VLSI-sorting evaluated under the linear model

AbstractThere are several different models of computation used on which to base evaluations of VLSI sorting algorithms and there are different measures of complexity. This paper revises complexity results under the linear model that have been gained under the constant model. This approach is due to expected technological development (see Mangir, 1983; Thompson and Raghavan, 1984; Vitanyi, 1984a, 1984b).For the constant model we know that for medium sized keys there are AT2and AP2 optimal sorting algorithms with T ranging from ω(log n) to O(√nk) and P ranging from Ω(1) to O(√nk) (Bilardi, 1984). The main results of asymptotic analysis of sorting algorithms under the linear model are that the lower bounds allow AT2 optimal sorting algorithms only for T = Θ(√nk) but allow AP2 algorithms in the same range as under the constant model. Furthermore the sorting algorithms presented in this paper meet these lower bounds. This proves that these bounds cannot be improved for k = Θ (log n). The building block for the realization of these sorting algorithms is a comparison exchange module that compares r × s bit matrices in time TC = Θ(r + s) on an area AC = Θ(r2) (not including the storage area for the keys).For problem sizes that exceed realistic chip capacities, chip-external sorting algorithms can be used. In this paper two different chip-external sorting algorithms (BBB(S) and TWB(S)) are presented. They are designed to be implemented on a single board. They use a sorting chip S to perform the sort-split operation on blocks of data BBB(S) and TWB(S) are systolic algorithms using local communication only so that their evaluation does not depend on whether the constant or the linear model is used. Furthermore it seems obvious that their design is technically feasible whenever the sorting chip S is technically feasible.TWB has optimal asymptotic time complexity, so its existence proves that under the linear model external sorting can be done asymptotically as fast as under the constant model. The time complexity of TWB(S) is linearly dependent on the speed gs = nsts. It is shown that the speed if looked at as a function of the chip capacity C is asymptotically maximal for AT2 optimal sorting algorithms. Thus S should be a sorting algorithm similar to the M-M-sorter presented in this paper. A major disadvantage of TWB(S) is that it cannot exploit the maximal throughput ds = ns/ps of a systolic sorting algorithm S.Therefore algorithm BBB(S) is introduced. The time complexity of BBB(S) is linearly dependent on ds. It is shown that the throughput is maximal for AP2 optimal algorithms. There is a wide range of such sorting algorithms including algorithms that can be realized in a way that is independent of the length of the keys. For example, BBB(S) with S being a highly parallel version of odd-even transposition sort has this kind of flexibility. A disadvantage of BBB(S) is that it is asymptotically slower than TWB(S)

A subquadratic algorithm for 3XOR

Given a set $X$ of $n$ binary words of equal length $w$, the 3XOR problem asks for three elements $a, b, c \in X$ such that $a \oplus b=c$, where $\oplus$ denotes the bitwise XOR operation. The problem can be easily solved on a word RAM with word length $w$ in time $O(n^2 \log{n})$. Using Han's fast integer sorting algorithm (2002/2004) this can be reduced to $O(n^2 \log{\log{n}})$. With randomization or a sophisticated deterministic dictionary construction, creating a hash table for $X$ with constant lookup time leads to an algorithm with (expected) running time $O(n^2)$. At present, seemingly no faster algorithms are known. We present a surprisingly simple deterministic, quadratic time algorithm for 3XOR. Its core is a version of the Patricia trie for $X$, which makes it possible to traverse the set $a \oplus X$ in ascending order for arbitrary $a\in \{0, 1\}^{w}$ in linear time. Furthermore, we describe a randomized algorithm for 3XOR with expected running time $O(n^2\cdot\min\{\log^3{w}/w, (\log\log{n})^2/\log^2 n\})$. The algorithm transfers techniques to our setting that were used by Baran, Demaine, and P\u{a}tra\c{s}cu (2005/2008) for solving the related int3SUM problem (the same problem with integer addition in place of binary XOR) in expected time $o(n^2)$. As suggested by Jafargholi and Viola (2016), linear hash functions are employed. The latter authors also showed that assuming 3XOR needs expected running time $n^{2-o(1)}$ one can prove conditional lower bounds for triangle enumeration just as with 3SUM. We demonstrate that 3XOR can be reduced to other problems as well, treating the examples offline SetDisjointness and offline SetIntersection, which were studied for 3SUM by Kopelowitz, Pettie, and Porat (2016)

Efficient Gauss Elimination for Near-Quadratic Matrices with One Short Random Block per Row, with Applications

In this paper we identify a new class of sparse near-quadratic random Boolean matrices that have full row rank over F_2 = {0,1} with high probability and can be transformed into echelon form in almost linear time by a simple version of Gauss elimination. The random matrix with dimensions n(1-epsilon) x n is generated as follows: In each row, identify a block of length L = O((log n)/epsilon) at a random position. The entries outside the block are 0, the entries inside the block are given by fair coin tosses. Sorting the rows according to the positions of the blocks transforms the matrix into a kind of band matrix, on which, as it turns out, Gauss elimination works very efficiently with high probability. For the proof, the effects of Gauss elimination are interpreted as a ("coin-flipping") variant of Robin Hood hashing, whose behaviour can be captured in terms of a simple Markov model from queuing theory. Bounds for expected construction time and high success probability follow from results in this area. They readily extend to larger finite fields in place of F_2. By employing hashing, this matrix family leads to a new implementation of a retrieval data structure, which represents an arbitrary function f: S -> {0,1} for some set S of m = (1-epsilon)n keys. It requires m/(1-epsilon) bits of space, construction takes O(m/epsilon^2) expected time on a word RAM, while queries take O(1/epsilon) time and access only one contiguous segment of O((log m)/epsilon) bits in the representation (O(1/epsilon) consecutive words on a word RAM). The method is readily implemented and highly practical, and it is competitive with state-of-the-art methods. In a more theoretical variant, which works only for unrealistically large S, we can even achieve construction time O(m/epsilon) and query time O(1), accessing O(1) contiguous memory words for a query. By well-established methods the retrieval data structure leads to efficient constructions of (static) perfect hash functions and (static) Bloom filters with almost optimal space and very local storage access patterns for queries

Self-Improving Algorithms

We investigate ways in which an algorithm can improve its expected performance by fine-tuning itself automatically with respect to an unknown input distribution D. We assume here that D is of product type. More precisely, suppose that we need to process a sequence I_1, I_2, ... of inputs I = (x_1, x_2, ..., x_n) of some fixed length n, where each x_i is drawn independently from some arbitrary, unknown distribution D_i. The goal is to design an algorithm for these inputs so that eventually the expected running time will be optimal for the input distribution D = D_1 * D_2 * ... * D_n. We give such self-improving algorithms for two problems: (i) sorting a sequence of numbers and (ii) computing the Delaunay triangulation of a planar point set. Both algorithms achieve optimal expected limiting complexity. The algorithms begin with a training phase during which they collect information about the input distribution, followed by a stationary regime in which the algorithms settle to their optimized incarnations.Comment: 26 pages, 8 figures, preliminary versions appeared at SODA 2006 and SoCG 2008. Thorough revision to improve the presentation of the pape

An Elegant Algorithm for the Construction of Suffix Arrays

The suffix array is a data structure that finds numerous applications in string processing problems for both linguistic texts and biological data. It has been introduced as a memory efficient alternative for suffix trees. The suffix array consists of the sorted suffixes of a string. There are several linear time suffix array construction algorithms (SACAs) known in the literature. However, one of the fastest algorithms in practice has a worst case run time of $O(n^2)$. The problem of designing practically and theoretically efficient techniques remains open. In this paper we present an elegant algorithm for suffix array construction which takes linear time with high probability; the probability is on the space of all possible inputs. Our algorithm is one of the simplest of the known SACAs and it opens up a new dimension of suffix array construction that has not been explored until now. Our algorithm is easily parallelizable. We offer parallel implementations on various parallel models of computing. We prove a lemma on the $\ell$-mers of a random string which might find independent applications. We also present another algorithm that utilizes the above algorithm. This algorithm is called RadixSA and has a worst case run time of $O(n\log{n})$. RadixSA introduces an idea that may find independent applications as a speedup technique for other SACAs. An empirical comparison of RadixSA with other algorithms on various datasets reveals that our algorithm is one of the fastest algorithms to date. The C++ source code is freely available at http://www.engr.uconn.edu/~man09004/radixSA.zi

Average-case analysis of perfect sorting by reversals (Journal Version)

Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any common interval. B\'erard et al. (2007) make use of strong interval trees to describe an algorithm for sorting signed permutations by reversals. Combinatorial properties of this family of trees are essential to the algorithm analysis. Here, we use the expected value of certain tree parameters to prove that the average run-time of the algorithm is at worst, polynomial, and additionally, for sufficiently long permutations, the sorting algorithm runs in polynomial time with probability one. Furthermore, our analysis of the subclass of commuting scenarios yields precise results on the average length of a reversal, and the average number of reversals.Comment: A preliminary version of this work appeared in the proceedings of Combinatorial Pattern Matching (CPM) 2009. See arXiv:0901.2847; Discrete Mathematics, Algorithms and Applications, vol. 3(3), 201