Related papers: Pure Parsimony Xor Haplotyping
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
We introduce sparse polynomial zonotopes, a new set representation for formal verification of hybrid systems. Sparse polynomial zonotopes can represent non-convex sets and are generalizations of zonotopes, polytopes, and Taylor models.…
Recently, sparsity-based algorithms are proposed for super-resolution spectrum estimation. However, to achieve adequately high resolution in real-world signal analysis, the dictionary atoms have to be close to each other in frequency,…
We present a new Hamiltonian-learning framework based on time-resolved measurement data from a fixed local IC-POVM and its application to inferring gene regulatory networks. We introduce the quantum Hamiltonian-based gene-expression model…
We study the isomorphism problem for random hypergraphs. We show that it is solvable in polynomial time for the binomial random $k$-uniform hypergraph $H_{n,p;k}$, for a wide range of $p$. We also show that it is solvable w.h.p. for random…
Selection and sorting the Cartesian sum, $X+Y$, are classic and important problems. Here, a new algorithm is presented, which generates the top $k$ values of the form $X_i+Y_j$. The algorithm relies only on median-of-medians and is simple…
Using discrete Morse theory, we give an algorithm that prunes the excess of information in the Taylor resolution and constructs a new cellular free resolution for an arbitrary monomial ideal. The pruned resolution is not simplicial in…
Variable selection for sparse linear regression is the problem of finding, given an m x p matrix B and a target vector y, a sparse vector x such that Bx approximately equals y. Assuming a standard complexity hypothesis, we show that no…
We study the problems of counting the homomorphisms, counting the copies, and counting the induced copies of a $k$-vertex graph $H$ in a $d$-degenerate $n$-vertex graph $G$. Our main result establishes exhaustive and explicit complexity…
The "rare type match problem" is the situation in which the suspect's DNA profile, matching the DNA profile of the crime stain, is not in the database of reference. The evaluation of this match in the light of the two competing hypotheses…
The (non-uniform) sparsest cut problem is the following graph-partitioning problem: given a "supply" graph, and demands on pairs of vertices, delete some subset of supply edges to minimize the ratio of the supply edges cut to the total…
Clustering genotypes based upon their phenotypic characteristics is used to obtain diverse sets of parents that are useful in their breeding programs. The Hierarchical Clustering (HC) algorithm is the current standard in clustering of…
How do phylogenetic reconstruction algorithms go astray when they return incorrect trees? This simple question has not been answered in detail, even for maximum parsimony (MP), the simplest phylogenetic criterion. Understanding MP has…
This paper categorizes the parameterized complexity of the algorithmic problems Perfect Phylogeny and Triangulating Colored Graphs when parameterized by the number of genes and colors, respectively. We show that they are complete for the…
We consider the following basic problem: given an $n$-variate degree-$d$ homogeneous polynomial $f$ with real coefficients, compute a unit vector $x \in \mathbb{R}^n$ that maximizes $|f(x)|$. Besides its fundamental nature, this problem…
Yang et al. (2013) introduced LORS, a method that jointly models the expression of genes, SNPs, and hidden factors for eQTL mapping. LORS solves a convex optimization problem and has guaranteed convergence. However, it can be…
We revisit the algorithmic problem of reconstructing a graph from homomorphism counts that has first been studied in (B\"oker et al., STACS 2024): given graphs $F_1,\ldots,F_k$ and counts $m_1,\ldots,m_k$, decide if there is a graph $G$…
In real life, it is always an urge to reach our goal in minimum effort i.e., it should have a minimum constrained path. The path may be shortest route in practical life, either physical or electronic medium. The scenario is to represents…
Many applications modeled by polynomial systems have positive dimensional solution components (e.g., the path synthesis problems for four-bar mechanisms) that are challenging to compute numerically by homotopy continuation methods. A…
Valiant introduced matchgate computation and holographic algorithms. A number of seemingly exponential time problems can be solved by this novel algorithmic paradigm in polynomial time. We show that, in a very strong sense, matchgate…