arXiv subjects

Oscar Mickelin

Publications and source records attributed to Oscar Mickelin.

At least 19 recordsLinked to original sources

arXiv2026

Two Datasets Are Better Than One: Method of Double Moments for 3-D Reconstruction in Cryo-EM

Cryo-electron microscopy (cryo-EM) is a powerful imaging technique for reconstructing three-dimensional molecular structures from noisy tomographic projection images of randomly oriented particles. We introduce a new data fusion framework, termed the method of double moments (MoDM), which reconstructs molecular structures from two instances of the second-order moment of projection images obtained under distinct orientation distributions: one uniform, the other non-uniform and unknown. We prove that these moments generically uniquely determine the underlying structure, up to a global rotation and reflection, and we develop a convex-relaxation-based algorithm that achieves accurate recovery using only second-order statistics. Our results demonstrate the advantage of collecting and modeling multiple datasets under different experimental conditions, illustrating that leveraging dataset diversity can substantially enhance reconstruction quality in computational imaging tasks.

cs.CV↗

arXiv2025

Subspace method of moments for ab initio 3-D single-particle cryo-EM reconstruction

Cryo-electron microscopy (cryo-EM) is a widely used technique for recovering the 3-D structure of biological molecules from a large number of experimentally generated noisy 2-D tomographic projection images of the 3-D structure, taken from unknown viewing angles. Through computationally intensive algorithms, these observed images are processed to reconstruct the 3-D structures. Many popular computational methods rely on estimating the unknown angles as part of the reconstruction process, which becomes particularly challenging at low signal-to-noise ratios. The method of moments (MoM) offers an alternative approach that circumvents the estimation of viewing orientations of individual projection images by instead estimating the underlying distribution of the viewing angles, and is robust to noise given sufficiently many images. However, the method of moments typically entails computing higher-order moments of the projection images, incurring significant computational and memory costs. To mitigate this, we propose a new approach called the subspace method of moments (SubspaceMoM), which compresses the first three moments using data-driven low-rank tensor techniques as well as expansion into a suitable function basis. The compressed moments can be efficiently computed from the set of projection images using numerical quadrature and can be employed to jointly reconstruct the 3-D structure and the distribution of viewing orientations. We illustrate the practical applicability of SubspaceMoM through numerical experiments using up to the third-order moment on synthetic datasets with a simplified cryo-EM image formation model, which significantly improves the reconstruction resolution compared to previous MoM approaches.

math.NA↗

arXiv2025

SO(3)-invariant PCA with application to molecular data

Principal component analysis (PCA) is a fundamental technique for dimensionality reduction and denoising; however, its application to three-dimensional data with arbitrary orientations -- common in structural biology -- presents significant challenges. A naive approach requires augmenting the dataset with many rotated copies of each sample, incurring prohibitive computational costs. In this paper, we extend PCA to 3D volumetric datasets with unknown orientations by developing an efficient and principled framework for SO(3)-invariant PCA that implicitly accounts for all rotations without explicit data augmentation. By exploiting underlying algebraic structure, we demonstrate that the computation involves only the square root of the total number of covariance entries, resulting in a substantial reduction in complexity. We validate the method on real-world molecular datasets, demonstrating its effectiveness and opening up new possibilities for large-scale, high-dimensional reconstruction problems.

eess.SP↗

arXiv2025

Diagonally-Weighted Generalized Method of Moments Estimation for Gaussian Mixture Modeling

Since Pearson [Philosophical Transactions of the Royal Society of London. A, 185 (1894), pp. 71-110] first applied the method of moments (MM) for modeling data as a mixture of one-dimensional Gaussians, moment-based estimation methods have proliferated. Among these methods, the generalized method of moments (GMM) improves the statistical efficiency of MM by weighting the moments appropriately. However, the computational complexity and storage complexity of MM and GMM grow exponentially with the dimension, making these methods impractical for high-dimensional data or when higher-order moments are required. Such computational bottlenecks are more severe in GMM since it additionally requires estimating a large weighting matrix. To overcome these bottlenecks, we propose the diagonally-weighted GMM (DGMM), which achieves a balance among statistical efficiency, computational complexity, and numerical stability. We apply DGMM to study the parameter estimation problem for weakly separated heteroscedastic low-rank Gaussian mixtures and design a computationally efficient and numerically stable algorithm that obtains the DGMM estimator without explicitly computing or storing the moment tensors. We implement the proposed algorithm and empirically validate the advantages of DGMM: in numerical studies, DGMM attains smaller estimation errors while requiring substantially shorter runtime than MM and GMM. The code and data will be available upon publication at https://github.com/liu-lzhang/dgmm.

cs.LG↗

arXiv2025

Fast expansion into harmonics on the ball

We devise fast and provably accurate algorithms to transform between an $N\times N \times N$ Cartesian voxel representation of a three-dimensional function and its expansion into the {ball harmonics}, that is, the eigenbasis of the Dirichlet Laplacian on the unit ball in $\mathbb{R}^3$. Given $\varepsilon > 0$, our algorithms achieve relative $\ell^1$ - $\ell^\infty$ accuracy $\varepsilon$ in time $O(N^3 (\log N)^2 + N^3 |\log \varepsilon|^2)$, while the naïve direct application of the expansion operators has time complexity $O(N^6)$. We illustrate our methods on numerical examples.

math.NA↗

arXiv2024

The beltway problem over orthogonal groups

The classical beltway problem entails recovering a set of points from their unordered pairwise distances on the circle. This problem can be viewed as a special case of the crystallographic phase retrieval problem of recovering a sparse signal from its periodic autocorrelation. Based on this interpretation, and motivated by cryo-electron microscopy, we suggest a natural generalization to orthogonal groups: recovering a sparse signal, up to an orthogonal transformation, from its autocorrelation over the orthogonal group. If the support of the signal is collision-free, we bound the number of solutions to the beltway problem over orthogonal groups, and prove that this bound is exactly one when the support of the signal is radially collision-free (i.e., the support points have distinct magnitudes). We also prove that if the pairwise products of the signal's weights are distinct, then the autocorrelation determines the signal uniquely, up to an orthogonal transformation. We conclude the paper by considering binary signals and show that in this case, the collision-free condition need not be sufficient to determine signals up to orthogonal transformation.

eess.SP↗

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

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↗

arXiv2022

Fast expansion into harmonics on the disk: a steerable basis with fast radial convolutions

We present a fast and numerically accurate method for expanding digitized $L \times L$ images representing functions on $[-1,1]^2$ supported on the disk $\{x \in \mathbb{R}^2 : |x|<1\}$ in the harmonics (Dirichlet Laplacian eigenfunctions) on the disk. Our method, which we refer to as the Fast Disk Harmonics Transform (FDHT), runs in $O(L^2 \log L)$ operations. This basis is also known as the Fourier-Bessel basis, and it has several computational advantages: it is orthogonal, ordered by frequency, and steerable in the sense that images expanded in the basis can be rotated by applying a diagonal transform to the coefficients. Moreover, we show that convolution with radial functions can also be efficiently computed by applying a diagonal transform to the coefficients.

math.NA↗

arXiv2022

Fast Principal Component Analysis for Cryo-EM Images

Principal component analysis (PCA) plays an important role in the analysis of cryo-EM images for various tasks such as classification, denoising, compression, and ab-initio modeling. We introduce a fast method for estimating a compressed representation of the 2-D covariance matrix of noisy cryo-electron microscopy projection images that enables fast PCA computation. Our method is based on a new algorithm for expanding images in the Fourier-Bessel basis (the harmonics on the disk), which provides a convenient way to handle the effect of the contrast transfer functions. For $N$ images of size $L\times L$, our method has time complexity $O(N L^3 + L^4)$ and space complexity $O(NL^2 + L^3)$. In contrast to previous work, these complexities are independent of the number of different contrast transfer functions of the images. We demonstrate our approach on synthetic and experimental data and show acceleration by factors of up to two orders of magnitude.

math.NA↗

arXiv2022

An optimal scheduled learning rate for a randomized Kaczmarz algorithm

We study how the learning rate affects the performance of a relaxed randomized Kaczmarz algorithm for solving $A x \approx b + \varepsilon$, where $A x =b$ is a consistent linear system and $\varepsilon$ has independent mean zero random entries. We derive a learning rate schedule which optimizes a bound on the expected error that is sharp in certain cases; in contrast to the exponential convergence of the standard randomized Kaczmarz algorithm, our optimized bound involves the reciprocal of the Lambert-$W$ function of an exponential.

math.NA↗

arXiv2022

The Role of Heterogeneity in Autonomous Perimeter Defense Problems

When is heterogeneity in the composition of an autonomous robotic team beneficial and when is it detrimental? We investigate and answer this question in the context of a minimally viable model that examines the role of heterogeneous speeds in perimeter defense problems, where defenders share a total allocated speed budget. We consider two distinct problem settings and develop strategies based on dynamic programming and on local interaction rules. We present a theoretical analysis of both approaches and our results are extensively validated using simulations. Interestingly, our results demonstrate that the viability of heterogeneous teams depends on the amount of information available to the defenders. Moreover, our results suggest a universality property: across a wide range of problem parameters the optimal ratio of the speeds of the defenders remains nearly constant.

cs.MA↗

arXiv2021

Sparse multi-reference alignment: sample complexity and computational hardness

Motivated by the problem of determining the atomic structure of macromolecules using single-particle cryo-electron microscopy (cryo-EM), we study the sample and computational complexities of the sparse multi-reference alignment (MRA) model: the problem of estimating a sparse signal from its noisy, circularly shifted copies. Based on its tight connection to the crystallographic phase retrieval problem, we establish that if the number of observations is proportional to the square of the variance of the noise, then the sparse MRA problem is statistically feasible for sufficiently sparse signals. To investigate its computational hardness, we consider three types of computational frameworks: projection-based algorithms, bispectrum inversion, and convex relaxations. We show that a state-of-the-art projection-based algorithm achieves the optimal estimation rate, but its computational complexity is exponential in the sparsity level. The bispectrum framework provides a statistical-computational trade-off: it requires more observations (so its estimation rate is suboptimal), but its computational load is provably polynomial in the signal's length. The convex relaxation approach provides polynomial time algorithms (with a large exponent) that recover sufficiently sparse signals at the optimal estimation rate. We conclude the paper by discussing potential statistical and algorithmic implications for cryo-EM.

cs.IT↗

arXiv2021

Recovering orthogonal tensors under arbitrarily strong, but locally correlated, noise

We consider the problem of recovering an orthogonally decomposable tensor with a subset of elements distorted by noise with arbitrarily large magnitude. We focus on the particular case where each mode in the decomposition is corrupted by noise vectors with components that are correlated locally, i.e., with nearby components. We show that this deterministic tensor completion problem has the unusual property that it can be solved in polynomial time if the rank of the tensor is sufficiently large. This is the polar opposite of the low-rank assumptions of typical low-rank tensor and matrix completion settings. We show that our problem can be solved through a system of coupled Sylvester-like equations and show how to accelerate their solution by an alternating solver. This enables recovery even with a substantial number of missing entries, for instance for $n$-dimensional tensors of rank $n$ with up to $40\%$ missing entries.

math.NA↗

arXiv2020

Multi-resolution Low-rank Tensor Formats

We describe a simple, black-box compression format for tensors with a multiscale structure. By representing the tensor as a sum of compressed tensors defined on increasingly coarse grids, we capture low-rank structures on each grid-scale, and we show how this leads to an increase in compression for a fixed accuracy. We devise an alternating algorithm to represent a given tensor in the multiresolution format and prove local convergence guarantees. In two dimensions, we provide examples that show that this approach can beat the Eckart-Young theorem, and for dimensions higher than two, we achieve higher compression than the tensor-train format on six real-world datasets. We also provide results on the closedness and stability of the tensor format and discuss how to perform common linear algebra operations on the level of the compressed tensors.

math.NA↗

arXiv2020

On Algorithms for and Computing with the Tensor Ring Decomposition

Tensor decompositions such as the canonical format and the tensor train format have been widely utilized to reduce storage costs and operational complexities for high-dimensional data, achieving linear scaling with the input dimension instead of exponential scaling. In this paper, we investigate even lower storage-cost representations in the tensor ring format, which is an extension of the tensor train format with variable end-ranks. Firstly, we introduce two algorithms for converting a tensor in full format to tensor ring format with low storage cost. Secondly, we detail a rounding operation for tensor rings and show how this requires new definitions of common linear algebra operations in the format to obtain storage-cost savings. Lastly, we introduce algorithms for transforming the graph structure of graph-based tensor formats, with orders of magnitude lower complexity than existing literature. The efficiency of all algorithms is demonstrated on a number of numerical examples, and in certain cases, we demonstrate significantly higher compression ratios when compared to previous approaches to using the tensor ring format.

math.NA↗

arXiv2019

Optimal orthogonal approximations to symmetric tensors cannot always be chosen symmetric

We study the problem of finding orthogonal low-rank approximations of symmetric tensors. In the case of matrices, the approximation is a truncated singular value decomposition which is then symmetric. Moreover, for rank-one approximations of tensors of any dimension, a classical result proven by Banach in 1938 shows that the optimal approximation can always be chosen to be symmetric. In contrast to these results, this article shows that the corresponding statement is no longer true for orthogonal approximations of higher rank. Specifically, for any of the four common notions of tensor orthogonality used in the literature, we show that optimal orthogonal approximations of rank greater than one cannot always be chosen to be symmetric.

math.NA↗

arXiv2018

On sufficient conditions for mixed monotonicity

Mixed monotone systems form an important class of nonlinear systems that have recently received attention in the abstraction-based control design area. Slightly different definitions exist in the literature, and it remains a challenge to verify mixed monotonicity of a system in general. In this paper, we first clarify the relation between different existing definitions of mixed monotone systems, and then give two sufficient conditions for mixed monotone functions defined on Euclidean space. These sufficient conditions are more general than the ones from the existing control literature, and they suggest that mixed monotonicity is a very generic property. Some discussions are provided on the computational usefulness of the proposed sufficient conditions.

math.OC↗