Proceedings of the 26th International Symposium on Theoretical Aspects of Computer Science (STACS'09)

The Symposium on Theoretical Aspects of Computer Science (STACS) is held alternately in France and in Germany. The conference of February 26-28, 2009, held in Freiburg, is the 26th in this series. Previous meetings took place in Paris (1984), Saarbr¨ucken (1985), Orsay (1986), Passau (1987), Bordeaux (1988), Paderborn (1989), Rouen (1990), Hamburg (1991), Cachan (1992), W¨urzburg (1993), Caen (1994), M¨unchen (1995), Grenoble (1996), L¨ubeck (1997), Paris (1998), Trier (1999), Lille (2000), Dresden (2001), Antibes (2002), Berlin (2003), Montpellier (2004), Stuttgart (2005), Marseille (2006), Aachen (2007), and Bordeaux (2008). ..

Recognition of generalized network matrices

In this PhD thesis, we deal with binet matrices, an extension of network matrices. The main result of this thesis is the following. A rational matrix A of size n times m can be tested for being binet in time O(n^6 m). If A is binet, our algorithm outputs a nonsingular matrix B and a matrix N such that [B N] is the node-edge incidence matrix of a bidirected graph (of full row rank) and A=B^{-1} N. Furthermore, we provide some results about Camion bases. For a matrix M of size n times m', we present a new characterization of Camion bases of M, whenever M is the node-edge incidence matrix of a connected digraph (with one row removed). Then, a general characterization of Camion bases as well as a recognition procedure which runs in O(n^2m') are given. An algorithm which finds a Camion basis is also presented. For totally unimodular matrices, it is proven to run in time O((nm)^2) where m=m'-n. The last result concerns specific network matrices. We give a characterization of nonnegative {r,s}-noncorelated network matrices, where r and s are two given row indexes. It also results a polynomial recognition algorithm for these matrices.Comment: 183 page

Combinatorial geometry of neural codes, neural data analysis, and neural networks

This dissertation explores applications of discrete geometry in mathematical neuroscience. We begin with convex neural codes, which model the activity of hippocampal place cells and other neurons with convex receptive fields. In Chapter 4, we introduce order-forcing, a tool for constraining convex realizations of codes, and use it to construct new examples of non-convex codes with no local obstructions. In Chapter 5, we relate oriented matroids to convex neural codes, showing that a code has a realization with convex polytopes iff it is the image of a representable oriented matroid under a neural code morphism. We also show that determining whether a code is convex is at least as difficult as determining whether an oriented matroid is representable, implying that the problem of determining whether a code is convex is NP-hard. Next, we turn to the problem of the underlying rank of a matrix. This problem is motivated by the problem of determining the dimensionality of (neural) data which has been corrupted by an unknown monotone transformation. In Chapter 6, we introduce two tools for computing underlying rank, the minimal nodes and the Radon rank. We apply these to analyze calcium imaging data from a larval zebrafish. In Chapter 7, we explore the underlying rank in more detail, establish connections to oriented matroid theory, and show that computing underlying rank is also NP-hard. Finally, we study the dynamics of threshold-linear networks (TLNs), a simple model of the activity of neural circuits. In Chapter 9, we describe the nullcline arrangement of a threshold linear network, and show that a subset of its chambers are an attracting set. In Chapter 10, we focus on combinatorial threshold linear networks (CTLNs), which are TLNs defined from a directed graph. We prove that if the graph of a CTLN is a directed acyclic graph, then all trajectories of the CTLN approach a fixed point.Comment: 193 pages, 69 figure

Proceedings of the 8th Cologne-Twente Workshop on Graphs and Combinatorial Optimization

International audienceThe Cologne-Twente Workshop (CTW) on Graphs and Combinatorial Optimization started off as a series of workshops organized bi-annually by either Köln University or Twente University. As its importance grew over time, it re-centered its geographical focus by including northern Italy (CTW04 in Menaggio, on the lake Como and CTW08 in Gargnano, on the Garda lake). This year, CTW (in its eighth edition) will be staged in France for the first time: more precisely in the heart of Paris, at the Conservatoire National d’Arts et Métiers (CNAM), between 2nd and 4th June 2009, by a mixed organizing committee with members from LIX, Ecole Polytechnique and CEDRIC, CNAM