A colimit decomposition for homotopy algebras in Cat

Badzioch showed that in the category of simplicial sets each homotopy algebra of a Lawvere theory is weakly equivalent to a strict algebra. In seeking to extend this result to other contexts Rosicky observed a key point to be that each homotopy colimit in simplicial sets admits a decomposition into a homotopy sifted colimit of finite coproducts, and asked the author whether a similar decomposition holds in the 2-category of categories Cat. Our purpose in the present paper is to show that this is the case.Comment: Some notation changed; small amount of exposition added in intr

The Drosophila genome nexus: a population genomic resource of 623 Drosophila melanogaster genomes, including 197 from a single ancestral range population.

Hundreds of wild-derived Drosophila melanogaster genomes have been published, but rigorous comparisons across data sets are precluded by differences in alignment methodology. The most common approach to reference-based genome assembly is a single round of alignment followed by quality filtering and variant detection. We evaluated variations and extensions of this approach and settled on an assembly strategy that utilizes two alignment programs and incorporates both substitutions and short indels to construct an updated reference for a second round of mapping prior to final variant detection. Utilizing this approach, we reassembled published D. melanogaster population genomic data sets and added unpublished genomes from several sub-Saharan populations. Most notably, we present aligned data from phase 3 of the Drosophila Population Genomics Project (DPGP3), which provides 197 genomes from a single ancestral range population of D. melanogaster (from Zambia). The large sample size, high genetic diversity, and potentially simpler demographic history of the DPGP3 sample will make this a highly valuable resource for fundamental population genetic research. The complete set of assemblies described here, termed the Drosophila Genome Nexus, presently comprises 623 consistently aligned genomes and is publicly available in multiple formats with supporting documentation and bioinformatic tools. This resource will greatly facilitate population genomic analysis in this model species by reducing the methodological differences between data sets

Environment and classical channels in categorical quantum mechanics

We present a both simple and comprehensive graphical calculus for quantum computing. In particular, we axiomatize the notion of an environment, which together with the earlier introduced axiomatic notion of classical structure enables us to define classical channels, quantum measurements and classical control. If we moreover adjoin the earlier introduced axiomatic notion of complementarity, we obtain sufficient structural power for constructive representation and correctness derivation of typical quantum informatic protocols.Comment: 26 pages, many pics; this third version has substantially more explanations than previous ones; Journal reference is of short 14 page version; Proceedings of the 19th EACSL Annual Conference on Computer Science Logic (CSL), Lecture Notes in Computer Science 6247, Springer-Verlag (2010

Three qubit entanglement within graphical Z/X-calculus

The compositional techniques of categorical quantum mechanics are applied to analyse 3-qubit quantum entanglement. In particular the graphical calculus of complementary observables and corresponding phases due to Duncan and one of the authors is used to construct representative members of the two genuinely tripartite SLOCC classes of 3-qubit entangled states, GHZ and W. This nicely illustrates the respectively pairwise and global tripartite entanglement found in the W- and GHZ-class states. A new concept of supplementarity allows us to characterise inhabitants of the W class within the abstract diagrammatic calculus; these method extends to more general multipartite qubit states.Comment: In Proceedings HPC 2010, arXiv:1103.226

Quantum Picturalism

The quantum mechanical formalism doesn't support our intuition, nor does it elucidate the key concepts that govern the behaviour of the entities that are subject to the laws of quantum physics. The arrays of complex numbers are kin to the arrays of 0s and 1s of the early days of computer programming practice. In this review we present steps towards a diagrammatic `high-level' alternative for the Hilbert space formalism, one which appeals to our intuition. It allows for intuitive reasoning about interacting quantum systems, and trivialises many otherwise involved and tedious computations. It clearly exposes limitations such as the no-cloning theorem, and phenomena such as quantum teleportation. As a logic, it supports `automation'. It allows for a wider variety of underlying theories, and can be easily modified, having the potential to provide the required step-stone towards a deeper conceptual understanding of quantum theory, as well as its unification with other physical theories. Specific applications discussed here are purely diagrammatic proofs of several quantum computational schemes, as well as an analysis of the structural origin of quantum non-locality. The underlying mathematical foundation of this high-level diagrammatic formalism relies on so-called monoidal categories, a product of a fairly recent development in mathematics. These monoidal categories do not only provide a natural foundation for physical theories, but also for proof theory, logic, programming languages, biology, cooking, ... The challenge is to discover the necessary additional pieces of structure that allow us to predict genuine quantum phenomena.Comment: Commissioned paper for Contemporary Physics, 31 pages, 84 pictures, some colo

The GHZ/W-calculus contains rational arithmetic

Graphical calculi for representing interacting quantum systems serve a number of purposes: compositionally, intuitive graphical reasoning, and a logical underpinning for automation. The power of these calculi stems from the fact that they embody generalized symmetries of the structure of quantum operations, which, for example, stretch well beyond the Choi-Jamiolkowski isomorphism. One such calculus takes the GHZ and W states as its basic generators. Here we show that this language allows one to encode standard rational calculus, with the GHZ state as multiplication, the W state as addition, the Pauli X gate as multiplicative inversion, and the Pauli Z gate as additive inversion.Comment: In Proceedings HPC 2010, arXiv:1103.226

Generalised Compositional Theories and Diagrammatic Reasoning

This chapter provides an introduction to the use of diagrammatic language, or perhaps more accurately, diagrammatic calculus, in quantum information and quantum foundations. We illustrate the use of diagrammatic calculus in one particular case, namely the study of complementarity and non-locality, two fundamental concepts of quantum theory whose relationship we explore in later part of this chapter. The diagrammatic calculus that we are concerned with here is not merely an illustrative tool, but it has both (i) a conceptual physical backbone, which allows it to act as a foundation for diverse physical theories, and (ii) a genuine mathematical underpinning, permitting one to relate it to standard mathematical structures.Comment: To appear as a Springer book chapter chapter, edited by G. Chirabella, R. Spekken

Picturing classical and quantum Bayesian inference

We introduce a graphical framework for Bayesian inference that is sufficiently general to accommodate not just the standard case but also recent proposals for a theory of quantum Bayesian inference wherein one considers density operators rather than probability distributions as representative of degrees of belief. The diagrammatic framework is stated in the graphical language of symmetric monoidal categories and of compact structures and Frobenius structures therein, in which Bayesian inversion boils down to transposition with respect to an appropriate compact structure. We characterize classical Bayesian inference in terms of a graphical property and demonstrate that our approach eliminates some purely conventional elements that appear in common representations thereof, such as whether degrees of belief are represented by probabilities or entropic quantities. We also introduce a quantum-like calculus wherein the Frobenius structure is noncommutative and show that it can accommodate Leifer's calculus of `conditional density operators'. The notion of conditional independence is also generalized to our graphical setting and we make some preliminary connections to the theory of Bayesian networks. Finally, we demonstrate how to construct a graphical Bayesian calculus within any dagger compact category.Comment: 38 pages, lots of picture