Analysis of Algorithms for Permutations Biased by Their Number of Records

The topic of the article is the parametric study of the complexity of algorithms on arrays of pairwise distinct integers. We introduce a model that takes into account the non-uniformness of data, which we call the Ewens-like distribution of parameter $\theta$ for records on permutations: the weight $\theta^r$ of a permutation depends on its number $r$ of records. We show that this model is meaningful for the notion of presortedness, while still being mathematically tractable. Our results describe the expected value of several classical permutation statistics in this model, and give the expected running time of three algorithms: the Insertion Sort, and two variants of the Min-Max search

Average-Case Complexity of Shellsort

We prove a general lower bound on the average-case complexity of Shellsort: the average number of data-movements (and comparisons) made by a $p$-pass Shellsort for any incremental sequence is \Omega (pn^{1 + 1/p) for all $p \leq \log n$. Using similar arguments, we analyze the average-case complexity of several other sorting algorithms.Comment: 11 pages. Submitted to ICALP'9

The combinatorics of biased riffle shuffles

This paper studies biased riffle shuffles, first defined by Diaconis, Fill, and Pitman. These shuffles generalize the well-studied Gilbert-Shannon-Reeds shuffle and convolve nicely. An upper bound is given for the time for these shuffles to converge to the uniform distribution; this matches lower bounds of Lalley. A careful version of a bijection of Gessel leads to a generating function for cycle structure after one of these shuffles and gives new results about descents in random permutations. Results are also obtained about the inversion and descent structure of a permutation after one of these shuffles.Comment: 11 page

Group-theoretic models of the inversion process in bacterial genomes

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent than longer, and those that move the terminus of replication are less probable than those that do not. Current methods for establishing the inversion distance between two bacterial genomes are unable to incorporate such information. In this paper we suggest a group-theoretic framework that in principle can take these constraints into account. In particular, we show that by lifting the problem from circular permutations to the affine symmetric group, the inversion distance can be found in polynomial time for a model in which inversions are restricted to acting on two regions. This requires the proof of new results in group theory, and suggests a vein of new combinatorial problems concerning permutation groups on which group theorists will be needed to collaborate with biologists. We apply the new method to inferring distances and phylogenies for published Yersinia pestis data.Comment: 19 pages, 7 figures, in Press, Journal of Mathematical Biolog