10 research outputs found
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
Data granulation by the principles of uncertainty
Researches in granular modeling produced a variety of mathematical models,
such as intervals, (higher-order) fuzzy sets, rough sets, and shadowed sets,
which are all suitable to characterize the so-called information granules.
Modeling of the input data uncertainty is recognized as a crucial aspect in
information granulation. Moreover, the uncertainty is a well-studied concept in
many mathematical settings, such as those of probability theory, fuzzy set
theory, and possibility theory. This fact suggests that an appropriate
quantification of the uncertainty expressed by the information granule model
could be used to define an invariant property, to be exploited in practical
situations of information granulation. In this perspective, a procedure of
information granulation is effective if the uncertainty conveyed by the
synthesized information granule is in a monotonically increasing relation with
the uncertainty of the input data. In this paper, we present a data granulation
framework that elaborates over the principles of uncertainty introduced by
Klir. Being the uncertainty a mesoscopic descriptor of systems and data, it is
possible to apply such principles regardless of the input data type and the
specific mathematical setting adopted for the information granules. The
proposed framework is conceived (i) to offer a guideline for the synthesis of
information granules and (ii) to build a groundwork to compare and
quantitatively judge over different data granulation procedures. To provide a
suitable case study, we introduce a new data granulation technique based on the
minimum sum of distances, which is designed to generate type-2 fuzzy sets. We
analyze the procedure by performing different experiments on two distinct data
types: feature vectors and labeled graphs. Results show that the uncertainty of
the input data is suitably conveyed by the generated type-2 fuzzy set models.Comment: 16 pages, 9 figures, 52 reference
Toward a multilevel representation of protein molecules: comparative approaches to the aggregation/folding propensity problem
This paper builds upon the fundamental work of Niwa et al. [34], which
provides the unique possibility to analyze the relative aggregation/folding
propensity of the elements of the entire Escherichia coli (E. coli) proteome in
a cell-free standardized microenvironment. The hardness of the problem comes
from the superposition between the driving forces of intra- and inter-molecule
interactions and it is mirrored by the evidences of shift from folding to
aggregation phenotypes by single-point mutations [10]. Here we apply several
state-of-the-art classification methods coming from the field of structural
pattern recognition, with the aim to compare different representations of the
same proteins gathered from the Niwa et al. data base; such representations
include sequences and labeled (contact) graphs enriched with chemico-physical
attributes. By this comparison, we are able to identify also some interesting
general properties of proteins. Notably, (i) we suggest a threshold around 250
residues discriminating "easily foldable" from "hardly foldable" molecules
consistent with other independent experiments, and (ii) we highlight the
relevance of contact graph spectra for folding behavior discrimination and
characterization of the E. coli solubility data. The soundness of the
experimental results presented in this paper is proved by the statistically
relevant relationships discovered among the chemico-physical description of
proteins and the developed cost matrix of substitution used in the various
discrimination systems.Comment: 17 pages, 3 figures, 46 reference
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
Relaxed Dissimilarity-based Symbolic Histogram Variants for Granular Graph Embedding
Graph embedding is an established and popular approach when designing graph-based pattern recognition systems. Amongst the several strategies, in the last ten years, Granular Computing emerged as a promising framework for structural pattern recognition. In the late 2000\u2019s, symbolic histograms have been proposed as the driving force in order to perform the graph embedding procedure by counting the number of times each granule of information appears in the graph to be embedded. Similarly to a bag-of-words representation of a text corpora, symbolic histograms have been originally conceived as integer-valued vectorial representation of the graphs. In this paper, we propose six \u2018relaxed\u2019 versions of symbolic histograms, where the proper dissimilarity values between the information granules and the constituent parts of the graph to be embedded are taken into account, information which is discarded in the original symbolic histogram formulation due to the hard-limited nature of the counting procedure. Experimental results on six open-access datasets of fully-labelled graphs show comparable performance in terms of classification accuracy with respect to the original symbolic histograms (average accuracy shift ranging from -7% to +2%), counterbalanced by a great improvement in terms of number of resulting information granules, hence number of features in the embedding space (up to 75% less features, on average)
Modelling and recognition of protein contact networks by multiple kernel learning and dissimilarity representations
Multiple kernel learning is a paradigm which employs a properly constructed chain of kernel functions able to simultaneously analyse different data or different representations of the same data. In this paper, we propose an hybrid classification system based on a linear combination of multiple kernels defined over multiple dissimilarity spaces. The core of the training procedure is the joint optimisation of kernel weights and representatives selection in the dissimilarity spaces. This equips the system with a two-fold knowledge discovery phase: by analysing the weights, it is possible to check which representations are more suitable for solving the classification problem, whereas the pivotal patterns selected as representatives can give further insights on the modelled system, possibly with the help of field-experts. The proposed classification system is tested on real proteomic data in order to predict proteins' functional role starting from their folded structure: specifically, a set of eight representations are drawn from the graph-based protein folded description. The proposed multiple kernel-based system has also been benchmarked against a clustering-based classification system also able to exploit multiple dissimilarities simultaneously. Computational results show remarkable classification capabilities and the knowledge discovery analysis is in line with current biological knowledge, suggesting the reliability of the proposed system
A Granular Computing approach to the design of optimized graph classification systems
Research on Graph-based pattern recognition and Soft Computing systems has attracted many scientists and engineers in several different contexts. This fact is motivated by the reason that graphs are general structures able to encode both topological and semantic information in data. While the data modeling properties of graphs are of indisputable power, there are still different concerns about the best way to compute similarity functions in an effective and efficient manner. To this end, suited transformation procedures are usually conceived to address the well-known Inexact Graph Matching problem in an explicit embedding space. In this paper, we propose two graph embedding algorithms based on the Granular Computing paradigm, which are engineered as key procedures of a general-purpose graph classification system. Tests have been conducted on benchmarking datasets relying on both synthetic and real-world data, achieving competitive results in terms of test set classification accuracy