A Parallel Algorithm for Exact Bayesian Structure Discovery in Bayesian Networks

Exact Bayesian structure discovery in Bayesian networks requires exponential time and space. Using dynamic programming (DP), the fastest known sequential algorithm computes the exact posterior probabilities of structural features in $O(2(d+1)n2^n)$ time and space, if the number of nodes (variables) in the Bayesian network is $n$ and the in-degree (the number of parents) per node is bounded by a constant $d$. Here we present a parallel algorithm capable of computing the exact posterior probabilities for all $n(n-1)$ edges with optimal parallel space efficiency and nearly optimal parallel time efficiency. That is, if $p=2^k$ processors are used, the run-time reduces to $O(5(d+1)n2^{n-k}+k(n-k)^d)$ and the space usage becomes $O(n2^{n-k})$ per processor. Our algorithm is based the observation that the subproblems in the sequential DP algorithm constitute a $n$-$D$ hypercube. We take a delicate way to coordinate the computation of correlated DP procedures such that large amount of data exchange is suppressed. Further, we develop parallel techniques for two variants of the well-known \emph{zeta transform}, which have applications outside the context of Bayesian networks. We demonstrate the capability of our algorithm on datasets with up to 33 variables and its scalability on up to 2048 processors. We apply our algorithm to a biological data set for discovering the yeast pheromone response pathways.Comment: 32 pages, 12 figure

Fast Parallel Fixed-Parameter Algorithms via Color Coding

Fixed-parameter algorithms have been successfully applied to solve numerous difficult problems within acceptable time bounds on large inputs. However, most fixed-parameter algorithms are inherently \emph{sequential} and, thus, make no use of the parallel hardware present in modern computers. We show that parallel fixed-parameter algorithms do not only exist for numerous parameterized problems from the literature -- including vertex cover, packing problems, cluster editing, cutting vertices, finding embeddings, or finding matchings -- but that there are parallel algorithms working in \emph{constant} time or at least in time \emph{depending only on the parameter} (and not on the size of the input) for these problems. Phrased in terms of complexity classes, we place numerous natural parameterized problems in parameterized versions of AC$^0$. On a more technical level, we show how the \emph{color coding} method can be implemented in constant time and apply it to embedding problems for graphs of bounded tree-width or tree-depth and to model checking first-order formulas in graphs of bounded degree

Partial-sum queries in OLAP data cubes using covering codes

A partial-sum query obtains the summation over a set of specified cells of a data cube. We establish a connection between the covering problem in the theory of error-correcting codes and the partial-sum problem and use this connection to devise algorithms for the partial-sum problem with efficient space-time trade-offs. For example, using our algorithms, with 44 percent additional storage, the query response time can be improved by about 12 percent; by roughly doubling the storage requirement, the query response time can be improved by about 34 percent

GPU-Accelerated BWT Construction for Large Collection of Short Reads

Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many state-of-the-art aligners, at their core, have used the Burrows-Wheeler transform (BWT) as a main-memory index of a reference genome (typical example, NCBI human genome). Recently, BWT has also found its use in string-graph assembly, for indexing the reads (i.e., raw data from DNA sequencers). In a typical data set, the volume of reads is tens of times of the sequenced genome and can be up to 100 Gigabases. Note that a reference genome is relatively stable and computing the index is not a frequent task. For reads, the index has to computed from scratch for each given input. The ability of efficient BWT construction becomes a much bigger concern than before. In this paper, we present a practical method called CX1 for constructing the BWT of very large string collections. CX1 is the first tool that can take advantage of the parallelism given by a graphics processing unit (GPU, a relative cheap device providing a thousand or more primitive cores), as well as simultaneously the parallelism from a multi-core CPU and more interestingly, from a cluster of GPU-enabled nodes. Using CX1, the BWT of a short-read collection of up to 100 Gigabases can be constructed in less than 2 hours using a machine equipped with a quad-core CPU and a GPU, or in about 43 minutes using a cluster with 4 such machines (the speedup is almost linear after excluding the first 16 minutes for loading the reads from the hard disk). The previously fastest tool BRC is measured to take 12 hours to process 100 Gigabases on one machine; it is non-trivial how BRC can be parallelized to take advantage a cluster of machines, let alone GPUs.Comment: 11 page

Highly parallel sparse Cholesky factorization

Several fine grained parallel algorithms were developed and compared to compute the Cholesky factorization of a sparse matrix. The experimental implementations are on the Connection Machine, a distributed memory SIMD machine whose programming model conceptually supplies one processor per data element. In contrast to special purpose algorithms in which the matrix structure conforms to the connection structure of the machine, the focus is on matrices with arbitrary sparsity structure. The most promising algorithm is one whose inner loop performs several dense factorizations simultaneously on a 2-D grid of processors. Virtually any massively parallel dense factorization algorithm can be used as the key subroutine. The sparse code attains execution rates comparable to those of the dense subroutine. Although at present architectural limitations prevent the dense factorization from realizing its potential efficiency, it is concluded that a regular data parallel architecture can be used efficiently to solve arbitrarily structured sparse problems. A performance model is also presented and it is used to analyze the algorithms

Answering Spatial Multiple-Set Intersection Queries Using 2-3 Cuckoo Hash-Filters

We show how to answer spatial multiple-set intersection queries in O(n(log w)/w + kt) expected time, where n is the total size of the t sets involved in the query, w is the number of bits in a memory word, k is the output size, and c is any fixed constant. This improves the asymptotic performance over previous solutions and is based on an interesting data structure, known as 2-3 cuckoo hash-filters. Our results apply in the word-RAM model (or practical RAM model), which allows for constant-time bit-parallel operations, such as bitwise AND, OR, NOT, and MSB (most-significant 1-bit), as exist in modern CPUs and GPUs. Our solutions apply to any multiple-set intersection queries in spatial data sets that can be reduced to one-dimensional range queries, such as spatial join queries for one-dimensional points or sets of points stored along space-filling curves, which are used in GIS applications.Comment: Full version of paper from 2017 ACM SIGSPATIAL International Conference on Advances in Geographic Information System