David I. Spivak

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.

Mapping spaces in quasi-categories

We apply the Dwyer-Kan theory of homotopy function complexes in model categories to the study of mapping spaces in quasi-categories. Using this, together with our work on rigidification from [DS1], we give a streamlined proof of the Quillen equivalence between quasi-categories and simplicial categories. Some useful material about relative mapping spaces in quasi-categories is developed along the way.

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 beta-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.

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

Anomaly-free sets of fermions

C^\infty

Reoccurring Patterns in Hierarchical Protein Materials and Music: The Power of Analogies

-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

Rigidification of quasi-categories

A\cap B

Relational foundations for functorial data migration

of submanifolds

Experience Implementing a Performant Category-Theory Library in Coq

A,B\subset X

Database queries and constraints via lifting problems

exists on the categorical level in our theory, and a cup product formula