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Alan Edelman

Publications and source records attributed to Alan Edelman.

At least 55 records · Page 3Linked to original sources

Locally Regularized Neural Differential Equations: Some Black Boxes Were Meant to Remain Closed!

Implicit layer deep learning techniques, like Neural Differential Equations, have become an important modeling framework due to their ability to adapt to new problems automatically. Training a neural differential equation is effectively a search over a space of plausible dynamical systems. However, controlling the computational cost for these models is difficult since it relies on the number of steps the adaptive solver takes. Most prior works have used higher-order methods to reduce prediction timings while greatly increasing training time or reducing both training and prediction timings by relying on specific training algorithms, which are harder to use as a drop-in replacement due to strict requirements on automatic differentiation. In this manuscript, we use internal cost heuristics of adaptive differential equation solvers at stochastic time points to guide the training toward learning a dynamical system that is easier to integrate. We "close the black-box" and allow the use of our method with any adjoint technique for gradient calculations of the differential equation solution. We perform experimental studies to compare our method to global regularization to show that we attain similar performance numbers without compromising the flexibility of implementation on ordinary differential equations (ODEs) and stochastic differential equations (SDEs). We develop two sampling strategies to trade off between performance and training time. Our method reduces the number of function evaluations to 0.556-0.733x and accelerates predictions by 1.3-2x.

cs.LG

Continuous Deep Equilibrium Models: Training Neural ODEs faster by integrating them to Infinity

Implicit models separate the definition of a layer from the description of its solution process. While implicit layers allow features such as depth to adapt to new scenarios and inputs automatically, this adaptivity makes its computational expense challenging to predict. In this manuscript, we increase the "implicitness" of the DEQ by redefining the method in terms of an infinite time neural ODE, which paradoxically decreases the training cost over a standard neural ODE by 2-4x. Additionally, we address the question: is there a way to simultaneously achieve the robustness of implicit layers while allowing the reduced computational expense of an explicit layer? To solve this, we develop Skip and Skip Reg. DEQ, an implicit-explicit (IMEX) layer that simultaneously trains an explicit prediction followed by an implicit correction. We show that training this explicit predictor is free and even decreases the training time by 1.11-3.19x. Together, this manuscript shows how bridging the dichotomy of implicit and explicit deep learning can combine the advantages of both techniques.

cs.LG

Signal Enhancement for Magnetic Navigation Challenge Problem

Harnessing the magnetic field of the Earth for navigation has shown promise as a viable alternative to other navigation systems. A magnetic navigation system collects its own magnetic field data using a magnetometer and uses magnetic anomaly maps to determine the current location. The greatest challenge with magnetic navigation arises when the magnetic field measurements from the magnetometer encompass the magnetic field from not just the Earth, but also from the vehicle on which it is mounted. It is difficult to separate the Earth magnetic anomaly field, which is crucial for navigation, from the total magnetic field reading from the sensor. The purpose of this challenge problem is to decouple the Earth and aircraft magnetic signals in order to derive a clean signal from which to perform magnetic navigation. Baseline testing on the dataset has shown that the Earth magnetic field can be extracted from the total magnetic field using machine learning (ML). The challenge is to remove the aircraft magnetic field from the total magnetic field using a trained model. This challenge offers an opportunity to construct an effective model for removing the aircraft magnetic field from the dataset by using a scientific machine learning (SciML) approach comprised of an ML algorithm integrated with the physics of magnetic navigation.

cs.LG

Bridging HPC Communities through the Julia Programming Language

The Julia programming language has evolved into a modern alternative to fill existing gaps in scientific computing and data science applications. Julia leverages a unified and coordinated single-language and ecosystem paradigm and has a proven track record of achieving high performance without sacrificing user productivity. These aspects make Julia a viable alternative to high-performance computing's (HPC's) existing and increasingly costly many-body workflow composition strategy in which traditional HPC languages (e.g., Fortran, C, C++) are used for simulations, and higher-level languages (e.g., Python, R, MATLAB) are used for data analysis and interactive computing. Julia's rapid growth in language capabilities, package ecosystem, and community make it a promising universal language for HPC. This paper presents the views of a multidisciplinary group of researchers from academia, government, and industry that advocate for an HPC software development paradigm that emphasizes developer productivity, workflow portability, and low barriers for entry. We believe that the Julia programming language, its ecosystem, and its community provide modern and powerful capabilities that enable this group's objectives. Crucially, we believe that Julia can provide a feasible and less costly approach to programming scientific applications and workflows that target HPC facilities. In this work, we examine the current practice and role of Julia as a common, end-to-end programming model to address major challenges in scientific reproducibility, data-driven AI/machine learning, co-design and workflows, scalability and performance portability in heterogeneous computing, network communication, data management, and community education. As a result, the diversification of current investments to fulfill the needs of the upcoming decade is crucial as more supercomputing centers prepare for the exascale era.

cs.DC

On the structure of the solutions to the matrix equation $G^*JG=J$

We study the mathematical structure of the solution set (and its tangent space) to the matrix equation $G^*JG=J$ for a given square matrix $J$. In the language of pure mathematics, this is a Lie group which is the isometry group for a bilinear (or a sesquilinear) form. Generally these groups are described as intersections of a few special groups. The tangent space to $\{G: G^*JG=J \}$ consists of solutions to the linear matrix equation $X^*J+JX=0$. For the complex case, the solution set of this linear equation was computed by De Ter{á}n and Dopico. We found that on its own, the equation $X^*J+JX=0$ is hard to solve. By throwing into the mix the complementary linear equation $X^*J-JX=0$, we find that rather than increasing the complexity, we reduce the complexity. Not only is it possible to now solve the original problem, but we can approach the broader algebraic and geometric structure. One implication is that the two equations form an $\mathfrak{h}$ and $\mathfrak{m}$ pair familiar in the study of pseudo-Riemannian symmetric spaces. We explicitly demonstrate the computation of the solutions to the equation $X^*J\pm XJ=0$ for real and complex matrices. However, any real, complex or quaternionic case with an arbitrary involution (e.g., transpose, conjugate transpose, and the various quaternion transposes) can be effectively solved with the same strategy. We provide numerical examples and visualizations.

math.NA

On the Cartan Decomposition for Classical Random Matrix Ensembles

We complete Dyson's dream by cementing the links between symmetric spaces and classical random matrix ensembles. Previous work has focused on a one-to-one correspondence between symmetric spaces and many but not all of the classical random matrix ensembles. This work shows that we can completely capture all of the classical random matrix ensembles from Cartan's symmetric spaces through the use of alternative coordinate systems. In the end, we have to let go of the notion of a one-to-one correspondence. We emphasize that the KAK decomposition traditionally favored by mathematicians is merely one coordinate system on the symmetric space, albeit a beautiful one. However, other matrix factorizations, especially the generalized singular value decomposition from numerical linear algebra reveal themselves to be perfectly valid coordinate systems revealing that one symmetric space can lead to many classical random matrix theories. We establish the connection between this numerical linear algebra viewpoint and the theory of generalized Cartan decomposition. This in turn allows us to produce yet more random matrix theories from a single symmetric space. Yet again these random matrix theories arise from matrix factorizations, through ones that we are not aware have appeared in the literature.

math-ph

AutoMat: Accelerated Computational Electrochemical systems Discovery

Large-scale electrification is vital to addressing the climate crisis, but several scientific and technological challenges remain to fully electrify both the chemical industry and transportation. In both of these areas, new electrochemical materials will be critical, but their development currently relies heavily on human-time-intensive experimental trial and error and computationally expensive first-principles, meso-scale and continuum simulations. We present an automated workflow, AutoMat, that accelerates these computational steps by introducing both automated input generation and management of simulations across scales from first principles to continuum device modeling. Furthermore, we show how to seamlessly integrate multi-fidelity predictions such as machine learning surrogates or automated robotic experiments "in-the-loop". The automated framework is implemented with design space search techniques to dramatically accelerate the overall materials discovery pipeline by implicitly learning design features that optimize device performance across several metrics. We discuss the benefits of AutoMat using examples in electrocatalysis and energy storage and highlight lessons learned.

cond-mat.mtrl-sci

Fifty Three Matrix Factorizations: A systematic approach

The success of matrix factorizations such as the singular value decomposition (SVD) has motivated the search for even more factorizations. We catalog 53 matrix factorizations, most of which we believe to be new. Our systematic approach, inspired by the generalized Cartan decomposition of Lie theory, also encompasses known factorizations such as the SVD, the symmetric eigendecomposition, the CS decomposition, the hyperbolic SVD, structured SVDs, the Takagi factorization, and others thereby covering familiar matrix factorizations as well as ones that were waiting to be discovered. We suggest that Lie theory has one way or another been lurking hidden in the foundations of the very successful field of matrix computations with applications routinely used in so many areas of computation. In this paper, we investigate consequences of the Cartan decomposition and the little known generalized Cartan decomposition for matrix factorizations. We believe that these factorizations once properly identified can lead to further work on algorithmic computations and applications.

math.NA

High-performance symbolic-numerics via multiple dispatch

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. We demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We showcase an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

cs.CL

Universal Differential Equations for Scientific Machine Learning

In the context of science, the well-known adage "a picture is worth a thousand words" might well be "a model is worth a thousand datasets." In this manuscript we introduce the SciML software ecosystem as a tool for mixing the information of physical laws and scientific models with data-driven machine learning approaches. We describe a mathematical object, which we denote universal differential equations (UDEs), as the unifying framework connecting the ecosystem. We show how a wide variety of applications, from automatically discovering biological mechanisms to solving high-dimensional Hamilton-Jacobi-Bellman equations, can be phrased and efficiently handled through the UDE formalism and its tooling. We demonstrate the generality of the software tooling to handle stochasticity, delays, and implicit constraints. This funnels the wide variety of SciML applications into a core set of training mechanisms which are highly optimized, stabilized for stiff equations, and compatible with distributed parallelism and GPU accelerators.

cs.LG

Composing Modeling and Simulation with Machine Learning in Julia

In this paper we introduce JuliaSim, a high-performance programming environment designed to blend traditional modeling and simulation with machine learning. JuliaSim can build accelerated surrogates from component-based models, such as those conforming to the FMI standard, using continuous-time echo state networks (CTESN). The foundation of this environment, ModelingToolkit.jl, is an acausal modeling language which can compose the trained surrogates as components within its staged compilation process. As a complementary factor we present the JuliaSim model library, a standard library with differential-algebraic equations and pre-trained surrogates, which can be composed using the modeling system for design, optimization, and control. We demonstrate the effectiveness of the surrogate-accelerated modeling and simulation approach on HVAC dynamics by showing that the CTESN surrogates accurately capture the dynamics of a HVAC cycle at less than 4\% error while accelerating its simulation by 340x. We illustrate the use of surrogate acceleration in the design process via global optimization of simulation parameters using the embedded surrogate, yielding a speedup of two orders of magnitude to find the optimum. We showcase the surrogate deployed in a co-simulation loop, as a drop-in replacement for one of the coupled FMUs, allowing engineers to effectively explore the design space of a coupled system. Together this demonstrates a workflow for automating the integration of machine learning techniques into traditional modeling and simulation processes.

cs.CE

Accelerating Simulation of Stiff Nonlinear Systems using Continuous-Time Echo State Networks

Modern design, control, and optimization often requires simulation of highly nonlinear models, leading to prohibitive computational costs. These costs can be amortized by evaluating a cheap surrogate of the full model. Here we present a general data-driven method, the continuous-time echo state network (CTESN), for generating surrogates of nonlinear ordinary differential equations with dynamics at widely separated timescales. We empirically demonstrate near-constant time performance using our CTESNs on a physically motivated scalable model of a heating system whose full execution time increases exponentially, while maintaining relative error of within 0.2 %. We also show that our model captures fast transients as well as slow dynamics effectively, while other techniques such as physics informed neural networks have difficulties trying to train and predict the highly nonlinear behavior of these models.

cs.LG

The GSVD: Where are the ellipses?, Matrix Trigonometry, and more

This paper provides an advanced mathematical theory of the Generalized Singular Value Decomposition (GSVD) and its applications. We explore the geometry of the GSVD which provides a long sought for ellipse picture which includes a horizontal and a vertical multiaxis. We further propose that the GSVD provides natural coordinates for the Grassmann manifold. This paper proves a theorem showing how the finite generalized singular values do or do not relate to the singular values of $AB^\dagger$. We then turn to the applications arguing that this geometrical theory is natural for understanding existing applications and recognizing opportunities for new applications. In particular the generalized singular vectors play a direct and as natural a mathematical role for certain applications as the singular vectors do for the SVD. In the same way that experts on the SVD often prefer not to cast SVD problems as eigenproblems, we propose that the GSVD, often cast as a generalized eigenproblem, is rather best cast in its natural setting. We illustrate this theoretical approach and the natural multiaxes (with labels from technical domains) in the context of applications where the GSVD arises: Tikhonov regularization (unregularized vs regularization), Genome Reconstruction (humans vs yeast), Signal Processing (signal vs noise), and statistical analysis such as ANOVA and discriminant analysis (between clusters vs within clusters.) With the aid of our ellipse figure, we encourage in the future the labelling of the natural multiaxes in any GSVD problem.

math.NA

A Differentiable Programming System to Bridge Machine Learning and Scientific Computing

Scientific computing is increasingly incorporating the advancements in machine learning and the ability to work with large amounts of data. At the same time, machine learning models are becoming increasingly sophisticated and exhibit many features often seen in scientific computing, stressing the capabilities of machine learning frameworks. Just as the disciplines of scientific computing and machine learning have shared common underlying infrastructure in the form of numerical linear algebra, we now have the opportunity to further share new computational infrastructure, and thus ideas, in the form of Differentiable Programming. We describe Zygote, a Differentiable Programming system that is able to take gradients of general program structures. We implement this system in the Julia programming language. Our system supports almost all language constructs (control flow, recursion, mutation, etc.) and compiles high-performance code without requiring any user intervention or refactoring to stage computations. This enables an expressive programming model for deep learning, but more importantly, it enables us to incorporate a large ecosystem of libraries in our models in a straightforward way. We discuss our approach to automatic differentiation, including its support for advanced techniques such as mixed-mode, complex and checkpointed differentiation, and present several examples of differentiating programs.

cs.PL

Circuitscape in Julia: High Performance Connectivity Modelling to Support Conservation Decisions

Connectivity across landscapes influences a wide range of conservation-relevant ecological processes, including species movements, gene flow, and the spread of wildfire, pests, and diseases. Recent improvements in remote sensing data suggest great potential to advance connectivity models, but computational constraints hinder these advances. To address this challenge, we upgraded the widely-used Circuitscape connectivity package to the high performance Julia programming language. Circuitscape.jl allows users to solve problems faster via improved parallel processing and solvers, and supports applications to larger problems (e.g., datasets with hundreds of millions of cells). We document speed improvements of up to 1800\%. We also demonstrate scaling of problem sizes up to 437 million grid cells. These improvements allow modelers to work with higher resolution data, larger landscapes and perform sensitivity analysis effortlessly. These improvements accelerate the pace of innovation, helping modelers address pressing challenges like species range shifts under climate change. Our collaboration between ecologists and computer scientists has led to the use of connectivity models to inform conservation decisions. Further, these next generation connectivity models will produce results faster, facilitating stronger engagement with decision-makers.

q-bio.QM

Fast computation of the principal components of genotype matrices in Julia

Finding the largest few principal components of a matrix of genetic data is a common task in genome-wide association studies (GWASs), both for dimensionality reduction and for identifying unwanted factors of variation. We describe a simple random matrix model for matrices that arise in GWASs, showing that the singular values have a bulk behavior that obeys a Marchenko-Pastur distributed with a handful of large outliers. We also implement Golub-Kahan-Lanczos (GKL) bidiagonalization in the Julia programming language, providing thick restarting and a choice between full and partial reorthogonalization strategies to control numerical roundoff. Our implementation of GKL bidiagonalization is up to 36 times faster than software tools used commonly in genomics data analysis for computing principal components, such as EIGENSOFT and FlashPCA, which use dense LAPACK routines and randomized subspace iteration respectively.

math.NA

TabulaROSA: Tabular Operating System Architecture for Massively Parallel Heterogeneous Compute Engines

The rise in computing hardware choices is driving a reevaluation of operating systems. The traditional role of an operating system controlling the execution of its own hardware is evolving toward a model whereby the controlling processor is distinct from the compute engines that are performing most of the computations. In this context, an operating system can be viewed as software that brokers and tracks the resources of the compute engines and is akin to a database management system. To explore the idea of using a database in an operating system role, this work defines key operating system functions in terms of rigorous mathematical semantics (associative array algebra) that are directly translatable into database operations. These operations possess a number of mathematical properties that are ideal for parallel operating systems by guaranteeing correctness over a wide range of parallel operations. The resulting operating system equations provide a mathematical specification for a Tabular Operating System Architecture (TabulaROSA) that can be implemented on any platform. Simulations of forking in TabularROSA are performed using an associative array implementation and compared to Linux on a 32,000+ core supercomputer. Using over 262,000 forkers managing over 68,000,000,000 processes, the simulations show that TabulaROSA has the potential to perform operating system functions on a massively parallel scale. The TabulaROSA simulations show 20x higher performance as compared to Linux while managing 2000x more processes in fully searchable tables.

cs.DC

Eigenvalue approximation of sums of Hermitian matrices from eigenvector localization/delocalization

We propose a technique for calculating and understanding the eigenvalue distribution of sums of random matrices from the known distribution of the summands. The exact problem is formidably hard. One extreme approximation to the true density amounts to classical probability, in which the matrices are assumed to commute; the other extreme is related to free probability, in which the eigenvectors are assumed to be in generic positions and sufficiently large. In practice, free probability theory can give a good approximation of the density. We develop a technique based on eigenvector localization/delocalization that works very well for important problems of interest where free probability is not sufficient, but certain uniformity properties apply. The localization/delocalization property appears in a convex combination parameter that notably, is independent of any eigenvalue properties and yields accurate eigenvalue density approximations. We demonstrate this technique on a number of examples as well as discuss a more general technique when the uniformity properties fail to apply.

quant-ph