Related papers: A semi-bijective algorithm for saturated extended …
We evaluate the configuration exponents of various ensembles of Hamiltonian paths drawn on random planar bicubic maps. These exponents are estimated from the extrapolations of exact enumeration results for finite sizes and compared with…
Many computer vision problems can be formulated as binary quadratic programs (BQPs). Two classic relaxation methods are widely used for solving BQPs, namely, spectral methods and semidefinite programming (SDP), each with their own…
Consider a real point configuration $\mathbf{A}$ of size $n$ and an integer $r \leq n$. The vertices of the $r$-lineup polytope of $\mathbf{A}$ correspond to the possible orderings of the top $r$ points of the configuration obtained by…
Using a fast tree-searching algorithm and a Pentium cluster, we enumerated all the sequences and compact conformations (structures) for a protein folding model on a cubic lattice of size $4\times3\times3$. We used two types of amino acids…
Quasi-median graphs are a tool commonly used by evolutionary biologists to visualise the evolution of molecular sequences. As with any graph, a quasi-median graph can contain cut vertices, that is, vertices whose removal disconnect the…
Frequent tree mining asks us to enumerate tree patterns that occur frequently in a database of rooted trees. This problem is motivated by tree-structured data in bioinformatics, such as glycans and pseudoknot-free RNA secondary structures.…
This article introduces a finite piecewise Euclidean cell complex homeomorphic to the space of monic centered complex polynomials of degree $d$ whose critical values lie in a fixed closed rectangular region. We call this the branched…
The question whether there exists an integral solution to the system of linear equations with non-negative constraints, $A\x = \b, \, \x \ge 0$, where $A \in \Z^{m\times n}$ and ${\mathbf b} \in \Z^m$, finds its applications in many areas,…
Two-dimensional (2D) materials are outstanding platforms for exotic physics and emerging applications by forming interfaces. In order to efficiently take into account the substrate screening in the quasiparticle energies of 2D materials,…
Our goal in this paper is to automatically extract a set of decision rules (rule set) that best explains a classification data set. First, a large set of decision rules is extracted from a set of decision trees trained on the data set. The…
The completely bounded trace and spectral norms, for finite-dimensional spaces, are known to be efficiently expressible by semidefinite programs (J. Watrous, Theory of Computing 5: 11, 2009). This paper presents two new, and arguably much…
Predicting protein secondary structure using lattice model is one of the most studied computational problem in bioinformatics. Here secondary structure or three dimensional structure of protein is predicted from its amino acid sequence.…
We consider the problem of counting motifs in bipartite affiliation networks, such as author-paper, user-product, and actor-movie relations. We focus on counting the number of occurrences of a "butterfly", a complete $2 \times 2$ biclique,…
Hierarchical matrices approximate a given matrix by a decomposition into low-rank submatrices that can be handled efficiently in factorized form. $\mathcal{H}^2$-matrices refine this representation following the ideas of fast multipole…
A major goal in nanoscience and nanotechnology is the self-assembly of any desired complex structure with a system of particles interacting through simple potentials. To achieve this objective, intense experimental and theoretical efforts…
In this paper, we propose iterative inner/outer approximations based on a recent notion of block factor-width-two matrices for solving semidefinite programs (SDPs). Our inner/outer approximating algorithms generate a sequence of upper/lower…
A recursive method is given for finding generating functions which enumerate rooted hypermaps by number of vertices, edges and faces for any given number of darts. It makes use of matrix-integral expressions arising from the study of…
The two tableaux assigned by the Robinson--Schensted correspondence are equal if and only if the input permutation is an involution, so the RS algorithm restricts to a bijection between involutions in the symmetric group and standard…
Finding large "cliquish" subgraphs is a central topic in graph mining and community detection. A popular clique relaxation are 2-clubs: instead of asking for subgraphs of diameter one (these are cliques), one asks for subgraphs of diameter…
An efficient algorithm to enumerate the vertices of a two-dimensional (2D) projection of a polytope, is presented in this paper. The proposed algorithm uses the support function of the polytope to be projected and enumerated for vertices.…