Interacting systems are prevalent in nature. It is challenging to accurately predict the dynamics of the system if its constituent components are analyzed independently. We develop a graph-based model that unveils the systemic interactions of time series observed at irregular time points, by using a directed acyclic graph to model the conditional dependencies (a form of causal notation) of the system components and learning this graph in tandem with a continuous-time model that parameterizes the solution curves of ordinary differential equations (ODEs). Our technique, a graph neural flow, leads to substantial enhancements over non-graph-based methods, as well as graph-based methods without the modeling of conditional dependencies. We validate our approach on several tasks, including time series classification and forecasting, to demonstrate its efficacy.

Real-world data is often assumed to lie within a low-dimensional structure embedded in high-dimensional space. In practical settings, we observe only a finite set of samples, forming what we refer to as the sample data subspace. It serves an essential approximation supporting tasks such as dimensionality reduction and generation. A major challenge lies in whether generative models can reliably synthesize samples that stay within this subspace rather than drifting away from the underlying structure. In this work, we provide theoretical insights into this challenge by leveraging Flow Matching models, which transform a simple prior into a complex target distribution via a learned velocity field. By treating the real data distribution as discrete, we derive analytical expressions for the optimal velocity field under a Gaussian prior, showing that generated samples memorize real data points and represent the sample data subspace exactly. To generalize to suboptimal scenarios, we introduce the Orthogonal Subspace Decomposition Network (OSDNet), which systematically decomposes the velocity field into subspace and off-subspace components. Our analysis shows that the off-subspace component decays, while the subspace component generalizes within the sample data subspace, ensuring generated samples preserve both proximity and diversity.

Reinforcement learning utilizing kernel ridge regression to predict the expected value function represents a powerful method with great representational capacity. This setting is a highly versatile framework amenable to analytical results. We consider kernel-based function approximation for RL in the infinite horizon average reward setting, also referred to as the undiscounted setting. We propose an optimistic algorithm, similar to acquisition function based algorithms in the special case of bandits. We establish novel no-regret performance guarantees for our algorithm, under kernel-based modelling assumptions. Additionally, we derive a novel confidence interval for the kernel-based prediction of the expected value function, applicable across various RL problems.

Data increasingly take the form of a multi-way array, or tensor, in several biomedical domains. Such tensors are often incompletely observed. For example, we are motivated by longitudinal microbiome studies in which several timepoints are missing for several subjects. There is a growing literature on missing data imputation for tensors. However, existing methods give a point estimate for missing values without capturing uncertainty. We propose a multiple imputation approach for tensors in a flexible Bayesian framework, that yields realistic simulated values for missing entries and can propagate uncertainty through subsequent analyses. Our model uses efficient and widely applicable conjugate priors for a CANDECOMP/PARAFAC (CP) factorization, with a separable residual covariance structure. This approach is shown to perform well with respect to both imputation accuracy and uncertainty calibration, for scenarios in which either single entries or entire fibers of the tensor are missing. For two microbiome applications, it is shown to accurately capture uncertainty in the full microbiome profile at missing timepoints and used to infer trends in species diversity for the population. Documented R code to perform our multiple imputation approach is available at https://github.com/lockEF/MultiwayImputation .

Causal discovery is essential for understanding relationships among variables of interest in many scientific domains. In this paper, we focus on permutation-based methods for learning causal graphs in Linear Gaussian Acyclic Models (LiGAMs), where the permutation encodes a causal ordering of the variables. Existing methods in this setting are not scalable due to their high computational complexity. These methods are comprised of two main components: (i) constructing a specific DAG, $\mathcal{G}^\pi$, for a given permutation $\pi$, which represents the best structure that can be learned from the available data while adhering to $\pi$, and (ii) searching over the space of permutations (i.e., causal orders) to minimize the number of edges in $\mathcal{G}^\pi$. We introduce QWO, a novel approach that significantly enhances the efficiency of computing $\mathcal{G}^\pi$ for a given permutation $\pi$. QWO has a speed-up of $O(n^2)$ ($n$ is the number of variables) compared to the state-of-the-art BIC-based method, making it highly scalable. We show that our method is theoretically sound and can be integrated into existing search strategies such as GRASP and hill-climbing-based methods to improve their performance.

We study the density estimation problem defined as follows: given $k$ distributions $p_1, \ldots, p_k$ over a discrete domain $[n]$, as well as a collection of samples chosen from a ``query'' distribution $q$ over $[n]$, output $p_i$ that is ``close'' to $q$. Recently~\cite{aamand2023data} gave the first and only known result that achieves sublinear bounds in {\em both} the sampling complexity and the query time while preserving polynomial data structure space. However, their improvement over linear samples and time is only by subpolynomial factors. Our main result is a lower bound showing that, for a broad class of data structures, their bounds cannot be significantly improved. In particular, if an algorithm uses $O(n/\log^c k)$ samples for some constant $c>0$ and polynomial space, then the query time of the data structure must be at least $k^{1-O(1)/\log \log k}$, i.e., close to linear in the number of distributions $k$. This is a novel \emph{statistical-computational} trade-off for density estimation, demonstrating that any data structure must use close to a linear number of samples or take close to linear query time. The lower bound holds even in the realizable case where $q=p_i$ for some $i$, and when the distributions are flat (specifically, all distributions are uniform over half of the domain $[n]$). We also give a simple data structure for our lower bound instance with asymptotically matching upper bounds. Experiments show that the data structure is quite efficient in practice.

Stein variational gradient descent (SVGD) [Liu and Wang, 2016] performs approximate Bayesian inference by representing the posterior with a set of particles. However, SVGD suffers from variance collapse, i.e. poor predictions due to underestimating uncertainty [Ba et al., 2021], even for moderately-dimensional models such as small Bayesian neural networks (BNNs). To address this issue, we generalize SVGD by letting each particle parameterize a component distribution in a mixture model. Our method, Stein Mixture Inference (SMI), optimizes a lower bound to the evidence (ELBO) and introduces user-specified guides parameterized by particles. SMI extends the Nonlinear SVGD framework [Wang and Liu, 2019] to the case of variational Bayes. SMI effectively avoids variance collapse, judging by a previously described test developed for this purpose, and performs well on standard data sets. In addition, SMI requires considerably fewer particles than SVGD to accurately estimate uncertainty for small BNNs. The synergistic combination of NSVGD, ELBO optimization and user-specified guides establishes a promising approach towards variational Bayesian inference in the case of tall and wide data.

Hyperparameters are configuration variables controlling the behavior of machine learning algorithms. They are ubiquitous in machine learning and artificial intelligence and the choice of their values determine the effectiveness of systems based on these technologies. Manual hyperparameter search is often unsatisfactory and becomes unfeasible when the number of hyperparameters is large. Automating the search is an important step towards automating machine learning, freeing researchers and practitioners alike from the burden of finding a good set of hyperparameters by trial and error. In this survey, we present a unified treatment of hyperparameter optimization, providing the reader with examples and insights into the state-of-the-art. We cover the main families of techniques to automate hyperparameter search, often referred to as hyperparameter optimization or tuning, including random and quasi-random search, bandit-, model- and gradient- based approaches. We further discuss extensions, including online, constrained, and multi-objective formulations, touch upon connections with other fields such as meta-learning and neural architecture search, and conclude with open questions and future research directions.

Kernel embeddings have emerged as a powerful tool for representing probability measures in a variety of statistical inference problems. By mapping probability measures into a reproducing kernel Hilbert space (RKHS), kernel embeddings enable flexible representations of complex relationships between variables. They serve as a mechanism for efficiently transferring the representation of a distribution downstream to other tasks, such as hypothesis testing or causal effect estimation. In the context of causal inference, the main challenges include identifying causal associations and estimating the average treatment effect from observational data, where confounding variables may obscure direct cause-and-effect relationships. Kernel embeddings provide a robust nonparametric framework for addressing these challenges. They allow for the representations of distributions of observational data and their seamless transformation into representations of interventional distributions to estimate relevant causal quantities.

In complex systems, processes operate across multiple time scales, such as rapid fluctuations in environmental conditions, intermediate responses like population dynamics, and slower shifts such as ecosystem succession or climate change. These dynamics are often nested, with fast processes embedded within slower ones. Fine-scale, rapid changes can accumulate over time to influence large-scale trends, while slower processes provide the conditions for fast dynamics to unfold. This interplay between processes at different time scales can lead to transient behaviors, where a system remains in one dynamic state for an extended period before abruptly shifting to another [4]. In ecological systems, these dynamics often manifest as long transients--periods of apparent stability followed by sudden regime shifts. These shifts can occur without any obvious external trigger, driven instead by internal processes or responses to environmental variability [6]. During these phases, a system may exhibit consistent behavior over time before transitioning to a different dynamic regime, which could involve altered oscillatory patterns or a completely new structure. Such transitions are difficult to predict, as they are nonlinear, involve systems operating at multiple interacting scales, and are influenced by stochasticity [5, 2]. Understanding these multiscale and nonlinear interactions is essential for anticipating regime shifts, which are often most consequential at the coarsest time scales, where changes in slow-moving processes like ecosystem succession or long-term climate changes lead to impactful, irreversible transitions [6].