On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given pattern of length $m$ in $O(\frac{m}{p}+ \lg p + \lg\lg p\cdot\lg\lg n)$ time for $p \le m$. For approximate pattern matching with $k$ differences or mismatches, we show how to compute all occurrences of a given pattern in $O(\frac{m^k\sigma^k}{p}\max\left(k,\lg\lg n\right)\!+\!(1+\frac{m}{p}) \lg p\cdot \lg\lg n + \text{occ})$ time, where $\sigma$ is the size of the alphabet and $p \le \sigma^k m^k$. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns $P$ and $P'$, we present a data structure for computing the interval of $PP'$ in $O(\lg\lg n)$ sequential time, or in $O(1+\lg_p\lg n)$ parallel time. All our data structures are of size $O(n)$ bits (in addition to the suffix array)

Fast antijamming timing acquisition using multilayer synchronization sequence

Pseudonoise (PN) sequences are widely used as preamble sequences to establish timing synchronization in military wireless communication systems. At the receiver, searching and detection techniques, such as the full parallel search (FPS) and the serial search (SS), are usually adopted to acquire correct timing position. However, the synchronization sequence has to be very long to combat jamming that reduces the signal-to-noise ratio (SNR) to an extremely low level. In this adverse scenario, the FPS scheme becomes too complex to implement, whereas the SS method suffers from the drawback of long mean acquisition time (MAT). In this paper, a fast timing acquisition method is proposed, using the multilayer synchronization sequence based on cyclical codes. Specifically, the transmitted preamble is the Kronecker product of Bose–Chaudhuri-Hocquenghem (BCH) codewords and PN sequences. At the receiver, the cyclical nature of BCH codes is exploited to test only a part of the entire sequence, resulting in shorter acquisition time. The algorithm is evaluated using the metrics of MAT and detection probability (DP). Theoretical expressions of MAT and DP are derived from the constant false-alarm rate (CFAR) criterion. Theoretical analysis and simulation results show that our proposed scheme dramatically reduces the acquisition time while achieving similar DP performance and maintaining a reasonably low real-time hardware implementation complexity, in comparison with the SS schem

An Efficient Multiway Mergesort for GPU Architectures

Sorting is a primitive operation that is a building block for countless algorithms. As such, it is important to design sorting algorithms that approach peak performance on a range of hardware architectures. Graphics Processing Units (GPUs) are particularly attractive architectures as they provides massive parallelism and computing power. However, the intricacies of their compute and memory hierarchies make designing GPU-efficient algorithms challenging. In this work we present GPU Multiway Mergesort (MMS), a new GPU-efficient multiway mergesort algorithm. MMS employs a new partitioning technique that exposes the parallelism needed by modern GPU architectures. To the best of our knowledge, MMS is the first sorting algorithm for the GPU that is asymptotically optimal in terms of global memory accesses and that is completely free of shared memory bank conflicts. We realize an initial implementation of MMS, evaluate its performance on three modern GPU architectures, and compare it to competitive implementations available in state-of-the-art GPU libraries. Despite these implementations being highly optimized, MMS compares favorably, achieving performance improvements for most random inputs. Furthermore, unlike MMS, state-of-the-art algorithms are susceptible to bank conflicts. We find that for certain inputs that cause these algorithms to incur large numbers of bank conflicts, MMS can achieve up to a 37.6% speedup over its fastest competitor. Overall, even though its current implementation is not fully optimized, due to its efficient use of the memory hierarchy, MMS outperforms the fastest comparison-based sorting implementations available to date

Learning Character Strings via Mastermind Queries, with a Case Study Involving mtDNA

We study the degree to which a character string, $Q$, leaks details about itself any time it engages in comparison protocols with a strings provided by a querier, Bob, even if those protocols are cryptographically guaranteed to produce no additional information other than the scores that assess the degree to which $Q$ matches strings offered by Bob. We show that such scenarios allow Bob to play variants of the game of Mastermind with $Q$ so as to learn the complete identity of $Q$. We show that there are a number of efficient implementations for Bob to employ in these Mastermind attacks, depending on knowledge he has about the structure of $Q$, which show how quickly he can determine $Q$. Indeed, we show that Bob can discover $Q$ using a number of rounds of test comparisons that is much smaller than the length of $Q$, under reasonable assumptions regarding the types of scores that are returned by the cryptographic protocols and whether he can use knowledge about the distribution that $Q$ comes from. We also provide the results of a case study we performed on a database of mitochondrial DNA, showing the vulnerability of existing real-world DNA data to the Mastermind attack.Comment: Full version of related paper appearing in IEEE Symposium on Security and Privacy 2009, "The Mastermind Attack on Genomic Data." This version corrects the proofs of what are now Theorems 2 and 4

Fast Parallel Operations on Search Trees

Using (a,b)-trees as an example, we show how to perform a parallel split with logarithmic latency and parallel join, bulk updates, intersection, union (or merge), and (symmetric) set difference with logarithmic latency and with information theoretically optimal work. We present both asymptotically optimal solutions and simplified versions that perform well in practice - they are several times faster than previous implementations

GPUSCAN++^{++}:Efficient Structural Graph Clustering on GPUs

Structural clustering is one of the most popular graph clustering methods, which has achieved great performance improvement by utilizing GPUs. Even though, the state-of-the-art GPU-based structural clustering algorithm, GPUSCAN, still suffers from efficiency issues since lots of extra costs are introduced for parallelization. Moreover, GPUSCAN assumes that the graph is resident in the GPU memory. However, the GPU memory capacity is limited currently while many real-world graphs are big and cannot fit in the GPU memory, which makes GPUSCAN unable to handle large graphs. Motivated by this, we present a new GPU-based structural clustering algorithm, GPUSCAN++, in this paper. To address the efficiency issue, we propose a new progressive clustering method tailored for GPUs that not only avoid high parallelization costs but also fully exploits the computing resources of GPUs. To address the GPU memory limitation issue, we propose a partition-based algorithm for structural clustering that can process large graphs with limited GPU memory. We conduct experiments on real graphs, and the experimental results demonstrate that our algorithm can achieve up to 168 times speedup compared with the state-of-the-art GPU-based algorithm when the graph can be resident in the GPU memory. Moreover, our algorithm is scalable to handle large graphs. As an example, our algorithm can finish the structural clustering on a graph with 1.8 billion edges using less than 2 GB GPU memory