1,051 research outputs found
The similarity metric
A new class of distances appropriate for measuring similarity relations
between sequences, say one type of similarity per distance, is studied. We
propose a new ``normalized information distance'', based on the noncomputable
notion of Kolmogorov complexity, and show that it is in this class and it
minorizes every computable distance in the class (that is, it is universal in
that it discovers all computable similarities). We demonstrate that it is a
metric and call it the {\em similarity metric}. This theory forms the
foundation for a new practical tool. To evidence generality and robustness we
give two distinctive applications in widely divergent areas using standard
compression programs like gzip and GenCompress. First, we compare whole
mitochondrial genomes and infer their evolutionary history. This results in a
first completely automatic computed whole mitochondrial phylogeny tree.
Secondly, we fully automatically compute the language tree of 52 different
languages.Comment: 13 pages, LaTex, 5 figures, Part of this work appeared in Proc. 14th
ACM-SIAM Symp. Discrete Algorithms, 2003. This is the final, corrected,
version to appear in IEEE Trans Inform. T
Test Set Diameter: Quantifying the Diversity of Sets of Test Cases
A common and natural intuition among software testers is that test cases need
to differ if a software system is to be tested properly and its quality
ensured. Consequently, much research has gone into formulating distance
measures for how test cases, their inputs and/or their outputs differ. However,
common to these proposals is that they are data type specific and/or calculate
the diversity only between pairs of test inputs, traces or outputs.
We propose a new metric to measure the diversity of sets of tests: the test
set diameter (TSDm). It extends our earlier, pairwise test diversity metrics
based on recent advances in information theory regarding the calculation of the
normalized compression distance (NCD) for multisets. An advantage is that TSDm
can be applied regardless of data type and on any test-related information, not
only the test inputs. A downside is the increased computational time compared
to competing approaches.
Our experiments on four different systems show that the test set diameter can
help select test sets with higher structural and fault coverage than random
selection even when only applied to test inputs. This can enable early test
design and selection, prior to even having a software system to test, and
complement other types of test automation and analysis. We argue that this
quantification of test set diversity creates a number of opportunities to
better understand software quality and provides practical ways to increase it.Comment: In submissio
Clustering by compression
We present a new method for clustering based on compression. The method
doesn't use subject-specific features or background knowledge, and works as
follows: First, we determine a universal similarity distance, the normalized
compression distance or NCD, computed from the lengths of compressed data files
(singly and in pairwise concatenation). Second, we apply a hierarchical
clustering method. The NCD is universal in that it is not restricted to a
specific application area, and works across application area boundaries. A
theoretical precursor, the normalized information distance, co-developed by one
of the authors, is provably optimal but uses the non-computable notion of
Kolmogorov complexity. We propose precise notions of similarity metric, normal
compressor, and show that the NCD based on a normal compressor is a similarity
metric that approximates universality. To extract a hierarchy of clusters from
the distance matrix, we determine a dendrogram (binary tree) by a new quartet
method and a fast heuristic to implement it. The method is implemented and
available as public software, and is robust under choice of different
compressors. To substantiate our claims of universality and robustness, we
report evidence of successful application in areas as diverse as genomics,
virology, languages, literature, music, handwritten digits, astronomy, and
combinations of objects from completely different domains, using statistical,
dictionary, and block sorting compressors. In genomics we presented new
evidence for major questions in Mammalian evolution, based on
whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta
hypothesis against the Theria hypothesis.Comment: LaTeX, 27 pages, 20 figure
The complexity landscape of viral genomes
Background Viruses are among the shortest yet highly abundant species that harbor minimal instructions to infect cells, adapt, multiply, and exist. However, with the current substantial availability of viral genome sequences, the scientific repertory lacks a complexity landscape that automatically enlights viral genomes' organization, relation, and fundamental characteristics. Results This work provides a comprehensive landscape of the viral genome's complexity (or quantity of information), identifying the most redundant and complex groups regarding their genome sequence while providing their distribution and characteristics at a large and local scale. Moreover, we identify and quantify inverted repeats abundance in viral genomes. For this purpose, we measure the sequence complexity of each available viral genome using data compression, demonstrating that adequate data compressors can efficiently quantify the complexity of viral genome sequences, including subsequences better represented by algorithmic sources (e.g., inverted repeats). Using a state-of-the-art genomic compressor on an extensive viral genomes database, we show that double-stranded DNA viruses are, on average, the most redundant viruses while single-stranded DNA viruses are the least. Contrarily, double-stranded RNA viruses show a lower redundancy relative to single-stranded RNA. Furthermore, we extend the ability of data compressors to quantify local complexity (or information content) in viral genomes using complexity profiles, unprecedently providing a direct complexity analysis of human herpesviruses. We also conceive a features-based classification methodology that can accurately distinguish viral genomes at different taxonomic levels without direct comparisons between sequences. This methodology combines data compression with simple measures such as GC-content percentage and sequence length, followed by machine learning classifiers. Conclusions This article presents methodologies and findings that are highly relevant for understanding the patterns of similarity and singularity between viral groups, opening new frontiers for studying viral genomes' organization while depicting the complexity trends and classification components of these genomes at different taxonomic levels. The whole study is supported by an extensive website (https://asilab.github.io/canvas/) for comprehending the viral genome characterization using dynamic and interactive approaches.Peer reviewe
Algorithmic Information Theory Applications in Bright Field Microscopy and Epithelial Pattern Formation
Algorithmic Information Theory (AIT), also known as Kolmogorov complexity, is a quantitative approach to defining information. AIT is mainly used to measure the amount of information present in the observations of a given phenomenon. In this dissertation we explore the applications of AIT in two case studies. The first examines bright field cell image segmentation and the second examines the information complexity of multicellular patterns. In the first study we demonstrate that our proposed AIT-based algorithm provides an accurate and robust bright field cell segmentation. Cell segmentation is the process of detecting cells in microscopy images, which is usually a challenging task for bright field microscopy due to the low contrast of the images. In the second study, which is the primary contribution of this dissertation, we employ an AIT-based algorithm to quantify the complexity of information content that arises during the development of multicellular organisms. We simulate multicellular organism development by coupling the Gene Regulatory Networks (GRN) within an epithelial field. Our results show that the configuration of GRNs influences the information complexity in the resultant multicellular patterns
A New Quartet Tree Heuristic for Hierarchical Clustering
We consider the problem of constructing an an optimal-weight tree from the
3*(n choose 4) weighted quartet topologies on n objects, where optimality means
that the summed weight of the embedded quartet topologiesis optimal (so it can
be the case that the optimal tree embeds all quartets as non-optimal
topologies). We present a heuristic for reconstructing the optimal-weight tree,
and a canonical manner to derive the quartet-topology weights from a given
distance matrix. The method repeatedly transforms a bifurcating tree, with all
objects involved as leaves, achieving a monotonic approximation to the exact
single globally optimal tree. This contrasts to other heuristic search methods
from biological phylogeny, like DNAML or quartet puzzling, which, repeatedly,
incrementally construct a solution from a random order of objects, and
subsequently add agreement values.Comment: 22 pages, 14 figure
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