Minimal Conflicting Sets for the Consecutive Ones Property in ancestral genome reconstruction

A binary matrix has the Consecutive Ones Property (C1P) if its columns can be ordered in such a way that all 1's on each row are consecutive. A Minimal Conflicting Set is a set of rows that does not have the C1P, but every proper subset has the C1P. Such submatrices have been considered in comparative genomics applications, but very little is known about their combinatorial structure and efficient algorithms to compute them. We first describe an algorithm that detects rows that belong to Minimal Conflicting Sets. This algorithm has a polynomial time complexity when the number of 1's in each row of the considered matrix is bounded by a constant. Next, we show that the problem of computing all Minimal Conflicting Sets can be reduced to the joint generation of all minimal true clauses and maximal false clauses for some monotone boolean function. We use these methods on simulated data related to ancestral genome reconstruction to show that computing Minimal Conflicting Set is useful in discriminating between true positive and false positive ancestral syntenies. We also study a dataset of yeast genomes and address the reliability of an ancestral genome proposal of the Saccahromycetaceae yeasts.Comment: 20 pages, 3 figure

Low-degree tests at large distances

We define tests of boolean functions which distinguish between linear (or quadratic) polynomials, and functions which are very far, in an appropriate sense, from these polynomials. The tests have optimal or nearly optimal trade-offs between soundness and the number of queries. In particular, we show that functions with small Gowers uniformity norms behave ``randomly'' with respect to hypergraph linearity tests. A central step in our analysis of quadraticity tests is the proof of an inverse theorem for the third Gowers uniformity norm of boolean functions. The last result has also a coding theory application. It is possible to estimate efficiently the distance from the second-order Reed-Muller code on inputs lying far beyond its list-decoding radius

Boolean Matrix Factorization Meets Consecutive Ones Property

Boolean matrix factorization is a natural and a popular technique for summarizing binary matrices. In this paper, we study a problem of Boolean matrix factorization where we additionally require that the factor matrices have consecutive ones property (OBMF). A major application of this optimization problem comes from graph visualization: standard techniques for visualizing graphs are circular or linear layout, where nodes are ordered in circle or on a line. A common problem with visualizing graphs is clutter due to too many edges. The standard approach to deal with this is to bundle edges together and represent them as ribbon. We also show that we can use OBMF for edge bundling combined with circular or linear layout techniques. We demonstrate that not only this problem is NP-hard but we cannot have a polynomial-time algorithm that yields a multiplicative approximation guarantee (unless P = NP). On the positive side, we develop a greedy algorithm where at each step we look for the best 1-rank factorization. Since even obtaining 1-rank factorization is NP-hard, we propose an iterative algorithm where we fix one side and and find the other, reverse the roles, and repeat. We show that this step can be done in linear time using pq-trees. We also extend the problem to cyclic ones property and symmetric factorizations. Our experiments show that our algorithms find high-quality factorizations and scale well

Learning pseudo-Boolean k-DNF and Submodular Functions

We prove that any submodular function f: {0,1}^n -> {0,1,...,k} can be represented as a pseudo-Boolean 2k-DNF formula. Pseudo-Boolean DNFs are a natural generalization of DNF representation for functions with integer range. Each term in such a formula has an associated integral constant. We show that an analog of Hastad's switching lemma holds for pseudo-Boolean k-DNFs if all constants associated with the terms of the formula are bounded. This allows us to generalize Mansour's PAC-learning algorithm for k-DNFs to pseudo-Boolean k-DNFs, and hence gives a PAC-learning algorithm with membership queries under the uniform distribution for submodular functions of the form f:{0,1}^n -> {0,1,...,k}. Our algorithm runs in time polynomial in n, k^{O(k \log k / \epsilon)}, 1/\epsilon and log(1/\delta) and works even in the agnostic setting. The line of previous work on learning submodular functions [Balcan, Harvey (STOC '11), Gupta, Hardt, Roth, Ullman (STOC '11), Cheraghchi, Klivans, Kothari, Lee (SODA '12)] implies only n^{O(k)} query complexity for learning submodular functions in this setting, for fixed epsilon and delta. Our learning algorithm implies a property tester for submodularity of functions f:{0,1}^n -> {0, ..., k} with query complexity polynomial in n for k=O((\log n/ \loglog n)^{1/2}) and constant proximity parameter \epsilon