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A FLOW ARTIST FOR HIGH-DIMENSIONAL CELLULAR DATA

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arXiv 2023年

作者： MacDonald, Kincaid Bhaskar, Dhananjay Thampakkul, Guy Nguyen, Nhi Zhang, Joia Perlmutter, Michael Adelstein, Ian Krishnaswamy, Smita Department of Mathematics Yale University United States Department of Genetics Yale School of Medicine United States Department of Computer Science Yale University United States Department of Mathematics Pomona College United States Applied Mathematics Program Yale University United States Department of Statistics University of Washington United States Department of Mathematics Boise State University United States Computational Biology and Bioinformatics Program Yale University United States

We consider the problem of embedding point cloud data sampled from an underlying manifold with an associated flow or velocity. Such data arises in many contexts where static snapshots of dynamic entities are measured, including in high-throughput biology such as single-cell transcriptomics. Existing embedding techniques either do not utilize velocity information or embed the coordinates and velocities independently, i.e., they either impose velocities on top of an existing point embedding or embed points within a prescribed vector field. Here we present FlowArtist, a neural network that embeds points while jointly learning a vector field around the points. The combination allows FlowArtist to better separate and visualize velocity-informed structures. Our results, on toy datasets and single-cell RNA velocity data, illustrate the value of utilizing coordinate and velocity information in tandem for embedding and visualizing high-dimensional data. © 2023, CC BY.

关键词： RNA

Marginal stability in jammed packings: Quasicontacts and weak contacts

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Physical Review E 2014年第2期90卷 022114-022114页

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

Maximally random jammed (MRJ) sphere packing is a prototypical example of a system naturally poised at the margin between underconstraint and overconstraint. This marginal stability has traditionally been understood in terms of isostaticity, the equality of the number of mechanical contacts and the number of degrees of freedom. Quasicontacts, pairs of spheres on the verge of coming in contact, are irrelevant for static stability, but they come into play when considering dynamic stability, as does the distribution of contact forces. We show that the effects of marginal dynamic stability, as manifested in the distributions of quasicontacts and weak contacts, are consequential and nontrivial. We study these ideas first in the context of MRJ packing of d-dimensional spheres, where we show that the abundance of quasicontacts grows at a faster rate than that of contacts. We reexamine a calculation of Jin et al. [Phys. Rev. E 82, 051126 (2010)], where quasicontacts were originally neglected, and we explore the effect of their inclusion in the calculation. This analysis yields an estimate of the asymptotic behavior of the packing density in high dimensions. We argue that this estimate should be reinterpreted as a lower bound. The latter part of the paper is devoted to Bravais lattice packings that possess the minimum number of contacts to maintain mechanical stability. We show that quasicontacts play an even more important role in these packings. We also show that jammed lattices are a useful setting for studying the Edwards ensemble, which weights each mechanically stable configuration equally and does not account for dynamics. This ansatz fails to predict the power-law distribution of near-zero contact forces, P(f)∼fθ.

关键词： SPHERE packings POWER law (mathematics) computational complexity NP-hard problems BRAVAIS lattice

Realizable hyperuniform and nonhyperuniform particle configurations with targeted spectral functions via effective pair interactions

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Physical Review E 2020年第3期101卷 032124-032124页

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

The capacity to identify realizable many-body configurations associated with targeted functional forms for the pair correlation function g2(r) or its corresponding structure factor S(k) is of great fundamental and practical importance. While there are obvious necessary conditions that a prescribed structure factor at number density ρ must satisfy to be configurationally realizable, sufficient conditions are generally not known due to the infinite degeneracy of configurations with different higher-order correlation functions. A major aim of this paper is to expand our theoretical knowledge of the class of pair correlation functions or structure factors that are realizable by classical disordered ensembles of particle configurations, including exotic “hyperuniform” varieties. We first introduce a theoretical formalism that provides a means to draw classical particle configurations from canonical ensembles with certain pairwise-additive potentials that could correspond to targeted analytical functional forms for the structure factor. This formulation enables us to devise an improved algorithm to construct systematically canonical-ensemble particle configurations with such targeted pair statistics, whenever realizable. As a proof of concept, we test the algorithm by targeting several different structure factors across dimensions that are known to be realizable and one hyperuniform target that is known to be nontrivially unrealizable. Our algorithm succeeds for all realizable targets and appropriately fails for the unrealizable target, demonstrating the accuracy and power of the method to numerically investigate the realizability problem. Subsequently, we also target several families of structure-factor functions that meet the known necessary realizability conditions but are not known to be realizable by disordered hyperuniform point configurations, including d-dimensional Gaussian structure factors, d-dimensional generalizations of the two-dimensional one-component plas

关键词： Classical statistical mechanics

Quantum phase transitions in long-range interacting hyperuniform spin chains in a transverse field

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Physical Review B 2021年第1期103卷 014118-014118页

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

Hyperuniform states of matter are characterized by anomalous suppression of long-wavelength density fluctuations. While most of the interesting cases of disordered hyperuniformity are provided by complex many-body systems such as liquids or amorphous solids, classical spin chains with certain long-range interactions have been shown to demonstrate the same phenomenon. Such spin-chain systems are ideal models for exploring the effects of quantum mechanics on hyperuniformity. It is well-known that the transverse field Ising model shows a quantum phase transition (QPT) at zero temperature. Under the quantum effects of a transverse magnetic field, classical hyperuniform spin chains are expected to lose their hyperuniformity. High-precision simulations of these cases are complicated because of the presence of highly nontrivial long-range interactions. We perform an extensive analysis of these systems using density matrix renormalization group simulations to study the possibilities of phase transitions and the mechanism by which they lose hyperuniformity. Even for a spin chain of length 30, we see discontinuous changes in properties like the “τ order metric” of the ground state, the measure of hyperuniformity, and the second cumulant of the total magnetization along the x-direction, all suggestive of first-order QPTs. An interesting feature of the phase transitions in these disordered hyperuniform spin chains is that, depending on the parameter values, the presence of a transverse magnetic field may lead remarkably to an increase in the order of the ground state as measured by the “τ order metric,” even if hyperuniformity is lost. Therefore, it would be possible to design materials to target specific novel quantum behaviors in the presence of a transverse magnetic field. Our numerical investigations suggest that these spin chains can show no more than two QPTs. We further analyze the long-range interacting spin chains via the Jordan-Wigner mapping onto a system of spinless

关键词： Long-range interactions Quantum phase transitions Spin chains

On the uniqueness of FROG methods

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arXiv 2017年

作者： Bendory, Tamir Sidorenko, Pavel Eldar, Yonina C. Program in Applied and Computational Mathematics Princeton University PrincetonNJ United States Department of Physics and Solid State Institute Technion-Israel Institute of Technology Haifa Israel Department of Electrical Engineering Technion-Israel Institute of Technology Haifa Israel

The problem of recovering a signal from its power spectrum, called phase retrieval, arises in many scientific fields. One of many examples is ultra-short laser pulse characterization in which the electromagnetic field is oscillating with ∼ 1015 Hz and phase information cannot be measured directly due to limitations of the electronic sensors. Phase retrieval is ill-posed in most cases as there are many different signals with the same Fourier transform magnitude. To overcome this fundamental ill-posedness, several measurement techniques are used in practice. One of the most popular methods for complete characterization of ultra-short laser pulses is the Frequency-Resolved Optical Gating (FROG). In FROG, the acquired data is the power spectrum of the product of the unknown pulse with its delayed replica. Therefore the measured signal is a quartic function of the unknown pulse. A generalized version of FROG, where the delayed replica is replaced by a second unknown pulse, is called blind FROG. In this case, the measured signal is quadratic with respect to both pulses. In this letter we introduce and formulate FROG-type techniques. We then show that almost all band-limited signals are determined uniquely, up to trivial ambiguities, by blind FROG measurements (and thus also by FROG), if in addition we have access to the signals power spectrum. Copyright © 2017, The Authors. All rights reserved.

关键词： Power spectrum

Model reduction with memory and the machine learning of dynamical systems

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arXiv 2018年

作者： Ma, Chao Wang, Jianchun Weinan, E. Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States Department of Mechanics and Aerospace Engineering Southern University of Science and Technology Shenzhen518055 China Beijing Institute of Big Data Research Beijing100871 China

The well-known Mori-Zwanzig theory tells us that model reduction leads to memory effect. For a long time, modeling the memory effect accurately and efficiently has been an important but nearly impossible task in developing a good reduced model. In this work, we explore a natural analogy between recurrent neural networks and the Mori-Zwanzig formalism to establish a systematic approach for developing reduced models with memory. Two training models-a direct training model and a dynamically coupled training model-are proposed and compared. We apply these methods to the Kuramoto-Sivashinsky equation and the Navier-Stokes equation. Numerical experiments show that the proposed method can produce reduced model with good performance on both short-term prediction and long-term statistical properties. Copyright © 2018, The Authors. All rights reserved.

关键词： Recurrent neural networks

Methodology to construct large realizations of perfectly hyperuniform disordered packings

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Physical Review E 2019年第5期99卷 052141-052141页

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

Disordered hyperuniform packings (or dispersions) are unusual amorphous two-phase materials that are endowed with exotic physical properties. Such hyperuniform systems are characterized by an anomalous suppression of volume-fraction fluctuations at infinitely long-wavelengths, compared to ordinary disordered materials. While there has been growing interest in such singular states of amorphous matter, a major obstacle has been an inability to produce large samples that are perfectly hyperuniform due to practical limitations of conventional numerical and experimental methods. To overcome these limitations, we introduce a general theoretical methodology to construct perfectly hyperuniform packings in d-dimensional Euclidean space Rd. Specifically, beginning with an initial general tessellation of space by disjoint cells that meets a “bounded-cell” condition, hard particles of general shape are placed inside each cell such that the local-cell particle packing fractions are identical to the global packing fraction. We prove that the constructed packings with a polydispersity in size are perfectly hyperuniform in the infinite-sample-size limit, regardless of particle shapes, positions, and numbers per cell. We use this theoretical formulation to devise an efficient and tunable algorithm to generate extremely large realizations of such packings. We employ two distinct initial tessellations: Voronoi as well as sphere tessellations. Beginning with Voronoi tessellations, we show that our algorithm can remarkably convert extremely large nonhyperuniform packings into hyperuniform ones in R2 and R3. Implementing our theoretical methodology on sphere tessellations, we establish the hyperuniformity of the classical Hashin-Shtrikman multiscale coated-spheres structures, which are known to be two-phase media microstructures that possess optimal effective transport and elastic properties. A consequence of our work is a rigorous demonstration that packings that have identical tessella

关键词： Fluctuations & noise

computational Methods for Single-Particle Electron Cryomicroscopy

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Biomedical Data Science 1000年第1期3卷 163-190页

作者： Amit Singer Fred J. Sigworth 1Department of Mathematics and Program in Applied and Computational Mathematics Princeton University Princeton New Jersey 08544 USA email: amits@math.princeton.edu 2Departments of Cellular and Molecular Physiology Biomedical Engineering and Molecular Biophysics and Biochemistry Yale University New Haven Connecticut 06520 USA email: fred.sigworth@yale.edu

Single-particle electron cryomicroscopy (cryo-EM) is an increasingly popular technique for elucidating the three-dimensional (3D) structure of proteins and other biologically significant complexes at near-atomic resolution. It is an imaging method that does not require crystallization and can capture molecules in their native states. In single-particle cryo-EM, the 3D molecular structure needs to be determined from many noisy 2D tomographic projections of individual molecules, whose orientations and positions are unknown. The high level of noise and the unknown pose parameters are two key elements that make reconstruction a challenging computational problem. Even more challenging is the inference of structural variability and flexible motions when the individual molecules being imaged are in different conformational states. This review discusses computational methods for structure determination by single-particle cryo-EM and their guiding principles from statistical inference, machine learning, and signal processing, which also play a significant role in many other data science applications.

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Hyperuniformity of generalized random organization models

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arXiv 2018年

作者： Ma, Zheng Torquato, Salvatore Department of Physics Princeton University and Princeton New Jersey08544 United States Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544 United States

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. Copyright © 2018, The Authors. All rights reserved.

关键词： Critical current density (superconductivity)