Abstract: Proteomics is one of the largest areas of research for
bioinformatics and medical science. An ambitious goal of proteomics
is to elucidate the structure, interactions and functions of all proteins
within cells and organisms. Predicting Protein-Protein Interaction
(PPI) is one of the crucial and decisive problems in current research.
Genomic data offer a great opportunity and at the same time a lot of
challenges for the identification of these interactions. Many methods
have already been proposed in this regard. In case of in-silico
identification, most of the methods require both positive and negative
examples of protein interaction and the perfection of these examples
are very much crucial for the final prediction accuracy. Positive
examples are relatively easy to obtain from well known databases. But
the generation of negative examples is not a trivial task. Current PPI
identification methods generate negative examples based on some
assumptions, which are likely to affect their prediction accuracy.
Hence, if more reliable negative examples are used, the PPI prediction
methods may achieve even more accuracy. Focusing on this issue, a
graph based negative example generation method is proposed, which
is simple and more accurate than the existing approaches. An
interaction graph of the protein sequences is created. The basic
assumption is that the longer the shortest path between two
protein-sequences in the interaction graph, the less is the possibility of
their interaction. A well established PPI detection algorithm is
employed with our negative examples and in most cases it increases
the accuracy more than 10% in comparison with the negative pair
selection method in that paper.
Abstract: Power System Security is a major concern in real time
operation. Conventional method of security evaluation consists of
performing continuous load flow and transient stability studies by
simulation program. This is highly time consuming and infeasible
for on-line application. Pattern Recognition (PR) is a promising
tool for on-line security evaluation. This paper proposes a Support
Vector Machine (SVM) based binary classification for static and
transient security evaluation. The proposed SVM based PR approach
is implemented on New England 39 Bus and IEEE 57 Bus systems.
The simulation results of SVM classifier is compared with the other
classifier algorithms like Method of Least Squares (MLS), Multi-
Layer Perceptron (MLP) and Linear Discriminant Analysis (LDA)
classifiers.
Abstract: We present an Electronic Nose (ENose), which is
aimed at identifying the presence of one out of two gases, possibly
detecting the presence of a mixture of the two. Estimation of the
concentrations of the components is also performed for a volatile
organic compound (VOC) constituted by methanol and acetone, for
the ranges 40-400 and 22-220 ppm (parts-per-million), respectively.
Our system contains 8 sensors, 5 of them being gas sensors (of the
class TGS from FIGARO USA, INC., whose sensing element is a tin
dioxide (SnO2) semiconductor), the remaining being a temperature
sensor (LM35 from National Semiconductor Corporation), a
humidity sensor (HIH–3610 from Honeywell), and a pressure sensor
(XFAM from Fujikura Ltd.).
Our integrated hardware–software system uses some machine
learning principles and least square regression principle to identify at
first a new gas sample, or a mixture, and then to estimate the
concentrations. In particular we adopt a training model using the
Support Vector Machine (SVM) approach with linear kernel to teach
the system how discriminate among different gases. Then we apply
another training model using the least square regression, to predict
the concentrations.
The experimental results demonstrate that the proposed
multiclassification and regression scheme is effective in the
identification of the tested VOCs of methanol and acetone with
96.61% correctness. The concentration prediction is obtained with
0.979 and 0.964 correlation coefficient for the predicted versus real
concentrations of methanol and acetone, respectively.
Abstract: Our study proposes an alternative method in building
Fuzzy Rule-Based System (FRB) from Support Vector Machine
(SVM). The first set of fuzzy IF-THEN rules is obtained through
an equivalence of the SVM decision network and the zero-ordered
Sugeno FRB type of the Adaptive Network Fuzzy Inference System
(ANFIS). The second set of rules is generated by combining the
first set based on strength of firing signals of support vectors using
Gaussian kernel. The final set of rules is then obtained from the
second set through input scatter partitioning. A distinctive advantage
of our method is the guarantee that the number of final fuzzy IFTHEN
rules is not more than the number of support vectors in the
trained SVM. The final FRB system obtained is capable of performing
classification with results comparable to its SVM counterpart, but it
has an advantage over the black-boxed SVM in that it may reveal
human comprehensible patterns.
Abstract: A New features are extracted and compared to
improve the prediction of protein-protein interactions. The basic idea
is to select and use the best set of features from the Tensor matrices
that are produced by the frequency vectors of the protein sequences.
Three set of features are compared, the first set is based on the
indices that are the most common in the interacting proteins, the
second set is based on the indices that tend to be common in the
interacting and non-interacting proteins, and the third set is
constructed by using random indices. Moreover, three encoding
strategies are compared; that are based on the amino asides polarity,
structure, and chemical properties. The experimental results indicate
that the highest accuracy can be obtained by using random indices
with chemical properties encoding strategy and support vector
machine.
Abstract: Evolutionary Algorithms are population-based,
stochastic search techniques, widely used as efficient global
optimizers. However, many real life optimization problems often
require finding optimal solution to complex high dimensional,
multimodal problems involving computationally very expensive
fitness function evaluations. Use of evolutionary algorithms in such
problem domains is thus practically prohibitive. An attractive
alternative is to build meta models or use an approximation of the
actual fitness functions to be evaluated. These meta models are order
of magnitude cheaper to evaluate compared to the actual function
evaluation. Many regression and interpolation tools are available to
build such meta models. This paper briefly discusses the
architectures and use of such meta-modeling tools in an evolutionary
optimization context. We further present two evolutionary algorithm
frameworks which involve use of meta models for fitness function
evaluation. The first framework, namely the Dynamic Approximate
Fitness based Hybrid EA (DAFHEA) model [14] reduces
computation time by controlled use of meta-models (in this case
approximate model generated by Support Vector Machine
regression) to partially replace the actual function evaluation by
approximate function evaluation. However, the underlying
assumption in DAFHEA is that the training samples for the metamodel
are generated from a single uniform model. This does not take
into account uncertain scenarios involving noisy fitness functions.
The second model, DAFHEA-II, an enhanced version of the original
DAFHEA framework, incorporates a multiple-model based learning
approach for the support vector machine approximator to handle
noisy functions [15]. Empirical results obtained by evaluating the
frameworks using several benchmark functions demonstrate their
efficiency