16,928 research outputs found
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
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
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
Multiscale modeling of granular flows with application to crowd dynamics
In this paper a new multiscale modeling technique is proposed. It relies on a
recently introduced measure-theoretic approach, which allows to manage the
microscopic and the macroscopic scale under a unique framework. In the
resulting coupled model the two scales coexist and share information. This
allows to perform numerical simulations in which the trajectories and the
density of the particles affect each other. Crowd dynamics is the motivating
application throughout the paper.Comment: 30 pages, 9 figure
Competition and cooperation:aspects of dynamics in sandpiles
In this article, we review some of our approaches to granular dynamics, now
well known to consist of both fast and slow relaxational processes. In the
first case, grains typically compete with each other, while in the second, they
cooperate. A typical result of {\it cooperation} is the formation of stable
bridges, signatures of spatiotemporal inhomogeneities; we review their
geometrical characteristics and compare theoretical results with those of
independent simulations. {\it Cooperative} excitations due to local density
fluctuations are also responsible for relaxation at the angle of repose; the
{\it competition} between these fluctuations and external driving forces, can,
on the other hand, result in a (rare) collapse of the sandpile to the
horizontal. Both these features are present in a theory reviewed here. An arena
where the effects of cooperation versus competition are felt most keenly is
granular compaction; we review here a random graph model, where three-spin
interactions are used to model compaction under tapping. The compaction curve
shows distinct regions where 'fast' and 'slow' dynamics apply, separated by
what we have called the {\it single-particle relaxation threshold}. In the
final section of this paper, we explore the effect of shape -- jagged vs.
regular -- on the compaction of packings near their jamming limit. One of our
major results is an entropic landscape that, while microscopically rough,
manifests {\it Edwards' flatness} at a macroscopic level. Another major result
is that of surface intermittency under low-intensity shaking.Comment: 36 pages, 23 figures, minor correction
A Fuzzy Petri Nets Model for Computing With Words
Motivated by Zadeh's paradigm of computing with words rather than numbers,
several formal models of computing with words have recently been proposed.
These models are based on automata and thus are not well-suited for concurrent
computing. In this paper, we incorporate the well-known model of concurrent
computing, Petri nets, together with fuzzy set theory and thereby establish a
concurrency model of computing with words--fuzzy Petri nets for computing with
words (FPNCWs). The new feature of such fuzzy Petri nets is that the labels of
transitions are some special words modeled by fuzzy sets. By employing the
methodology of fuzzy reasoning, we give a faithful extension of an FPNCW which
makes it possible for computing with more words. The language expressiveness of
the two formal models of computing with words, fuzzy automata for computing
with words and FPNCWs, is compared as well. A few small examples are provided
to illustrate the theoretical development.Comment: double columns 14 pages, 8 figure
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