Related papers: Polynomial cases of the Discretizable Molecular Di…
Graph polynomials encode fundamental combinatorial invariants of graphs. Their computation is investigated using tree and path decomposition frameworks, with formal definitions of treewidth, k-trees, and pathwidth establishing the…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
Graph edit distance (GED) is a powerful and flexible graph matching paradigm that can be used to address different tasks in structural pattern recognition, machine learning, and data mining. In this paper, some new binary linear programming…
Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive…
We study Voronoi diagrams of manifolds and varieties with respect to polyhedral norms. We provide upper and lower bounds on the dimensions of Voronoi cells. For algebraic varieties, we count their full-dimensional Voronoi cells. As an…
The \textit{biharmonic distance} (BD) is a fundamental metric that measures the distance of two nodes in a graph. It has found applications in network coherence, machine learning, and computational graphics, among others. In spite of BD's…
The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over…
Given a connected undirected weighted graph, we are concerned with problems related to partitioning the graph. First of all we look for the closest disconnected graph (the minimum cut problem), here with respect to the Euclidean norm. We…
We study the problem of supervised learning a metric space under discriminative constraints. Given a universe $X$ and sets ${\cal S}, {\cal D}\subset {X \choose 2}$ of similar and dissimilar pairs, we seek to find a mapping $f:X\to Y$, into…
In distance query reconstruction, we wish to reconstruct the edge set of a hidden graph by asking as few distance queries as possible to an oracle. Given two vertices $u$ and $v$, the oracle returns the shortest path distance between $u$…
Graphs on integer points of polytopes whose edges come from a set of allowed differences are studied. It is shown that any simple graph can be embedded in that way. The minimal dimension of such a representation is the fiber dimension of…
We show that given $m$ proteins (or protein backbones, which are modeled as 3D polygonal chains each of length O(n)) the problem of protein local structure alignment under the discrete Fr\'{e}chet distance is as hard as Independent Set. So…
We study a large family of graph covering problems, whose definitions rely on distances, for graphs of bounded cyclomatic number (that is, the minimum number of edges that need to be removed from the graph to destroy all cycles). These…
A quasi-metric is a distance function which satisfies the triangle inequality but is not symmetric: it can be thought of as an asymmetric metric. The central result of this thesis, developed in Chapter 3, is that a natural correspondence…
We present a paralell approach to discrete geometry: the first one introduces Voronoi cell complexes from statistical tessellations in order to know the mean scalar curvature in term of the mean number of edges of a cell. The second one…
A resolving set $S$ of a graph $G$ is a subset of its vertices such that no two vertices of $G$ have the same distance vector to $S$. The Metric Dimension problem asks for a resolving set of minimum size, and in its decision form, a…
A threshold graph G on n vertices is defined by binary sequence of length n. In this paper we present an explicit formula for computing the distance characteristic polynomial of a threshold graph from its binary sequence. As application, we…
The treedepth of a graph $G$ is the least possible depth of an elimination forest of $G$: a rooted forest on the same vertex set where every pair of vertices adjacent in $G$ is bound by the ancestor/descendant relation. We propose an…
We propose a multiscale method for elliptic problems on complex domains, e.g. domains with cracks or complicated boundary. For local singularities this paper also offers a discrete alternative to enrichment techniques such as XFEM. We…
We study a class of complex polynomial equations on a finite graph with a view to understanding how holistic phenomena emerge from combinatorial structure. Particular solutions arise from orthogonal projections of regular polytopes,…