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In this work, we study the metric Steiner Tree problem on graphs focusing on computing lower bounds for the integrality gap of the bi-directed cut (DCUT) formulation and introducing a novel formulation, the Complete Metric (CM) model, specifically designed to address the weakness of the DCUT formulation on metric instances. A key contribution of our work is extending of the Gap problem, previously explored in the context of the Traveling Salesman problems, to the metric Steiner Tree problem. To tackle the Gap problem for Steiner Tree instances, we first establish several structural properties of the CM formulation. We then classify the isomorphism classes of the vertices within the CM polytope, revealing a correspondence between the vertices of the DCUT and CM polytopes. Computationally, we exploit these structural properties to design two complementary heuristics for finding nontrivial small metric Steiner instances with a large integrality gap. We present several vertices for graphs with a number of nodes $\leq 10$, which realize the best-known lower bounds on the integrality gap for the CM and the DCUT formulations. We conclude the paper by presenting three new conjectures on the integrality gap of the DCUT and CM formulations for small graphs., Comment: 27 pages, 4 figures

In this paper, by resorting to classical methods of statistical mechanics, we build a kinetic model able to reproduce the observed statistical weight distribution of many diverse species. The kinetic description of the time variations of the weight distribution is based on elementary interactions that describe in a qualitative and quantitative way successive evolutionary updates, and determine explicit equilibrium distributions. Numerical fittings on mammalian eutherians of the order Chiroptera population illustrates the effectiveness of the approach.

This paper introduces a computational method for generating metric Travelling Salesman Problem (TSP) instances having a large integrality gap. The method is based on the solution of an integer programming problem, called IH-OPT, that takes as input a fractional solution of the Subtour Elimination Problem (SEP) on a TSP instance and computes a TSP instance having an integrality gap larger than or equal to the integrality gap of the first instance. The decision variables of IH-OPT are the entries of the TSP cost matrix, and the constraints are defined by the intersection of the metric cone with an exponential number of inequalities, one for each possible TSP tour. Given the very large number of constraints, we have implemented a branch-and-cut algorithm for solving IH-OPT. Then, by sampling cost vectors over the metric polytope and by solving the corresponding SEP, we can generate random fractional vertices of the SEP polytope. If we solve the IH-OPT problem for every sampled vertex using our branch-and-cut algorithm, we can select the generated TSP instance (i.e., cost vector), yielding the longest runtime for Concorde, the state-of-the-art TSP solver. Our computational results show that our method is very effective in producing challenging instances. As a by-product, we release the Hard-TSPLIB, a library of 41 small metric TSP instances which have a large integrality gap and are challenging in terms of runtime for Concorde.

This paper introduces the Gene Mover's Distance, a measure of similarity between a pair of cells based on their gene expression profiles obtained via single-cell RNA sequencing. The underlying idea of the proposed distance is to interpret the gene expression array of a single cell as a discrete probability measure. The distance between two cells is hence computed by solving an Optimal Transport problem between the two corresponding discrete measures. In the Optimal Transport model, we use two types of cost function for measuring the distance between a pair of genes. The first cost function exploits a gene embedding, called gene2vec, which is used to map each gene to a high dimensional vector: the cost of moving a unit of mass of gene expression from a gene to another is set to the Euclidean distance between the corresponding embedded vectors. The second cost function is based on a Pearson distance among pairs of genes. In both cost functions, the more two genes are correlated, the lower is their distance. We exploit the Gene Mover's Distance to solve two classification problems: the classification of cells according to their condition and according to their type. To assess the impact of our new metric, we compare the performances of a $k$-Nearest Neighbor classifier using different distances. The computational results show that the Gene Mover's Distance is competitive with the state-of-the-art distances used in the literature., Comment: 16 pages, 8 figures. The data used in this paper is available online at: https://zenodo.org/record/4604569