Abstract: The problem of natural convection about a cone embedded in a porous medium at local Rayleigh numbers based on the boundary layer approximation and the Darcy-s law have been studied before. Similarity solutions for a full cone with the prescribed wall temperature or surface heat flux boundary conditions which is the power function of distance from the vertex of the inverted cone give us a third-order nonlinear differential equation. In this paper, an approximate method for solving higher-order ordinary differential equations is proposed. The approach is based on a rational Chebyshev Tau (RCT) method. The operational matrices of the derivative and product of rational Chebyshev (RC) functions are presented. These matrices together with the Tau method are utilized to reduce the solution of the higher-order ordinary differential equations to the solution of a system of algebraic equations. We also present the comparison of this work with others and show that the present method is applicable.
Abstract: The literature reports a large number of approaches for
measuring the similarity between protein sequences. Most of these
approaches estimate this similarity using alignment-based techniques
that do not necessarily yield biologically plausible results, for two
reasons.
First, for the case of non-alignable (i.e., not yet definitively aligned
and biologically approved) sequences such as multi-domain, circular
permutation and tandem repeat protein sequences, alignment-based
approaches do not succeed in producing biologically plausible results.
This is due to the nature of the alignment, which is based on the
matching of subsequences in equivalent positions, while non-alignable
proteins often have similar and conserved domains in non-equivalent
positions.
Second, the alignment-based approaches lead to similarity measures
that depend heavily on the parameters set by the user for the alignment
(e.g., gap penalties and substitution matrices). For easily alignable
protein sequences, it's possible to supply a suitable combination of
input parameters that allows such an approach to yield biologically
plausible results. However, for difficult-to-align protein sequences,
supplying different combinations of input parameters yields different
results. Such variable results create ambiguities and complicate the
similarity measurement task.
To overcome these drawbacks, this paper describes a novel and
effective approach for measuring the similarity between protein
sequences, called SAF for Substitution and Alignment Free. Without
resorting either to the alignment of protein sequences or to substitution
relations between amino acids, SAF is able to efficiently detect the
significant subsequences that best represent the intrinsic properties of
protein sequences, those underlying the chronological dependencies of
structural features and biochemical activities of protein sequences.
Moreover, by using a new efficient subsequence matching scheme,
SAF more efficiently handles protein sequences that contain similar
structural features with significant meaning in chronologically
non-equivalent positions. To show the effectiveness of SAF, extensive
experiments were performed on protein datasets from different
databases, and the results were compared with those obtained by
several mainstream algorithms.
Abstract: There are several approaches for handling multiclass classification. Aside from one-against-one (OAO) and one-against-all (OAA), hierarchical classification technique is also commonly used. A binary classification tree is a hierarchical classification structure that breaks down a k-class problem into binary sub-problems, each solved by a binary classifier. In each node, a set of classes is divided into two subsets. A good class partition should be able to group similar classes together. Many algorithms measure similarity in term of distance between class centroids. Classes are grouped together by a clustering algorithm when distances between their centroids are small. In this paper, we present a binary classification tree with tuned observation-based clustering (BCT-TOB) that finds a class partition by performing clustering on observations instead of class centroids. A merging step is introduced to merge any insignificant class split. The experiment shows that performance of BCT-TOB is comparable to other algorithms.
Abstract: In this paper we present a method of abrupt cut detection with a novel logic of frames- comparison. Actual frame is compared with its motion estimated prediction instead of comparison with successive frame. Four different similarity metrics were employed to estimate the resemblance of compared frames. Obtained results were evaluated by standard used measures of test accuracy and compared with existing approach. Based on the results, we claim the proposed method is more effective and Pearson correlation coefficient obtained the best results among chosen similarity metrics.
Abstract: Pattern recognition is the research area of Artificial Intelligence that studies the operation and design of systems that recognize patterns in the data. Important application areas are image analysis, character recognition, fingerprint classification, speech analysis, DNA sequence identification, man and machine diagnostics, person identification and industrial inspection. The interest in improving the classification systems of data analysis is independent from the context of applications. In fact, in many studies it is often the case to have to recognize and to distinguish groups of various objects, which requires the need for valid instruments capable to perform this task. The objective of this article is to show several methodologies of Artificial Intelligence for data classification applied to biomedical patterns. In particular, this work deals with the realization of a Computer-Aided Detection system (CADe) that is able to assist the radiologist in identifying types of mammary tumor lesions. As an additional biomedical application of the classification systems, we present a study conducted on blood samples which shows how these methods may help to distinguish between carriers of Thalassemia (or Mediterranean Anaemia) and healthy subjects.
Abstract: The paper presents an on-line recognition machine
(RM) for continuous/isolated, dynamic and static gestures that arise
in Flight Deck Officer (FDO) training. RM is based on generic pattern
recognition framework. Gestures are represented as templates using
summary statistics. The proposed recognition algorithm exploits temporal
and spatial characteristics of gestures via dynamic programming
and Markovian process. The algorithm predicts corresponding index
of incremental input data in the templates in an on-line mode.
Accumulated consistency in the sequence of prediction provides a
similarity measurement (Score) between input data and the templates.
The algorithm provides an intuitive mechanism for automatic detection
of start/end frames of continuous gestures. In the present paper,
we consider isolated gestures. The performance of RM is evaluated
using four datasets - artificial (W TTest), hand motion (Yang) and
FDO (tracker, vision-based ). RM achieves comparable results which
are in agreement with other on-line and off-line algorithms such as
hidden Markov model (HMM) and dynamic time warping (DTW).
The proposed algorithm has the additional advantage of providing
timely feedback for training purposes.
Abstract: We present a method to create special domain
collections from news sites. The method only requires a single
sample article as a seed. No prior corpus statistics are needed and the
method is applicable to multiple languages. We examine various
similarity measures and the creation of document collections for
English and Japanese. The main contributions are as follows. First,
the algorithm can build special domain collections from as little as
one sample document. Second, unlike other algorithms it does not
require a second “general" corpus to compute statistics. Third, in our
testing the algorithm outperformed others in creating collections
made up of highly relevant articles.
Abstract: In April 2009, a new variant of Influenza A virus
subtype H1N1 emerged in Mexico and spread all over the world. The
influenza has three subtypes in human (H1N1, H1N2 and H3N2)
Types B and C influenza tend to be associated with local or regional
epidemics. Preliminary genetic characterization of the influenza
viruses has identified them as swine influenza A (H1N1) viruses.
Nucleotide sequence analysis of the Haemagglutinin (HA) and
Neuraminidase (NA) are similar to each other and the majority of
their genes of swine influenza viruses, two genes coding for the
neuraminidase (NA) and matrix (M) proteins are similar to
corresponding genes of swine influenza. Sequence similarity between
the 2009 A (H1N1) virus and its nearest relatives indicates that its
gene segments have been circulating undetected for an extended
period. Nucleic acid sequence Maximum Likelihood (MCL) and
DNA Empirical base frequencies, Phylogenetic relationship amongst
the HA genes of H1N1 virus isolated in Genbank having high
nucleotide sequence homology.
In this paper we used 16 HA nucleotide sequences from NCBI for
computing sequence relationships similarity of swine influenza A
virus using the following method MCL the result is 28%, 36.64% for
Optimal tree with the sum of branch length, 35.62% for Interior
branch phylogeny Neighber – Join Tree, 1.85% for the overall
transition/transversion, and 8.28% for Overall mean distance.
Abstract: The complexity of today-s software systems makes
collaborative development necessary to accomplish tasks.
Frameworks are necessary to allow developers perform their tasks
independently yet collaboratively. Similarity detection is one of the
major issues to consider when developing such frameworks. It allows
developers to mine existing repositories when developing their own
views of a software artifact, and it is necessary for identifying the
correspondences between the views to allow merging them and
checking their consistency. Due to the importance of the
requirements specification stage in software development, this paper
proposes a framework for collaborative development of Object-
Oriented formal specifications along with a similarity detection
approach to support the creation, merging and consistency checking
of specifications. The paper also explores the impact of using
additional concepts on improving the matching results. Finally, the
proposed approach is empirically evaluated.
Abstract: The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.
Abstract: Most of fuzzy clustering algorithms have some
discrepancies, e.g. they are not able to detect clusters with convex
shapes, the number of the clusters should be a priori known, they
suffer from numerical problems, like sensitiveness to the
initialization, etc. This paper studies the synergistic combination of
the hierarchical and graph theoretic minimal spanning tree based
clustering algorithm with the partitional Gath-Geva fuzzy clustering
algorithm. The aim of this hybridization is to increase the robustness
and consistency of the clustering results and to decrease the number
of the heuristically defined parameters of these algorithms to
decrease the influence of the user on the clustering results. For the
analysis of the resulted fuzzy clusters a new fuzzy similarity measure
based tool has been presented. The calculated similarities of the
clusters can be used for the hierarchical clustering of the resulted
fuzzy clusters, which information is useful for cluster merging and
for the visualization of the clustering results. As the examples used
for the illustration of the operation of the new algorithm will show,
the proposed algorithm can detect clusters from data with arbitrary
shape and does not suffer from the numerical problems of the
classical Gath-Geva fuzzy clustering algorithm.
Abstract: Approximate tandem repeats in a genomic sequence are
two or more contiguous, similar copies of a pattern of nucleotides.
They are used in DNA mapping, studying molecular evolution
mechanisms, forensic analysis and research in diagnosis of inherited
diseases. All their functions are still investigated and not well
defined, but increasing biological databases together with tools for
identification of these repeats may lead to discovery of their specific
role or correlation with particular features. This paper presents a new
approach for finding approximate tandem repeats in a given sequence,
where the similarity between consecutive repeats is measured using
the Hamming distance. It is an enhancement of a method for finding
exact tandem repeats in DNA sequences based on the Burrows-
Wheeler transform.
Abstract: The need of high frame-rate imaging has been triggered by the new applications of ultrasound imaging to transient elastography and real-time 3D ultrasound. Using plane wave excitation (PWE) is one of the methods to achieve very high frame-rate imaging since an image can be formed with a single insonification. However, due to the lack of transmit focusing, the image quality with PWE is lower compared with those using conventional focused transmission. To solve this problem, we propose a filter-retrieved transmit focusing (FRF) technique combined with cross-correlation weighting (FRF+CC weighting) for high frame-rate imaging with PWE. A restrospective focusing filter is designed to simultaneously minimize the predefined sidelobe energy associated with single PWE and the filter energy related to the signal-to-noise-ratio (SNR). This filter attempts to maintain the mainlobe signals and to reduce the sidelobe ones, which gives similar mainlobe signals and different sidelobes between the original PWE and the FRF baseband data. Normalized cross-correlation coefficient at zero lag is calculated to quantify the degree of similarity at each imaging point and used as a weighting matrix to the FRF baseband data to further suppress sidelobes, thus improving the filter-retrieved focusing quality.
Abstract: Intuitionistic fuzzy sets as proposed by Atanassov,
have gained much attention from past and latter researchers for
applications in various fields. Similarity measures between
intuitionistic fuzzy sets were developed afterwards. However, it does
not cater the conflicting behavior of each element evaluated. We
therefore made some modification to the similarity measure of IFS
by considering conflicting concept to the model. In this paper, we
concentrate on Zhang and Fu-s similarity measures for IFSs and
some examples are given to validate these similarity measures. A
simple modification to Zhang and Fu-s similarity measures of IFSs
was proposed to find the best result according to the use of degree of
indeterminacy. Finally, we mark up with the application to real
decision making problems.
Abstract: One of the major problems in genomic field is to perform sequence comparison on DNA and protein sequences. Executing sequence comparison on the DNA and protein data is a computationally intensive task. Sequence comparison is the basic step for all algorithms in protein sequences similarity. Parallel computing is an attractive solution to provide the computational power needed to speedup the lengthy process of the sequence comparison. Our main research is to enhance the protein sequence algorithm using dynamic programming method. In our approach, we parallelize the dynamic programming algorithm using multithreaded program to perform the sequence comparison and also developed a distributed protein database among many PCs using Remote Method Interface (RMI). As a result, we showed how different sizes of protein sequences data and computation of scoring matrix of these protein sequence on different number of processors affected the processing time and speed, as oppose to sequential processing.
Abstract: In this paper, we present a novel objective nonreference
performance assessment algorithm for image fusion. It takes
into account local measurements to estimate how well the important
information in the source images is represented by the fused image.
The metric is based on the Universal Image Quality Index and uses
the similarity between blocks of pixels in the input images and the
fused image as the weighting factors for the metrics. Experimental
results confirm that the values of the proposed metrics correlate well
with the subjective quality of the fused images, giving a significant
improvement over standard measures based on mean squared error
and mutual information.
Abstract: There is an urgent need to develop novel
Mycobacterium tuberculosis (Mtb) drugs that are active against drug
resistant bacteria but, more importantly, kill persistent bacteria. Our
study structured based on integrated analysis of metabolic pathways,
small molecule screening and similarity Search in PubChem
Database. Metabolic analysis approaches based on Unified weighted
used for potent target selection. Our results suggest that pantothenate
synthetase (panC) and and 3-methyl-2-oxobutanoate hydroxymethyl
transferase (panB) as a appropriate drug targets. In our study, we
used pantothenate synthetase because of existence inhibitors. We
have reported the discovery of new antitubercular compounds
through ligand based approaches using computational tools.
Abstract: Retrieval image by shape similarity, given a template
shape is particularly challenging, owning to the difficulty to derive a
similarity measurement that closely conforms to the common
perception of similarity by humans. In this paper, a new method for the
representation and comparison of shapes is present which is based on
the shape matrix and snake model. It is scaling, rotation, translation
invariant. And it can retrieve the shape images with some missing or
occluded parts. In the method, the deformation spent by the template
to match the shape images and the matching degree is used to evaluate
the similarity between them.
Abstract: In this paper we present a method for gene ranking
from DNA microarray data. More precisely, we calculate the correlation
networks, which are unweighted and undirected graphs, from
microarray data of cervical cancer whereas each network represents
a tissue of a certain tumor stage and each node in the network
represents a gene. From these networks we extract one tree for
each gene by a local decomposition of the correlation network. The
interpretation of a tree is that it represents the n-nearest neighbor
genes on the n-th level of a tree, measured by the Dijkstra distance,
and, hence, gives the local embedding of a gene within the correlation
network. For the obtained trees we measure the pairwise similarity
between trees rooted by the same gene from normal to cancerous
tissues. This evaluates the modification of the tree topology due to
progression of the tumor. Finally, we rank the obtained similarity
values from all tissue comparisons and select the top ranked genes.
For these genes the local neighborhood in the correlation networks
changes most between normal and cancerous tissues. As a result
we find that the top ranked genes are candidates suspected to be
involved in tumor growth and, hence, indicates that our method
captures essential information from the underlying DNA microarray
data of cervical cancer.
Abstract: This paper introduces new algorithms (Fuzzy relative
of the CLARANS algorithm FCLARANS and Fuzzy c Medoids
based on randomized search FCMRANS) for fuzzy clustering of
relational data. Unlike existing fuzzy c-medoids algorithm (FCMdd)
in which the within cluster dissimilarity of each cluster is minimized
in each iteration by recomputing new medoids given current
memberships, FCLARANS minimizes the same objective function
minimized by FCMdd by changing current medoids in such away
that that the sum of the within cluster dissimilarities is minimized.
Computing new medoids may be effected by noise because outliers
may join the computation of medoids while the choice of medoids in
FCLARANS is dictated by the location of a predominant fraction of
points inside a cluster and, therefore, it is less sensitive to the
presence of outliers. In FCMRANS the step of computing new
medoids in FCMdd is modified to be based on randomized search.
Furthermore, a new initialization procedure is developed that add
randomness to the initialization procedure used with FCMdd. Both
FCLARANS and FCMRANS are compared with the robust and
linearized version of fuzzy c-medoids (RFCMdd). Experimental
results with different samples of the Reuter-21578, Newsgroups
(20NG) and generated datasets with noise show that FCLARANS is
more robust than both RFCMdd and FCMRANS. Finally, both
FCMRANS and FCLARANS are more efficient and their outputs
are almost the same as that of RFCMdd in terms of classification
rate.