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Francois Nicolas

Publications and source records attributed to Francois Nicolas.

12 recordsLinked to original sources
arXiv2014

Tighter Undecidability Bounds for Matrix Mortality, Zero-in-the-Corner Problems, and More

We study the decidability of three well-known problems related to integer matrix multiplication: Mortality (M), Zero in the Left-Upper Corner (Z), and Zero in the Right-Upper Corner (R). Let d and k be positive integers. Define M(k, d x d) as the following special case of the Mortality problem: given a set X of d -by-d integer matrices such that the cardinality of X is not greater than k, decide whether the d-by-d zero matrix belongs to X^+, where X^+ denotes the closure of X under the usual matrix multiplication. In the same way, define the Z(k, d x d) problem as: given an instance X of M(k, d x d) (the instances of Z(k, d x d) are the same as those of M(k, d x d)), decide whether at least one matrix in X^+ has a zero in the left-upper corner. Define R(k, d x d) as the variant of Z(k, d x d) where "left-upper corner" is replaced with "right-upper corner". In the paper, we prove that M(6, 3 x 3), M(4, 5 x 5), M(3, 9 x 9), M(2, 15 x 15), Z(5, 3 x 3), Z(3, 5 x 5), Z(2, 9 x 9), R(6, 3 x 3), R(5, 4 x 4), and R(3, 6 x 6) are undecidable. The previous best comparable results were the undecidabilities of M(7, 3 x 3), M(3, 13 x 13), M(2, 21 x 21), Z(7, 3 x 3), Z(2, 13 x 13), R(7, 3 x 3), and R(2, 10 x 10).

cs.DM↗
arXiv2012

On the decidability of semigroup freeness

This paper deals with the decidability of semigroup freeness. More precisely, the freeness problem over a semigroup S is defined as: given a finite subset X of S, decide whether each element of S has at most one factorization over X. To date, the decidabilities of two freeness problems have been closely examined. In 1953, Sardinas and Patterson proposed a now famous algorithm for the freeness problem over the free monoid. In 1991, Klarner, Birget and Satterfield proved the undecidability of the freeness problem over three-by-three integer matrices. Both results led to the publication of many subsequent papers. The aim of the present paper is three-fold: (i) to present general results concerning freeness problems, (ii) to study the decidability of freeness problems over various particular semigroups (special attention is devoted to multiplicative matrix semigroups), and (iii) to propose precise, challenging open questions in order to promote the study of the topic.

cs.DM↗
arXiv2012

Various complexity results for computational mass spectrometry problems

Define Minimum Soapy Union (MinSU) as the following optimization problem: given a $k$-tuple $(X_1, X_2,..., X_k)$ of finite integer sets, find a $k$-tuple $(t_1, t_2,..., t_k)$ of integers that minimizes the cardinality of $(X_1 + t_1) \cup (X_2 + t_2) \cup ... \cup (X_n + t_k)$. We show that MinSU is NP-complete, APX-hard, and polynomial for fixed $k$. MinSU appears naturally in the context of protein shotgun sequencing: Here, the protein is cleaved into short and overlapping peptides, which are then analyzed by tandem mass spectrometry. To improve the quality of such spectra, one then asks for the mass of the unknown prefix (the shift) of the spectrum, such that the resulting shifted spectra show a maximum agreement. For real-world data the problem is even more complicated than our definition of MinSU; but our intractability results clearly indicate that it is unlikely to find a polynomial time algorithm for shotgun protein sequencing.

cs.CC↗
arXiv2012

On the Morse-Hedlund complexity gap

In 1938, Morse and Hedlund proved that the subword complexity function of an infinite word is either bounded or at least linearly growing. In 1982, Ehrenfeucht and Rozenberg proved that this gap property holds for the subword complexity function of any language. The aim of the present paper is to present a self-contained, compact proof of Ehrenfeucht and Rozenberg's result.

cs.FL↗
arXiv2011

Intractability of the Minimum-Flip Supertree problem and its variants

Computing supertrees is a central problem in phylogenetics. The supertree method that is by far the most widely used today was introduced in 1992 and is called Matrix Representation with Parsimony analysis (MRP). Matrix Representation using Flipping (MRF)}, which was introduced in 2002, is an interesting variant of MRP: MRF is arguably more relevant that MRP and various efficient implementations of MRF have been presented. From a theoretical point of view, implementing MRF or MRP is solving NP-hard optimization problems. The aim of this paper is to study the approximability and the fixed-parameter tractability of the optimization problem corresponding to MRF, namely Minimum-Flip Supertree. We prove strongly negative results.

cs.CC↗
arXiv2009

Asymptotic behavior of growth functions of D0L-systems

A D0L-system is a triple (A, f, w) where A is a finite alphabet, f is an endomorphism of the free monoid over A, and w is a word over A. The D0L-sequence generated by (A, f, w) is the sequence of words (w, f(w), f(f(w)), f(f(f(w))), ...). The corresponding sequence of lengths, that is the function mapping each non-negative integer n to |f^n(w)|, is called the growth function of (A, f, w). In 1978, Salomaa and Soittola deduced the following result from their thorough study of the theory of rational power series: if the D0L-sequence generated by (A, f, w) is not eventually the empty word then there exist a non-negative integer d and a real number b greater than or equal to one such that |f^n(w)| behaves like n^d b^n as n tends to infinity. The aim of the present paper is to present a short, direct, elementary proof of this theorem.

cs.DM↗
arXiv2009

A simple, polynomial-time algorithm for the matrix torsion problem

The Matrix Torsion Problem (MTP) is: given a square matrix M with rational entries, decide whether two distinct powers of M are equal. It has been shown by Cassaigne and the author that the MTP reduces to the Matrix Power Problem (MPP) in polynomial time: given two square matrices A and B with rational entries, the MTP is to decide whether B is a power of A. Since the MPP is decidable in polynomial time, it is also the case of the MTP. However, the algorithm for MPP is highly non-trivial. The aim of this note is to present a simple, direct, polynomial-time algorithm for the MTP.

cs.DM↗
arXiv2008

(Generalized) Post Correspondence Problem and semi-Thue systems

Let PCP(k) denote the Post Correspondence Problem for k input pairs of strings. Let ACCESSIBILITY(k) denote the the word problem for k-rule semi-Thue systems. In 1980, Claus showed that if ACCESSIBILITY(k) is undecidable then PCP(k + 4) is also undecidable. The aim of the paper is to present a clean, detailed proof of the statement. We proceed in two steps, using the Generalized Post Correspondence Problem as an auxiliary. First, we prove that if ACCESSIBILITY(k) is undecidable then GPCP(k + 2) is also undecidable. Then, we prove that if GPCP(k) is undecidable then PCP(k + 2) is also undecidable. (The latter result has also been shown by Harju and Karhumaki.) To date, the sharpest undecidability bounds for both PCP and GPCP have been deduced from Claus's result: since Matiyasevich and Senizergues showed that ACCESSIBILITY(3) is undecidable, GPCP(5) and PCP(7) are undecidable.

cs.DM↗
arXiv2008

Solving the Maximum Agreement SubTree and the Maximum Compatible Tree problems on many bounded degree trees

Given a set of leaf-labeled trees with identical leaf sets, the well-known "Maximum Agreement SubTree" problem (MAST) consists of finding a subtree homeomorphically included in all input trees and with the largest number of leaves. Its variant called "Maximum Compatible Tree" (MCT) is less stringent, as it allows the input trees to be refined. Both problems are of particular interest in computational biology, where trees encountered have often small degrees. In this paper, we study the parameterized complexity of MAST and MCT with respect to the maximum degree, denoted by D, of the input trees. It is known that MAST is polynomial for bounded D. As a counterpart, we show that the problem is W[1]-hard with respect to parameter D. Moreover, relying on recent advances in parameterized complexity we obtain a tight lower bound: while MAST can be solved in O(N^{O(D)}) time where N denotes the input length, we show that an O(N^{o(D)}) bound is not achievable, unless SNP is contained in SE. We also show that MCT is W[1]-hard with respect to D, and that MCT cannot be solved in O(N^{o(2^{D/2})}) time, SNP is contained in SE.

cs.CC↗