String Reconstruction from Substring Compositions

Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than twice a prime, can be reconstructed uniquely up to reversal. For all other lengths we show that reconstruction is not always possible and provide sometimes-tight bounds on the largest number of strings with given substring compositions. The lower bounds are derived by combinatorial arguments and the upper bounds by algebraic considerations that precisely characterize the set of strings with the same substring compositions in terms of the factorization of bivariate polynomials. The problem can be viewed as a combinatorial simplification of the turnpike problem, and its solution may shed light on this long-standing problem as well. Using well known results on transience of multi-dimensional random walks, we also provide a reconstruction algorithm that reconstructs random strings over alphabets of size $\ge4$ in optimal near-quadratic time

Separation probabilities for products of permutations

We study the mixing properties of permutations obtained as a product of two uniformly random permutations of fixed cycle types. For instance, we give an exact formula for the probability that elements $1,2,...,k$ are in distinct cycles of the random permutation of $\{1,2,...,n\}$ obtained as product of two uniformly random $n$-cycles

Bijections and symmetries for the factorizations of the long cycle

We study the factorizations of the permutation $(1,2,...,n)$ into $k$ factors of given cycle types. Using representation theory, Jackson obtained for each $k$ an elegant formula for counting these factorizations according to the number of cycles of each factor. In the cases $k=2,3$ Schaeffer and Vassilieva gave a combinatorial proof of Jackson's formula, and Morales and Vassilieva obtained more refined formulas exhibiting a surprising symmetry property. These counting results are indicative of a rich combinatorial theory which has remained elusive to this point, and it is the goal of this article to establish a series of bijections which unveil some of the combinatorial properties of the factorizations of $(1,2,...,n)$ into $k$ factors for all $k$. We thereby obtain refinements of Jackson's formulas which extend the cases $k=2,3$ treated by Morales and Vassilieva. Our bijections are described in terms of "constellations", which are graphs embedded in surfaces encoding the transitive factorizations of permutations

Tame Decompositions and Collisions

A univariate polynomial f over a field is decomposable if f = g o h = g(h) for nonlinear polynomials g and h. It is intuitively clear that the decomposable polynomials form a small minority among all polynomials over a finite field. The tame case, where the characteristic p of Fq does not divide n = deg f, is fairly well-understood, and we have reasonable bounds on the number of decomposables of degree n. Nevertheless, no exact formula is known if $n$ has more than two prime factors. In order to count the decomposables, one wants to know, under a suitable normalization, the number of collisions, where essentially different (g, h) yield the same f. In the tame case, Ritt's Second Theorem classifies all 2-collisions. We introduce a normal form for multi-collisions of decompositions of arbitrary length with exact description of the (non)uniqueness of the parameters. We obtain an efficiently computable formula for the exact number of such collisions at degree n over a finite field of characteristic coprime to p. This leads to an algorithm for the exact number of decomposable polynomials at degree n over a finite field Fq in the tame case

Matrix Factorizations and Representations of Quivers II: type ADE case

We study a triangulated category of graded matrix factorizations for a polynomial of type ADE. We show that it is equivalent to the derived category of finitely generated modules over the path algebra of the corresponding Dynkin quiver. Also, we discuss a special stability condition for the triangulated category in the sense of T. Bridgeland, which is naturally defined by the grading.Comment: v2: typos corrected, added an appendix by K.Ued