Publications

The brain effortlessly solves blind source separation (BSS) problems, but the algorithm it uses remains elusive. In signal processing, linear BSS problems are often solved by Independent Component Analysis (ICA). To serve as a model of a biological circuit, the ICA neural network (NN) must satisfy at least the following requirements: 1. The algorithm must operate in the online setting where data samples are streamed one at a time, and the NN computes the sources on the fly without storing any significant fraction of the data in memory. 2. The synaptic weight update is local, i.e., it depends only on the biophysical variables present in the vicinity of a synapse. Here, we propose a novel objective function for ICA from which we derive a biologically plausible NN, including both the neural architecture and the synaptic learning rules. Interestingly, our algorithm relies on modulating synaptic plasticity by the total activity of the output neurons. In the brain, this could be accomplished by neuromodulators, extracellular calcium, local field potential, or nitric oxide.

Recently introduced shadow tomography protocols use “classical shadows” of quantum states to predict many target functions of an unknown quantum state. Unlike full quantum state tomography, shadow tomography does not insist on accurate recovery of the density matrix for high rank mixed states. Yet, such a protocol makes multiple accurate predictions with high confidence, based on a moderate number of quantum measurements. One particular influential algorithm, proposed by Huang et al. [Huang, Kueng, and Preskill, Nat. Phys. 16, 1050 (2020)], requires additional circuits for performing certain random unitary transformations. In this paper, we avoid these transformations but employ an arbitrary informationally complete positive operator-valued measure and show that such a procedure can compute k-bit correlation functions for quantum states reliably. We also show that, for this application, we do not need the median of means procedure of Huang et al. Finally, we discuss the contrast between the computation of correlation functions and fidelity of reconstruction of low rank density matrices.

Numerical methods for approximately solving partial differential equations (PDE) are at the core of scientific computing. Often, this requires high-resolution or adaptive discretization grids to capture relevant spatio-temporal features in the PDE solution, e.g., in applications like turbulence, combustion, and shock propagation. Numerical approximation also requires knowing the PDE in order to construct problem-specific discretizations. Systematically deriving such solution-adaptive discrete operators, however, is a current challenge. Here we present an artificial neural network architecture for data-driven learning of problemand resolution-specific local discretizations of nonlinear PDEs. Our proposed method achieves numerically stable discretization of the operators in an unknown nonlinear PDE by spatially and temporally adaptive parametric pooling on regular Cartesian grids, and by incorporating knowledge about discrete time integration. Knowing the actual PDE is not necessary, as solution data is sufficient to train the network to learn the discrete operators. A once-trained neural architecture model can be used to predict solutions of the PDE on larger spatial domains and for longer times than it was trained for, hence addressing the problem of PDE-constrained extrapolation from data. We present demonstrative examples on long-term forecasting of hard numerical problems including equation-free forecasting of non-linear dynamics of forced Burgers problem on coarse spatio-temporal grids.

We introduce c-lasso, a Python package that enables sparse and robust linear regression and classification with linear equality constraints. The underlying statistical forward model is assumed to be of the following form: [ y = X β+ σε subject to Cβ=0 ] Here, X ∈ℝ

mathematical illustrations by Alex H. Barnett: In Discriminating Data, Wendy Hui Kyong Chun reveals how polarization is a goal—not an error—within big data and machine learning. These methods, she argues, encode segregation, eugenics, and identity politics through their default assumptions and conditions. Correlation, which grounds big data's predictive potential, stems from twentieth-century eugenic attempts to “breed” a better future. Recommender systems foster angry clusters of sameness through homophily. Users are “trained” to become authentically predictable via a politics and technology of recognition. Machine learning and data analytics thus seek to disrupt the future by making disruption impossible.

In this paper we analyze the dynamics of single-excitation states, which model the scattering of a single photon from multiple two level atoms. For short times and weak atom-field couplings we show that the atomic amplitudes are given by a sum of decaying exponentials, where the decay rates and Lamb shifts are given by the poles of a certain analytic function. This result is a refinement of the "pole approximation" appearing in the standard Wigner-Weisskopf analysis of spontaneous emission. On the other hand, at large times, the atomic field decays like O(1/t3) with a known constant expressed in terms of the coupling parameter and the resonant frequency of the atoms. Moreover, we show that for stronger coupling, the solutions also feature a collection of oscillatory exponentials which dominate the behavior at long times. Finally, we extend the analysis to the continuum limit in which atoms are distributed according to a given density.

Abstract Several antimicrobial peptides, including magainin and the human cathelicidin LL-37, act by forming pores in bacterial membranes. Bacteria such as Staphylococcus aureus modify their membrane's cardiolipin composition to resist such types of perturbations that compromise their membrane stability. Here, we used molecular dynamics simulations to quantify the role of cardiolipin on the formation of pores in simple bacterial-like membrane models composed of phosphatidylglycerol and cardiolipin mixtures. Cardiolopin modified the structure and ordering of the lipid bilayer, making it less susceptible to mechanical changes. Accordingly, the free-energy barrier for the formation of a transmembrane pore and its kinetic instability augmented by increasing the cardiolipin concentration. This is attributed to the unfavorable positioning of cardiolipin near the formed pore, due to its small polar-head and bulky hydrophobic-body. Overall, our study demonstrates how cardiolipin prevents membrane-pore formation and this constitutes a plausible mechanism used by bacteria to act against stress perturbations and, thereby, gain resistance to antimicrobial agents.

Stacking is a widely used model averaging technique that asymptotically yields optimal predictions among linear averages. We show that stacking is most effective when model predictive performance is heterogeneous in inputs, and we can further improve the stacked mixture with a hierarchical model. We generalize stacking to Bayesian hierarchical stacking. The model weights are varying as a function of data, partially-pooled, and inferred using Bayesian inference. We further incorporate discrete and continuous inputs, other structured priors, and time series and longitudinal data. To verify the performance gain of the proposed method, we derive theory bounds, and demonstrate on several applied problems.

The Portable Extensible Toolkit for Scientific computation (PETSc) library delivers scalable solvers for nonlinear time-dependent differential and algebraic equations and for numerical optimization. The PETSc design for performance portability addresses fundamental GPU accelerator challenges and stresses flexibility and extensibility by separating the programming model used by the application from that used by the library, and it enables application developers to use their preferred programming model, such as Kokkos, RAJA, SYCL, HIP, CUDA, or OpenCL, on upcoming exascale systems. A blueprint for using GPUs from PETSc-based codes is provided, and case studies emphasize the flexibility and high performance achieved on current GPU-based systems.

We present `latentcor`, an R package for correlation estimation from data with mixed variable types. Mixed variables types, including continuous, binary, ordinal, zero-inflated, or truncated data are routinely collected in many areas of science. Accurate estimation of correlations among such variables is often the first critical step in statistical analysis workflows. Pearson correlation as the default choice is not well suited for mixed data types as the underlying normality assumption is violated. The concept of semi-parametric latent Gaussian copula models, on the other hand, provides a unifying way to estimate correlations between mixed data types. The R package `latentcor` comprises a comprehensive list of these models, enabling the estimation of correlations between any of continuous/binary/ternary/zero-inflated (truncated) variable types. The underlying implementation takes advantage of a fast multi-linear interpolation scheme with an efficient choice of interpolation grid points, thus giving the package a small memory footprint without compromising estimation accuracy. This makes latent correlation estimation readily available for modern high-throughput data analysis.