Graphical model selection is a seemingly impossible task when many pairs of variables are never jointly observed; this requires inference of conditional dependencies with no observations of corresponding marginal dependencies. This under-explored statistical problem arises in neuroimaging, for example, when different partially overlapping subsets of neurons are recorded in non-simultaneous sessions. We call this statistical challenge the "Graph Quilting" problem. We study this problem in the context of sparse inverse covariance learning, and focus on Gaussian graphical models where we show that missing parts of the covariance matrix yields an unidentifiable precision matrix specifying the graph. Nonetheless, we show that, under mild conditions, it is possible to correctly identify edges connecting the observed pairs of nodes. Additionally, we show that we can recover a minimal superset of edges connecting variables that are never jointly observed. Thus, one can infer conditional relationships even when marginal relationships are unobserved, a surprising result! To accomplish this, we propose an $\ell_1$-regularized partially observed likelihood-based graph estimator and provide performance guarantees in population and in high-dimensional finite-sample settings. We illustrate our approach using synthetic data, as well as for learning functional neural connectivity from calcium imaging data.
We extend the well-known $\beta$-model for directed graphs to dynamic network setting, where we observe snapshots of adjacency matrices at different time points. We propose a kernel-smoothed likelihood approach for estimating $2n$ time-varying parameters in a network with $n$ nodes, from $N$ snapshots. We establish consistency and asymptotic normality properties of our kernel-smoothed estimators as either $n$ or $N$ diverges. Our results contrast their counterparts in single-network analyses, where $n\to\infty$ is invariantly required in asymptotic studies. We conduct comprehensive simulation studies that confirm our theory's prediction and illustrate the performance of our method from various angles. We apply our method to an email data set and obtain meaningful results.
Machine learning can benefit from causal discovery for interpretation and from causal inference for generalization. In this line of research, a few invariant learning algorithms for out-of-distribution (OOD) generalization have been proposed by using multiple training environments to find invariant relationships. Some of them are focused on causal discovery as Invariant Causal Prediction (ICP), which finds causal parents of a variable of interest, and some directly provide a causal optimal predictor that generalizes well in OOD environments as Invariant Risk Minimization (IRM). This group of algorithms works under the assumption of multiple environments that represent different interventions in the causal inference context. Those environments are not normally available when working with observational data and real-world applications. Here we propose a method to generate them in an efficient way. We assess the performance of this unsupervised learning problem by implementing ICP on simulated data. We also show how to apply ICP efficiently integrated with our method for causal discovery. Finally, we proposed an improved version of our method in combination with ICP for datasets with multiple covariates where ICP and other causal discovery methods normally degrade in performance.
We consider the classic 1-center problem: Given a set $P$ of $n$ points in a metric space find the point in $P$ that minimizes the maximum distance to the other points of $P$. We study the complexity of this problem in $d$-dimensional $\ell_p$-metrics and in edit and Ulam metrics over strings of length $d$. Our results for the 1-center problem may be classified based on $d$ as follows. $\bullet$ Small $d$: Assuming the hitting set conjecture (HSC), we show that when $d=\omega(\log n)$, no subquadratic algorithm can solve 1-center problem in any of the $\ell_p$-metrics, or in edit or Ulam metrics. $\bullet$ Large $d$: When $d=\Omega(n)$, we extend our conditional lower bound to rule out subquartic algorithms for 1-center problem in edit metric (assuming Quantified SETH). On the other hand, we give a $(1+\epsilon)$-approximation for 1-center in Ulam metric with running time $\tilde{O_{\varepsilon}}(nd+n^2\sqrt{d})$. We also strengthen some of the above lower bounds by allowing approximations or by reducing the dimension $d$, but only against a weaker class of algorithms which list all requisite solutions. Moreover, we extend one of our hardness results to rule out subquartic algorithms for the well-studied 1-median problem in the edit metric, where given a set of $n$ strings each of length $n$, the goal is to find a string in the set that minimizes the sum of the edit distances to the rest of the strings in the set.
In Selk and Gertheiss (2022) a nonparametric prediction method for models with multiple functional and categorical covariates is introduced. The dependent variable can be categorical (binary or multi-class) or continuous, thus both classification and regression problems are considered. In the paper at hand the asymptotic properties of this method are developed. A uniform rate of convergence for the regression / classification estimator is given. Further it is shown that, asymptotically, a data-driven least squares cross-validation method can automatically remove irrelevant, noise variables.
Obtaining guarantees on the convergence of the minimizers of empirical risks to the ones of the true risk is a fundamental matter in statistical learning. Instead of deriving guarantees on the usual estimation error, the goal of this paper is to provide concentration inequalities on the distance between the sets of minimizers of the risks for a broad spectrum of estimation problems. In particular, the risks are defined on metric spaces through probability measures that are also supported on metric spaces. A particular attention will therefore be given to include unbounded spaces and non-convex cost functions that might also be unbounded. This work identifies a set of assumptions allowing to describe a regime that seem to govern the concentration in many estimation problems, where the empirical minimizers are stable. This stability can then be leveraged to prove parametric concentration rates in probability and in expectation. The assumptions are verified, and the bounds showcased, on a selection of estimation problems such as barycenters on metric space with positive or negative curvature, subspaces of covariance matrices, regression problems and entropic-Wasserstein barycenters.
Comparison-based learning addresses the problem of learning when, instead of explicit features or pairwise similarities, one only has access to comparisons of the form: \emph{Object $A$ is more similar to $B$ than to $C$.} Recently, it has been shown that, in Hierarchical Clustering, single and complete linkage can be directly implemented using only such comparisons while several algorithms have been proposed to emulate the behaviour of average linkage. Hence, finding hierarchies (or dendrograms) using only comparisons is a well understood problem. However, evaluating their meaningfulness when no ground-truth nor explicit similarities are available remains an open question. In this paper, we bridge this gap by proposing a new revenue function that allows one to measure the goodness of dendrograms using only comparisons. We show that this function is closely related to Dasgupta's cost for hierarchical clustering that uses pairwise similarities. On the theoretical side, we use the proposed revenue function to resolve the open problem of whether one can approximately recover a latent hierarchy using few triplet comparisons. On the practical side, we present principled algorithms for comparison-based hierarchical clustering based on the maximisation of the revenue and we empirically compare them with existing methods.
Bayesian optimization is a methodology for global optimization of unknown and expensive objectives. It combines a surrogate Bayesian regression model with an acquisition function to decide where to evaluate the objective. Typical regression models are given by Gaussian processes with stationary covariance functions. However, these functions are unable to express prior input-dependent information, including possible locations of the optimum. The ubiquity of stationary models has led to the common practice of exploiting prior information via informative mean functions. In this paper, we highlight that these models can perform poorly, especially in high dimensions. We propose novel informative covariance functions for optimization, leveraging nonstationarity to encode preferences for certain regions of the search space and adaptively promote local exploration during optimization. We demonstrate that the proposed functions can increase the sample efficiency of Bayesian optimization in high dimensions, even under weak prior information.
We consider the problem of discovering $K$ related Gaussian directed acyclic graphs (DAGs), where the involved graph structures share a consistent causal order and sparse unions of supports. Under the multi-task learning setting, we propose a $l_1/l_2$-regularized maximum likelihood estimator (MLE) for learning $K$ linear structural equation models. We theoretically show that the joint estimator, by leveraging data across related tasks, can achieve a better sample complexity for recovering the causal order (or topological order) than separate estimations. Moreover, the joint estimator is able to recover non-identifiable DAGs, by estimating them together with some identifiable DAGs. Lastly, our analysis also shows the consistency of union support recovery of the structures. To allow practical implementation, we design a continuous optimization problem whose optimizer is the same as the joint estimator and can be approximated efficiently by an iterative algorithm. We validate the theoretical analysis and the effectiveness of the joint estimator in experiments.
Graph Neural Networks (GNNs) have proven to be useful for many different practical applications. However, many existing GNN models have implicitly assumed homophily among the nodes connected in the graph, and therefore have largely overlooked the important setting of heterophily, where most connected nodes are from different classes. In this work, we propose a novel framework called CPGNN that generalizes GNNs for graphs with either homophily or heterophily. The proposed framework incorporates an interpretable compatibility matrix for modeling the heterophily or homophily level in the graph, which can be learned in an end-to-end fashion, enabling it to go beyond the assumption of strong homophily. Theoretically, we show that replacing the compatibility matrix in our framework with the identity (which represents pure homophily) reduces to GCN. Our extensive experiments demonstrate the effectiveness of our approach in more realistic and challenging experimental settings with significantly less training data compared to previous works: CPGNN variants achieve state-of-the-art results in heterophily settings with or without contextual node features, while maintaining comparable performance in homophily settings.
With the rapid increase of large-scale, real-world datasets, it becomes critical to address the problem of long-tailed data distribution (i.e., a few classes account for most of the data, while most classes are under-represented). Existing solutions typically adopt class re-balancing strategies such as re-sampling and re-weighting based on the number of observations for each class. In this work, we argue that as the number of samples increases, the additional benefit of a newly added data point will diminish. We introduce a novel theoretical framework to measure data overlap by associating with each sample a small neighboring region rather than a single point. The effective number of samples is defined as the volume of samples and can be calculated by a simple formula $(1-\beta^{n})/(1-\beta)$, where $n$ is the number of samples and $\beta \in [0,1)$ is a hyperparameter. We design a re-weighting scheme that uses the effective number of samples for each class to re-balance the loss, thereby yielding a class-balanced loss. Comprehensive experiments are conducted on artificially induced long-tailed CIFAR datasets and large-scale datasets including ImageNet and iNaturalist. Our results show that when trained with the proposed class-balanced loss, the network is able to achieve significant performance gains on long-tailed datasets.