arXiv subjects

David I. Spivak

Publications and source records attributed to David I. Spivak.

At least 73 records · Page 4Linked to original sources

arXiv2015

Nesting of dynamic systems and mode-dependent networks

For many networks, the connection pattern (often called the topology) can vary in time, depending on the changing state, or mode, of the modules within the network. For example, "airplane mode" is the name for one communicative mode of a modern cellphone, in which it will not connect with any cellphone towers; thus the topology of the cellular network is dependent on the modes of its modules. This paper addresses the issue of nesting such mode-dependent networks, in which a local network can be abstracted as a single module in a larger network. Each module in the network represents a dynamic system, whose behavior includes repeatedly updating its communicative mode. It is in this way that the dynamics of the modules controls the topology of the networks at all levels. This paper provides a formal semantics, using the category-theoretic framework of operads and their algebras, to capture the nesting property and dynamics of mode-dependent networks. We provide a detailed running example to ground the mathematics.

math.DS↗

arXiv2015

QINL: Query-integrated Languages

We describe an alternative solution to the impedance-mismatch problem between programming and query languages: rather than embed queries in a programming language, as done in LINQ systems, we embed programs in a query language, and dub the result QINL.

cs.PL↗

arXiv2015

Algebras of Open Dynamical Systems on the Operad of Wiring Diagrams

In this paper, we use the language of operads to study open dynamical systems. More specifically, we study the algebraic nature of assembling complex dynamical systems from an interconnection of simpler ones. The syntactic architecture of such interconnections is encoded using the visual language of wiring diagrams. We define the symmetric monoidal category W, from which we may construct an operad O(W), whose objects are black boxes with input and output ports, and whose morphisms are wiring diagrams, thus prescribing the algebraic rules for interconnection. We then define two W-algebras, G and L, which associate semantic content to the structures in W. Respectively, they correspond to general and to linear systems of differential equations, in which an internal state is controlled by inputs and produces outputs. As an example, we use these algebras to formalize the classical problem of systems of tanks interconnected by pipes, and hence make explicit the algebraic relationships among systems at different levels of granularity.

math.CT↗

arXiv2015

Relational Foundations For Functorial Data Migration

We study the data transformation capabilities associated with schemas that are presented by directed multi-graphs and path equations. Unlike most approaches which treat graph-based schemas as abbreviations for relational schemas, we treat graph-based schemas as categories. A schema $S$ is a finitely-presented category, and the collection of all $S$-instances forms a category, $S$-inst. A functor $F$ between schemas $S$ and $T$, which can be generated from a visual mapping between graphs, induces three adjoint data migration functors, $Σ_F:S$-inst$\to T$-inst, $Π_F: S$-inst $\to T$-inst, and $Δ_F:T$-inst $\to S$-inst. We present an algebraic query language FQL based on these functors, prove that FQL is closed under composition, prove that FQL can be implemented with the select-project-product-union relational algebra (SPCU) extended with a key-generation operation, and prove that SPCU can be implemented with FQL.

cs.DB↗

arXiv2015

Categories as mathematical models

Written to be contributed as the "mathematical modeling" chapter of a book, edited by Elaine Landry, to be titled "Categories for the Working Philosopher". In this chapter, category theory is presented as a mathematical modeling framework that highlights the relationships between objects, rather than the objects in themselves. A working definition of model is given, and several examples of mathematical objects, such as vector spaces, groups, and dynamical systems, are considered as categorical models.

math.CT↗

arXiv2015

Toward formalizing ologs: Linguistic structures, instantiations, and mappings

We define the notion of linguistic structure on a small category, in order to provide a more formal description of ontology logs, also known as ologs, introduced by R. E. Kent and D. I. Spivak in their paper "Ologs: A categorical framework for knowledge representation." In particular, we construct a bicategory $\mathsf{Eng}$, of English noun phrases and verb phrases, endorsed as functional by varying sets of authors. An olog is then defined as a lax functor to $\mathsf{Eng}$. We then present a new notion of linguistic functor, which extends Spivak's notion of meaningful functors. Finally, we discuss the relationship between ologs and databases in this context.

math.CT↗

arXiv2015

Functorial Data Migration: From Theory to Practice

In this paper we describe a functorial data migration scenario about the manufacturing service capability of a distributed supply chain. The scenario is a category-theoretic analog of an OWL ontology-based semantic enrichment scenario developed at the National Institute of Standards and Technology (NIST). The scenario is presented using, and is included with, the open-source FQL tool, available for download at categoricaldata.net/fql.html.

cs.DB↗

arXiv2014

Type theoretical databases

We present a soundness theorem for a dependent type theory with context constants with respect to an indexed category of (finite, abstract) simplical complexes. The point of interest for computer science is that this category can be seen to represent tables in a natural way. Thus the category is a model for databases, a single mathematical structure in which all database schemas and instances (of a suitable, but sufficiently general form) are represented. The type theory then allows for the specification of database schemas and instances, the manipulation of the same with the usual type-theoretic operations, and the posing of queries.

math.LO↗

arXiv2014

Experience Implementing a Performant Category-Theory Library in Coq

We describe our experience implementing a broad category-theory library in Coq. Category theory and computational performance are not usually mentioned in the same breath, but we have needed substantial engineering effort to teach Coq to cope with large categorical constructions without slowing proof script processing unacceptably. In this paper, we share the lessons we have learned about how to represent very abstract mathematical objects and arguments in Coq and how future proof assistants might be designed to better support such reasoning. One particular encoding trick to which we draw attention allows category-theoretic arguments involving duality to be internalized in Coq's logic with definitional equality. Ours may be the largest Coq development to date that uses the relatively new Coq version developed by homotopy type theorists, and we reflect on which new features were especially helpful.

math.CT↗

arXiv2013

Category theory for scientists (Old version)

There are many books designed to introduce category theory to either a mathematical audience or a computer science audience. In this book, our audience is the broader scientific community. We attempt to show that category theory can be applied throughout the sciences as a framework for modeling phenomena and communicating results. In order to target the scientific audience, this book is example-based rather than proof-based. For example, monoids are framed in terms of agents acting on objects, sheaves are introduced with primary examples coming from geography, and colored operads are discussed in terms of their ability to model self-similarity. A new version with solutions to exercises will be available through MIT Press.

math.CT↗

arXiv2013

The operad of temporal wiring diagrams: formalizing a graphical language for discrete-time processes

We investigate the hierarchical structure of processes using the mathematical theory of operads. Information or material enters a given process as a stream of inputs, and the process converts it to a stream of outputs. Output streams can then be supplied to other processes in an organized manner, and the resulting system of interconnected processes can itself be considered a macro process. To model the inherent structure in this kind of system, we define an operad $\mathcal{W}$ of black boxes and directed wiring diagrams, and we define a $\mathcal{W}$-algebra $\mathcal{P}$ of processes (which we call propagators, after Radul and Sussman). Previous operadic models of wiring diagrams use undirected wires without length, useful for modeling static systems of constraints, whereas we use directed wires with length, useful for modeling dynamic flows of information. We give multiple examples throughout to ground the ideas.

math.CT↗

arXiv2013

Database queries and constraints via lifting problems

Previous work has demonstrated that categories are useful and expressive models for databases. In the present paper we build on that model, showing that certain queries and constraints correspond to lifting problems, as found in modern approaches to algebraic topology. In our formulation, each so-called SPARQL graph pattern query corresponds to a category-theoretic lifting problem, whereby the set of solutions to the query is precisely the set of lifts. We interpret constraints within the same formalism and then investigate some basic properties of queries and constraints. In particular, to any database $π$ we can associate a certain derived database $\Qry(π)$ of queries on $π$. As an application, we explain how giving users access to certain parts of $\Qry(π)$, rather than direct access to $π$, improves ones ability to manage the impact of schema evolution.

math.CT↗

arXiv2013

The operad of wiring diagrams: formalizing a graphical language for databases, recursion, and plug-and-play circuits

Wiring diagrams, as seen in digital circuits, can be nested hierarchically and thus have an aspect of self-similarity. We show that wiring diagrams form the morphisms of an operad $\mcT$, capturing this self-similarity. We discuss the algebra $\Rel$ of mathematical relations on $\mcT$, and in so doing use wiring diagrams as a graphical language with which to structure queries on relational databases. We give the example of circuit diagrams as a special case. We move on to show how plug-and-play devices and also recursion can be formulated in the operadic framework as well. Throughout we include many examples and figures.

cs.DB↗

arXiv2013

Functorial Data Migration

In this paper we present a simple database definition language: that of categories and functors. A database schema is a small category and an instance is a set-valued functor on it. We show that morphisms of schemas induce three "data migration functors", which translate instances from one schema to the other in canonical ways. These functors parameterize projections, unions, and joins over all tables simultaneously and can be used in place of conjunctive and disjunctive queries. We also show how to connect a database and a functional programming language by introducing a functorial connection between the schema and the category of types for that language. We begin the paper with a multitude of examples to motivate the definitions, and near the end we provide a dictionary whereby one can translate database concepts into category-theoretic concepts and vice-versa.

cs.DB↗

arXiv2012

Kleisli Database Instances

We use monads to relax the atomicity requirement for data in a database. Depending on the choice of monad, the database fields may contain generalized values such as lists or sets of values, or they may contain exceptions such as various types of nulls. The return operation for monads ensures that any ordinary database instance will count as one of these generalized instances, and the bind operation ensures that generalized values behave well under joins of foreign key sequences. Different monads allow for vastly different types of information to be stored in the database. For example, we show that classical concepts like Markov chains, graphs, and finite state automata are each perfectly captured by a different monad on the same schema.

cs.DB↗

arXiv2011

Ologs: a categorical framework for knowledge representation

In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as semantic networks) cannot. An olog is similar to a relational database schema; in fact an olog can serve as a data repository if desired. Unlike database schemas, which are generally difficult to create or modify, ologs are designed to be user-friendly enough that authoring or reconfiguring an olog is a matter of course rather than a difficult chore. It is hoped that learning to author ologs is much simpler than learning a database definition language, despite their similarity. We describe ologs carefully and illustrate with many examples. As an application we show that any primitive recursive function can be described by an olog. We also show that ologs can be aligned or connected together into a larger network using functors. The various methods of information flow and institutions can then be used to integrate local and global world-views. We finish by providing several different avenues for future research.

cs.LO↗

arXiv2011

Category theoretic analysis of hierarchical protein materials and social networks

Materials in biology span all the scales from Angstroms to meters and typically consist of complex hierarchical assemblies of simple building blocks. Here we describe an application of category theory to describe structural and resulting functional properties of biological protein materials by developing so-called ologs. An olog is like a "concept web" or "semantic network" except that it follows a rigorous mathematical formulation based on category theory. This key difference ensures that an olog is unambiguous, highly adaptable to evolution and change, and suitable for sharing concepts with other olog. We consider simple cases of alpha-helical and amyloid-like protein filaments subjected to axial extension and develop an olog representation of their structural and resulting mechanical properties. We also construct a representation of a social network in which people send text-messages to their nearest neighbors and act as a team to perform a task. We show that the olog for the protein and the olog for the social network feature identical category-theoretic representations, and we proceed to precisely explicate the analogy or isomorphism between them. The examples presented here demonstrate that the intrinsic nature of a complex system, which in particular includes a precise relationship between structure and function at different hierarchical levels, can be effectively represented by an olog. This, in turn, allows for comparative studies between disparate materials or fields of application, and results in novel approaches to derive functionality in the design of de novo hierarchical systems. We discuss opportunities and challenges associated with the description of complex biological materials by using ologs as a powerful tool for analysis and design in the context of materiomics, and we present the potential impact of this approach for engineering, life sciences, and medicine.

math.CT↗

arXiv2010

Derived Smooth Manifolds

We define a simplicial category called the category of derived manifolds. It contains the category of smooth manifolds as a full discrete subcategory, and it is closed under taking arbitrary intersections in a manifold. A derived manifold is a space together with a sheaf of local $C^\infty$-rings that is obtained by patching together homotopy zero-sets of smooth functions on Euclidean spaces. We show that derived manifolds come equipped with a stable normal bundle and can be imbedded into Euclidean space. We define a cohomology theory called derived cobordism, and use a Pontrjagin-Thom argument to show that the derived cobordism theory is isomorphic to the classical cobordism theory. This allows us to define fundamental classes in cobordism for all derived manifolds. In particular, the intersection $A\cap B$ of submanifolds $A,B\subset X$ exists on the categorical level in our theory, and a cup product formula $$[A]\smile[B]=[A\cap B]$$ holds, even if the submanifolds are not transverse. One can thus consider the theory of derived manifolds as a {\em categorification} of intersection theory.

math.AT↗