Classical Structures Based on Unitaries

Starting from the observation that distinct notions of copying have arisen in different categorical fields (logic and computation, contrasted with quantum mechanics) this paper addresses the question of when, or whether, they may coincide. Provided all definitions are strict in the categorical sense, we show that this can never be the case. However, allowing for the defining axioms to be taken up to canonical isomorphism, a close connection between the classical structures of categorical quantum mechanics, and the categorical property of self-similarity familiar from logical and computational models becomes apparent. The required canonical isomorphisms are non-trivial, and mix both typed (multi-object) and untyped (single-object) tensors and structural isomorphisms; we give coherence results that justify this approach. We then give a class of examples where distinct self-similar structures at an object determine distinct matrix representations of arrows, in the same way as classical structures determine matrix representations in Hilbert space. We also give analogues of familiar notions from linear algebra in this setting such as changes of basis, and diagonalisation.Comment: 24 pages,7 diagram

BOOL-AN: A method for comparative sequence analysis and phylogenetic reconstruction

A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar or vector) and visual characteristics (graphs). The binary encoded sequence information is transformed into a compact analytical form, called the Iterative Canonical Form (or ICF) of Boolean functions, which can then be used as a generalized molecular descriptor. The method provides raw vector data for calculating different distance matrices, which in turn can be analyzed by neighbor-joining or UPGMA to derive a phylogenetic tree, or by principal coordinates analysis to get an ordination scattergram. The new method and the associated software for inferring phylogenetic trees are called the Boolean analysis or BOOL-AN

Computing k-Modal Embeddings of Planar Digraphs

Given a planar digraph G and a positive even integer k, an embedding of G in the plane is k-modal, if every vertex of G is incident to at most k pairs of consecutive edges with opposite orientations, i.e., the incoming and the outgoing edges at each vertex are grouped by the embedding into at most k sets of consecutive edges with the same orientation. In this paper, we study the k-Modality problem, which asks for the existence of a k-modal embedding of a planar digraph. This combinatorial problem is at the very core of a variety of constrained embedding questions for planar digraphs and flat clustered networks. First, since the 2-Modality problem can be easily solved in linear time, we consider the general k-Modality problem for any value of k>2 and show that the problem is NP-complete for planar digraphs of maximum degree Delta <= k+3. We relate its computational complexity to that of two notions of planarity for flat clustered networks: Planar Intersection-Link and Planar NodeTrix representations. This allows us to answer in the strongest possible way an open question by Di Giacomo [https://doi.org/10.1007/978-3-319-73915-1_37], concerning the complexity of constructing planar NodeTrix representations of flat clustered networks with small clusters, and to address a research question by Angelini et al. [https://doi.org/10.7155/jgaa.00437], concerning intersection-link representations based on geometric objects that determine complex arrangements. On the positive side, we provide a simple FPT algorithm for partial 2-trees of arbitrary degree, whose running time is exponential in k and linear in the input size. Second, motivated by the recently-introduced planar L-drawings of planar digraphs [https://doi.org/10.1007/978-3-319-73915-1_36], which require the computation of a 4-modal embedding, we focus our attention on k=4. On the algorithmic side, we show a complexity dichotomy for the 4-Modality problem with respect to Delta, by providing a linear-time algorithm for planar digraphs with Delta <= 6. This algorithmic result is based on decomposing the input digraph into its blocks via BC-trees and each of these blocks into its triconnected components via SPQR-trees. In particular, we are able to show that the constraints imposed on the embedding by the rigid triconnected components can be tackled by means of a small set of reduction rules and discover that the algorithmic core of the problem lies in special instances of NAESAT, which we prove to be always NAE-satisfiable - a result of independent interest that improves on Porschen et al. [https://doi.org/10.1007/978-3-540-24605-3_14]. Finally, on the combinatorial side, we consider outerplanar digraphs and show that any such a digraph always admits a k-modal embedding with k=4 and that this value of k is best possible for the digraphs in this family

Effective Marking Equivalence Checking in Systems with Dynamic Process Creation

The starting point of this work is a framework allowing to model systems with dynamic process creation, equipped with a procedure to detect symmetric executions (ie., which differ only by the identities of processes). This allows to reduce the state space, potentially to an exponentially smaller size, and, because process identifiers are never reused, this also allows to reduce to finite size some infinite state spaces. However, in this approach, the procedure to detect symmetries does not allow for computationally efficient algorithms, mainly because each newly computed state has to be compared with every already reached state. In this paper, we propose a new approach to detect symmetries in this framework that will solve this problem, thus enabling for efficient algorithms. We formalise a canonical representation of states and identify a sufficient condition on the analysed model that guarantees that every symmetry can be detected. For the models that do not fall into this category, our approach is still correct but does not guarantee a maximal reduction of state space.Comment: In Proceedings Infinity 2012, arXiv:1302.310

An Etude on Recursion Relations and Triangulations

Following~\cite{Arkani-Hamed:2017thz}, we derive a recursion relation by applying a one-parameter deformation of kinematic variables for tree-level scattering amplitudes in bi-adjoint $\phi^3$ theory. The recursion relies on properties of the amplitude that can be made manifest in the underlying kinematic associahedron, and it provides triangulations for the latter. Furthermore, we solve the recursion relation and present all-multiplicity results for the amplitude: by reformulating the associahedron in terms of its vertices, it is given explicitly as a sum of "volume" of simplicies for any triangulation, which is an analogy of BCFW representation/triangulation of amplituhedron for ${\cal N}=4$ SYM.Comment: 26 pages, 3 figure

Learning by stochastic serializations

Complex structures are typical in machine learning. Tailoring learning algorithms for every structure requires an effort that may be saved by defining a generic learning procedure adaptive to any complex structure. In this paper, we propose to map any complex structure onto a generic form, called serialization, over which we can apply any sequence-based density estimator. We then show how to transfer the learned density back onto the space of original structures. To expose the learning procedure to the structural particularities of the original structures, we take care that the serializations reflect accurately the structures' properties. Enumerating all serializations is infeasible. We propose an effective way to sample representative serializations from the complete set of serializations which preserves the statistics of the complete set. Our method is competitive or better than state of the art learning algorithms that have been specifically designed for given structures. In addition, since the serialization involves sampling from a combinatorial process it provides considerable protection from overfitting, which we clearly demonstrate on a number of experiments.Comment: Submission to NeurIPS 201