Workshop on Applied Category Theory: Bridging Theory and Practice
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Experience Implementing a Performant Category-Theory Library in Coq
Experience Implementing a Performant Category-Theory Library in Coq Jason Gross, Adam Chlipala, and David I. Spivak Massachusetts Institute of Technology, Cambridge, MA, USA [email protected], [email protected], [email protected] Abstract. 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 sub- stantial 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 repre- sent very abstract mathematical objects and arguments in Coq and how future proof assistants might be designed to better support such rea- soning. One particular encoding trick to which we draw attention al- lows 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. Keywords: Coq · category theory · homotopy type theory · duality · performance 1 Introduction Category theory [36] is a popular all-encompassing mathematical formalism that casts familiar mathematical ideas from many domains in terms of a few unifying concepts. A category can be described as a directed graph plus algebraic laws stating equivalences between paths through the graph. Because of this spar- tan philosophical grounding, category theory is sometimes referred to in good humor as \formal abstract nonsense." Certainly the popular perception of cat- egory theory is quite far from pragmatic issues of implementation. -
Double Categories of Open Dynamical Systems (Extended Abstract)
Double Categories of Open Dynamical Systems (Extended Abstract) David Jaz Myers Johns Hopkins University A (closed) dynamical system is a notion of how things can be, together with a notion of how they may change given how they are. The idea and mathematics of closed dynamical systems has proven incredibly useful in those sciences that can isolate their object of study from its environment. But many changing situations in the world cannot be meaningfully isolated from their environment – a cell will die if it is removed from everything beyond its walls. To study systems that interact with their environment, and to design such systems in a modular way, we need a robust theory of open dynamical systems. In this extended abstract, we put forward a general definition of open dynamical system. We define two general sorts of morphisms between these systems: covariant morphisms which include trajectories, steady states, and periodic orbits; and contravariant morphisms which allow for plugging variables of some systems into parameters of other systems. We define an indexed double category of open dynamical systems indexed by their interface and use a double Grothendieck construction to construct a double category of open dynamical systems. In our main theorem, we construct covariantly representable indexed double functors from the indexed double category of dynamical systems to an indexed double category of spans. This shows that all covariantly representable structures of dynamical systems — including trajectories, steady states, and periodic orbits — compose according to the laws of matrix arithmetic. 1 Open Dynamical Systems The notion of a dynamical system pervades mathematical modeling in the sciences. -
Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
A Category-Theoretic Approach to Representation and Analysis of Inconsistency in Graph-Based Viewpoints
A Category-Theoretic Approach to Representation and Analysis of Inconsistency in Graph-Based Viewpoints by Mehrdad Sabetzadeh A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Computer Science University of Toronto Copyright c 2003 by Mehrdad Sabetzadeh Abstract A Category-Theoretic Approach to Representation and Analysis of Inconsistency in Graph-Based Viewpoints Mehrdad Sabetzadeh Master of Science Graduate Department of Computer Science University of Toronto 2003 Eliciting the requirements for a proposed system typically involves different stakeholders with different expertise, responsibilities, and perspectives. This may result in inconsis- tencies between the descriptions provided by stakeholders. Viewpoints-based approaches have been proposed as a way to manage incomplete and inconsistent models gathered from multiple sources. In this thesis, we propose a category-theoretic framework for the analysis of fuzzy viewpoints. Informally, a fuzzy viewpoint is a graph in which the elements of a lattice are used to specify the amount of knowledge available about the details of nodes and edges. By defining an appropriate notion of morphism between fuzzy viewpoints, we construct categories of fuzzy viewpoints and prove that these categories are (finitely) cocomplete. We then show how colimits can be employed to merge the viewpoints and detect the inconsistencies that arise independent of any particular choice of viewpoint semantics. Taking advantage of the same category-theoretic techniques used in defining fuzzy viewpoints, we will also introduce a more general graph-based formalism that may find applications in other contexts. ii To my mother and father with love and gratitude. Acknowledgements First of all, I wish to thank my supervisor Steve Easterbrook for his guidance, support, and patience. -
Knowledge Representation in Bicategories of Relations
Knowledge Representation in Bicategories of Relations Evan Patterson Department of Statistics, Stanford University Abstract We introduce the relational ontology log, or relational olog, a knowledge representation system based on the category of sets and relations. It is inspired by Spivak and Kent’s olog, a recent categorical framework for knowledge representation. Relational ologs interpolate between ologs and description logic, the dominant formalism for knowledge representation today. In this paper, we investigate relational ologs both for their own sake and to gain insight into the relationship between the algebraic and logical approaches to knowledge representation. On a practical level, we show by example that relational ologs have a friendly and intuitive—yet fully precise—graphical syntax, derived from the string diagrams of monoidal categories. We explain several other useful features of relational ologs not possessed by most description logics, such as a type system and a rich, flexible notion of instance data. In a more theoretical vein, we draw on categorical logic to show how relational ologs can be translated to and from logical theories in a fragment of first-order logic. Although we make extensive use of categorical language, this paper is designed to be self-contained and has considerable expository content. The only prerequisites are knowledge of first-order logic and the rudiments of category theory. 1. Introduction arXiv:1706.00526v2 [cs.AI] 1 Nov 2017 The representation of human knowledge in computable form is among the oldest and most fundamental problems of artificial intelligence. Several recent trends are stimulating continued research in the field of knowledge representation (KR). -
The ACT Pipeline from Abstraction to Application
Addressing hypercomplexity: The ACT pipeline from abstraction to application David I. Spivak (Joint with Brendan Fong, Paolo Perrone, Evan Patterson) Department of Mathematics Massachusetts Institute of Technology 0 / 25 Introduction Outline 1 Introduction Why? How? What? Plan of the talk 2 Some new applications 3 Catlab.jl 4 Conclusion 0 / 25 Introduction Why? What's wrong? As problem complexity increases, good organization becomes crucial. (Courtesy of Spencer Breiner, NIST) 1 / 25 Introduction Why? The problem is hypercomplexity The world is becoming more complex. We need to deal with more and more diverse sorts of interaction. Rather than closed dynamical systems, everything is open. The state of one system affects those of systems in its environment. Examples are everywhere. Designing anything requires input from more diverse stakeholders. Software is developed by larger teams, touching a common codebase. Scientists need to use experimental data obtained by their peers. (But the data structure and assumptions don't simply line up.) We need to handle this new complexity; traditional methods are faltering. 2 / 25 Introduction How? How might we deal with hypercomplexity? Organize the problem spaces effectively, as objects in their own right. Find commonalities in the various problems we work on. Consider the ways we build complex problems out of simple ones. Think of problem spaces and solutions as mathematical entities. With that in hand, how do you solve a hypercomplex problem? Migrating subproblems to groups who can solve them. Take the returned solutions and fit them together. Ensure in advance that these solutions will compose. Do this according the mathematical problem-space structure. -
Diagrammatics in Categorification and Compositionality
Diagrammatics in Categorification and Compositionality by Dmitry Vagner Department of Mathematics Duke University Date: Approved: Ezra Miller, Supervisor Lenhard Ng Sayan Mukherjee Paul Bendich Dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Mathematics in the Graduate School of Duke University 2019 ABSTRACT Diagrammatics in Categorification and Compositionality by Dmitry Vagner Department of Mathematics Duke University Date: Approved: Ezra Miller, Supervisor Lenhard Ng Sayan Mukherjee Paul Bendich An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Mathematics in the Graduate School of Duke University 2019 Copyright c 2019 by Dmitry Vagner All rights reserved Abstract In the present work, I explore the theme of diagrammatics and their capacity to shed insight on two trends|categorification and compositionality|in and around contemporary category theory. The work begins with an introduction of these meta- phenomena in the context of elementary sets and maps. Towards generalizing their study to more complicated domains, we provide a self-contained treatment|from a pedagogically novel perspective that introduces almost all concepts via diagrammatic language|of the categorical machinery with which we may express the broader no- tions found in the sequel. The work then branches into two seemingly unrelated disciplines: dynamical systems and knot theory. In particular, the former research defines what it means to compose dynamical systems in a manner analogous to how one composes simple maps. The latter work concerns the categorification of the slN link invariant. In particular, we use a virtual filtration to give a more diagrammatic reconstruction of Khovanov-Rozansky homology via a smooth TQFT. -
2019 AMS Prize Announcements
FROM THE AMS SECRETARY 2019 Leroy P. Steele Prizes The 2019 Leroy P. Steele Prizes were presented at the 125th Annual Meeting of the AMS in Baltimore, Maryland, in January 2019. The Steele Prizes were awarded to HARUZO HIDA for Seminal Contribution to Research, to PHILIppE FLAJOLET and ROBERT SEDGEWICK for Mathematical Exposition, and to JEFF CHEEGER for Lifetime Achievement. Haruzo Hida Philippe Flajolet Robert Sedgewick Jeff Cheeger Citation for Seminal Contribution to Research: Hamadera (presently, Sakai West-ward), Japan, he received Haruzo Hida an MA (1977) and Doctor of Science (1980) from Kyoto The 2019 Leroy P. Steele Prize for Seminal Contribution to University. He did not have a thesis advisor. He held po- Research is awarded to Haruzo Hida of the University of sitions at Hokkaido University (Japan) from 1977–1987 California, Los Angeles, for his highly original paper “Ga- up to an associate professorship. He visited the Institute for Advanced Study for two years (1979–1981), though he lois representations into GL2(Zp[[X ]]) attached to ordinary cusp forms,” published in 1986 in Inventiones Mathematicae. did not have a doctoral degree in the first year there, and In this paper, Hida made the fundamental discovery the Institut des Hautes Études Scientifiques and Université that ordinary cusp forms occur in p-adic analytic families. de Paris Sud from 1984–1986. Since 1987, he has held a J.-P. Serre had observed this for Eisenstein series, but there full professorship at UCLA (and was promoted to Distin- the situation is completely explicit. The methods and per- guished Professor in 1998). -
Parametrized Higher Category Theory
Parametrized higher category theory Jay Shah MIT May 1, 2017 Jay Shah (MIT) Parametrized higher category theory May 1, 2017 1 / 32 Answer: depends on the class of weak equivalences one inverts in the larger category of G-spaces. Inverting the class of maps that induce a weak equivalence of underlying spaces, X ; the homotopy type of the underlying space X , together with the homotopy coherent G-action. Can extract homotopy fixed points and hG orbits X , XhG from this. Equivariant homotopy theory Let G be a finite group and let X be a topological space with G-action (e.g. G = C2 and X = U(n) with the complex conjugation action). What is the \homotopy type" of X ? Jay Shah (MIT) Parametrized higher category theory May 1, 2017 2 / 32 Inverting the class of maps that induce a weak equivalence of underlying spaces, X ; the homotopy type of the underlying space X , together with the homotopy coherent G-action. Can extract homotopy fixed points and hG orbits X , XhG from this. Equivariant homotopy theory Let G be a finite group and let X be a topological space with G-action (e.g. G = C2 and X = U(n) with the complex conjugation action). What is the \homotopy type" of X ? Answer: depends on the class of weak equivalences one inverts in the larger category of G-spaces. Jay Shah (MIT) Parametrized higher category theory May 1, 2017 2 / 32 Equivariant homotopy theory Let G be a finite group and let X be a topological space with G-action (e.g. -
Category Theory Cheat Sheet
Musa Al-hassy https://github.com/alhassy/CatsCheatSheet July 5, 2019 Even when morphisms are functions, the objects need not be sets: Sometimes the objects . are operations —with an appropriate definition of typing for the functions. The categories Reference Sheet for Elementary Category Theory of F -algebras are an example of this. “Gluing” Morphisms Together Categories Traditional function application is replaced by the more generic concept of functional A category C consists of a collection of “objects” Obj C, a collection of “(homo)morphisms” composition suggested by morphism-arrow chaining: HomC(a; b) for any a; b : Obj C —also denoted “a !C b”—, an operation Id associating Whenever we have two morphisms such that the target type of one of them, say g : B A a morphism Ida : Hom(a; a) to each object a, and a dependently-typed “composition” is the same as the source type of the other, say f : C B then “f after g”, their composite operation _ ◦ _ : 8fABC : Objg ! Hom(B; C) ! Hom(A; B) ! Hom(A; C) that is morphism, f ◦ g : C A can be defined. It “glues” f and g together, “sequentially”: required to be associative with Id as identity. It is convenient to define a pair of operations src; tgt from morphisms to objects as follows: f g f◦g C − B − A ) C − A composition-Type f : X !C Y ≡ src f = X ^ tgt f = Y src; tgt-Definition Composition is the basis for gluing morphisms together to build more complex morphisms. Instead of HomC we can instead assume primitive a ternary relation _ : _ !C _ and However, not every two morphisms can be glued together by composition. -
Logic and Categories As Tools for Building Theories
Logic and Categories As Tools For Building Theories Samson Abramsky Oxford University Computing Laboratory 1 Introduction My aim in this short article is to provide an impression of some of the ideas emerging at the interface of logic and computer science, in a form which I hope will be accessible to philosophers. Why is this even a good idea? Because there has been a huge interaction of logic and computer science over the past half-century which has not only played an important r^olein shaping Computer Science, but has also greatly broadened the scope and enriched the content of logic itself.1 This huge effect of Computer Science on Logic over the past five decades has several aspects: new ways of using logic, new attitudes to logic, new questions and methods. These lead to new perspectives on the question: What logic is | and should be! Our main concern is with method and attitude rather than matter; nevertheless, we shall base the general points we wish to make on a case study: Category theory. Many other examples could have been used to illustrate our theme, but this will serve to illustrate some of the points we wish to make. 2 Category Theory Category theory is a vast subject. It has enormous potential for any serious version of `formal philosophy' | and yet this has hardly been realized. We shall begin with introduction to some basic elements of category theory, focussing on the fascinating conceptual issues which arise even at the most elementary level of the subject, and then discuss some its consequences and philosophical ramifications. -
Yoneda's Lemma for Internal Higher Categories
YONEDA'S LEMMA FOR INTERNAL HIGHER CATEGORIES LOUIS MARTINI Abstract. We develop some basic concepts in the theory of higher categories internal to an arbitrary 1- topos. We define internal left and right fibrations and prove a version of the Grothendieck construction and of Yoneda's lemma for internal categories. Contents 1. Introduction 2 Motivation 2 Main results 3 Related work 4 Acknowledgment 4 2. Preliminaries 4 2.1. General conventions and notation4 2.2. Set theoretical foundations5 2.3. 1-topoi 5 2.4. Universe enlargement 5 2.5. Factorisation systems 8 3. Categories in an 1-topos 10 3.1. Simplicial objects in an 1-topos 10 3.2. Categories in an 1-topos 12 3.3. Functoriality and base change 16 3.4. The (1; 2)-categorical structure of Cat(B) 18 3.5. Cat(S)-valued sheaves on an 1-topos 19 3.6. Objects and morphisms 21 3.7. The universe for groupoids 23 3.8. Fully faithful and essentially surjective functors 26 arXiv:2103.17141v2 [math.CT] 2 May 2021 3.9. Subcategories 31 4. Groupoidal fibrations and Yoneda's lemma 36 4.1. Left fibrations 36 4.2. Slice categories 38 4.3. Initial functors 42 4.4. Covariant equivalences 49 4.5. The Grothendieck construction 54 4.6. Yoneda's lemma 61 References 71 Date: May 4, 2021. 1 2 LOUIS MARTINI 1. Introduction Motivation. In various areas of geometry, one of the principal strategies is to study geometric objects by means of algebraic invariants such as cohomology, K-theory and (stable or unstable) homotopy groups.