6,685 research outputs found
Elephant Search with Deep Learning for Microarray Data Analysis
Even though there is a plethora of research in Microarray gene expression
data analysis, still, it poses challenges for researchers to effectively and
efficiently analyze the large yet complex expression of genes. The feature
(gene) selection method is of paramount importance for understanding the
differences in biological and non-biological variation between samples. In
order to address this problem, a novel elephant search (ES) based optimization
is proposed to select best gene expressions from the large volume of microarray
data. Further, a promising machine learning method is envisioned to leverage
such high dimensional and complex microarray dataset for extracting hidden
patterns inside to make a meaningful prediction and most accurate
classification. In particular, stochastic gradient descent based Deep learning
(DL) with softmax activation function is then used on the reduced features
(genes) for better classification of different samples according to their gene
expression levels. The experiments are carried out on nine most popular Cancer
microarray gene selection datasets, obtained from UCI machine learning
repository. The empirical results obtained by the proposed elephant search
based deep learning (ESDL) approach are compared with most recent published
article for its suitability in future Bioinformatics research.Comment: 12 pages, 5 Tabl
Examining applying high performance genetic data feature selection and classification algorithms for colon cancer diagnosis
Background and Objectives: This paper examines the accuracy and efficiency (time complexity) of high performance genetic data feature selection and classification algorithms for colon cancer diagnosis. The need for this research derives from the urgent and increasing need for accurate and efficient algorithms. Colon cancer is a leading cause of death worldwide, hence it is vitally important for the cancer tissues to be expertly identified and classified in a rapid and timely manner, to assure both a fast detection of the disease and to expedite the drug discovery process.
Methods: In this research, a three-phase approach was proposed and implemented: Phases One and Two examined the feature selection algorithms and classification algorithms employed separately, and Phase Three examined the performance of the combination of these.
Results: It was found from Phase One that the Particle Swarm Optimization (PSO) algorithm performed best with the colon dataset as a feature selection (29 genes selected) and from Phase Two that the Sup- port Vector Machine (SVM) algorithm outperformed other classifications, with an accuracy of almost 86%. It was also found from Phase Three that the combined use of PSO and SVM surpassed other algorithms in accuracy and performance, and was faster in terms of time analysis (94%).
Conclusions: It is concluded that applying feature selection algorithms prior to classification algorithms results in better accuracy than when the latter are applied alone. This conclusion is important and significant to industry and society
An Evolutionary Variable Neighborhood Search for Selecting Combinational Gene Signatures in Predicting Chemo-Response of Osteosarcoma
In genomic studies of cancers, identification of genetic biomarkers from analyzing microarray chip that interrogate thousands of genes is important for diagnosis and therapeutics. However, the commonly used statistical significance analysis can only provide information of each single gene, thus neglecting the intrinsic interactions among genes. Therefore, methods aiming at combinational gene signatures are highly valuable. Supervised classification is an effective way to assess the function of a gene combination in differentiating various groups of samples. In this paper, an evolutionary variable neighborhood search (EVNS) that integrated the approaches of evolutionary algorithm and variable neighborhood search (VNS) is introduced.It consists of a population of solutions that evolution is performed by a variable neighborhood search operator, instead of the more usual reproduction operators, crossover and mutation used in evolutionary algorithms. It is an efficient search algorithm especially suitable for tremendous solution space. The proposed EVNS can simultaneously optimize the feature subset and the classifier through a common solution coding mechanism. This method was applied in searching the combinational gene signatures for predicting histologic response of chemotherapy on osteosarcoma patients, which is the most common malignant bone tumor in children. Cross-validation results show that EVNS outperforms the other existing approaches in classifying initial biopsy samples
An integrated approach of particle swarm optimization and support vector machine for gene signature selection and cancer prediction
To improve cancer diagnosis and drug development, the classification of tumor types based on genomic information is important. As DNA micro array studies produce a large amount of data, expression data are highly redundant and noisy, and most genes are believed to be uninformative with respect to the studied classes. Only a fraction of genes may present distinct profiles for different classes of samples. Classification tools to deal with these issues are thus important. These tools should learn to robustly identify a subset of informative genes embedded in a large dataset that is contaminated with high dimensional noises. In this paper, an integrated approach of support vector machine (SVM) and particle swarm optimization (PSO) is proposed for this purpose. The proposed approach can simultaneously optimize the selection of feature subset and the classifier through a common solution coding mechanism. As an illustration, the proposed approach is applied to search the combinational gene signatures for predicting histologic response to chemotherapy of osteosarcoma patients. Cross validation results show that the proposed approach outperforms other existing methods in terms of classification accuracy. Further validation using an independent dataset shows misclassification of only one out of fourteen patient samples, suggesting that the selected gene signatures can reflect the chemoresistance in osteosarcoma
RasBhari: optimizing spaced seeds for database searching, read mapping and alignment-free sequence comparison
Many algorithms for sequence analysis rely on word matching or word
statistics. Often, these approaches can be improved if binary patterns
representing match and don't-care positions are used as a filter, such that
only those positions of words are considered that correspond to the match
positions of the patterns. The performance of these approaches, however,
depends on the underlying patterns. Herein, we show that the overlap complexity
of a pattern set that was introduced by Ilie and Ilie is closely related to the
variance of the number of matches between two evolutionarily related sequences
with respect to this pattern set. We propose a modified hill-climbing algorithm
to optimize pattern sets for database searching, read mapping and
alignment-free sequence comparison of nucleic-acid sequences; our
implementation of this algorithm is called rasbhari. Depending on the
application at hand, rasbhari can either minimize the overlap complexity of
pattern sets, maximize their sensitivity in database searching or minimize the
variance of the number of pattern-based matches in alignment-free sequence
comparison. We show that, for database searching, rasbhari generates pattern
sets with slightly higher sensitivity than existing approaches. In our Spaced
Words approach to alignment-free sequence comparison, pattern sets calculated
with rasbhari led to more accurate estimates of phylogenetic distances than the
randomly generated pattern sets that we previously used. Finally, we used
rasbhari to generate patterns for short read classification with CLARK-S. Here
too, the sensitivity of the results could be improved, compared to the default
patterns of the program. We integrated rasbhari into Spaced Words; the source
code of rasbhari is freely available at http://rasbhari.gobics.de
Combined optimization algorithms applied to pattern classification
Accurate classification by minimizing the error on test samples is the main
goal in pattern classification. Combinatorial optimization is a well-known
method for solving minimization problems, however, only a few examples of
classifiers axe described in the literature where combinatorial optimization is
used in pattern classification. Recently, there has been a growing interest
in combining classifiers and improving the consensus of results for a greater
accuracy. In the light of the "No Ree Lunch Theorems", we analyse the combination
of simulated annealing, a powerful combinatorial optimization method
that produces high quality results, with the classical perceptron algorithm.
This combination is called LSA machine. Our analysis aims at finding paradigms
for problem-dependent parameter settings that ensure high classifica,
tion results. Our computational experiments on a large number of benchmark
problems lead to results that either outperform or axe at least competitive to
results published in the literature. Apart from paxameter settings, our analysis
focuses on a difficult problem in computation theory, namely the network
complexity problem. The depth vs size problem of neural networks is one of
the hardest problems in theoretical computing, with very little progress over
the past decades. In order to investigate this problem, we introduce a new
recursive learning method for training hidden layers in constant depth circuits.
Our findings make contributions to a) the field of Machine Learning, as the
proposed method is applicable in training feedforward neural networks, and to
b) the field of circuit complexity by proposing an upper bound for the number
of hidden units sufficient to achieve a high classification rate. One of the major
findings of our research is that the size of the network can be bounded by
the input size of the problem and an approximate upper bound of 8 + ā2n/n
threshold gates as being sufficient for a small error rate, where n := log/SL
and SL is the training set
A cDNA Microarray Gene Expression Data Classifier for Clinical Diagnostics Based on Graph Theory
Despite great advances in discovering cancer molecular profiles, the proper application of microarray technology to routine clinical diagnostics is still a challenge. Current practices in the classification of microarrays' data show two main limitations: the reliability of the training data sets used to build the classifiers, and the classifiers' performances, especially when the sample to be classified does not belong to any of the available classes. In this case, state-of-the-art algorithms usually produce a high rate of false positives that, in real diagnostic applications, are unacceptable. To address this problem, this paper presents a new cDNA microarray data classification algorithm based on graph theory and is able to overcome most of the limitations of known classification methodologies. The classifier works by analyzing gene expression data organized in an innovative data structure based on graphs, where vertices correspond to genes and edges to gene expression relationships. To demonstrate the novelty of the proposed approach, the authors present an experimental performance comparison between the proposed classifier and several state-of-the-art classification algorithm
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