performance by +24% on average. Our project website is available at https://chongyi-zheng.github.io/onestep-fb.

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.

Many empirical studies of labor market questions rely on estimating relatively simple predictive models using small, carefully constructed longitudinal survey datasets based on hand-engineered features. Large Language Models (LLMs), trained on massive datasets, encode vast quantities of world knowledge and can be used for the next job prediction problem. However, while an off-the-shelf LLM produces plausible career trajectories when prompted, the probability with which an LLM predicts a particular job transition conditional on career history will not, in general, align with the true conditional probability in a given population. Recently, Vafa et al. (2024) introduced a transformer-based "foundation model", CAREER, trained using a large, unrepresentative resume dataset, that predicts transitions between jobs; it further demonstrated how transfer learning techniques can be used to leverage the foundation model to build better predictive models of both transitions and wages that reflect conditional transition probabilities found in nationally representative survey datasets. This paper considers an alternative where the fine-tuning of the CAREER foundation model is replaced by fine-tuning LLMs. For the task of next job prediction, we demonstrate that models trained with our approach outperform several alternatives in terms of predictive performance on the survey data, including traditional econometric models, CAREER, and LLMs with in-context learning, even though the LLM can in principle predict job titles that are not allowed in the survey data. Further, we show that our fine-tuned LLM-based models' predictions are more representative of the career trajectories of various workforce subpopulations than off-the-shelf LLM models and CAREER. We conduct experiments and analyses that highlight the sources of the gains in the performance of our models for representative predictions.

Learning curve extrapolation aims to predict model performance in later epochs of training, based on the performance in earlier epochs. In this work, we argue that, while the inherent uncertainty in the extrapolation of learning curves warrants a Bayesian approach, existing methods are (i) overly restrictive, and/or (ii) computationally expensive. We describe the first application of prior-data fitted neural networks (PFNs) in this context. A PFN is a transformer, pre-trained on data generated from a prior, to perform approximate Bayesian inference in a single forward pass. We propose LC-PFN, a PFN trained to extrapolate 10 million artificial right-censored learning curves generated from a parametric prior proposed in prior art using MCMC. We demonstrate that LC-PFN can approximate the posterior predictive distribution more accurately than MCMC, while being over 10 000 times faster. We also show that the same LC-PFN achieves competitive performance extrapolating a total of 20 000 real learning curves from four learning curve benchmarks (LCBench, NAS-Bench-201, Taskset, and PD1) that stem from training a wide range of model architectures (MLPs, CNNs, RNNs, and Transformers) on 53 different datasets with varying input modalities (tabular, image, text, and protein data). Finally, we investigate its potential in the context of model selection and find that a simple LC-PFN based predictive early stopping criterion obtains 2 - 6x speed-ups on 45 of these datasets, at virtually no overhead.

Safety performance evaluation is critical for developing and deploying connected and automated vehicles (CAVs). One prevailing way is to design testing scenarios using prior knowledge of CAVs, test CAVs in these scenarios, and then evaluate their safety performances. However, significant differences between CAVs and prior knowledge could severely reduce the evaluation efficiency. Towards addressing this issue, most existing studies focus on the adaptive design of testing scenarios during the CAV testing process, but so far they cannot be applied to high-dimensional scenarios. In this paper, we focus on the adaptive safety performance evaluation by leveraging the testing results, after the CAV testing process. It can significantly improve the evaluation efficiency and be applied to high-dimensional scenarios. Specifically, instead of directly evaluating the unknown quantity (e.g., crash rates) of CAV safety performances, we evaluate the differences between the unknown quantity and known quantity (i.e., control variates). By leveraging the testing results, the control variates could be well designed and optimized such that the differences are close to zero, so the evaluation variance could be dramatically reduced for different CAVs. To handle the high-dimensional scenarios, we propose the sparse control variates method, where the control variates are designed only for the sparse and critical variables of scenarios. According to the number of critical variables in each scenario, the control variates are stratified into strata and optimized within each stratum using multiple linear regression techniques. We justify the proposed method's effectiveness by rigorous theoretical analysis and empirical study of high-dimensional overtaking scenarios.

Stochastic gradient Markov Chain Monte Carlo (SGMCMC) is considered the gold standard for Bayesian inference in large-scale models, such as Bayesian neural networks. Since practitioners face speed versus accuracy tradeoffs in these models, variational inference (VI) is often the preferable option. Unfortunately, VI makes strong assumptions on both the factorization and functional form of the posterior. In this work, we propose a new non-parametric variational approximation that makes no assumptions about the approximate posterior's functional form and allows practitioners to specify the exact dependencies the algorithm should respect or break. The approach relies on a new Langevin-type algorithm that operates on a modified energy function, where parts of the latent variables are averaged over samples from earlier iterations of the Markov chain. This way, statistical dependencies can be broken in a controlled way, allowing the chain to mix faster. This scheme can be further modified in a "dropout" manner, leading to even more scalability. We test our scheme for ResNet-20 on CIFAR-10, SVHN, and FMNIST. In all cases, we find improvements in convergence speed and/or final accuracy compared to SG-MCMC and VI.

It is commonplace to encounter heterogeneous or nonstationary data, of which the underlying generating process changes across domains or over time. Such a distribution shift feature presents both challenges and opportunities for causal discovery. In this paper, we develop a framework for causal discovery from such data, called Constraint-based causal Discovery from heterogeneous/NOnstationary Data (CD-NOD), to find causal skeleton and directions and estimate the properties of mechanism changes. First, we propose an enhanced constraint-based procedure to detect variables whose local mechanisms change and recover the skeleton of the causal structure over observed variables. Second, we present a method to determine causal orientations by making use of independent changes in the data distribution implied by the underlying causal model, benefiting from information carried by changing distributions. After learning the causal structure, next, we investigate how to efficiently estimate the "driving force" of the nonstationarity of a causal mechanism. That is, we aim to extract from data a low-dimensional representation of changes. The proposed methods are nonparametric, with no hard restrictions on data distributions and causal mechanisms, and do not rely on window segmentation. Furthermore, we find that data heterogeneity benefits causal structure identification even with particular types of confounders. Finally, we show the connection between heterogeneity/nonstationarity and soft intervention in causal discovery. Experimental results on various synthetic and real-world data sets (task-fMRI and stock market data) are presented to demonstrate the efficacy of the proposed methods.

Conformal prediction is a theoretically grounded framework for constructing predictive intervals. We study conformal prediction with missing values in the covariates -- a setting that brings new challenges to uncertainty quantification. We first show that the marginal coverage guarantee of conformal prediction holds on imputed data for any missingness distribution and almost all imputation functions. However, we emphasize that the average coverage varies depending on the pattern of missing values: conformal methods tend to construct prediction intervals that under-cover the response conditionally to some missing patterns. This motivates our novel generalized conformalized quantile regression framework, missing data augmentation, which yields prediction intervals that are valid conditionally to the patterns of missing values, despite their exponential number. We then show that a universally consistent quantile regression algorithm trained on the imputed data is Bayes optimal for the pinball risk, thus achieving valid coverage conditionally to any given data point. Moreover, we examine the case of a linear model, which demonstrates the importance of our proposal in overcoming the heteroskedasticity induced by missing values. Using synthetic and data from critical care, we corroborate our theory and report improved performance of our methods.

Various stuff and things in visual data possess specific traits, which can be learned by deep neural networks and are implicitly represented as the visual prior, e.g., object location and shape, in the model. Such prior potentially impacts many vision tasks. For example, in conditional image synthesis, spatial conditions failing to adhere to the prior can result in visually inaccurate synthetic results. This work aims to explicitly learn the visual prior and enable the customization of sampling. Inspired by advances in language modeling, we propose to learn Visual prior via Generative Pre-Training, dubbed VisorGPT. By discretizing visual locations of objects, e.g., bounding boxes, human pose, and instance masks, into sequences, \our~can model visual prior through likelihood maximization. Besides, prompt engineering is investigated to unify various visual locations and enable customized sampling of sequential outputs from the learned prior. Experimental results demonstrate that \our~can effectively model the visual prior, which can be employed for many vision tasks, such as customizing accurate human pose for conditional image synthesis models like ControlNet. Code will be released at https://github.com/Sierkinhane/VisorGPT.

Causal sensitivity analysis aims to provide bounds for causal effect estimates in the presence of unobserved confounding. However, existing methods for causal sensitivity analysis are per-instance procedures, meaning that changes to the dataset, causal query, sensitivity level, or treatment require new computation. Here, we instead present an in-context learning approach. Specifically, we propose an amortized approach to causal sensitivity analysis based on prior-data fitted networks. A key challenge is that the sensitivity bounds are not directly available when sampling training data. To address this, we develop a general prior-data construction that is applicable across the class of generalized treatment sensitivity models. Our construction involves a Lagrangian scalarization of the objective to generate training labels for the bounds through a tradeoff between causal effect min/max-imization and sensitivity model violation, which avoids model-specific analytical derivations. We further show that, under standard convexity and linearity conditions, our objective recovers the full Pareto frontier of solutions. Empirically, we demonstrate our amortized approach across various datasets, causal queries, and sensitivity levels, where our approach achieves a test-time computation that is orders of magnitude faster than per-instance methods. To the best of our knowledge, ours is the first foundation model for in-context learning for causal sensitivity analysis.

Autoregressive video diffusion models hold promise for world simulation but are vulnerable to exposure bias arising from the train-test mismatch. While recent works address this via post-training, they typically rely on a bidirectional teacher model or online discriminator. To achieve an end-to-end solution, we introduce Resampling Forcing, a teacher-free framework that enables training autoregressive video models from scratch and at scale. Central to our approach is a self-resampling scheme that simulates inference-time model errors on history frames during training. Conditioned on these degraded histories, a sparse causal mask enforces temporal causality while enabling parallel training with frame-level diffusion loss. To facilitate efficient long-horizon generation, we further introduce history routing, a parameter-free mechanism that dynamically retrieves the top-k most relevant history frames for each query. Experiments demonstrate that our approach achieves performance comparable to distillation-based baselines while exhibiting superior temporal consistency on longer videos owing to native-length training.

Users of music streaming, video streaming, news recommendation, and e-commerce services often engage with content in a sequential manner. Providing and evaluating good sequences of recommendations is therefore a central problem for these services. Prior reweighting-based counterfactual evaluation methods either suffer from high variance or make strong independence assumptions about rewards. We propose a new counterfactual estimator that allows for sequential interactions in the rewards with lower variance in an asymptotically unbiased manner. Our method uses graphical assumptions about the causal relationships of the slate to reweight the rewards in the logging policy in a way that approximates the expected sum of rewards under the target policy. Extensive experiments in simulation and on a live recommender system show that our approach outperforms existing methods in terms of bias and data efficiency for the sequential track recommendations problem.

We propose a novel hierarchical Bayesian model for learning with a large (possibly infinite) number of tasks/episodes, which suits well the few-shot meta learning problem. We consider episode-wise random variables to model episode-specific target generative processes, where these local random variables are governed by a higher-level global random variate. The global variable helps memorize the important information from historic episodes while controlling how much the model needs to be adapted to new episodes in a principled Bayesian manner. Within our model framework, the prediction on a novel episode/task can be seen as a Bayesian inference problem. However, a main obstacle in learning with a large/infinite number of local random variables in online nature, is that one is not allowed to store the posterior distribution of the current local random variable for frequent future updates, typical in conventional variational inference. We need to be able to treat each local variable as a one-time iterate in the optimization. We propose a Normal-Inverse-Wishart model, for which we show that this one-time iterate optimization becomes feasible due to the approximate closed-form solutions for the local posterior distributions. The resulting algorithm is more attractive than the MAML in that it is not required to maintain computational graphs for the whole gradient optimization steps per episode. Our approach is also different from existing Bayesian meta learning methods in that unlike dealing with a single random variable for the whole episodes, our approach has a hierarchical structure that allows one-time episodic optimization, desirable for principled Bayesian learning with many/infinite tasks. The code is available at https://github.com/minyoungkim21/niwmeta.

Minibatch optimal transport coupling straightens paths in unconditional flow matching. This leads to computationally less demanding inference as fewer integration steps and less complex numerical solvers can be employed when numerically solving an ordinary differential equation at test time. However, in the conditional setting, minibatch optimal transport falls short. This is because the default optimal transport mapping disregards conditions, resulting in a conditionally skewed prior distribution during training. In contrast, at test time, we have no access to the skewed prior, and instead sample from the full, unbiased prior distribution. This gap between training and testing leads to a subpar performance. To bridge this gap, we propose conditional optimal transport C^2OT that adds a conditional weighting term in the cost matrix when computing the optimal transport assignment. Experiments demonstrate that this simple fix works with both discrete and continuous conditions in 8gaussians-to-moons, CIFAR-10, ImageNet-32x32, and ImageNet-256x256. Our method performs better overall compared to the existing baselines across different function evaluation budgets. Code is available at https://hkchengrex.github.io/C2OT

Out-of-distribution (OOD) prediction is often approached by restricting models to causal or invariant covariates, avoiding non-causal spurious associations that may be unstable across environments. Despite its theoretical appeal, this strategy frequently underperforms empirical risk minimization (ERM) in practice. We investigate the source of this gap and show that such failures naturally arise when only a subset of the true causes of the outcome is observed. In these settings, non-causal spurious covariates can serve as informative proxies for unobserved causes and substantially improve prediction, except under distribution shifts that break these proxy relationships. Consequently, the optimal set of predictive covariates is neither universal nor necessarily exhibits invariant relationships with the outcome across all environments, but instead depends on the specific type of shift encountered. Crucially, we observe that different covariate shifts induce distinct, observable signatures in the covariate distribution itself. Moreover, these signatures can be extracted from unlabeled data in the target OOD environment and used to assess when proxy covariates remain reliable and when they fail. Building on this observation, we propose an environment-adaptive covariate selection (EACS) algorithm that maps environment-level covariate summaries to environment-specific covariate sets, while allowing the incorporation of prior causal knowledge as constraints. Across simulations and applied datasets, EACS consistently outperforms static causal, invariant, and ERM-based predictors under diverse distribution shifts.

Egocentric manipulation videos are highly challenging due to severe occlusions during interactions and frequent object entries and exits from the camera view as the person moves. Current methods typically focus on recovering either hand or object pose in isolation, but both struggle during interactions and fail to handle out-of-sight cases. Moreover, their independent predictions often lead to inconsistent hand-object relations. We introduce WHOLE, a method that holistically reconstructs hand and object motion in world space from egocentric videos given object templates. Our key insight is to learn a generative prior over hand-object motion to jointly reason about their interactions. At test time, the pretrained prior is guided to generate trajectories that conform to the video observations. This joint generative reconstruction substantially outperforms approaches that process hands and objects separately followed by post-processing. WHOLE achieves state-of-the-art performance on hand motion estimation, 6D object pose estimation, and their relative interaction reconstruction. Project website: https://judyye.github.io/whole-www

A desired closure property in Bayesian probability is that an updated posterior distribution be in the same class of distributions --- say Gaussians --- as the prior distribution. When the updating takes place via a statistical model, one calls the class of prior distributions the `conjugate priors' of the model. This paper gives (1) an abstract formulation of this notion of conjugate prior, using channels, in a graphical language, (2) a simple abstract proof that such conjugate priors yield Bayesian inversions, and (3) a logical description of conjugate priors that highlights the required closure of the priors under updating. The theory is illustrated with several standard examples, also covering multiple updating.

We present an approach to learn general robot manipulation priors from 3D hand-object interaction trajectories. We build a framework to use in-the-wild videos to generate sensorimotor robot trajectories. We do so by lifting both the human hand and the manipulated object in a shared 3D space and retargeting human motions to robot actions. Generative modeling on this data gives us a task-agnostic base policy. This policy captures a general yet flexible manipulation prior. We empirically demonstrate that finetuning this policy, with both reinforcement learning (RL) and behavior cloning (BC), enables sample-efficient adaptation to downstream tasks and simultaneously improves robustness and generalizability compared to prior approaches. Qualitative experiments are available at: https://hgaurav2k.github.io/hop/.

Large Vision-Language Models (LVLMs) have demonstrated outstanding performance across various multimodal tasks. However, they suffer from a problem known as language prior, where responses are generated based solely on textual patterns while disregarding image information. Addressing the issue of language prior is crucial, as it can lead to undesirable biases or hallucinations when dealing with images that are out of training distribution. Despite its importance, current methods for accurately measuring language priors in LVLMs are poorly studied. Although existing benchmarks based on counterfactual or out-of-distribution images can partially be used to measure language priors, they fail to disentangle language priors from other confounding factors. To this end, we propose a new benchmark called VLind-Bench, which is the first benchmark specifically designed to measure the language priors, or blindness, of LVLMs. It not only includes tests on counterfactual images to assess language priors but also involves a series of tests to evaluate more basic capabilities such as commonsense knowledge, visual perception, and commonsense biases. For each instance in our benchmark, we ensure that all these basic tests are passed before evaluating the language priors, thereby minimizing the influence of other factors on the assessment. The evaluation and analysis of recent LVLMs in our benchmark reveal that almost all models exhibit a significant reliance on language priors, presenting a strong challenge in the field.

Specifying rewards for reinforcement learned (RL) agents is challenging. Preference-based RL (PbRL) mitigates these challenges by inferring a reward from feedback over sets of trajectories. However, the effectiveness of PbRL is limited by the amount of feedback needed to reliably recover the structure of the target reward. We present the PRIor Over Rewards (PRIOR) framework, which incorporates priors about the structure of the reward function and the preference feedback into the reward learning process. Imposing these priors as soft constraints on the reward learning objective reduces the amount of feedback required by half and improves overall reward recovery. Additionally, we demonstrate that using an abstract state space for the computation of the priors further improves the reward learning and the agent's performance.

In Online Continual Learning (OCL) a learning system receives a stream of data and sequentially performs prediction and training steps. Important challenges in OCL are concerned with automatic adaptation to the particular non-stationary structure of the data, and with quantification of predictive uncertainty. Motivated by these challenges we introduce a probabilistic Bayesian online learning model by using a (possibly pretrained) neural representation and a state space model over the linear predictor weights. Non-stationarity over the linear predictor weights is modelled using a parameter drift transition density, parametrized by a coefficient that quantifies forgetting. Inference in the model is implemented with efficient Kalman filter recursions which track the posterior distribution over the linear weights, while online SGD updates over the transition dynamics coefficient allows to adapt to the non-stationarity seen in data. While the framework is developed assuming a linear Gaussian model, we also extend it to deal with classification problems and for fine-tuning the deep learning representation. In a set of experiments in multi-class classification using data sets such as CIFAR-100 and CLOC we demonstrate the predictive ability of the model and its flexibility to capture non-stationarity.