Publications

The performance of objective image quality assessment (IQA) models has been evaluated primarily by comparing model predictions to human quality judgments. Perceptual datasets gathered for this purpose have provided useful benchmarks for improving IQA methods, but their heavy use creates a risk of overfitting. Here, we perform a large-scale comparison of IQA models in terms of their use as objectives for the optimization of image processing algorithms. Specifically, we use eleven full-reference IQA models to train deep neural networks for four low-level vision tasks: denoising, deblurring, super-resolution, and compression. Subjective testing on the optimized images allows us to rank the competing models in terms of their perceptual performance, elucidate their relative advantages and disadvantages in these tasks, and propose a set of desirable properties for incorporation into future IQA models.

We describe a new algorithm to solve the time dependent, frequency integrated radiation transport (RT) equation implicitly, which is coupled to an explicit solver for equations of magnetohydrodynamics (MHD) using {\sf Athena++}. The radiation filed is represented by specific intensities along discrete rays, which are evolved using a conservative finite volume approach for both cartesian and curvilinear coordinate systems. All the terms for spatial transport of photons and interactions between gas and radiation are calculated implicitly together. An efficient Jacobi-like iteration scheme is used to solve the implicit equations. This removes any time step constrain due to the speed of light in RT. We evolve the specific intensities in the lab frame to simplify the transport step. The lab-frame specific intensities are transformed to the co-moving frame via Lorentz transformation when the source term is calculated. Therefore, the scheme does not need any expansion in terms of v/c. The radiation energy and momentum source terms for the gas are calculated via direct quadrature in the angular space. The time step for the whole scheme is determined by the normal Courant -- Friedrichs -- Lewy condition in the MHD module. We provide a variety of test problems for this algorithm including both optically thick and thin regimes, and for both gas and radiation pressure dominated flows to demonstrate its accuracy and efficiency.

Active galactic nuclei (AGNs) are powered by geometrically thin accretion disks surrounding a central supermassive black hole. Here we explore the evolution of stars embedded in these extreme astrophysical environments (AGN stars). Because AGN disks are much hotter and denser than most components of the interstellar medium, AGN stars are subject to very different boundary conditions than normal stars. They are also strongly affected by both mass accretion, which can run away given the vast mass of the disk, and mass loss due to super-Eddington winds. Moreover, chemical mixing plays a critical role in the evolution of these stars by allowing fresh hydrogen accreted from the disk to mix into their cores. We find that, depending on the local AGN density and sound speed and the duration of the AGN phase, AGN stars can rapidly become very massive (M > 100 M⊙). These stars undergo core collapse, leave behind compact remnants, and contribute to polluting the disk with heavy elements. We show that the evolution of AGN stars can have a profound impact on the evolution of AGN metallicities, as well as the production of gravitational wave sources observed by LIGO-Virgo. We point to our Galactic Center as a region well suited to testing some of our predictions for this exotic stellar evolutionary channel.

Latent Gaussian copula models provide a powerful means to perform multi-view data integration since these models can seamlessly express dependencies between mixed variable types (binary, continuous, zero-inflated) via latent Gaussian correlations. The estimation of these latent correlations, however, comes at considerable computational cost, having prevented the routine use of these models on high-dimensional data. Here, we propose a new computational approach for estimating latent correlations via a hybrid multi-linear interpolation and optimization scheme. Our approach speeds up the current state of the art computation by several orders of magnitude, thus allowing fast computation of latent Gaussian copula models even when the number of variables p is large. We provide theoretical guarantees for the approximation error of our numerical scheme and support its excellent performance on simulated and real-world data. We illustrate the practical advantages of our method on high-dimensional sparse quantitative and relative abundance microbiome data as well as multi-view data from The Cancer Genome Atlas Project. Our method is implemented in the R package mixedCCA, available at https://github.com/irinagain/mixedCCA this https URL.

Cortical pyramidal neurons receive inputs from multiple distinct neural populations and integrate these inputs in separate dendritic compartments. We explore the possibility that cortical microcircuits implement Canonical Correlation Analysis (CCA), an unsupervised learning method that projects the inputs onto a common subspace so as to maximize the correlations between the projections. To this end, we seek a multi-channel CCA algorithm that can be implemented in a biologically plausible neural network. For biological plausibility, we require that the network operates in the online setting and its synaptic update rules are local. Starting from a novel CCA objective function, we derive an online optimization algorithm whose optimization steps can be implemented in a single-layer neural network with multi-compartmental neurons and local non-Hebbian learning rules. We also derive an extension of our online CCA algorithm with adaptive output rank and output whitening. Interestingly, the extension maps onto a neural network whose neural architecture and synaptic updates resemble neural circuitry and synaptic plasticity observed experimentally in cortical pyramidal neurons.

In cells, cytoskeletal filament networks are responsible for cell movement, growth, and division. Filaments in the cytoskeleton are driven and organized by crosslinking molecular motors. In reconstituted cytoskeletal systems, motor activity is responsible for far-from-equilibrium phenomena such as active stress, self-organized flow, and spontaneous nematic defect generation. How microscopic interactions between motors and filaments lead to larger-scale dynamics remains incompletely understood. To build from motor–filament interactions to predict bulk behavior of cytoskeletal systems, more computationally efficient techniques for modeling motor–filament interactions are needed. Here, we derive a coarse-graining hierarchy of explicit and continuum models for crosslinking motors that bind to and walk on filament pairs. We compare the steady-state motor distribution and motor-induced filament motion for the different models and analyze their computational cost. All three models agree well in the limit of fast motor binding kinetics. Evolving a truncated moment expansion of motor density speeds the computation by 103–106 compared to the explicit or continuous-density simulations, suggesting an approach for more efficient simulation of large networks. These tools facilitate further study of motor–filament networks on micrometer to millimeter length scales.

Active fluids consume fuel at the microscopic scale, converting this energy into forces that can drive macroscopic motions over scales far larger than their microscopic constituents. In some cases, the mechanisms that give rise to this phenomenon have been well characterized, and can explain experimentally observed behaviors in both bulk fluids and those confined in simple stationary geometries. More recently, active fluids have been encapsulated in viscous drops or elastic shells so as to interact with an outer environment or a deformable boundary. Such systems are not as well understood. In this work, we examine the behavior of droplets of an active nematic fluid. We study their linear stability about the isotropic equilibrium over a wide range of parameters, identifying regions in which different modes of instability dominate. Simulations of their full dynamics are used to identify their nonlinear behavior within each region. When a single mode dominates, the droplets behave simply: as rotors, swimmers, or extensors. When parameters are tuned so that multiple modes have nearly the same growth rate, a pantheon of modes appears, including zigzaggers, washing machines, wanderers, and pulsators.

The Hubbard model represents the fundamental model for interacting quantum systems and electronic correlations. Using the two-dimensional half-filled Hubbard model at weak coupling as testing grounds, we perform a comparative study of a comprehensive set of state of the art quantum many-body methods. Upon cooling into its insulating antiferromagnetic ground-state, the model hosts a rich sequence of distinct physical regimes with crossovers between a high-temperature incoherent regime, an intermediate temperature metallic regime and a low-temperature insulating regime with a pseudogap created by antiferromagnetic fluctuations. We assess the ability of each method to properly address these physical regimes and crossovers through the computation of several observables probing both quasiparticle properties and magnetic correlations, with two numerically exact methods (diagrammatic and determinantal quantum Monte Carlo) serving as a benchmark. By combining computational results and analytical insights, we elucidate the nature and role of spin fluctuations in each of these regimes and explain, in particular, how quasiparticles can coexist with increasingly long-range antiferromagnetic correlations in the metallic regime. We also critically discuss whether imaginary time methods are able to capture the non-Fermi liquid singularities of this fully nested system.

Developing oocytes need large supplies of macromolecules and organelles. A conserved strategy for accumulating these products is to pool resources of oocyte-associated germline nurse cells. In Drosophila, these cells grow more than 100-fold to boost their biosynthetic capacity. No previously known mechanism explains how nurse cells coordinate growth collectively. Here, we report a cell cycle-regulating mechanism that depends on bidirectional communication between the oocyte and nurse cells, revealing the oocyte as a critical regulator of germline cyst growth. Transcripts encoding the cyclin-dependent kinase inhibitor, Dacapo, are synthesized by the nurse cells and actively localized to the oocyte. Retrograde movement of the oocyte-synthesized Dacapo protein to the nurse cells generates a network of coupled oscillators that controls the cell cycle of the nurse cells to regulate cyst growth. We propose that bidirectional nurse cell-oocyte communication establishes a growth-sensing feedback mechanism that regulates the quantity of maternal resources loaded into the oocyte.

This paper presents the gravitational-wave measurement of the Hubble constant (H0) using the detections from the first and second observing runs of the Advanced LIGO and Virgo detector network. The presence of the transient electromagnetic counterpart of the binary neutron star GW170817 led to the first standard-siren measurement of H0. Here we additionally use binary black hole detections in conjunction with galaxy catalogs and report a joint measurement. Our updated measurement is H0=68.7+17.0−7.8 km/s/Mpc (68.3\% of the highest density posterior interval with a flat-in-log prior) which is an improvement by a factor of 1.04 (about 4\%) over the GW170817-only value of 68.7+17.5−8.3 km/s/Mpc. A significant additional contribution currently comes from GW170814, a loud and well-localized detection from a part of the sky thoroughly covered by the Dark Energy Survey. With numerous detections anticipated over the upcoming years, an exhaustive understanding of other systematic effects are also going to become increasingly important. These results establish the path to cosmology using gravitational-wave observations with and without transient electromagnetic counterparts.