Automata in SageMath---Combinatorics meet Theoretical Computer Science

The new finite state machine package in the mathematics software system SageMath is presented and illustrated by many examples. Several combinatorial problems, in particular digit problems, are introduced, modeled by automata and transducers and solved using SageMath. In particular, we compute the asymptotic Hamming weight of a non-adjacent-form-like digit expansion, which was not known before

Combinatorics of the Permutahedra, Associahedra, and Friends

I present an overview of the research I have conducted for the past ten years in algebraic, bijective, enumerative, and geometric combinatorics. The two main objects I have studied are the permutahedron and the associahedron as well as the two partial orders they are related to: the weak order on permutations and the Tamari lattice. This document contains a general introduction (Chapters 1 and 2) on those objects which requires very little previous knowledge and should be accessible to non-specialist such as master students. Chapters 3 to 8 present the research I have conducted and its general context. You will find: * a presentation of the current knowledge on Tamari interval and a precise description of the family of Tamari interval-posets which I have introduced along with the rise-contact involution to prove the symmetry of the rises and the contacts in Tamari intervals; * my most recent results concerning q, t-enumeration of Catalan objects and Tamari intervals in relation with triangular partitions; * the descriptions of the integer poset lattice and integer poset Hopf algebra and their relations to well known structures in algebraic combinatorics; * the construction of the permutree lattice, the permutree Hopf algebra and permutreehedron; * the construction of the s-weak order and s-permutahedron along with the s-Tamari lattice and s-associahedron. Chapter 9 is dedicated to the experimental method in combinatorics research especially related to the SageMath software. Chapter 10 describes the outreach efforts I have participated in and some of my approach towards mathematical knowledge and inclusion.Comment: 163 pages, m\'emoire d'Habilitation \`a diriger des Recherche

Quantitative and Algorithmic aspects of Barrier Synchronization in Concurrency

In this paper we address the problem of understanding Concurrency Theory from a combinatorial point of view. We are interested in quantitative results and algorithmic tools to refine our understanding of the classical combinatorial explosion phenomenon arising in concurrency. This paper is essentially focusing on the the notion of synchronization from the point of view of combinatorics. As a first step, we address the quantitative problem of counting the number of executions of simple processes interacting with synchronization barriers. We elaborate a systematic decomposition of processes that produces a symbolic integral formula to solve the problem. Based on this procedure, we develop a generic algorithm to generate process executions uniformly at random. For some interesting sub-classes of processes we propose very efficient counting and random sampling algorithms. All these algorithms have one important characteristic in common: they work on the control graph of processes and thus do not require the explicit construction of the state-space

FORMULAE AND ASYMPTOTICS FOR COEFFICIENTS OF ALGEBRAIC FUNCTIONS

International audienc

Continuous-time temporal logic specification and verification for nonlinear biological systems in uncertain contexts

In this thesis we introduce a complete framework for modelling and verification of biological systems in uncertain contexts based on the bond-calculus process algebra and the LBUC spatio-temporal logic. The bond-calculus is a biological process algebra which captures complex patterns of interaction based on affinity patterns, a novel communication mechanism using pattern matching to express multiway interaction affinities and general kinetic laws, whilst retaining an agent-centric modelling style for biomolecular species. The bond-calculus is equipped with a novel continuous semantics which maps models to systems of Ordinary Differential Equations (ODEs) in a compositional way. We then extend the bond-calculus to handle uncertain models, featuring interval uncertainties in their species concentrations and reaction rate parameters. Our semantics is also extended to handle uncertainty in every aspect of a model, producing non-deterministic continuous systems whose behaviour depends either on time-independent uncertain parameters and initial conditions, corresponding to our partial knowledge of the system at hand, or time-varying uncertain inputs, corresponding to genuine variability in a system’s behaviour based on environmental factors. This language is then coupled with the LBUC spatio-temporal logic which combines Signal Temporal Logic (STL) temporal operators with an uncertain context operator which quantifies over an uncertain context model describing the range of environments over which a property must hold. We develop model-checking procedures for STL and LBUC properties based on verified signal monitoring over flowpipes produced by the Flow* verified integrator, including the technique of masking which directs monitoring for atomic propositions to time regions relevant to the overall verification problem at hand. This allows us to monitor many interesting nested contextual properties and frequently reduces monitoring costs by an order of magnitude. Finally, we explore the technique of contextual signal monitoring which can use a single Flow* flowpipe representing a functional dependency to complete a whole tree of signals corresponding to different uncertain contexts. This allows us to produce refined monitoring results over the whole space and to explore the variation in system behaviour in different contexts

On the treewidth of triangulated 3-manifolds

In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann, Schultens and Saito by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 18(k+1) (resp. 4(3k+1))

Q(sqrt(-3))-Integral Points on a Mordell Curve

We use an extension of quadratic Chabauty to number fields,recently developed by the author with Balakrishnan, Besser and M ̈uller,combined with a sieving technique, to determine the integral points overQ(√−3) on the Mordell curve y2 = x3 − 4