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Many discrete optimization problems amount to selecting a feasible set of edges of least weight. We consider in this paper the context of spatial graphs where the positions of the vertices are uncertain and belong to known uncertainty sets.…
The Distance Geometry Problem asks for a realization of a given weighted graph in $\mathbb{R}^K$. Two variants of this problem, both originating from protein conformation, are based on a given vertex order (which abstracts the protein…
A graph is called (generically) rigid in $\mathbb{R}^d$ if, for any choice of sufficiently generic edge lengths, it can be embedded in $\mathbb{R}^d$ in a finite number of distinct ways, modulo rigid transformations. Here we deal with the…
In this paper we investigate the geometry of a discrete Bayesian network whose graph is a tree all of whose variables are binary and the only observed variables are those labeling its leaves. We provide the full geometric description of…
Although recovering an Euclidean distance matrix from noisy observations is a common problem in practice, how well this could be done remains largely unknown. To fill in this void, we study a simple distance matrix estimate based upon the…
Distance Geometry is based on the inverse problem that asks to find the positions of points, in a Euclidean space of given dimension, that are compatible with a given set of distances. We briefly introduce the field, and discuss some open…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
The tree-depth problem can be seen as finding an elimination tree of minimum height for a given input graph $G$. We introduce a bicriteria generalization in which additionally the width of the elimination tree needs to be bounded by some…
The natural pseudo-distance of spaces endowed with filtering functions is precious for shape classification and retrieval; its optimal estimate coming from persistence diagrams is the bottleneck distance, which unfortunately suffers from…
We study geometric random graphs defined on the points of a Poisson process in $d$-dimensional space, which additionally carry independent random marks. Edges are established at random using the marks of the endpoints and the distance…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
A searcher is tasked with exploring a graph with edge lengths and vertex weights, starting from a designated vertex. Initially, only the starting vertex is considered explored. At each step, the searcher adds an edge to the solution,…
We study the projective geometry of algebraic neural layers, namely families of maps induced by a polynomial activation function, with particular emphasis on the generic Euclidean Distance degree ($\mathrm{gED}$). This invariant is…
Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and geometric aspects of the…
Many combinatorial optimization problems can be formulated as the search for a subgraph that satisfies certain properties and minimizes the total weight. We assume here that the vertices correspond to points in a metric space and can take…
The Vertex Cover problem plays an essential role in the study of polynomial kernelization in parameterized complexity, i.e., the study of provable and efficient preprocessing for NP-hard problems. Motivated by the great variety of positive…
We introduce new distance measures for comparing straight-line embedded graphs based on the Fr\'echet distance and the weak Fr\'echet distance. These graph distances are defined using continuous mappings and thus take the combinatorial…
A protein is traditionally visualised as a piecewise linear discrete curve, and its geometry is conventionally characterised by the extrinsically determined Ramachandran angles. However, a protein backbone has also two independent intrinsic…
Combining the techniques of approximation algorithms and parameterized complexity has long been considered a promising research area, but relatively few results are currently known. In this paper we study the parameterized approximability…
We present a geometric formulation of the Multiple Kernel Learning (MKL) problem. To do so, we reinterpret the problem of learning kernel weights as searching for a kernel that maximizes the minimum (kernel) distance between two convex…