EHR repositories contain large amounts of wide-ranging patient and treatment information and are essential for the development of individualized treatments in the context of disease progression [14]. With the broad adoption of EHR in the US, a large variety of data types are now routinely collected over long periods of time. This has ushered in an era of research focused on the applications and development of data-analytic tools for mining historical records of medical data to drive novel insight. Broadly, the extraction of meaningful patterns through unsupervised learning [31, 23, 17, 10] and the prediction of outcomes through supervised learning [22, 43, 41, 40, 37, 16, 13, 34, 3] are two important directions. Unsupervised methods can be applied towards many different tasks, such as prediction, imputation, and simulation; and often contain a model of the underlying structure in the data [29]. This underlying structure is not directly observed and can lead to insights that are otherwise difficult to produce, especially for large and complex data sets.

Diffusion-based generative models have achieved promising results recently, but raise an array of open questions in terms of conceptual understanding, theoretical analysis, algorithm improvement and extensions to discrete, structured, non-Euclidean domains. This work tries to re-exam the overall framework, in order to gain better theoretical understandings and develop algorithmic extensions for data from arbitrary domains. By viewing diffusion models as latent variable models with unobserved diffusion trajectories and applying maximum likelihood estimation (MLE) with latent trajectories imputed from an auxiliary distribution, we show that both the model construction and the imputation of latent trajectories amount to constructing diffusion bridge processes that achieve deterministic values and constraints at end point, for which we provide a systematic study and a suit of tools. Leveraging our framework, we present 1) a first theoretical error analysis for learning diffusion generation models, and 2) a simple and unified approach to learning on data from different discrete and constrained domains. Experiments show that our methods perform superbly on generating images, semantic segments and 3D point clouds.

In many scenarios such as genome-wide association studies where dependences between variables commonly exist, it is often of interest to infer the interaction effects in the model. However, testing pairwise interactions among millions of variables in complex and high-dimensional data suffers from low statistical power and huge computational cost. To address these challenges, we propose a two-stage testing procedure with false discovery rate (FDR) control, which is known as a less conservative multiple-testing correction. Theoretically, the difficulty in the FDR control dues to the data dependence among test statistics in two stages, and the fact that the number of hypothesis tests conducted in the second stage depends on the screening result in the first stage. By using the Cram\'er type moderate deviation technique, we show that our procedure controls FDR at the desired level asymptotically in the generalized linear model (GLM), where the model is allowed to be misspecified. In addition, the asymptotic power of the FDR control procedure is rigorously established. We demonstrate via comprehensive simulation studies that our two-stage procedure is computationally more efficient than the classical BH procedure, with a comparable or improved statistical power. Finally, we apply the proposed method to a bladder cancer data from dbGaP where the scientific goal is to identify genetic susceptibility loci for bladder cancer.

This paper attempts to establish the theoretical foundation for the emerging super-model paradigm via domain adaptation, where one first trains a very large-scale model, {\it i.e.}, super model (or foundation model in some other papers), on a large amount of data and then adapts it to various specific domains. Super-model paradigms help reduce computational and data cost and carbon emission, which is critical to AI industry, especially enormous small and medium-sized enterprises. We model the super-model paradigm as a two-stage diffusion process: (1) in the pre-training stage, the model parameter diffuses from random initials and converges to a steady distribution; and (2) in the fine-tuning stage, the model parameter is transported to another steady distribution. Both training stages can be mathematically modeled by the Uhlenbeck-Ornstein process which converges to two Maxwell-Boltzmann distributions, respectively, each of which characterizes the corresponding convergent model. An $\mathcal O(1/\sqrt{N})$ generalization bound is then established via PAC-Bayesian framework. The theory finds that the generalization error of the fine-tuning stage is dominant in domain adaptation. In addition, our theory suggests that the generalization is determined by a new measure that characterizes the domain discrepancy between the source domain and target domain, based on the covariance matrices and the shift of the converged local minimum.

However, estimating treatment effects using EHR data poses several challenges, including time-varying confounding, repeated and temporally non-aligned measurements of covariates, treatment assignments and outcomes, and loss-to-follow-up due to dropout. Here, we develop the Subgroup Discovery for Longitudinal Data (SDLD) algorithm, a tree-based algorithm for discovering subgroups with heterogeneous treatment effects using longitudinal data by combining the generalized interaction tree algorithm, a general data-driven method for subgroup discovery, with longitudinal targeted maximum likelihood estimation. We apply the algorithm to EHR data to discover subgroups of people living with human immunodeficiency virus (HIV) who are at higher risk of weight gain when receiving dolutegravir-containing antiretroviral therapies (ARTs) versus when receiving non dolutegravir-containing ARTs. Key words: Causal Inference; Dolutegravir; Electronic health record; Heterogeneity of treatment effects; Longitudinal targeted maximum likelihood estimation; Machine learning; Recursive partitioning; Subgroup discovery.

Structural health monitoring (SHM) has been an active research area for the last three decades, and has accumulated a number of critical advances over that period, as can be seen in the literature. However, SHM is still facing challenges because of the paucity of damage-state data, operational and environmental fluctuations, repeatability issues, and changes in boundary conditions. These issues present as inconsistencies in the captured features and can have a huge impact on the practical implementation, but more critically, on the generalisation of the technology. Population-based SHM has been designed to address some of these concerns by modelling and transferring missing information using data collected from groups of similar structures. In this work, vibration data were collected from four healthy, nominally-identical, full-scale composite helicopter blades. Manufacturing differences (e.g., slight differences in geometry and/or material properties), among the blades presented as variability in their structural dynamics, which can be very problematic for SHM based on machine learning from vibration data. This work aims to address this variability by defining a general model for the frequency response functions of the blades, called a form, using mixtures of Gaussian processes.

This article studies the estimation of latent community memberships from pairwise interactions in a network of $N$ nodes, where the observed interactions can be of arbitrary type, including binary, categorical, and vector-valued, and not excluding even more general objects such as time series or spatial point patterns. As a generative model for such data, we introduce a stochastic block model with a general measurable interaction space $\mathcal S$, for which we derive information-theoretic bounds for the minimum achievable error rate. These bounds yield sharp criteria for the existence of consistent and strongly consistent estimators in terms of data sparsity, statistical similarity between intra- and inter-block interaction distributions, and the shape and size of the interaction space. The general framework makes it possible to study temporal and multiplex networks with $\mathcal S = \{0,1\}^T$, in settings where both $N \to \infty$ and $T \to \infty$, and the temporal interaction patterns are correlated over time. For temporal Markov interactions, we derive sharp consistency thresholds. We also present fast online estimation algorithms which fully utilise the non-binary nature of the observed data. Numerical experiments on synthetic and real data show that these algorithms rapidly produce accurate estimates even for very sparse data arrays.

We study the application of the factor graph framework for symbol detection on linear inter-symbol interference channels. Cyclic factor graphs have the potential to yield low-complexity symbol detectors, but are suboptimal if the ubiquitous sum-product algorithm is applied. In this paper, we present and evaluate strategies to improve the performance of cyclic factor graph-based symbol detection algorithms by means of neural enhancement. In particular, we apply neural belief propagation as an effective way to counteract the effect of cycles within the factor graph. We further propose the application and optimization of a linear preprocessor of the channel output. By modifying the observation model, the preprocessing can effectively change the underlying factor graph, thereby significantly improving the detection performance as well as reducing the complexity.

While sample efficiency is the main motive for use of Bayesian optimisation when black-box functions are expensive to evaluate, the standard approach based on type II maximum likelihood (ML-II) may fail and result in disappointing performance in small-sample trials. The paper provides three compelling reasons to adopt fully Bayesian optimisation (FBO) as an alternative. First, failures of ML-II are more commonplace than implied by the existing studies using the contrived settings. Second, FBO is more robust than ML-II, and the price of robustness is almost trivial. Third, FBO has become simple to implement and fast enough to be practical. The paper supports the argument using relevant experiments, which reflect the current practice regarding models, algorithms, and software platforms. Since the benefits seem to outweigh the costs, researchers should consider adopting FBO for their applications so that they can guard against potential failures that end up wasting precious research resources.

Modern approaches for simulation-based inference rely upon deep learning surrogates to enable approximate inference with computer simulators. In practice, the estimated posteriors' computational faithfulness is, however, rarely guaranteed. For example, Hermans et al. (2021) show that current simulation-based inference algorithms can produce posteriors that are overconfident, hence risking false inferences. In this work, we introduce Balanced Neural Ratio Estimation (BNRE), a variation of the NRE algorithm designed to produce posterior approximations that tend to be more conservative, hence improving their reliability, while sharing the same Bayes optimal solution. We achieve this by enforcing a balancing condition that increases the quantified uncertainty in small simulation budget regimes while still converging to the exact posterior as the budget increases. We provide theoretical arguments showing that BNRE tends to produce posterior surrogates that are more conservative than NRE's. We evaluate BNRE on a wide variety of tasks and show that it produces conservative posterior surrogates on all tested benchmarks and simulation budgets. Finally, we emphasize that BNRE is straightforward to implement over NRE and does not introduce any computational overhead.