arXiv subjects

Joe Kileel

Publications and source records attributed to Joe Kileel.

At least 37 records · Page 2Linked to original sources

arXiv2024

The G-invariant graph Laplacian

Graph Laplacian based algorithms for data lying on a manifold have been proven effective for tasks such as dimensionality reduction, clustering, and denoising. In this work, we consider data sets whose data points lie on a manifold that is closed under the action of a known unitary matrix Lie group G. We propose to construct the graph Laplacian by incorporating the distances between all the pairs of points generated by the action of G on the data set. We deem the latter construction the ``G-invariant Graph Laplacian'' (G-GL). We show that the G-GL converges to the Laplace-Beltrami operator on the data manifold, while enjoying a significantly improved convergence rate compared to the standard graph Laplacian which only utilizes the distances between the points in the given data set. Furthermore, we show that the G-GL admits a set of eigenfunctions that have the form of certain products between the group elements and eigenvectors of certain matrices, which can be estimated from the data efficiently using FFT-type algorithms. We demonstrate our construction and its advantages on the problem of filtering data on a noisy manifold closed under the action of the special unitary group SU(2).

cs.LG↗

arXiv2024

Algebraic Constraints and Algorithms for Common Lines in Cryo-EM

We revisit the topic of common lines between projection images in single particle cryo-electron microscopy (cryo-EM). We derive a novel low-rank constraint on a certain $2n \times n$ matrix storing properly-scaled basis vectors for the common lines between $n$ projection images of one molecular conformation. Using this algebraic constraint and others, we give optimization algorithms to denoise common lines and recover the unknown 3D rotations associated to the images. As an application, we develop a clustering algorithm to partition a set of noisy images into homogeneous communities using common lines, in the case of discrete heterogeneity in cryo-EM. We demonstrate the methods on synthetic and experimental datasets.

math.OC↗

arXiv2024

The effect of smooth parametrizations on nonconvex optimization landscapes

We develop new tools to study landscapes in nonconvex optimization. Given one optimization problem, we pair it with another by smoothly parametrizing the domain. This is either for practical purposes (e.g., to use smooth optimization algorithms with good guarantees) or for theoretical purposes (e.g., to reveal that the landscape satisfies a strict saddle property). In both cases, the central question is: how do the landscapes of the two problems relate? More precisely: how do desirable points such as local minima and critical points in one problem relate to those in the other problem? A key finding in this paper is that these relations are often determined by the parametrization itself, and are almost entirely independent of the cost function. Accordingly, we introduce a general framework to study parametrizations by their effect on landscapes. The framework enables us to obtain new guarantees for an array of problems, some of which were previously treated on a case-by-case basis in the literature. Applications include: optimizing low-rank matrices and tensors through factorizations; solving semidefinite programs via the Burer-Monteiro approach; training neural networks by optimizing their weights and biases; and quotienting out symmetries.

math.OC↗

arXiv2024

Moment-based metrics for molecules computable from cryo-EM images

Single particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution 3-D structure of biological macromolecules from many noisy and randomly oriented projection images. One notable approach to 3-D reconstruction, known as Kam's method, relies on the moments of the 2-D images. Inspired by Kam's method, we introduce a rotationally invariant metric between two molecular structures, which does not require 3-D alignment. Further, we introduce a metric between a stack of projection images and a molecular structure, which is invariant to rotations and reflections and does not require performing 3-D reconstruction. Additionally, the latter metric does not assume a uniform distribution of viewing angles. We demonstrate uses of the new metrics on synthetic and experimental datasets, highlighting their ability to measure structural similarity.

q-bio.BM↗

arXiv2023

Symmetry Breaking in Symmetric Tensor Decomposition

In this note, we consider the highly nonconvex optimization problem associated with computing the rank decomposition of symmetric tensors. We formulate the invariance properties of the loss function and show that critical points detected by standard gradient based methods are \emph{symmetry breaking} with respect to the target tensor. The phenomena, seen for different choices of target tensors and norms, make possible the use of recently developed analytic and algebraic tools for studying nonconvex optimization landscapes exhibiting symmetry breaking phenomena of similar nature.

math.OC↗

arXiv2023

Snapshot of Algebraic Vision

In this survey article, we present interactions between algebraic geometry and computer vision, which have recently come under the header of algebraic vision. The subject has given new insights in multiple view geometry and its application to 3D scene reconstruction and carried a host of novel problems and ideas back into algebraic geometry.

math.AG↗

arXiv2023

Moment Estimation for Nonparametric Mixture Models Through Implicit Tensor Decomposition

We present an alternating least squares type numerical optimization scheme to estimate conditionally-independent mixture models in $\mathbb{R}^n$, without parameterizing the distributions. Following the method of moments, we tackle an incomplete tensor decomposition problem to learn the mixing weights and componentwise means. Then we compute the cumulative distribution functions, higher moments and other statistics of the component distributions through linear solves. Crucially for computations in high dimensions, the steep costs associated with high-order tensors are evaded, via the development of efficient tensor-free operations. Numerical experiments demonstrate the competitive performance of the algorithm, and its applicability to many models and applications. Furthermore we provide theoretical analyses, establishing identifiability from low-order moments of the mixture and guaranteeing local linear convergence of the ALS algorithm.

math.NA↗

arXiv2023

Estimation under group actions: recovering orbits from invariants

We study a class of orbit recovery problems in which we observe independent copies of an unknown element of $\mathbb{R}^p$, each linearly acted upon by a random element of some group (such as $\mathbb{Z}/p$ or $\mathrm{SO}(3)$) and then corrupted by additive Gaussian noise. We prove matching upper and lower bounds on the number of samples required to approximately recover the group orbit of this unknown element with high probability. These bounds, based on quantitative techniques in invariant theory, give a precise correspondence between the statistical difficulty of the estimation problem and algebraic properties of the group. Furthermore, we give computer-assisted procedures to certify these properties that are computationally efficient in many cases of interest. The model is motivated by geometric problems in signal processing, computer vision, and structural biology, and applies to the reconstruction problem in cryo-electron microscopy (cryo-EM), a problem of significant practical interest. Our results allow us to verify (for a given problem size) that if cryo-EM images are corrupted by noise with variance $σ^2$, the number of images required to recover the molecule structure scales as $σ^6$. We match this bound with a novel (albeit computationally expensive) algorithm for ab initio reconstruction in cryo-EM, based on invariant features of degree at most 3. We further discuss how to recover multiple molecular structures from mixed (or heterogeneous) cryo-EM samples.

math.ST↗

arXiv2023

Scalable symmetric Tucker tensor decomposition

We study the best low-rank Tucker decomposition of symmetric tensors. The motivating application is decomposing higher-order multivariate moments. Moment tensors have special structure and are important to various data science problems. We advocate for projected gradient descent (PGD) method and higher-order eigenvalue decomposition (HOEVD) approximation as computation schemes. Most importantly, we develop scalable adaptations of the basic PGD and HOEVD methods to decompose sample moment tensors. With the help of implicit and streaming techniques, we evade the overhead cost of building and storing the moment tensor. Such reductions make computing the Tucker decomposition realizable for large data instances in high dimensions. Numerical experiments demonstrate the efficiency of the algorithms and the applicability of moment tensor decompositions to real-world datasets. Finally we study the convergence on the Grassmannian manifold, and prove that the update sequence derived by the PGD solver achieves first- and second-order criticality.

math.NA↗

arXiv2023

Moment Varieties for Mixtures of Products

The setting of this article is nonparametric algebraic statistics. We study moment varieties of conditionally independent mixture distributions on $\mathbb{R}^n$. These are the secant varieties of toric varieties that express independence in terms of univariate moments. Our results revolve around the dimensions and defining polynomials of these varieties.

math.AG↗

arXiv2023

Autocorrelation analysis for cryo-EM with sparsity constraints: Improved sample complexity and projection-based algorithms

The number of noisy images required for molecular reconstruction in single-particle cryo-electron microscopy (cryo-EM) is governed by the autocorrelations of the observed, randomly-oriented, noisy projection images. In this work, we consider the effect of imposing sparsity priors on the molecule. We use techniques from signal processing, optimization, and applied algebraic geometry to obtain new theoretical and computational contributions for this challenging non-linear inverse problem with sparsity constraints. We prove that molecular structures modeled as sums of Gaussians are uniquely determined by the second-order autocorrelation of their projection images, implying that the sample complexity is proportional to the square of the variance of the noise. This theory improves upon the non-sparse case, where the third-order autocorrelation is required for uniformly-oriented particle images and the sample complexity scales with the cube of the noise variance. Furthermore, we build a computational framework to reconstruct molecular structures which are sparse in the wavelet basis. This method combines the sparse representation for the molecule with projection-based techniques used for phase retrieval in X-ray crystallography.

math.NA↗

arXiv2023

Diffusion Maps for Group-Invariant Manifolds

In this article, we consider the manifold learning problem when the data set is invariant under the action of a compact Lie group $K$. Our approach consists in augmenting the data-induced graph Laplacian by integrating over the $K$-orbits of the existing data points, which yields a $K$-invariant graph Laplacian $L$. We prove that $L$ can be diagonalized by using the unitary irreducible representation matrices of $K$, and we provide an explicit formula for computing its eigenvalues and eigenfunctions. In addition, we show that the normalized Laplacian operator $L_N$ converges to the Laplace-Beltrami operator of the data manifold with an improved convergence rate, where the improvement grows with the dimension of the symmetry group $K$. This work extends the steerable graph Laplacian framework of Landa and Shkolnisky from the case of $\operatorname{SO}(2)$ to arbitrary compact Lie groups.

cs.LG↗

arXiv2022

Finding stationary points on bounded-rank matrices: A geometric hurdle and a smooth remedy

We consider the problem of provably finding a stationary point of a smooth function to be minimized on the variety of bounded-rank matrices. This turns out to be unexpectedly delicate. We trace the difficulty back to a geometric obstacle: On a nonsmooth set, there may be sequences of points along which standard measures of stationarity tend to zero, but whose limit points are not stationary. We name such events apocalypses, as they can cause optimization algorithms to converge to non-stationary points. We illustrate this explicitly for an existing optimization algorithm on bounded-rank matrices. To provably find stationary points, we modify a trust-region method on a standard smooth parameterization of the variety. The method relies on the known fact that second-order stationary points on the parameter space map to stationary points on the variety. Our geometric observations and proposed algorithm generalize beyond bounded-rank matrices. We give a geometric characterization of apocalypses on general constraint sets, which implies that Clarke-regular sets do not admit apocalypses. Such sets include smooth manifolds, manifolds with boundaries, and convex sets. Our trust-region method supports parameterization by any complete Riemannian manifold.

math.OC↗

arXiv2022

Tensor Moments of Gaussian Mixture Models: Theory and Applications

Gaussian mixture models (GMMs) are fundamental tools in statistical and data sciences. We study the moments of multivariate Gaussians and GMMs. The $d$-th moment of an $n$-dimensional random variable is a symmetric $d$-way tensor of size $n^d$, so working with moments naively is assumed to be prohibitively expensive for $d>2$ and larger values of $n$. In this work, we develop theory and numerical methods for \emph{implicit computations} with moment tensors of GMMs, reducing the computational and storage costs to $\mathcal{O}(n^2)$ and $\mathcal{O}(n^3)$, respectively, for general covariance matrices, and to $\mathcal{O}(n)$ and $\mathcal{O}(n)$, respectively, for diagonal ones. We derive concise analytic expressions for the moments in terms of symmetrized tensor products, relying on the correspondence between symmetric tensors and homogeneous polynomials, and combinatorial identities involving Bell polynomials. The primary application of this theory is to estimating GMM parameters (means and covariances) from a set of observations, when formulated as a moment-matching optimization problem. If there is a known and common covariance matrix, we also show it is possible to debias the data observations, in which case the problem of estimating the unknown means reduces to symmetric CP tensor decomposition. Numerical results validate and illustrate the numerical efficiency of our approaches. This work potentially opens the door to the competitiveness of the method of moments as compared to expectation maximization methods for parameter estimation of GMMs.

stat.ML↗

arXiv2021

On the Instability of Relative Pose Estimation and RANSAC's Role

In this paper we study the numerical instabilities of the 5- and 7-point problems for essential and fundamental matrix estimation in multiview geometry. In both cases we characterize the ill-posed world scenes where the condition number for epipolar estimation is infinite. We also characterize the ill-posed instances in terms of the given image data. To arrive at these results, we present a general framework for analyzing the conditioning of minimal problems in multiview geometry, based on Riemannian manifolds. Experiments with synthetic and real-world data then reveal a striking conclusion: that Random Sample Consensus (RANSAC) in Structure-from-Motion (SfM) does not only serve to filter out outliers, but RANSAC also selects for well-conditioned image data, sufficiently separated from the ill-posed locus that our theory predicts. Our findings suggest that, in future work, one could try to accelerate and increase the success of RANSAC by testing only well-conditioned image data.

cs.CV↗

arXiv2021

Landscape analysis of an improved power method for tensor decomposition

In this work, we consider the optimization formulation for symmetric tensor decomposition recently introduced in the Subspace Power Method (SPM) of Kileel and Pereira. Unlike popular alternative functionals for tensor decomposition, the SPM objective function has the desirable properties that its maximal value is known in advance, and its global optima are exactly the rank-1 components of the tensor when the input is sufficiently low-rank. We analyze the non-convex optimization landscape associated with the SPM objective. Our analysis accounts for working with noisy tensors. We derive quantitative bounds such that any second-order critical point with SPM objective value exceeding the bound must equal a tensor component in the noiseless case, and must approximate a tensor component in the noisy case. For decomposing tensors of size $D^{\times m}$, we obtain a near-global guarantee up to rank $\widetilde{o}(D^{\lfloor m/2 \rfloor})$ under a random tensor model, and a global guarantee up to rank $\mathcal{O}(D)$ assuming deterministic frame conditions. This implies that SPM with suitable initialization is a provable, efficient, robust algorithm for low-rank symmetric tensor decomposition. We conclude with numerics that show a practical preferability for using the SPM functional over a more established counterpart.

math.OC↗

arXiv2021

Manifold learning with arbitrary norms

Manifold learning methods play a prominent role in nonlinear dimensionality reduction and other tasks involving high-dimensional data sets with low intrinsic dimensionality. Many of these methods are graph-based: they associate a vertex with each data point and a weighted edge with each pair. Existing theory shows that the Laplacian matrix of the graph converges to the Laplace-Beltrami operator of the data manifold, under the assumption that the pairwise affinities are based on the Euclidean norm. In this paper, we determine the limiting differential operator for graph Laplacians constructed using $\textit{any}$ norm. Our proof involves an interplay between the second fundamental form of the manifold and the convex geometry of the given norm's unit ball. To demonstrate the potential benefits of non-Euclidean norms in manifold learning, we consider the task of mapping the motion of large molecules with continuous variability. In a numerical simulation we show that a modified Laplacian eigenmaps algorithm, based on the Earthmover's distance, outperforms the classic Euclidean Laplacian eigenmaps, both in terms of computational cost and the sample size needed to recover the intrinsic geometry.

cs.LG↗

arXiv2019

Method of moments for 3-D single particle ab initio modeling with non-uniform distribution of viewing angles

Single-particle reconstruction in cryo-electron microscopy (cryo-EM) is an increasingly popular technique for determining the 3-D structure of a molecule from several noisy 2-D projections images taken at unknown viewing angles. Most reconstruction algorithms require a low-resolution initialization for the 3-D structure, which is the goal of ab initio modeling. Suggested by Zvi Kam in 1980, the method of moments (MoM) offers one approach, wherein low-order statistics of the 2-D images are computed and a 3-D structure is estimated by solving a system of polynomial equations. Unfortunately, Kam's method suffers from restrictive assumptions, most notably that viewing angles should be distributed uniformly. Often unrealistic, uniformity entails the computation of higher-order correlations, as in this case first and second moments fail to determine the 3-D structure. In the present paper, we remove this hypothesis, by permitting an unknown, non-uniform distribution of viewing angles in MoM. Perhaps surprisingly, we show that this case is statistically easier than the uniform case, as now first and second moments generically suffice to determine low-resolution expansions of the molecule. In the idealized setting of a known, non-uniform distribution, we find an efficient provable algorithm inverting first and second moments. For unknown, non-uniform distributions, we use non-convex optimization methods to solve for both the molecule and distribution.

math.NA↗