An Efficient Algorithm for Enumerating Chordless Cycles and Chordless Paths

A chordless cycle (induced cycle) $C$ of a graph is a cycle without any chord, meaning that there is no edge outside the cycle connecting two vertices of the cycle. A chordless path is defined similarly. In this paper, we consider the problems of enumerating chordless cycles/paths of a given graph $G=(V,E),$ and propose algorithms taking $O(|E|)$ time for each chordless cycle/path. In the existing studies, the problems had not been deeply studied in the theoretical computer science area, and no output polynomial time algorithm has been proposed. Our experiments showed that the computation time of our algorithms is constant per chordless cycle/path for non-dense random graphs and real-world graphs. They also show that the number of chordless cycles is much smaller than the number of cycles. We applied the algorithm to prediction of NMR (Nuclear Magnetic Resonance) spectra, and increased the accuracy of the prediction

A constant-time algorithm for middle levels Gray codes

For any integer $n\geq 1$ a middle levels Gray code is a cyclic listing of all $n$-element and $(n+1)$-element subsets of $\{1,2,\ldots,2n+1\}$ such that any two consecutive subsets differ in adding or removing a single element. The question whether such a Gray code exists for any $n\geq 1$ has been the subject of intensive research during the last 30 years, and has been answered affirmatively only recently [T. M\"utze. Proof of the middle levels conjecture. Proc. London Math. Soc., 112(4):677--713, 2016]. In a follow-up paper [T. M\"utze and J. Nummenpalo. An efficient algorithm for computing a middle levels Gray code. To appear in ACM Transactions on Algorithms, 2018] this existence proof was turned into an algorithm that computes each new set in the Gray code in time $\mathcal{O}(n)$ on average. In this work we present an algorithm for computing a middle levels Gray code in optimal time and space: each new set is generated in time $\mathcal{O}(1)$ on average, and the required space is $\mathcal{O}(n)$

On the probability of planarity of a random graph near the critical point

Consider the uniform random graph $G(n,M)$ with $n$ vertices and $M$ edges. Erd\H{o}s and R\'enyi (1960) conjectured that the limit \lim_{n \to \infty} \Pr\{G(n,\textstyle{n\over 2}) is planar}} exists and is a constant strictly between 0 and 1. \L uczak, Pittel and Wierman (1994) proved this conjecture and Janson, \L uczak, Knuth and Pittel (1993) gave lower and upper bounds for this probability. In this paper we determine the exact probability of a random graph being planar near the critical point $M=n/2$. For each $\lambda$, we find an exact analytic expression for $$p(\lambda) = \lim_{n \to \infty} \Pr{G(n,\textstyle{n\over 2}(1+\lambda n^{-1/3})) is planar}.$$ In particular, we obtain $p(0) \approx 0.99780$. We extend these results to classes of graphs closed under taking minors. As an example, we show that the probability of $G(n,\textstyle{n\over 2})$ being series-parallel converges to 0.98003. For the sake of completeness and exposition we reprove in a concise way several basic properties we need of a random graph near the critical point.Comment: 10 pages, 1 figur

Pure Parsimony Xor Haplotyping

The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies. The xor-genotype data is a cheaply obtainable type of data distinguishing heterozygous from homozygous sites without identifying the homozygous alleles. In this paper we propose a formulation based on a well-known model used in haplotype inference: pure parsimony. We exhibit exact solutions of the problem by providing polynomial time algorithms for some restricted cases and a fixed-parameter algorithm for the general case. These results are based on some interesting combinatorial properties of a graph representation of the solutions. Furthermore, we show that the problem has a polynomial time k-approximation, where k is the maximum number of xor-genotypes containing a given SNP. Finally, we propose a heuristic and produce an experimental analysis showing that it scales to real-world large instances taken from the HapMap project