Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userOn Alternative Models for Leaf Powers
67
0
0.0
(
0
)
Added by
Benjamin Bergougnoux
Publication date
2021
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
A fundamental problem in computational biology is the construction of phylogenetic trees, also called evolutionary trees, for a set of organisms. A graph-theoretic approach takes as input a similarity graph $G$ on the set of organisms, with adjacency denoting evolutionary closeness, and asks for a tree $T$ whose leaves are the set of organisms, with two vertices adjacent in $G$ if and only if the distance between them in the tree is less than some specified distance bound. If this exists $G$ is called a leaf power. Over 20 years ago, [Nishimura et al., J. Algorithms, 2002] posed the question if leaf powers could be recognized in polynomial time. In this paper we explore this still unanswered question from the perspective of two alternative models of leaf powers that have been rather overlooked. These models do not rely on a variable distance bound and are therefore more apt for generalization. Our first result concerns leaf powers with a linear structure and uses a model where the edges of the tree $T$ are weighted by rationals between 0 and 1, and the distance bound is fixed to 1. We show that the graphs having such a model with $T$ a caterpillar are exactly the co-threshold tolerance graphs and can therefore be recognized in $O(n^2)$ time by an algorithm of [Golovach et al., Discret. Appl. Math., 2017]. Our second result concerns leaf powers with a star structure and concerns the geometric NeS model used by [Brandstadt et al., Discret. Math., 2010]. We show that the graphs having a NeS model where the main embedding tree is a star can be recognized in polynomial time. These results pave the way for an attack on the main question, to settle the issue if leaf powers can be recognized in polynomial time.
rate research
Read More
A string $S[1,n]$ is a power (or tandem repeat) of order $k$ and period $n/k$ if it can decomposed into $k$ consecutive equal-length blocks of letters. Powers and periods are fundamental to string processing, and algorithms for their efficient computation have wide application and are heavily studied. Recently, Fici et al. (Proc. ICALP 2016) defined an {em anti-power} of order $k$ to be a string composed of $k$ pairwise-distinct blocks of the same length ($n/k$, called {em anti-period}). Anti-powers are a natural converse to powers, and are objects of combinatorial interest in their own right. In this paper we initiate the algorithmic study of anti-powers. Given a string $S$, we describe an optimal algorithm for locating all substrings of $S$ that are anti-powers of a specified order. The optimality of the algorithm follows form a combinatorial lemma that provides a lower bound on the number of distinct anti-powers of a given order: we prove that a string of length $n$ can contain $Theta(n^2/k)$ distinct anti-powers of order $k$.
The problem of finding a common refinement of a set of rooted trees with common leaf set $L$ appears naturally in mathematical phylogenetics whenever poorly resolved information on the same taxa from different sources is to be reconciled. This constitutes a special case of the well-studied supertree problem, where the leaf sets of the input trees may differ. Algorithms that solve the rooted tree compatibility problem are of course applicable to this special case. However, they require sophisticated auxiliary data structures and have a running time of at least $O(k|L|log^2(k|L|))$ for $k$ input trees. Here, we show that the problem can be solved in $O(k|L|)$ time using a simple bottom-up algorithm called LinCR. An implementation of LinCR in Python is freely available at https://github.com/david-schaller/tralda.
We study a simple Markov chain, the switch chain, on the set of all perfect matchings in a bipartite graph. This Markov chain was proposed by Diaconis, Graham and Holmes as a possible approach to a sampling problem arising in Statistics. We ask: for which classes of graphs is the Markov chain ergodic and for which is it rapidly mixing? We provide a precise answer to the ergodicity question and close bounds on the mixing question. We show for the first time that the mixing time of the switch chain is polynomial in the case of monotone graphs, a class that includes examples of interest in the statistical setting.
The $k$-leaf power graph $G$ of a tree $T$ is a graph whose vertices are the leaves of $T$ and whose edges connect pairs of leaves at unweighted distance at most~$k$ in $T$. Recognition of the $k$-leaf power graphs for $k geq 7$ is still an open problem. In this paper, we provide two algorithms for this problem for sparse leaf power graphs. Our results shows that the problem of recognizing these graphs is fixed-parameter tractable when parameterized both by $k$ and by the degeneracy of the given graph. To prove this, we first describe how to embed the leaf root of a leaf power graph into a product of the graph with a cycle graph. We bound the treewidth of the resulting product in terms of $k$ and the degeneracy of $G$. The first presented algorithm uses methods based on monadic second-order logic (MSO$_2$) to recognize the existence of a leaf power as a subgraph of the product graph. Using the same embedding in the product graph, the second algorithm presents a dynamic programming approach to solve the problem and provide a better dependence on the parameters.
We study the problem of sampling an approximately uniformly random satisfying assignment for atomic constraint satisfaction problems i.e. where each constraint is violated by only one assignment to its variables. Let $p$ denote the maximum probability of violation of any constraint and let $Delta$ denote the maximum degree of the line graph of the constraints. Our main result is a nearly-linear (in the number of variables) time algorithm for this problem, which is valid in a Lovasz local lemma type regime that is considerably less restrictive compared to previous works. In particular, we provide sampling algorithms for the uniform distribution on: (1) $q$-colorings of $k$-uniform hypergraphs with $Delta lesssim q^{(k-4)/3 + o_{q}(1)}.$ The exponent $1/3$ improves the previously best-known $1/7$ in the case $q, Delta = O(1)$ [Jain, Pham, Vuong; arXiv, 2020] and $1/9$ in the general case [Feng, He, Yin; STOC 2021]. (2) Satisfying assignments of Boolean $k$-CNF formulas with $Delta lesssim 2^{k/5.741}.$ The constant $5.741$ in the exponent improves the previously best-known $7$ in the case $k = O(1)$ [Jain, Pham, Vuong; arXiv, 2020] and $13$ in the general case [Feng, He, Yin; STOC 2021]. (3) Satisfying assignments of general atomic constraint satisfaction problems with $pcdot Delta^{7.043} lesssim 1.$ The constant $7.043$ improves upon the previously best-known constant of $350$ [Feng, He, Yin; STOC 2021]. At the heart of our analysis is a novel information-percolation type argument for showing the rapid mixing of the Glauber dynamics for a carefully constructed projection of the uniform distribution on satisfying assignments. Notably, there is no natural partial order on the space, and we believe that the techniques developed for the analysis may be of independent interest.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
