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Combinatorial enumeration of various RNA secondary structures and protein contact maps, is of great interest for both combinatorists and computational biologists. Enumeration of protein contact maps has considerable difficulties due to the…
We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…
In this paper, we establish a one-to-one correspondence between the set of biclosed sets in an irreducible root system of type $A_n$ and the set of quasitrivial semigroup structures on a set with $n+1$ elements. Building on this…
Various specifiable combinatorial structures, with d extensive parameters, can be exactly sampled both by the recursive method, with linear arithmetic complexity if a heavy preprocessing is performed, or by the Boltzmann method, with…
We consider systems of recursively defined combinatorial structures. We give algorithms checking that these systems are well founded, computing generating series and providing numerical values. Our framework is an articulation of the…
We present an algorithm for recovering planted solutions in two well-known models, the stochastic block model and planted constraint satisfaction problems, via a common generalization in terms of random bipartite graphs. Our algorithm…
A derivative structure is a nonequivalent substitutional atomic configuration derived from a given primitive cell. The enumeration of derivative structures plays an essential role in searching for the ground states in multicomponent…
The contact map of a protein fold is a graph that represents the patterns of contacts in the fold. It is known that the contact map can be decomposed into stacks and queues. RNA secondary structures are special stacks in which the degree of…
We present a purely combinatorial solution of the problem of enumerating planar bicubic maps with hard particles. This is done by use of a bijection with a particular class of blossom trees with particles, obtained by an appropriate cutting…
Biclustering, also called co-clustering, block clustering, or two-way clustering, involves the simultaneous clustering of both the rows and columns of a data matrix into distinct groups, such that the rows and columns within a group display…
In this paper, we survey some properties, encoding, and bijections involving combinatorial maps, double occurrence words, and chord diagrams. We particularly study quasi-trees from a purely combinatorial point of view and derive a…
Bipartite graphs are a prevalent modeling tool for real-world networks, capturing interactions between vertices of two different types. Within this framework, bicliques emerge as crucial structures when studying dense subgraphs: they are…
We provide geometric methods and algorithms to verify, construct and enumerate pairs of words (of specified length over a fixed $m$-letter alphabet) that form identities in the semigroup $\ut{n}$ of $n\times n$ upper triangular tropical…
We present recursive formulas giving the maximal number of leaves in tree-like polyforms living in two-dimensional regular lattices and in tree-like polycubes in the three-dimensional cubic lattice. We call these tree-like polyforms and…
A (convex) polytope $P$ is said to be $2$-level if for every direction of hyperplanes which is facet-defining for $P$, the vertices of $P$ can be covered with two hyperplanes of that direction. The study of these polytopes is motivated by…
This article describes a normal form algorithm for the Brieskorn lattice of an isolated hypersurface singularity. It is the basis of efficient algorithms to compute the Bernstein-Sato polynomial, the complex monodromy, and Hodge-theoretic…
We investigate pattern avoidance in permutations satisfying some additional restrictions. These are naturally considered in terms of avoiding patterns in linear extensions of certain forest-like partially ordered sets, which we call binary…
We study planted problems---finding hidden structures in random noisy inputs---through the lens of the sum-of-squares semidefinite programming hierarchy (SoS). This family of powerful semidefinite programs has recently yielded many new…
We present a bijective algorithm with which an arbitrary permutation decomposes canonically into elementary blocks which we call families, which are sets with a specified number of ascents and descents. We show that families, arranged in an…
Distributed algorithms for solving coupled semidefinite programs (SDPs) commonly require many iterations to converge. They also put high computational demand on the computational agents. In this paper we show that in case the coupled…