On Matrices, Automata, and Double Counting

Matrix models are ubiquitous for constraint problems. Many such problems have a matrix of variables M, with the same constraint defined by a finite-state automaton A on each row of M and a global cardinality constraint gcc on each column of M. We give two methods for deriving, by double counting, necessary conditions on the cardinality variables of the gcc constraints from the automaton A. The first method yields linear necessary conditions and simple arithmetic constraints. The second method introduces the cardinality automaton, which abstracts the overall behaviour of all the row automata and can be encoded by a set of linear constraints. We evaluate the impact of our methods on a large set of nurse rostering problem instances

Algebraic properties of structured context-free languages: old approaches and novel developments

The historical research line on the algebraic properties of structured CF languages initiated by McNaughton's Parenthesis Languages has recently attracted much renewed interest with the Balanced Languages, the Visibly Pushdown Automata languages (VPDA), the Synchronized Languages, and the Height-deterministic ones. Such families preserve to a varying degree the basic algebraic properties of Regular languages: boolean closure, closure under reversal, under concatenation, and Kleene star. We prove that the VPDA family is strictly contained within the Floyd Grammars (FG) family historically known as operator precedence. Languages over the same precedence matrix are known to be closed under boolean operations, and are recognized by a machine whose pop or push operations on the stack are purely determined by terminal letters. We characterize VPDA's as the subclass of FG having a peculiarly structured set of precedence relations, and balanced grammars as a further restricted case. The non-counting invariance property of FG has a direct implication for VPDA too.Comment: Extended version of paper presented at WORDS2009, Salerno,Italy, September 200

Revisiting Waiting Times in DNA evolution

Transcription factors are short stretches of DNA (or $k$-mers) mainly located in promoters sequences that enhance or repress gene expression. With respect to an initial distribution of letters on the DNA alphabet, Behrens and Vingron consider a random sequence of length $n$ that does not contain a given $k$-mer or word of size $k$. Under an evolution model of the DNA, they compute the probability $\mathfrak{p}_n$ that this $k$-mer appears after a unit time of 20 years. They prove that the waiting time for the first apparition of the $k$-mer is well approximated by $T_n=1/\mathfrak{p}_n$. Their work relies on the simplifying assumption that the $k$-mer is not self-overlapping. They observe in particular that the waiting time is mostly driven by the initial distribution of letters. Behrens et al. use an approach by automata that relaxes the assumption related to words overlaps. Their numerical evaluations confirms the validity of Behrens and Vingron approach for non self-overlapping words, but provides up to 44% corrections for highly self-overlapping words such as $\mathtt{AAAAA}$. We devised an approach of the problem by clump analysis and generating functions; this approach leads to prove a quasi-linear behaviour of $\mathfrak{p}_n$ for a large range of values of $n$, an important result for DNA evolution. We present here this clump analysis, first by language decomposition, and next by an automaton construction; finally, we describe an equivalent approach by construction of Markov automata.Comment: 19 pages, 3 Figures, 2 Table

Diagonalizing transfer matrices and matrix product operators: a medley of exact and computational methods

Transfer matrices and matrix product operators play an ubiquitous role in the field of many body physics. This paper gives an ideosyncratic overview of applications, exact results and computational aspects of diagonalizing transfer matrices and matrix product operators. The results in this paper are a mixture of classic results, presented from the point of view of tensor networks, and of new results. Topics discussed are exact solutions of transfer matrices in equilibrium and non-equilibrium statistical physics, tensor network states, matrix product operator algebras, and numerical matrix product state methods for finding extremal eigenvectors of matrix product operators.Comment: Lecture notes from a course at Vienna Universit

Algebraic Methods in the Congested Clique

In this work, we use algebraic methods for studying distance computation and subgraph detection tasks in the congested clique model. Specifically, we adapt parallel matrix multiplication implementations to the congested clique, obtaining an $O(n^{1-2/\omega})$ round matrix multiplication algorithm, where $\omega < 2.3728639$ is the exponent of matrix multiplication. In conjunction with known techniques from centralised algorithmics, this gives significant improvements over previous best upper bounds in the congested clique model. The highlight results include: -- triangle and 4-cycle counting in $O(n^{0.158})$ rounds, improving upon the $O(n^{1/3})$ triangle detection algorithm of Dolev et al. [DISC 2012], -- a $(1 + o(1))$-approximation of all-pairs shortest paths in $O(n^{0.158})$ rounds, improving upon the $\tilde{O} (n^{1/2})$-round $(2 + o(1))$-approximation algorithm of Nanongkai [STOC 2014], and -- computing the girth in $O(n^{0.158})$ rounds, which is the first non-trivial solution in this model. In addition, we present a novel constant-round combinatorial algorithm for detecting 4-cycles.Comment: This is work is a merger of arxiv:1412.2109 and arxiv:1412.266

On the Wilf-Stanley limit of 4231-avoiding permutations and a conjecture of Arratia

We construct a sequence of finite automata that accept subclasses of the class of 4231-avoiding permutations. We thereby show that the Wilf-Stanley limit for the class of 4231-avoiding permutations is bounded below by 9.35. This bound shows that this class has the largest such limit among all classes of permutations avoiding a single permutation of length 4 and refutes the conjecture that the Wilf-Stanley limit of a class of permutations avoiding a single permutation of length k cannot exceed (k-1)^2.Comment: Submitted to Advances in Applied Mathematic

Partial Derivative Automaton for Regular Expressions with Shuffle

We generalize the partial derivative automaton to regular expressions with shuffle and study its size in the worst and in the average case. The number of states of the partial derivative automata is in the worst case at most 2^m, where m is the number of letters in the expression, while asymptotically and on average it is no more than (4/3)^m

Quantum geometry and quantum algorithms

Motivated by algorithmic problems arising in quantum field theories whose dynamical variables are geometric in nature, we provide a quantum algorithm that efficiently approximates the colored Jones polynomial. The construction is based on the complete solution of Chern-Simons topological quantum field theory and its connection to Wess-Zumino-Witten conformal field theory. The colored Jones polynomial is expressed as the expectation value of the evolution of the q-deformed spin-network quantum automaton. A quantum circuit is constructed capable of simulating the automaton and hence of computing such expectation value. The latter is efficiently approximated using a standard sampling procedure in quantum computation.Comment: Submitted to J. Phys. A: Math-Gen, for the special issue ``The Quantum Universe'' in honor of G. C. Ghirard