arXiv subjects

James Fairbanks

Publications and source records attributed to James Fairbanks.

29 records · Page 2Linked to original sources

arXiv2023

Characterizing Compositionality of LQR from the Categorical Perspective

Composing systems is a fundamental concept in modern control systems, yet it remains challenging to formally analyze how controllers designed for individual subsystems can differ from controllers designed for the composition of those subsystems. To address this challenge, we propose a novel approach to composing control systems based on resource sharing machines, a concept from applied category theory. We use resource sharing machines to investigate the differences between (i) the linear-quadratic regulator (LQR) designed directly for a composite system and (ii) the LQR that is attained through the composition of LQRs designed for each subsystem. We first establish novel formalisms to compose LQR control designs using resource sharing machines. Then we develop new sufficient conditions to guarantee that the LQR designed for a composite system is equal to the LQR attained through composition of LQRs for its subsystems. In addition, we reduce the developed condition to that of checking the controllability and observability of a certain linear, time-invariant system, which provides a simple, computationally efficient procedure for evaluating the equivalence of controllers for composed systems.

eess.SY↗

arXiv2023

Computational category-theoretic rewriting

We demonstrate how category theory provides specifications that can efficiently be implemented via imperative algorithms and apply this to the field of graph rewriting. By examples, we show how this paradigm of software development makes it easy to quickly write correct and performant code. We provide a modern implementation of graph rewriting techniques at the level of abstraction of finitely-presented C-sets and clarify the connections between C-sets and the typed graphs supported in existing rewriting software. We emphasize that our open-source library is extensible: by taking new categorical constructions (such as slice categories, structured cospans, and distributed graphs) and relating their limits and colimits to those of their underlying categories, users inherit efficient algorithms for pushout complements and (final) pullback complements. This allows one to perform double-, single-, and sesqui-pushout rewriting over a broad class of data structures.

cs.LO↗

arXiv2022

Operadic Modeling of Dynamical Systems: Mathematics and Computation

Dynamical systems are ubiquitous in science and engineering as models of phenomena that evolve over time. Although complex dynamical systems tend to have important modular structure, conventional modeling approaches suppress this structure. Building on recent work in applied category theory, we show how deterministic dynamical systems, discrete and continuous, can be composed in a hierarchical style. In mathematical terms, we reformulate some existing operads of wiring diagrams and introduce new ones, using the general formalism of C-sets (copresheaves). We then establish dynamical systems as algebras of these operads. In a computational vein, we show that Euler's method is functorial for undirected systems, extending a previous result for directed systems. All of the ideas in this paper are implemented as practical software using Catlab and the AlgebraicJulia ecosystem, written in the Julia programming language for scientific computing.

math.CT↗

arXiv2022

Categorical Data Structures for Technical Computing

Many mathematical objects can be represented as functors from finitely-presented categories $\mathsf{C}$ to $\mathsf{Set}$. For instance, graphs are functors to $\mathsf{Set}$ from the category with two parallel arrows. Such functors are known informally as $\mathsf{C}$-sets. In this paper, we describe and implement an extension of $\mathsf{C}$-sets having data attributes with fixed types, such as graphs with labeled vertices or real-valued edge weights. We call such structures "acsets," short for "attributed $\mathsf{C}$-sets." Derived from previous work on algebraic databases, acsets are a joint generalization of graphs and data frames. They also encompass more elaborate graph-like objects such as wiring diagrams and Petri nets with rate constants. We develop the mathematical theory of acsets and then describe a generic implementation in the Julia programming language, which uses advanced language features to achieve performance comparable with specialized data structures.

math.CT↗

arXiv2022

A diagrammatic view of differential equations in physics

Presenting systems of differential equations in the form of diagrams has become common in certain parts of physics, especially electromagnetism and computational physics. In this work, we aim to put such use of diagrams on a firm mathematical footing, while also systematizing a broadly applicable framework to reason formally about systems of equations and their solutions. Our main mathematical tools are category-theoretic diagrams, which are well known, and morphisms between diagrams, which have been less appreciated. As an application of the diagrammatic framework, we show how complex, multiphysical systems can be modularly constructed from basic physical principles. A wealth of examples, drawn from electromagnetism, transport phenomena, fluid mechanics, and other fields, is included.

math-ph↗

arXiv2022

Compositional Exploration of Combinatorial Scientific Models

We implement a novel representation of model search spaces as diagrams over a category of models, where we have restricted attention to a broad class of models whose structure is presented by \C-sets. (Co)limits in these diagram categories allow the creation of composite model spaces from more primitive spaces. We present a novel implementation of the computer algebra of finitely presented categories and diagram categories (including their limits and colimits), which formalizes a notion of model space exploration. This is coupled with strategies to facilitate the selection of desired models from these model spaces. We demonstrate our framework by generating a tool which fits experimental data, searching an epidemiology-relevant subspace of mass-action kinetic models.

cs.LO↗

arXiv2022

An Algebraic Framework for Structured Epidemic Modeling

Pandemic management requires that scientists rapidly formulate and analyze epidemiological models in order to forecast the spread of disease and the effects of mitigation strategies. Scientists must modify existing models and create novel ones in light of new biological data and policy changes such as social distancing and vaccination. Traditional scientific modeling workflows detach the structure of a model -- its submodels and their interactions -- from its implementation in software. Consequently, incorporating local changes to model components may require global edits to the code-base through a manual, time-intensive, and error-prone process. We propose a compositional modeling framework that uses high-level algebraic structures to capture domain-specific scientific knowledge and bridge the gap between how scientists think about models and the code that implements them. These algebraic structures, grounded in applied category theory, simplify and expedite modeling tasks such as model specification, stratification, analysis, and calibration. With their structure made explicit, models also become easier to communicate, criticize, and refine in light of stakeholder feedback.

cs.PL↗

arXiv2020

A Compositional Framework for Scientific Model Augmentation

Scientists construct and analyze computational models to understand the world. That understanding comes from efforts to augment, combine, and compare models of related phenomena. We propose SemanticModels.jl, a system that leverages techniques from static and dynamic program analysis to process executable versions of scientific models to perform such metamodeling tasks. By framing these metamodeling tasks as metaprogramming problems, SemanticModels.jl enables writing programs that generate and expand models. To this end, we present a category theory-based framework for defining metamodeling tasks, and extracting semantic information from model implementations, and show how this framework can be used to enhance scientific workflows in a working case study.

cs.PL↗

arXiv2020

Compositional Scientific Computing with Catlab and SemanticModels

Scientific computing is currently performed by writing domain specific modeling frameworks for solving special classes of mathematical problems. Since applied category theory provides abstract reasoning machinery for describing and analyzing diverse areas of math, it is a natural platform for building generic and reusable software components for scientific computing. We present Catlab.jl, which provides the category-theoretic infrastructure for this project, together with SemanticModels.jl, which leverages this infrastructure for particular modeling tasks. This approach enhances and automates scientific computing workflows by applying recent advances in mathematical modeling of interconnected systems as cospan algebras.

math.CT↗

arXiv2019

Unsupervised Construction of Knowledge Graphs From Text and Code

The scientific literature is a rich source of information for data mining with conceptual knowledge graphs; the open science movement has enriched this literature with complementary source code that implements scientific models. To exploit this new resource, we construct a knowledge graph using unsupervised learning methods to identify conceptual entities. We associate source code entities to these natural language concepts using word embedding and clustering techniques. Practical naming conventions for methods and functions tend to reflect the concept(s) they implement. We take advantage of this specificity by presenting a novel process for joint clustering text concepts that combines word-embeddings, nonlinear dimensionality reduction, and clustering techniques to assist in understanding, organizing, and comparing software in the open science ecosystem. With our pipeline, we aim to assist scientists in building on existing models in their discipline when making novel models for new phenomena. By combining source code and conceptual information, our knowledge graph enhances corpus-wide understanding of scientific literature.

cs.LG↗

arXiv2011

A Ramsey Theorem for Indecomposable Matchings

A matching is indecomposable if it does not contain a nontrivial contiguous segment of vertices whose neighbors are entirely contained in the segment. We prove a Ramsey-like result for indecomposable matchings, showing that every sufficiently long indecomposable matching contains a long indecomposable matching of one of three types: interleavings, broken nestings, and proper pin sequences.

math.CO↗