79,805 research outputs found
Indexing large genome collections on a PC
Motivation: The availability of thousands of invidual genomes of one species
should boost rapid progress in personalized medicine or understanding of the
interaction between genotype and phenotype, to name a few applications. A key
operation useful in such analyses is aligning sequencing reads against a
collection of genomes, which is costly with the use of existing algorithms due
to their large memory requirements.
Results: We present MuGI, Multiple Genome Index, which reports all
occurrences of a given pattern, in exact and approximate matching model,
against a collection of thousand(s) genomes. Its unique feature is the small
index size fitting in a standard computer with 16--32\,GB, or even 8\,GB, of
RAM, for the 1000GP collection of 1092 diploid human genomes. The solution is
also fast. For example, the exact matching queries are handled in average time
of 39\,s and with up to 3 mismatches in 373\,s on the test PC with
the index size of 13.4\,GB. For a smaller index, occupying 7.4\,GB in memory,
the respective times grow to 76\,s and 917\,s.
Availability: Software and Suuplementary material:
\url{http://sun.aei.polsl.pl/mugi}
GraphMatch: Efficient Large-Scale Graph Construction for Structure from Motion
We present GraphMatch, an approximate yet efficient method for building the
matching graph for large-scale structure-from-motion (SfM) pipelines. Unlike
modern SfM pipelines that use vocabulary (Voc.) trees to quickly build the
matching graph and avoid a costly brute-force search of matching image pairs,
GraphMatch does not require an expensive offline pre-processing phase to
construct a Voc. tree. Instead, GraphMatch leverages two priors that can
predict which image pairs are likely to match, thereby making the matching
process for SfM much more efficient. The first is a score computed from the
distance between the Fisher vectors of any two images. The second prior is
based on the graph distance between vertices in the underlying matching graph.
GraphMatch combines these two priors into an iterative "sample-and-propagate"
scheme similar to the PatchMatch algorithm. Its sampling stage uses Fisher
similarity priors to guide the search for matching image pairs, while its
propagation stage explores neighbors of matched pairs to find new ones with a
high image similarity score. Our experiments show that GraphMatch finds the
most image pairs as compared to competing, approximate methods while at the
same time being the most efficient.Comment: Published at IEEE 3DV 201
Random Indexing K-tree
Random Indexing (RI) K-tree is the combination of two algorithms for
clustering. Many large scale problems exist in document clustering. RI K-tree
scales well with large inputs due to its low complexity. It also exhibits
features that are useful for managing a changing collection. Furthermore, it
solves previous issues with sparse document vectors when using K-tree. The
algorithms and data structures are defined, explained and motivated. Specific
modifications to K-tree are made for use with RI. Experiments have been
executed to measure quality. The results indicate that RI K-tree improves
document cluster quality over the original K-tree algorithm.Comment: 8 pages, ADCS 2009; Hyperref and cleveref LaTeX packages conflicted.
Removed clevere
Lightweight LCP Construction for Very Large Collections of Strings
The longest common prefix array is a very advantageous data structure that,
combined with the suffix array and the Burrows-Wheeler transform, allows to
efficiently compute some combinatorial properties of a string useful in several
applications, especially in biological contexts. Nowadays, the input data for
many problems are big collections of strings, for instance the data coming from
"next-generation" DNA sequencing (NGS) technologies. In this paper we present
the first lightweight algorithm (called extLCP) for the simultaneous
computation of the longest common prefix array and the Burrows-Wheeler
transform of a very large collection of strings having any length. The
computation is realized by performing disk data accesses only via sequential
scans, and the total disk space usage never needs more than twice the output
size, excluding the disk space required for the input. Moreover, extLCP allows
to compute also the suffix array of the strings of the collection, without any
other further data structure is needed. Finally, we test our algorithm on real
data and compare our results with another tool capable to work in external
memory on large collections of strings.Comment: This manuscript version is made available under the CC-BY-NC-ND 4.0
license http://creativecommons.org/licenses/by-nc-nd/4.0/ The final version
of this manuscript is in press in Journal of Discrete Algorithm
Topic Similarity Networks: Visual Analytics for Large Document Sets
We investigate ways in which to improve the interpretability of LDA topic
models by better analyzing and visualizing their outputs. We focus on examining
what we refer to as topic similarity networks: graphs in which nodes represent
latent topics in text collections and links represent similarity among topics.
We describe efficient and effective approaches to both building and labeling
such networks. Visualizations of topic models based on these networks are shown
to be a powerful means of exploring, characterizing, and summarizing large
collections of unstructured text documents. They help to "tease out"
non-obvious connections among different sets of documents and provide insights
into how topics form larger themes. We demonstrate the efficacy and
practicality of these approaches through two case studies: 1) NSF grants for
basic research spanning a 14 year period and 2) the entire English portion of
Wikipedia.Comment: 9 pages; 2014 IEEE International Conference on Big Data (IEEE BigData
2014
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