Nonrigid registration is conventionally divided into point set registration, which aligns sparse geometries, and image registration, which aligns continuous intensity fields on regular grids. However, this dichotomy creates a critical bottleneck for emerging scientific data, such as spatial transcriptomics, where high-dimensional vector-valued functions, e.g., gene expression, are defined on irregular, sparse manifolds. Consequently, researchers currently face a forced choice: either sacrifice single-cell resolution via voxelization to utilize image-based tools, or ignore the critical functional signal to utilize geometric tools. To resolve this dilemma, we propose Domain Elastic Transform (DET), a grid-free probabilistic framework that unifies geometric and functional alignment. By treating data as functions on irregular domains, DET registers high-dimensional signals directly without binning. We formulate the problem within a rigorous Bayesian framework, modeling domain deformation as an elastic motion guided by a joint spatial-functional likelihood. The method is fully unsupervised and scalable, utilizing feature-sensitive downsampling to handle massive atlases. We demonstrate that DET achieves 92\% topological preservation on MERFISH data where state-of-the-art optimal transport methods struggle ($<$5\%), and successfully registers whole-embryo Stereo-seq atlases across developmental stages -- a task involving massive scale and complex nonrigid growth. The implementation of DET is available on {https://github.com/ohirose/bcpd} (since Mar, 2025).

This paper develops a unified framework for measuring concentration in weighted systems embedded in networks of interactions. While traditional indices such as the Herfindahl-Hirschman Index capture dispersion in weights, they neglect the topology of relationships among the elements receiving those weights. To address this limitation, we introduce a family of topology-aware concentration indices that jointly account for weight distributions and network structure. At the core of the framework lies a baseline Network Concentration Index (NCI), defined as a normalized quadratic form that measures the fraction of potential weighted interconnection realized along observed network links. Building on this foundation, we construct a flexible class of extensions that modify either the interaction structure or the normalization benchmark, including weighted, density-adjusted, null-model, degree-constrained, transformed-data, and multi-layer variants. This family of indices preserves key properties such as normalization, invariance, and interpretability, while allowing concentration to be evaluated across different dimensions of dependence, including intensity, higher-order interactions, and extreme events. Theoretical results characterize the indices and establish their relationship with classical concentration and network measures. Empirical and simulation evidence demonstrate that systems with identical weight distributions may exhibit markedly different levels of structural concentration depending on network topology, highlighting the additional information captured by the proposed framework. The approach is broadly applicable to economic, financial, and complex systems in which weighted elements interact through networks.

Uncertainty quantification for image data is dominated by complex deep learning methods, yet the field lacks an interpretable, mathematically grounded baseline. We propose Bayesian scattering to fill this gap, serving as a first-step baseline akin to the role of Bayesian linear regression for tabular data. Our method couples the wavelet scattering transform-a deep, non-learned feature extractor-with a simple probabilistic head. Because scattering features are derived from geometric principles rather than learned, they avoid overfitting the training distribution. This helps provide sensible uncertainty estimates even under significant distribution shifts. We validate this on diverse tasks, including medical imaging under institution shift, wealth mapping under country-to-country shift, and Bayesian optimization of molecular properties. Our results suggest that Bayesian scattering is a solid baseline for complex uncertainty quantification methods.

Learning causal relations from observational data is a fundamental problem with wide-ranging applications across many fields. Constraint-based methods infer the underlying causal structure by performing conditional independence tests. However, existing algorithms such as the prominent PC algorithm need to perform a large number of independence tests, which in the worst case is exponential in the maximum degree of the causal graph. Despite extensive research, it remains unclear if there exist algorithms with better complexity without additional assumptions. Here, we establish an algorithm that achieves a better complexity of $p^{\mathcal{O}(s)}$ tests, where $p$ is the number of nodes in the graph and $s$ denotes the maximum undirected clique size of the underlying essential graph. Complementing this result, we prove that any constraint-based algorithm must perform at least $2^{Ω(s)}$ conditional independence tests, establishing that our proposed algorithm achieves exponent-optimality up to a logarithmic factor in terms of the number of conditional independence tests needed. Finally, we validate our theoretical findings through simulations, on semi-synthetic gene-expression data, and real-world data, demonstrating the efficiency of our algorithm compared to existing methods in terms of number of conditional independence tests needed.

Bayesian neural network (BNN) posteriors are often considered impractical for inference, as symmetries fragment them, non-identifiabilities inflate dimensionality, and weight-space priors are seen as meaningless. In this work, we study how overparametrization and priors together reshape BNN posteriors and derive implications allowing us to better understand their interplay. We show that redundancy introduces three key phenomena that fundamentally reshape the posterior geometry: balancedness, weight reallocation on equal-probability manifolds, and prior conformity. We validate our findings through extensive experiments with posterior sampling budgets that far exceed those of earlier works, and demonstrate how overparametrization induces structured, prior-aligned weight posterior distributions.

Data assimilation algorithms estimate the state of a dynamical system from partial observations, where the successful performance of these algorithms hinges on costly parameter tuning and on employing an accurate model for the dynamics. This paper introduces a framework for jointly learning the state, dynamics, and parameters of filtering algorithms in data assimilation through a process we refer to as auto-differentiable filtering. The framework leverages a theoretically motivated loss function that enables learning from partial, noisy observations via gradient-based optimization using auto-differentiation. We further demonstrate how several well-known data assimilation methods can be learned or tuned within this framework. To underscore the versatility of auto-differentiable filtering, we perform experiments on dynamical systems spanning multiple scientific domains, such as the Clohessy-Wiltshire equations from aerospace engineering, the Lorenz-96 system from atmospheric science, and the generalized Lotka-Volterra equations from systems biology. Finally, we provide guidelines for practitioners to customize our framework according to their observation model, accuracy requirements, and computational budget.

Diffusion language models (DLMs) have emerged as a promising alternative to autoregressive (AR) models for language modeling, allowing flexible generation order and parallel generation of multiple tokens. However, this flexibility introduces a challenge absent in AR models: the \emph{decoding strategy} -- which determines the order and number of tokens generated at each iteration -- critically affects sampling efficiency. Among decoding strategies explored in practice, confidence-based methods, which adaptively select which and how many tokens to unmask based on prediction confidence, have shown strong empirical performance. Despite this success, our theoretical understanding of confidence-based decoding remains limited. In this work, we develop the first theoretical analysis framework for confidence-based decoding in DLMs. We focus on an entropy sum-based strategy that continues unmasking tokens within each iteration until the cumulative entropy exceeds a threshold, and show that it achieves $\varepsilon$-accurate sampling in KL divergence with an expected number of iterations $\widetilde O(H(X_0)/\varepsilon)$, where $H(X_0)$ denotes the entropy of the target data distribution. Notably, this strategy yields substantial sampling acceleration when the data distribution has low entropy relative to the sequence length, while automatically adapting to the intrinsic complexity of data without requiring prior knowledge or hyperparameter tuning. Overall, our results provide a theoretical foundation for confidence-based decoding and may inform the design of more efficient decoding strategies for DLMs.

The Riesz representer is a central object in semiparametric statistics and debiased/doubly-robust estimation. Two literatures in econometrics have highlighted the role for directly estimating Riesz representers: the automatic debiased machine learning literature (as in Chernozhukov et al., 2022b), and an independent literature on sieve methods for conditional moment models (as in Chen et al., 2014). These two literatures solve distinct optimization problems that in the population both have the Riesz representer as their solution. We show that with unregularized or ridge-regularized linear, sieve, or RKHS models, the two resulting estimators are numerically equivalent. However, for other regularization schemes such as the Lasso, or more general machine learning function classes including neural networks, the estimators are not necessarily equivalent. In the latter case, the Chen et al. (2014) formulation yields a novel constrained optimization problem for directly estimating Riesz representers with machine learning. Drawing on results from Birrell et al. (2022), we conjecture that this approach may offer statistical advantages at the cost of greater computational complexity.

Time-dependent reliability analysis of nonlinear dynamical systems under stochastic excitations is a critical yet computationally demanding task. Conventional approaches, such as Monte Carlo simulation, necessitate repeated evaluations of computationally expensive numerical solvers, leading to significant computational bottlenecks. To address this challenge, we propose \textit{CoNBONet}, a neuroscience-inspired surrogate model that enables fast, energy-efficient, and uncertainty-aware reliability analysis, providing a scalable alternative to techniques such as Monte Carlo simulations. CoNBONet, short for \textbf{Co}nformalized \textbf{N}euroscience-inspired \textbf{B}ayesian \textbf{O}perator \textbf{Net}work, leverages the expressive power of deep operator networks while integrating neuroscience-inspired neuron models to achieve fast, low-power inference. Unlike traditional surrogates such as Gaussian processes, polynomial chaos expansions, or support vector regression, that may face scalability challenges for high-dimensional, time-dependent reliability problems, CoNBONet offers \textit{fast and energy-efficient inference} enabled by a neuroscience-inspired network architecture, \textit{calibrated uncertainty quantification with theoretical guarantees} via split conformal prediction, and \textit{strong generalization capability} through an operator-learning paradigm that maps input functions to system response trajectories. Validation of the proposed CoNBONet for various nonlinear dynamical systems demonstrates that CoNBONet preserves predictive fidelity, and achieves reliable coverage of failure probabilities, making it a powerful tool for robust and scalable reliability analysis in engineering design.

Based on some recent work of the author on stochastic approximation in non-markovian environments, the situation when the driving random process is non-ergodic in addition to being non-markovian is considered. Using this, we propose an analytic framework for understanding transformer based learning, specifically, the `attention' mechanism, and continual learning, both of which depend on the entire past in principle.