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Manifold learning-based methods for analyzing single-cell RNA-sequencing data

Current Opinion in Systems Biology 2018年 7卷 36-46页

作者： Moon, Kevin R. Stanley, Jay S. Burkhardt, Daniel van Dijk, David Wolf, Guy Krishnaswamy, Smita Department of Genetics Yale University New Haven CT United States Applied Mathematics Program Yale University New Haven CT United States Computational Biology and Bioinformatics Program Yale University New Haven CT United States Department of Computer Science Yale University New Haven CT United States

Recent advances in single-cell RNA sequencing technologies enable deep insights into cellular development, gene regulation, and phenotypic diversity by measuring gene expression for thousands of cells in a single experiment. While these technologies hold great potential for improving our understanding of cellular states and progression, they also pose new challenges and require advanced mathematical and algorithmic tools to extract underlying biological signals. In this review, we cover one of the most promising avenues of research into unlocking the potential of scRNA-seq data: the field of manifold learning, and the related manifold assumption in data analysis. Manifold learning provides a powerful structure for algorithmic approaches to process the data, extract its dynamics, and infer patterns in it. In particular, we cover manifold learning-based methods for denoising the data, revealing gene interactions, extracting pseudotime progressions with model fitting, visualizing the cellular state space via dimensionality reduction, and clustering the data. © 2017 Published by Elsevier Ltd.

关键词： Data mining Gene regulatory networks Imputation Manifold learning Pseudotime trends Single cell RNA sequencing

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Reducing bias and variance for CTF estimation in single particle cryo-EM

arXiv

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arXiv 2019年

作者： Heimowitz, Ayelet Andén, Joakim Singer, Amit Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Center for Computational Mathematics Flatiron Institute New YorkNY10010 United States Program in Applied and Computational Mathematics Department of Mathematics Princeton University PrincetonNJ08544 United States

When using an electron microscope for imaging of particles embedded in vitreous ice, the recorded image, or micrograph, is a significantly degraded version of the tomographic projection of the sample. Apart from noise, the image is affected by the optical configuration of the microscope. This transformation is typically modeled as a convolution with a point spread function. The Fourier transform of this function, known as the contrast transfer function (CTF), is oscillatory, attenuating and amplifying different frequency bands, and sometimes flipping their signs. High-resolution reconstruction requires this CTF to be accounted for, but as its form depends on experimental parameters, it must first be estimated from the micrograph. We present a new method for CTF estimation based on multitaper methods, which reduces bias and variance in the estimate. We also use known properties of the CTF and the background noise power spectrum to further reduce the variance through background subtraction and steerable basis projection. We show that the resulting power spectrum estimates better capture the zero-crossings of the CTF and yield accurate CTF estimates on several experimental micrographs. Copyright © 2019, The Authors. All rights reserved.

关键词： Linear programming

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Characterization of maximally random jammed sphere packings: Voronoi correlation functions

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Physical Review E 2014年第5期90卷 052120-052120页

作者： Michael A. Klatt Salvatore Torquato Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

We characterize the structure of maximally random jammed (MRJ) sphere packings by computing the Minkowski functionals (volume, surface area, and integrated mean curvature) of their associated Voronoi cells. The probability distribution functions of these functionals of Voronoi cells in MRJ sphere packings are qualitatively similar to those of an equilibrium hard-sphere liquid and partly even to the uncorrelated Poisson point process, implying that such local statistics are relatively structurally insensitive. This is not surprising because the Minkowski functionals of a single Voronoi cell incorporate only local information and are insensitive to global structural information. To improve upon this, we introduce descriptors that incorporate nonlocal information via the correlation functions of the Minkowski functionals of two cells at a given distance as well as certain cell-cell probability density functions. We evaluate these higher-order functions for our MRJ packings as well as equilibrium hard spheres and the Poisson point process. It is shown that these Minkowski correlation and density functions contain visibly more information than the corresponding standard pair-correlation functions. We find strong anticorrelations in the Voronoi volumes for the hyperuniform MRJ packings, consistent with previous findings for other pair correlations [A. Donev et al., Phys. Rev. Lett. 95, 090604 (2005)], indicating that large-scale volume fluctuations are suppressed by accompanying large Voronoi cells with small cells, and vice versa. In contrast to the aforementioned local Voronoi statistics, the correlation functions of the Voronoi cells qualitatively distinguish the structure of MRJ sphere packings (prototypical glasses) from that of not only the Poisson point process but also the correlated equilibrium hard-sphere liquids. Moreover, while we did not find any perfect icosahedra (the locally densest possible structure in which a central sphere contacts 12 neighbors) in th

关键词： RANDOM variables VORONOI polygons MINKOWSKI space POISSON processes FUNCTIONS (mathematics)

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Effect of dimensionality on the percolation thresholds of various d-dimensional lattices

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Physical Review E 2013年第3期87卷 032149-032149页

作者： S. Torquato Y. Jiao []Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

We show analytically that the [0,1], [1,1], and [2,1] Padé approximants of the mean cluster number S(p) for site and bond percolation on general d-dimensional lattices are upper bounds on this quantity in any Euclidean dimension d, where p is the occupation probability. These results lead to certain lower bounds on the percolation threshold pc that become progressively tighter as d increases and asymptotically exact as d becomes large. These lower-bound estimates depend on the structure of the d-dimensional lattice and whether site or bond percolation is being considered. We obtain explicit bounds on pc for both site and bond percolation on five different lattices: d-dimensional generalizations of the simple-cubic, body-centered-cubic, and face-centered-cubic Bravais lattices as well as the d-dimensional generalizations of the diamond and kagomé (or pyrochlore) non-Bravais lattices. These analytical estimates are used to assess available simulation results across dimensions (up through d=13 in some cases). It is noteworthy that the tightest lower bound provides reasonable estimates of pc in relatively low dimensions and becomes increasingly accurate as d grows. We also derive high-dimensional asymptotic expansions for pc for the 10 percolation problems and compare them to the Bethe-lattice approximation. Finally, we remark on the radius of convergence of the series expansion of S in powers of p as the dimension grows.

关键词： Solvents

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Effect of dimensionality on the percolation threshold of overlapping nonspherical hyperparticles

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Physical Review E 2013年第2期87卷 022111-022111页

We study the effect of dimensionality on the percolation threshold ηc of identical overlapping nonspherical convex hyperparticles in d-dimensional Euclidean space Rd. This is done by formulating a scaling relation for ηc that is based on a rigorous lower bound [Torquato, J. Chem. Phys. 136, 054106 (2012)] and a conjecture that hyperspheres provide the highest threshold, for any d, among all convex hyperparticle shapes (that are not a trivial affine transformation of a hypersphere). This scaling relation also exploits the recently discovered principle that low-dimensional continuum percolation behavior encodes high-dimensional information. We derive an explicit formula for the exclusion volume vex of a hyperparticle of arbitrary shape in terms of its d-dimensional volume v, surface area s, and radius of mean curvature R¯ (or, equivalently, mean width). These basic geometrical properties are computed for a wide variety of nonspherical hyperparticle shapes with random orientations across all dimensions, including, among other shapes, various polygons for d=2, Platonic solids, spherocylinders, parallepipeds, and zero-volume plates for d=3 and their appropriate generalizations for d≥4. Using this information, we compute the lower bound and scaling relation for ηc for this comprehensive set of continuum percolation models across dimensions. We demonstrate that the scaling relation provides accurate upper-bound estimates of the threshold ηc across dimensions and becomes increasingly accurate as the space dimension increases.

关键词： DIMENSIONAL analysis PERCOLATION (Statistical physics) EUCLIDEAN geometry SCALING laws (Statistical physics) POLYGONS SHAPES

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Hyperuniformity of generalized random organization models

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Physical Review E 2019年第2期99卷 022115-022115页

作者： Zheng Ma Salvatore Torquato Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Studies of random organization models of monodisperse (i.e., identical) spherical particles have shown that a hyperuniform state is achievable when the system goes through an absorbing phase transition to a critical state. Here we investigate to what extent hyperuniformity is preserved when the model is generalized to particles with a size distribution and/or nonspherical shapes. We begin by examining binary disks in two dimensions and demonstrate that their critical states are hyperuniform as two-phase media, but not hyperuniform nor multihyperuniform as point patterns formed by the particle centroids. We further confirm the generality of our findings by studying particles with a continuous size distribution. Finally, to study the effect of rotational degrees of freedom, we extend our model to noncircular particles, namely, hard rectangles with various aspect ratios, including the hard-needle limit. Although these systems exhibit only short-range orientational order, hyperuniformity is still preserved. Our analysis reveals that the redistribution of the “mass” of the particles rather than the particle centroids is central to this dynamical process. The consideration of the “active volume fraction” of generalized random organization models may help to resolve which universality class they belong to and hence may lead to a deeper theoretical understanding of absorbing-state models. Our results suggest that general particle systems subject to random organization can be a robust way to fabricate a wide class of hyperuniform states of matter by tuning the structures via different particle-size and -shape distributions. This in turn potentially enables the creation of multifunctional hyperuniform materials with desirable optical, transport, and mechanical properties.

关键词： Classical statistical mechanics

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Characterization of maximally random jammed sphere packings. III. Transport and electromagnetic properties via correlation functions

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Physical Review E 2018年第1期97卷 012118-012118页

In the first two papers of this series, we characterized the structure of maximally random jammed (MRJ) sphere packings across length scales by computing a variety of different correlation functions, spectral functions, hole probabilities, and local density fluctuations. From the remarkable structural features of the MRJ packings, especially its disordered hyperuniformity, exceptional physical properties can be expected. Here we employ these structural descriptors to estimate effective transport and electromagnetic properties via rigorous bounds, exact expansions, and accurate analytical approximation formulas. These property formulas include interfacial bounds as well as universal scaling laws for the mean survival time and the fluid permeability. We also estimate the principal relaxation time associated with Brownian motion among perfectly absorbing traps. For the propagation of electromagnetic waves in the long-wavelength limit, we show that a dispersion of dielectric MRJ spheres within a matrix of another dielectric material forms, to a very good approximation, a dissipationless disordered and isotropic two-phase medium for any phase dielectric contrast ratio. We compare the effective properties of the MRJ sphere packings to those of overlapping spheres, equilibrium hard-sphere packings, and lattices of hard spheres. Moreover, we generalize results to micro- and macroscopically anisotropic packings of spheroids with tensorial effective properties. The analytic bounds predict the qualitative trend in the physical properties associated with these structures, which provides guidance to more time-consuming simulations and experiments. They especially provide impetus for experiments to design materials with unique bulk properties resulting from hyperuniformity, including structural-color and color-sensing applications.

关键词： Classical statistical mechanics

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Structural characterization of many-particle systems on approach to hyperuniform states

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Physical Review E 2021年第5期103卷 052126-052126页

作者： Salvatore Torquato Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

The study of hyperuniform states of matter is an emerging multidisciplinary field, impinging on topics in the physical sciences, mathematics, and biology. The focus of this work is the exploration of quantitative descriptors that herald when a many-particle system in d-dimensional Euclidean space Rd approaches a hyperuniform state as a function of the relevant control parameter. We establish quantitative criteria to ascertain the extent of hyperuniform and nonhyperuniform distance-scaling regimes as well as the crossover point between them in terms of the “volume” coefficient A and “surface-area” coefficient B associated with the local number variance σ2(R) for a spherical window of radius R. The larger the ratio B/A, the larger the hyperuniform scaling regime, which becomes of infinite extent in the limit B/A→∞. To complement the known direct-space representation of the coefficient B in terms of the total correlation function h(r), we derive its corresponding Fourier representation in terms of the structure factor S(k), which is especially useful when scattering information is available experimentally or theoretically. We also demonstrate that the free-volume theory of the pressure of equilibrium packings of identical hard spheres that approach a strictly jammed state either along the stable crystal or metastable disordered branch dictates that such end states be exactly hyperuniform. Using the ratio B/A, as well as other diagnostic measures of hyperuniformity, including the hyperuniformity index H and the direct-correlation function length scale ξc, we study three different exactly solvable models as a function of the relevant control parameter, either density or temperature, with end states that are perfectly hyperuniform. Specifically, we analyze equilibrium systems of hard rods and “sticky” hard-sphere systems in arbitrary space dimension d as a function of density. We also examine low-temperature excited states of many-particle systems interacting with “stealt

关键词： Fluctuations & noise

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Precise algorithms to compute surface correlation functions of two-phase heterogeneous media and their applications

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Physical Review E 2018年第1期98卷 013307-013307页

The quantitative characterization of the microstructure of random heterogeneous media in d-dimensional Euclidean space Rd via a variety of n-point correlation functions is of great importance, since the respective infinite set determines the effective physical properties of the media. In particular, surface-surface Fss and surface-void Fsv correlation functions (obtainable from radiation scattering experiments) contain crucial interfacial information that enables one to estimate transport properties of the media (e.g., the mean survival time and fluid permeability) and complements the information content of the conventional two-point correlation function. However, the current technical difficulty involved in sampling surface correlation functions has been a stumbling block in their widespread use. We first present a concise derivation of the small-r behaviors of these functions, which are linked to the mean curvature of the system. Then we demonstrate that one can reduce the computational complexity of the problem, without sacrificing accuracy, by extracting the necessary interfacial information from a cut of the d-dimensional statistically homogeneous and isotropic system with an infinitely long line. Accordingly, we devise algorithms based on this idea and test them for two-phase media in continuous and discrete spaces. Specifically for the exact benchmark model of overlapping spheres, we find excellent agreement between numerical and exact results. We compute surface correlation functions and corresponding local surface-area variances for a variety of other model microstructures, including hard spheres in equilibrium, decorated “stealthy” patterns, as well as snapshots of evolving pattern formation processes (e.g., spinodal decomposition). It is demonstrated that the precise determination of surface correlation functions provides a powerful means to characterize a wide class of complex multiphase microstructures.

关键词： Structural properties

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Confined disordered strictly jammed binary sphere packings

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Physical Review E 2015年第6期92卷 062207-062207页

作者： D. Chen S. Torquato Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA

Disordered jammed packings under confinement have received considerably less attention than their bulk counterparts and yet arise in a variety of practical situations. In this work, we study binary sphere packings that are confined between two parallel hard planes and generalize the Torquato-Jiao (TJ) sequential linear programming algorithm [Phys. Rev. E 82, 061302 (2010)] to obtain putative maximally random jammed (MRJ) packings that are exactly isostatic with high fidelity over a large range of plane separation distances H, small to large sphere radius ratio α, and small sphere relative concentration x. We find that packing characteristics can be substantially different from their bulk analogs, which is due to what we term “confinement frustration.” Rattlers in confined packings are generally more prevalent than those in their bulk counterparts. We observe that packing fraction, rattler fraction, and degree of disorder of MRJ packings generally increase with H, though exceptions exist. Discontinuities in the packing characteristics as H varies in the vicinity of certain values of H are due to associated discontinuous transitions between different jammed states. When the plane separation distance is on the order of two large-sphere diameters or less, the packings exhibit salient two-dimensional features; when the plane separation distance exceeds about 30 large-sphere diameters, the packings approach three-dimensional bulk packings. As the size contrast increases (as α decreases), the rattler fraction dramatically increases due to what we call “size-disparity” frustration. We find that at intermediate α and when x is about 0.5 (50-50 mixture), the disorder of packings is maximized, as measured by an order metric ψ that is based on the number density fluctuations in the direction perpendicular to the hard walls. We also apply the local volume-fraction variance στ2(R) to characterize confined packings and find that these packings possess essentially the same level of

关键词： RESEARCH Combinatorial packing & covering Linear programming Density Powders Sphere packings

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