2,683 research outputs found
Substructure Discovery Using Minimum Description Length and Background Knowledge
The ability to identify interesting and repetitive substructures is an
essential component to discovering knowledge in structural data. We describe a
new version of our SUBDUE substructure discovery system based on the minimum
description length principle. The SUBDUE system discovers substructures that
compress the original data and represent structural concepts in the data. By
replacing previously-discovered substructures in the data, multiple passes of
SUBDUE produce a hierarchical description of the structural regularities in the
data. SUBDUE uses a computationally-bounded inexact graph match that identifies
similar, but not identical, instances of a substructure and finds an
approximate measure of closeness of two substructures when under computational
constraints. In addition to the minimum description length principle, other
background knowledge can be used by SUBDUE to guide the search towards more
appropriate substructures. Experiments in a variety of domains demonstrate
SUBDUE's ability to find substructures capable of compressing the original data
and to discover structural concepts important to the domain. Description of
Online Appendix: This is a compressed tar file containing the SUBDUE discovery
system, written in C. The program accepts as input databases represented in
graph form, and will output discovered substructures with their corresponding
value.Comment: See http://www.jair.org/ for an online appendix and other files
accompanying this articl
Designing labeled graph classifiers by exploiting the R\'enyi entropy of the dissimilarity representation
Representing patterns as labeled graphs is becoming increasingly common in
the broad field of computational intelligence. Accordingly, a wide repertoire
of pattern recognition tools, such as classifiers and knowledge discovery
procedures, are nowadays available and tested for various datasets of labeled
graphs. However, the design of effective learning procedures operating in the
space of labeled graphs is still a challenging problem, especially from the
computational complexity viewpoint. In this paper, we present a major
improvement of a general-purpose classifier for graphs, which is conceived on
an interplay between dissimilarity representation, clustering,
information-theoretic techniques, and evolutionary optimization algorithms. The
improvement focuses on a specific key subroutine devised to compress the input
data. We prove different theorems which are fundamental to the setting of the
parameters controlling such a compression operation. We demonstrate the
effectiveness of the resulting classifier by benchmarking the developed
variants on well-known datasets of labeled graphs, considering as distinct
performance indicators the classification accuracy, computing time, and
parsimony in terms of structural complexity of the synthesized classification
models. The results show state-of-the-art standards in terms of test set
accuracy and a considerable speed-up for what concerns the computing time.Comment: Revised versio
Structural graph matching using the EM algorithm and singular value decomposition
This paper describes an efficient algorithm for inexact graph matching. The method is purely structural, that is, it uses only the edge or connectivity structure of the graph and does not draw on node or edge attributes. We make two contributions: 1) commencing from a probability distribution for matching errors, we show how the problem of graph matching can be posed as maximum-likelihood estimation using the apparatus of the EM algorithm; and 2) we cast the recovery of correspondence matches between the graph nodes in a matrix framework. This allows one to efficiently recover correspondence matches using the singular value decomposition. We experiment with the method on both real-world and synthetic data. Here, we demonstrate that the method offers comparable performance to more computationally demanding method
Classifying sequences by the optimized dissimilarity space embedding approach: a case study on the solubility analysis of the E. coli proteome
We evaluate a version of the recently-proposed classification system named
Optimized Dissimilarity Space Embedding (ODSE) that operates in the input space
of sequences of generic objects. The ODSE system has been originally presented
as a classification system for patterns represented as labeled graphs. However,
since ODSE is founded on the dissimilarity space representation of the input
data, the classifier can be easily adapted to any input domain where it is
possible to define a meaningful dissimilarity measure. Here we demonstrate the
effectiveness of the ODSE classifier for sequences by considering an
application dealing with the recognition of the solubility degree of the
Escherichia coli proteome. Solubility, or analogously aggregation propensity,
is an important property of protein molecules, which is intimately related to
the mechanisms underlying the chemico-physical process of folding. Each protein
of our dataset is initially associated with a solubility degree and it is
represented as a sequence of symbols, denoting the 20 amino acid residues. The
herein obtained computational results, which we stress that have been achieved
with no context-dependent tuning of the ODSE system, confirm the validity and
generality of the ODSE-based approach for structured data classification.Comment: 10 pages, 49 reference
Graph ambiguity
In this paper, we propose a rigorous way to define the concept of ambiguity in the domain of graphs. In past studies, the classical definition of ambiguity has been derived starting from fuzzy set and fuzzy information theories. Our aim is to show that also in the domain of the graphs it is possible to derive a formulation able to capture the same semantic and mathematical concept. To strengthen the theoretical results, we discuss the application of the graph ambiguity concept to the graph classification setting, conceiving a new kind of inexact graph matching procedure. The results prove that the graph ambiguity concept is a characterizing and discriminative property of graphs. (C) 2013 Elsevier B.V. All rights reserved
Link Prediction by De-anonymization: How We Won the Kaggle Social Network Challenge
This paper describes the winning entry to the IJCNN 2011 Social Network
Challenge run by Kaggle.com. The goal of the contest was to promote research on
real-world link prediction, and the dataset was a graph obtained by crawling
the popular Flickr social photo sharing website, with user identities scrubbed.
By de-anonymizing much of the competition test set using our own Flickr crawl,
we were able to effectively game the competition. Our attack represents a new
application of de-anonymization to gaming machine learning contests, suggesting
changes in how future competitions should be run.
We introduce a new simulated annealing-based weighted graph matching
algorithm for the seeding step of de-anonymization. We also show how to combine
de-anonymization with link prediction---the latter is required to achieve good
performance on the portion of the test set not de-anonymized---for example by
training the predictor on the de-anonymized portion of the test set, and
combining probabilistic predictions from de-anonymization and link prediction.Comment: 11 pages, 13 figures; submitted to IJCNN'201
Structured Sparsity: Discrete and Convex approaches
Compressive sensing (CS) exploits sparsity to recover sparse or compressible
signals from dimensionality reducing, non-adaptive sensing mechanisms. Sparsity
is also used to enhance interpretability in machine learning and statistics
applications: While the ambient dimension is vast in modern data analysis
problems, the relevant information therein typically resides in a much lower
dimensional space. However, many solutions proposed nowadays do not leverage
the true underlying structure. Recent results in CS extend the simple sparsity
idea to more sophisticated {\em structured} sparsity models, which describe the
interdependency between the nonzero components of a signal, allowing to
increase the interpretability of the results and lead to better recovery
performance. In order to better understand the impact of structured sparsity,
in this chapter we analyze the connections between the discrete models and
their convex relaxations, highlighting their relative advantages. We start with
the general group sparse model and then elaborate on two important special
cases: the dispersive and the hierarchical models. For each, we present the
models in their discrete nature, discuss how to solve the ensuing discrete
problems and then describe convex relaxations. We also consider more general
structures as defined by set functions and present their convex proxies.
Further, we discuss efficient optimization solutions for structured sparsity
problems and illustrate structured sparsity in action via three applications.Comment: 30 pages, 18 figure
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