scholarly journals A Bound on Partitioning Clusters

10.37236/6797 ◽  
2017 ◽  
Vol 24 (2) ◽  
Author(s):  
Daniel Kane ◽  
Terence Tao

Let $X$ be a finite collection of sets (or "clusters"). We consider the problem of counting the number of ways a cluster $A \in X$ can be partitioned into two disjoint clusters $A_1, A_2 \in X$, thus $A = A_1 \uplus A_2$ is the disjoint union of $A_1$ and $A_2$; this problem arises in the run time analysis of the ASTRAL algorithm in phylogenetic reconstruction. We obtain the bound$$ | \{ (A_1,A_2,A) \in X \times X \times X: A = A_1 \uplus A_2 \} | \leq |X|^{3/p} $$where $|X|$ denotes the cardinality of $X$, and $p := \log_3 \frac{27}{4} = 1.73814\dots$, so that $\frac{3}{p} = 1.72598\dots$. Furthermore, the exponent $p$ cannot be replaced by any larger quantity. This improves upon the trivial bound of $|X|^2$. The argument relies on establishing a one-dimensional convolution inequality that can be established by elementary calculus combined with some numerical verification.In a similar vein, we show that for any subset $A$ of a discrete cube $\{0,1\}^n$, the additive energy of $A$ (the number of quadruples $(a_1,a_2,a_3,a_4)$ in $A^4$ with $a_1+a_2=a_3+a_4$) is at most $|A|^{\log_2 6}$, and that this exponent is best possible.

2003 ◽  
Vol 89 (2) ◽  
pp. 191-209 ◽  
Author(s):  
Liqiang Wang ◽  
Scott D. Stoller

2005 ◽  
Vol 113 ◽  
pp. 105-121 ◽  
Author(s):  
D. Garbervetsky ◽  
C. Nakhli ◽  
S. Yovine ◽  
H. Zorgati

2012 ◽  
Vol 10 (02) ◽  
pp. 1241007 ◽  
Author(s):  
SLAVICA DIMITRIEVA ◽  
PHILIPP BUCHER

Commonly used RNA folding programs compute the minimum free energy structure of a sequence under the pseudoknot exclusion constraint. They are based on Zuker's algorithm which runs in time O(n3). Recently, it has been claimed that RNA folding can be achieved in average time O(n2) using a sparsification technique. A proof of quadratic time complexity was based on the assumption that computational RNA folding obeys the "polymer-zeta property". Several variants of sparse RNA folding algorithms were later developed. Here, we present our own version, which is readily applicable to existing RNA folding programs, as it is extremely simple and does not require any new data structure. We applied it to the widely used Vienna RNAfold program, to create sibRNAfold, the first public sparsified version of a standard RNA folding program. To gain a better understanding of the time complexity of sparsified RNA folding in general, we carried out a thorough run time analysis with synthetic random sequences, both in the context of energy minimization and base pairing maximization. Contrary to previous claims, the asymptotic time complexity of a sparsified RNA folding algorithm using standard energy parameters remains O(n3) under a wide variety of conditions. Consistent with our run-time analysis, we found that RNA folding does not obey the "polymer-zeta property" as claimed previously. Yet, a basic version of a sparsified RNA folding algorithm provides 15- to 50-fold speed gain. Surprisingly, the same sparsification technique has a different effect when applied to base pairing optimization. There, its asymptotic running time complexity appears to be either quadratic or cubic depending on the base composition. The code used in this work is available at: http://sibRNAfold.sourceforge.net/ .


1992 ◽  
Vol 112 (3) ◽  
pp. 527-534 ◽  
Author(s):  
Zbigniew Szafraniec

Let F = (F1, …, Fn-1): (ℝn, 0)→(ℝn-1, 0) and G:(ℝn, 0)→(ℝ, 0) be germs of analytic mappings, and let X = F-1(0). Assume that 0 ∈ ℝn is an isolated singular point in X, i.e. 0 ∈ ℝn is isolated in {x ∈ X|rank[DF(x)] < n-1}. Hence a germ of X/{0} at the origin is either void or a finite disjoint union of analytic curves. Let b denote the number of branches, i.e. connected components, of X/{0} and let b+ (resp. b-, b0) denote the number of branches of X/{0} on which G is positive (resp. G is negative, G vanishes). The problem is to calculate the numbers b, b+, b-, b0 in terms of F and G.


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