Efficient computation of hashes

The sequential computation of hashes at the core of many distributed storage systems and found, for example, in grid services can hinder efficiency in service quality and even pose security challenges that can only be addressed by the use of parallel hash tree modes. The main contributions of this paper are, first, the identification of several efficiency and security challenges posed by the use of sequential hash computation based on the Merkle-Damgard engine. In addition, alternatives for the parallel computation of hash trees are discussed, and a prototype for a new parallel implementation of the Keccak function, the SHA-3 winner, is introduced

Efficient Computation of Sequence Mappability

Sequence mappability is an important task in genome re-sequencing. In the $(k,m)$-mappability problem, for a given sequence $T$ of length $n$, our goal is to compute a table whose $i$th entry is the number of indices $j \ne i$ such that length-$m$ substrings of $T$ starting at positions $i$ and $j$ have at most $k$ mismatches. Previous works on this problem focused on heuristic approaches to compute a rough approximation of the result or on the case of $k=1$. We present several efficient algorithms for the general case of the problem. Our main result is an algorithm that works in $\mathcal{O}(n \min\{m^k,\log^{k+1} n\})$ time and $\mathcal{O}(n)$ space for $k=\mathcal{O}(1)$. It requires a carefu l adaptation of the technique of Cole et al.~[STOC 2004] to avoid multiple counting of pairs of substrings. We also show $\mathcal{O}(n^2)$-time algorithms to compute all results for a fixed $m$ and all $k=0,\ldots,m$ or a fixed $k$ and all $m=k,\ldots,n-1$. Finally we show that the $(k,m)$-mappability problem cannot be solved in strongly subquadratic time for $k,m = \Theta(\log n)$ unless the Strong Exponential Time Hypothesis fails.Comment: Accepted to SPIRE 201

Efficient computation of middle levels Gray codes

For any integer $n\geq 1$ a middle levels Gray code is a cyclic listing of all bitstrings of length $2n+1$ that have either $n$ or $n+1$ entries equal to 1 such that any two consecutive bitstrings in the list differ in exactly one bit. The question whether such a Gray code exists for every $n\geq 1$ has been the subject of intensive research during the last 30 years, and has been answered affirmatively only recently [T. M\"utze. Proof of the middle levels conjecture. Proc. London Math. Soc., 112(4):677--713, 2016]. In this work we provide the first efficient algorithm to compute a middle levels Gray code. For a given bitstring, our algorithm computes the next $\ell$ bitstrings in the Gray code in time $\mathcal{O}(n\ell(1+\frac{n}{\ell}))$, which is $\mathcal{O}(n)$ on average per bitstring provided that $\ell=\Omega(n)$

Efficient Computation of the Characteristic Polynomial

This article deals with the computation of the characteristic polynomial of dense matrices over small finite fields and over the integers. We first present two algorithms for the finite fields: one is based on Krylov iterates and Gaussian elimination. We compare it to an improvement of the second algorithm of Keller-Gehrig. Then we show that a generalization of Keller-Gehrig's third algorithm could improve both complexity and computational time. We use these results as a basis for the computation of the characteristic polynomial of integer matrices. We first use early termination and Chinese remaindering for dense matrices. Then a probabilistic approach, based on integer minimal polynomial and Hensel factorization, is particularly well suited to sparse and/or structured matrices

Efficient Computation of the Kauffman Bracket

This paper bounds the computational cost of computing the Kauffman bracket of a link in terms of the crossing number of that link. Specifically, it is shown that the image of a tangle with $g$ boundary points and $n$ crossings in the Kauffman bracket skein module is a linear combination of $O(2^g)$ basis elements, with each coefficient a polynomial with at most $n$ nonzero terms, each with integer coefficients, and that the link can be built one crossing at a time as a sequence of tangles with maximum number of boundary points bounded by $C\sqrt{n}$ for some $C.$ From this it follows that the computation of the Kauffman bracket of the link takes time and memory a polynomial in $n$ times $2^{C\sqrt{n}}.

Fuel Efficient Computation in Passive Self-Assembly

In this paper we show that passive self-assembly in the context of the tile self-assembly model is capable of performing fuel efficient, universal computation. The tile self-assembly model is a premiere model of self-assembly in which particles are modeled by four-sided squares with glue types assigned to each tile edge. The assembly process is driven by positive and negative force interactions between glue types, allowing for tile assemblies floating in the plane to combine and break apart over time. We refer to this type of assembly model as passive in that the constituent parts remain unchanged throughout the assembly process regardless of their interactions. A computationally universal system is said to be fuel efficient if the number of tiles used up per computation step is bounded by a constant. Work within this model has shown how fuel guzzling tile systems can perform universal computation with only positive strength glue interactions. Recent work has introduced space-efficient, fuel-guzzling universal computation with the addition of negative glue interactions and the use of a powerful non-diagonal class of glue interactions. Other recent work has shown how to achieve fuel efficient computation within active tile self-assembly. In this paper we utilize negative interactions in the tile self-assembly model to achieve the first computationally universal passive tile self-assembly system that is both space and fuel-efficient. In addition, we achieve this result using a limited diagonal class of glue interactions