arXiv subjects

Armeen Taeb

Publications and source records attributed to Armeen Taeb.

At least 19 recordsLinked to original sources

arXiv2025

Consensus Tree Estimation with False Discovery Control via Partially Ordered Sets

Trees are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, machine learning, social sciences and anatomy. Summarizing a collection of trees by a single representative is challenging, in part due to the dimensions of both the sample space and the parameter space. We frame consensus tree estimation as a structured feature-selection problem, where leaves and edges are the features. We introduce a partial order on trees, use it to define false discoveries for a candidate summary tree, and develop novel estimation algorithms that control the false discovery rate at a nominal level for a broad class of generative models. We also use the partial order to assess the stability of features in a selected tree. Importantly, our method accommodates unequal leaf sets and non-binary trees, which commonly arise in modern datasets. Our feature-selection perspective yields finite-sample and model-free guarantees and provides a foundation for integrating multiple testing tools into tree estimation. We apply the method to study the origins of complex life. Our estimated tree recapitulates well-known divisions but highlights that there is insufficient data to determine the most recent archaeal ancestor of eukaryotic life.

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arXiv2025

Convex Mixed-Integer Programming for Causal Additive Models with Optimization and Statistical Guarantees

We study the problem of learning a directed acyclic graph from data generated according to an additive, non-linear structural equation model with Gaussian noise. We express each non-linear function through a basis expansion, and derive a maximum likelihood estimator with a group l0-regularization that penalizes the number of edges in the graph. The resulting estimator is formulated through a convex mixed-integer program, enabling the use of branch-and-bound methods to obtain a solution that is guaranteed to be accurate up to a pre-specified optimality gap. Our formulation can naturally encode background knowledge, such as the presence or absence of edges and partial order constraints among the variables. We establish consistency guarantees for our estimator in terms of graph recovery, even when the number of variables grows with the sample size. Additionally, by connecting the optimality guarantees with our statistical error bounds, we derive an early stopping criterion that allows terminating the branch-and-bound procedure while preserving consistency. Compared with existing approaches that either assume equal error variances, restrict to linear structural equation models, or rely on heuristic procedures, our method enjoys both optimization and statistical guarantees. Extensive simulations and real-data analysis show that the proposed method achieves markedly better graph recovery performance.

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arXiv2025

Model-oriented Graph Distances via Partially Ordered Sets

A well-defined distance on the parameter space is key to evaluating estimators, ensuring consistency, and building confidence sets. While there are typically standard distances to adopt in a continuous space, this is not the case for combinatorial parameters such as graphs that represent statistical models. Defined on the graphs alone, existing proposals like the structural Hamming distance ignore the structure of the model space and can thus exhibit undesirable behaviors. We propose a model-oriented framework for defining the distance between graphs that is applicable across different graph classes. Our approach treats each graph as a statistical model and organizes the graphs in a partially ordered set based on model inclusion. This induces a neighborhood structure, from which we define the model-oriented distance as the length of a shortest path through neighbors, yielding a metric in the space of graphs. We apply this framework to probabilistic undirected graphs, causal directed acyclic graphs, {causal acyclic directed mixed graphs}, probabilistic completed partially directed acyclic graphs, and causal maximally oriented partially directed acyclic graphs. We analyze theoretical and empirical behaviors of the model-oriented distance. By exploiting the underlying poset structures, we develop algorithms for computing and bounding the proposed distance that scale to moderate-sized graphs. Finally, we showcase its utility for quantifying the robustness of adjustment sets to errors in specifying the causal graph.

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arXiv2025

An Asymptotically Optimal Coordinate Descent Algorithm for Learning Bayesian Networks from Gaussian Models

This paper studies the problem of learning Bayesian networks from continuous observational data, generated according to a linear Gaussian structural equation model. We consider an $\ell_0$-penalized maximum likelihood estimator for this problem which is known to have favorable statistical properties but is computationally challenging to solve, especially for medium-sized Bayesian networks. We propose a new coordinate descent algorithm to approximate this estimator and prove several remarkable properties of our procedure: the algorithm converges to a coordinate-wise minimum, and despite the non-convexity of the loss function, as the sample size tends to infinity, the objective value of the coordinate descent solution converges to the optimal objective value of the $\ell_0$-penalized maximum likelihood estimator. Finite-sample statistical consistency guarantees are also established. To the best of our knowledge, our proposal is the first coordinate descent procedure endowed with optimality and statistical guarantees in the context of learning Bayesian networks. Numerical experiments on synthetic and real data demonstrate that our coordinate descent method can obtain near-optimal solutions while being scalable.

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arXiv2025

A spectral method for multi-view subspace learning using the product of projections

Multi-view data provides complementary information on the same set of observations, with multi-omics and multimodal sensor data being common examples. Analyzing such data typically requires distinguishing between shared (joint) and unique (individual) signal subspaces from noisy, high-dimensional measurements. Despite many proposed methods, the conditions for reliably identifying joint and individual subspaces remain unclear. We rigorously quantify these conditions, which depend on the ratio of the signal rank to the ambient dimension, principal angles between true subspaces, and noise levels. Our approach characterizes how spectrum perturbations of the product of projection matrices, derived from each view's estimated subspaces, affect subspace separation. Using these insights, we provide an easy-to-use and scalable estimation algorithm. In particular, we employ rotational bootstrap and random matrix theory to partition the observed spectrum into joint, individual, and noise subspaces. Diagnostic plots visualize this partitioning, providing practical and interpretable insights into the estimation performance. In simulations, our method estimates joint and individual subspaces more accurately than existing approaches. Applications to multi-omics data from colorectal cancer patients and nutrigenomic study of mice demonstrate improved performance in downstream predictive tasks.

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arXiv2025

Quantifying uncertainty and stability among highly correlated predictors: a subspace perspective

We study the problem of linear feature selection when features are highly correlated. Such settings pose two fundamental challenges. First, how should model similarity be defined? Simply counting features in common can be misleading: two models may share no features, yet highly correlated features can make the two models very similar in terms of predictive ability. Second, how can feature stability be assessed across runs of a variable selection method? High correlation can yield very different feature sets, so counting how often a feature is selected may label most features as unstable, and selecting stable features would result in models that are too small with poor predictive performance. In essence, these issues arise because existing notions of similarity and stability are "discrete" in nature. To overcome these challenges, we propose a novel framework based on feature subspaces -- the subspaces spanned by selected columns of the feature matrix. This new perspective leads to "continuous" measures of similarity and stability, as well as false positive error, all of which are defined in terms of "closeness" of feature subspaces. Our measures naturally account for feature correlation and reduce to existing discrete notions when features are uncorrelated. To obtain stable models, we propose and theoretically analyze a subspace-based generalization of stability selection (Meinshausen & B\"uhlmann 2010, Taeb et al. 2020), which combines a discrete model search with a continuous subspace-based assessment of stability. On synthetic and real gene expression data, our method improves on existing stability-based approaches by (i) producing multiple stable models that capture feature interchangeability, and (ii) generating larger models with better predictive performance. Our method is implemented in the R package substab.

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arXiv2025

Model Selection over Partially Ordered Sets

In problems such as variable selection and graph estimation, models are characterized by Boolean logical structure such as presence or absence of a variable or an edge. Consequently, false positive error or false negative error can be specified as the number of variables/edges that are incorrectly included or excluded in an estimated model. However, there are several other problems such as ranking, clustering, and causal inference in which the associated model classes do not admit transparent notions of false positive and false negative errors due to the lack of an underlying Boolean logical structure. In this paper, we present a generic approach to endow a collection of models with partial order structure, which leads to a hierarchical organization of model classes as well as natural analogs of false positive and false negative errors. We describe model selection procedures that provide false positive error control in our general setting and we illustrate their utility with numerical experiments.

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arXiv2025

Extremal graphical modeling with latent variables via convex optimization

Extremal graphical models encode the conditional independence structure of multivariate extremes and provide a powerful tool for quantifying the risk of rare events. Prior work on learning these graphs from data has focused on the setting where all relevant variables are observed. For the popular class of Hüsler-Reiss models, we propose the \texttt{eglatent} method, a tractable convex program for learning extremal graphical models in the presence of latent variables. Our approach decomposes the Hüsler-Reiss precision matrix into a sparse component encoding the graphical structure among the observed variables after conditioning on the latent variables, and a low-rank component encoding the effect of a few latent variables on the observed variables. We provide finite-sample guarantees of \texttt{eglatent} and show that it consistently recovers the conditional graph as well as the number of latent variables. We highlight the improved performances of our approach on synthetic and real data.

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arXiv2025

Integer Programming for Learning Directed Acyclic Graphs from Non-identifiable Gaussian Models

We study the problem of learning directed acyclic graphs from continuous observational data, generated according to a linear Gaussian structural equation model. State-of-the-art structure learning methods for this setting have at least one of the following shortcomings: i) they cannot provide optimality guarantees and can suffer from learning sub-optimal models; ii) they rely on the stringent assumption that the noise is homoscedastic, and hence the underlying model is fully identifiable. We overcome these shortcomings and develop a computationally efficient mixed-integer programming framework for learning medium-sized problems that accounts for arbitrary heteroscedastic noise. We present an early stopping criterion under which we can terminate the branch-and-bound procedure to achieve an asymptotically optimal solution and establish the consistency of this approximate solution. In addition, we show via numerical experiments that our method outperforms state-of-the-art algorithms and is robust to noise heteroscedasticity, whereas the performance of some competing methods deteriorates under strong violations of the identifiability assumption. The software implementation of our method is available as the Python package \emph{micodag}.

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arXiv2025

Causality-oriented robustness: exploiting general noise interventions

Since distribution shifts are common in real-world applications, there is a pressing need to develop prediction models that are robust against such shifts. Existing frameworks, such as empirical risk minimization or distributionally robust optimization, either lack generalizability for unseen distributions or rely on postulated distance measures. Alternatively, causality offers a data-driven and structural perspective to robust predictions. However, the assumptions necessary for causal inference can be overly stringent, and the robustness offered by such causal models often lacks flexibility. In this paper, we focus on causality-oriented robustness and propose Distributional Robustness via Invariant Gradients (DRIG), a method that exploits general noise interventions in training data for robust predictions against unseen interventions, and naturally interpolates between in-distribution prediction and causality. In a linear setting, we prove that DRIG yields predictions that are robust among a data-dependent class of distribution shifts. Furthermore, we show that our framework includes anchor regression as a special case, and that it yields prediction models that protect against more diverse perturbations. We establish finite-sample results and extend our approach to semi-supervised domain adaptation to further improve prediction performance. Finally, we empirically validate our methods on synthetic simulations and on single-cell and intensive health care datasets.

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arXiv2025

Characterization and Greedy Learning of Gaussian Structural Causal Models under Unknown Interventions

We consider the problem of recovering the causal structure underlying observations from different experimental conditions when the targets of the interventions in each experiment are unknown. We assume a linear structural causal model with additive Gaussian noise and consider interventions that perturb their targets while maintaining the causal relationships in the system. Different models may entail the same distributions, offering competing causal explanations for the given observations. We fully characterize this equivalence class and offer identifiability results, which we use to derive a greedy algorithm called GnIES to recover the equivalence class of the data-generating model without knowledge of the intervention targets. In addition, we develop a novel procedure to generate semi-synthetic data sets with known causal ground truth but distributions closely resembling those of a real data set of choice. We leverage this procedure and evaluate the performance of GnIES on an array of synthetic and semi-synthetic data sets, and real data from a biological system and a tightly controlled physical system. We provide, in the Python packages gnies and sempler, implementations of GnIES and our semi-synthetic data generation procedure.

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arXiv2023

Learning and scoring Gaussian latent variable causal models with unknown additive interventions

With observational data alone, causal structure learning is a challenging problem. The task becomes easier when having access to data collected from perturbations of the underlying system, even when the nature of these is unknown. Existing methods either do not allow for the presence of latent variables or assume that these remain unperturbed. However, these assumptions are hard to justify if the nature of the perturbations is unknown. We provide results that enable scoring causal structures in the setting with additive, but unknown interventions. Specifically, we propose a maximum-likelihood estimator in a structural equation model that exploits system-wide invariances to output an equivalence class of causal structures from perturbation data. Furthermore, under certain structural assumptions on the population model, we provide a simple graphical characterization of all the DAGs in the interventional equivalence class. We illustrate the utility of our framework on synthetic data as well as real data involving California reservoirs and protein expressions. The software implementation is available as the Python package \emph{utlvce}.

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arXiv2023

Inverse Problems and Data Assimilation

We provide a clear and concise introduction to the subjects of inverse problems and data assimilation, and their inter-relations. The first part of our notes covers inverse problems; this refers to the study of how to estimate unknown model parameters from data. The second part of our notes covers data assimilation; this refers to a particular class of inverse problems in which the unknown parameter is the initial condition (and/or state) of a dynamical system, and the data comprises partial and noisy observations of the state. The third and final part of our notes describes the use of data assimilation methods to solve generic inverse problems by introducing an artificial algorithmic time. Our notes cover, among other topics, maximum a posteriori estimation, (stochastic) gradient descent, variational Bayes, Monte Carlo, importance sampling and Markov chain Monte Carlo for inverse problems; and 3DVAR, 4DVAR, extended and ensemble Kalman filters, and particle filters for data assimilation. Each of parts one and two starts with a chapter on the Bayesian formulation, in which the problem solution is given by a posterior distribution on the unknown parameter. Then the following chapter specializes the Bayesian formulation to a linear-Gaussian setting where explicit characterization of the posterior is possible and insightful. The next two chapters explore methods to extract information from the posterior in nonlinear and non-Gaussian settings using optimization and Gaussian approximations. The final two chapters describe sampling methods that can reproduce the full posterior in the large sample limit. Each chapter closes with a bibliography containing citations to alternative pedagogical literature and to relevant research literature. We also include a set of exercises at the end of parts one and two. Our notes are thus useful for both classroom teaching and self-guided study.

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arXiv2022

Provable concept learning for interpretable predictions using variational autoencoders

In safety-critical applications, practitioners are reluctant to trust neural networks when no interpretable explanations are available. Many attempts to provide such explanations revolve around pixel-based attributions or use previously known concepts. In this paper we aim to provide explanations by provably identifying \emph{high-level, previously unknown ground-truth concepts}. To this end, we propose a probabilistic modeling framework to derive (C)oncept (L)earning and (P)rediction (CLAP) -- a VAE-based classifier that uses visually interpretable concepts as predictors for a simple classifier. Assuming a generative model for the ground-truth concepts, we prove that CLAP is able to identify them while attaining optimal classification accuracy. Our experiments on synthetic datasets verify that CLAP identifies distinct ground-truth concepts on synthetic datasets and yields promising results on the medical Chest X-Ray dataset.

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arXiv2022

A Fast Non-parametric Approach for Local Causal Structure Learning

We study the problem of causal structure learning with essentially no assumptions on the functional relationships and noise. We develop DAG-FOCI, a computationally fast algorithm for this setting that is based on the FOCI variable selection algorithm in~\cite{azadkia2021simple}. DAG-FOCI outputs the set of parents of a response variable of interest. We provide theoretical guarantees of our procedure when the underlying graph does not contain any (undirected) cycle containing the response variable of interest. Furthermore, in the absence of this assumption, we give a conservative guarantee against false positive causal claims when the set of parents is identifiable. We demonstrate the applicability of DAG-FOCI on simulated as well as a real dataset from computational biology~\cite{sachs2005causal}.

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arXiv2020

Learning Exponential Family Graphical Models with Latent Variables using Regularized Conditional Likelihood

Fitting a graphical model to a collection of random variables given sample observations is a challenging task if the observed variables are influenced by latent variables, which can induce significant confounding statistical dependencies among the observed variables. We present a new convex relaxation framework based on regularized conditional likelihood for latent-variable graphical modeling in which the conditional distribution of the observed variables conditioned on the latent variables is given by an exponential family graphical model. In comparison to previously proposed tractable methods that proceed by characterizing the marginal distribution of the observed variables, our approach is applicable in a broader range of settings as it does not require knowledge about the specific form of distribution of the latent variables and it can be specialized to yield tractable approaches to problems in which the observed data are not well-modeled as Gaussian. We demonstrate the utility and flexibility of our framework via a series of numerical experiments on synthetic as well as real data.

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arXiv2020

False Discovery and Its Control in Low Rank Estimation

Models specified by low-rank matrices are ubiquitous in contemporary applications. In many of these problem domains, the row/column space structure of a low-rank matrix carries information about some underlying phenomenon, and it is of interest in inferential settings to evaluate the extent to which the row/column spaces of an estimated low-rank matrix signify discoveries about the phenomenon. However, in contrast to variable selection, we lack a formal framework to assess true/false discoveries in low-rank estimation; in particular, the key source of difficulty is that the standard notion of a discovery is a discrete one that is ill-suited to the smooth structure underlying low-rank matrices. We address this challenge via a geometric reformulation of the concept of a discovery, which then enables a natural definition in the low-rank case. We describe and analyze a generalization of the Stability Selection method of Meinshausen and Bühlmann to control for false discoveries in low-rank estimation, and we demonstrate its utility compared to previous approaches via numerical experiments.

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arXiv2016

Interpreting Latent Variables in Factor Models via Convex Optimization

Latent or unobserved phenomena pose a significant difficulty in data analysis as they induce complicated and confounding dependencies among a collection of observed variables. Factor analysis is a prominent multivariate statistical modeling approach that addresses this challenge by identifying the effects of (a small number of) latent variables on a set of observed variables. However, the latent variables in a factor model are purely mathematical objects that are derived from the observed phenomena, and they do not have any interpretation associated to them. A natural approach for attributing semantic information to the latent variables in a factor model is to obtain measurements of some additional plausibly useful covariates that may be related to the original set of observed variables, and to associate these auxiliary covariates to the latent variables. In this paper, we describe a systematic approach for identifying such associations. Our method is based on solving computationally tractable convex optimization problems, and it can be viewed as a generalization of the minimum-trace factor analysis procedure for fitting factor models via convex optimization. We analyze the theoretical consistency of our approach in a high-dimensional setting as well as its utility in practice via experimental demonstrations with real data.

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