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which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Fractal MapReduce decomposition of sequence alignment
, 2011
"... This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Fractal MapReduce decomposition of sequence alignment ..."
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This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Fractal MapReduce decomposition of sequence alignment
Factoring wavelet transforms into lifting steps
 J. FOURIER ANAL. APPL
, 1998
"... This paper is essentially tutorial in nature. We show how any discrete wavelet transform or two band subband filtering with finite filters can be decomposed into a finite sequence of simple filtering steps, which we call lifting steps but that are also known as ladder structures. This decompositio ..."
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Cited by 584 (8 self)
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in the biorthogonal, i.e, nonunitary case. Like the lattice factorization, the decomposition presented here asymptotically reduces the computational complexity of the transform by a factor two. It has other applications, such as the possibility of defining a waveletlike transform that maps integers to integers.
Support vector machine learning for interdependent and structured output spaces
 In ICML
, 2004
"... Learning general functional dependencies is one of the main goals in machine learning. Recent progress in kernelbased methods has focused on designing flexible and powerful input representations. This paper addresses the complementary issue of problems involving complex outputs suchas multiple depe ..."
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Cited by 450 (20 self)
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the sparseness and structural decomposition of the problem. We demonstrate the versatility and effectiveness of our method on problems ranging from supervised grammar learning and namedentity recognition, to taxonomic text classification and sequence alignment. 1.
Human DNA methylomes at base resolution show widespread epigenomic differences.
 Nature,
, 2009
"... DNA cytosine methylation is a central epigenetic modification that has essential roles in cellular processes including genome regulation, development and disease. Here we present the first genomewide, singlebaseresolution maps of methylated cytosines in a mammalian genome, from both human embryo ..."
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Cited by 401 (6 self)
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embryonic stem cells 17 and IMR90 fetal lung fibroblasts 18 , generating 1.16 and 1.18 billion reads, respectively, that aligned uniquely to the human reference sequence (NCBI build 36/HG18). The total sequence yield was 87.5 and 91.0 gigabases (Gb), with an average read depth of 14.23 and 14.83 per strand
MapReduce in the Clouds for Science
 In Proceedings of the 2010 IEEE Second International Conference on Cloud Computing Technology and Science
, 2010
"... Abstract — The utility computing model introduced by cloud computing combined with the rich set of cloud infrastructure services offers a very viable alternative to traditional servers and computing clusters. MapReduce distributed data processing architecture has become the weapon of choice for dat ..."
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Cited by 21 (2 self)
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Abstract — The utility computing model introduced by cloud computing combined with the rich set of cloud infrastructure services offers a very viable alternative to traditional servers and computing clusters. MapReduce distributed data processing architecture has become the weapon of choice
Bounded geometries, fractals, and lowdistortion embeddings
"... The doubling constant of a metric space (X; d) is thesmallest value * such that every ball in X can be covered by * balls of half the radius. The doubling dimension of X isthen defined as dim(X) = log2 *. A metric (or sequence ofmetrics) is called doubling precisely when its doubling dimension is ..."
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Cited by 198 (40 self)
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arising from trees, from graphs excludinga fixed minor, and from snowflaked metrics. Our techniques include decomposition theorems for doubling metrics, andan analysis of a fractal in the plane due to Laakso [21]. Finally, we discuss some applications and point out a centralopen question regarding
RASL: Robust Alignment by Sparse and Lowrank Decomposition for Linearly Correlated Images
, 2010
"... This paper studies the problem of simultaneously aligning a batch of linearly correlated images despite gross corruption (such as occlusion). Our method seeks an optimal set of image domain transformations such that the matrix of transformed images can be decomposed as the sum of a sparse matrix of ..."
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Cited by 161 (6 self)
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of errors and a lowrank matrix of recovered aligned images. We reduce this extremely challenging optimization problem to a sequence of convex programs that minimize the sum of ℓ1norm and nuclear norm of the two component matrices, which can be efficiently solved by scalable convex optimization techniques
Cloudenabling Sequence Alignment with Hadoop MapReduce: A Performance Analysis. IPCBEE
, 2012
"... Abstract. The Bio Sequence alignment involves arranging DNA, RNA or protein sequences in order to find similarity between the aligned sequences, which helps us to find the structural, functional and evolutionary relationships among organisms. Next generation sequencing has led to the generation of b ..."
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Cited by 1 (0 self)
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predictable since the cloud implementation has many overheads which may sometimes negatively affect the performance. In this paper, we investigate this issue and provide a detailed study of the performance of a canonical MapReduce implementation of sequence alignment algorithm, CloudBurst: Highly sensitive
MapReduce and Data Intensive Applications
"... Distributed and parallel computing have emerged as a well developed field in computer science. Cloud computing offers new approaches for commercial and scientific applications because it incorporates different perspectives for the use of both hardware and software. MapReducedistributed data processi ..."
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processing architecture, instantiating the new paradigm of “bring the computation to data ” has become a popular solution for large scale scientific applications, such as data/textmining, bioinformatics sequence alignment, Matrix Multiplication, etc. To understand whether the MapReduce computing model
Open Access CloudAligner: A fast and fullfeatured MapReduce
"... based tool for sequence mapping ..."
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