Seferina Mavroudi

A PROBABILISTIC SYMMETRIC ENCRYPTION SCHEME FOR VERY FAST SECURE COMMUNICATION BASED ON CHAOTIC SYSTEMS OF DIFFERENCE EQUATIONS

We present a new probabilistic symmetric key encryption scheme based on the chaotic dynamics of properly designed chaotic systems. This technique exploits the concept of virtual attractors, which are not real attractors of the underlying chaotic dynamics but are created and maintained artificially. Each virtual attractor represents a symbol of the alphabet used to encode messages. The state space is partitioned over the virtual attractors creating clusters of states. The enciphering process randomizes over the set of states mapped to a virtual attractor in order to construct the ciphertext for the transmited symbol. The receiver can reconstruct perfectly this virtual state space, given the possession of the same chaotic system of difference equations with parameters tuned perfectly to those of the transmitter. Therefore, from the ciphertext chunk corresponding to a state, the virtual attractor can be derived from the details of the virtual state space. The knowledge of the virtual attractor leads to the recovery of the transmitted symbol. We demonstrate that the new algorithm is secure, reliable and very fast. It uses discrete time chaotic recurrent systems and is simple, flexible and modular. These systems can be constructed easily dynamically from an alphanumeric encryption key. The cryptographic security of the algorithm is evaluated with combinatorial arguments.

Gene expression data analysis with a dynamically extended self-organized map that exploits class information

MOTIVATION Currently the most popular approach to analyze genome-wide expression data is clustering. One of the major drawbacks of most of the existing clustering methods is that the number of clusters has to be specified a priori. Furthermore, by using pure unsupervised algorithms prior biological knowledge is totally ignored Moreover, most current tools lack an effective framework for tight integration of unsupervised and supervised learning for the analysis of high-dimensional expression data and only very few multi-class supervised approaches are designed with the provision for effectively utilizing multiple functional class labeling. RESULTS The paper adapts a novel Self-Organizing map called supervised Network Self-Organized Map (sNet-SOM) to the peculiarities of multi-labeled gene expression data. The sNet-SOM determines adaptively the number of clusters with a dynamic extension process. This process is driven by an inhomogeneous measure that tries to balance unsupervised, supervised and model complexity criteria. Nodes within a rectangular grid are grown at the boundary nodes, weights rippled from the internal nodes towards the outer nodes of the grid, and whole columns inserted within the map The appropriate level of expansion is determined automatically. Multiple sNet-SOM models are constructed dynamically each for a different unsupervised/supervised balance and model selection criteria are used to select the one optimum one. The results indicate that sNet-SOM yields competitive performance to other recently proposed approaches for supervised classification at a significantly reduced computational cost and it provides extensive exploratory analysis potentiality within the analysis framework. Furthermore, it explores simple design decisions that are easier to comprehend and computationally efficient.

YamiPred: A Novel Evolutionary Method for Predicting Pre-miRNAs and Selecting Relevant Features

MicroRNAs (miRNAs) are small non-coding RNAs, which play a significant role in gene regulation. Predicting miRNA genes is a challenging bioinformatics problem and existing experimental and computational methods fail to deal with it effectively. We developed YamiPred, an embedded classification method that combines the efficiency and robustness of support vector machines (SVM) with genetic algorithms (GA) for feature selection and parameters optimization. YamiPred was tested in a new and realistic human dataset and was compared with state-of-the-art computational intelligence approaches and the prevalent SVM-based tools for miRNA prediction. Experimental results indicate that YamiPred outperforms existing approaches in terms of accuracy and of geometric mean of sensitivity and specificity. The embedded feature selection component selects a compact feature subset that contributes to the performance optimization. Further experimentation with this minimal feature subset has achieved very high classification performance and revealed the minimum number of samples required for developing a robust predictor. YamiPred also confirmed the important role of commonly used features such as entropy and enthalpy, and uncovered the significance of newly introduced features, such as %A-U aggregate nucleotide frequency and positional entropy. The best model trained on human data has successfully predicted pre-miRNAs to other organisms including the category of viruses.

Scientific Scripting for the Java Platform with jLab

By modifying Groovy with Matlab-like constructs, the authors created a compiled mathematical scripting language called GroovySci for the jLab platform. The resulting code generation enhancements could ultimately extend Javas potential for scientific computing.

Exploiting java scientific libraries with the scala language within the scalalab environment

Since Java is one of the most popular languages in the academic and research community a lot of robust and effective scientific libraries have been developed. However, the utilisation of these libraries is very awkward especially for the average scientist that does not expertise in software development. The study presents the framework that has constructed for the utilisation of Java scientific libraries within the ScalaLab environment. The flexibility and extensibility of the Scala language allows the implementation of simple, coherent and efficient Matlab-like interfaces to those libraries. Moreover, other specialised Java libraries can be exploited much more easily and productively from within ScalaLab with the toolbox import mechanism that this work describes. Additionally, the system offers facilities such as on-line help, code completion, graphical control of the class-path and a specialised text editor with code colouring facilities that greatly facilitate the development of scientific software.

ScalaLab: An Effective Scala-Based Scientific Programming Environment for Java

Scala offers many benefits for constructing scientific programming environments. Extending Scala with Matlab-like constructs enabled the creation of ScalaSci, a compiled mathematical scripting framework, and ScalaLab, an efficient integrated scientific programming environment. ScalaLab offers an interesting open source alternative to commercial packages, especially for the scientific community familiar with Java.

A Hybrid Support Vector Fuzzy Inference System for the Classification of Leakage Current Waveforms Portraying Discharges

Abstract Several techniques have been applied on leakage current waveforms in order to extract information regarding electrical activity on high-voltage insulators. However, a fully representative value is yet to be defined. In this article, a hybrid support vector fuzzy inference system is introduced as a classification tool. The system incorporates fuzzy logic, genetic algorithms, and support vector machines. Apart from the classification accuracy achieved, the system also produces a set of fuzzy rules under which the classification is made, allowing a further insight of the process. A comparison is made to other classification tools previously applied on the same data set.

The Supervised Network Self-Organizing Map for Classification of Large Data Sets

Complex application domains involve difficult pattern classification problems. The state space of these problems consists of regions that lie near class separation boundaries and require the construction of complex discriminants while for the rest regions the classification task is significantly simpler. The motivation for developing the Supervised Network Self-Organizing Map (SNet-SOM) model is to exploit this fact for designing computationally effective solutions. Specifically, the SNet-SOM utilizes unsupervised learning for classifying at the simple regions and supervised learning for the difficult ones in a two stage learning process. The unsupervised learning approach is based on the Self-Organizing Map (SOM) of Kohonen. The basic SOM is modified with a dynamic node insertion/deletion process controlled with an entropy based criterion that allows an adaptive extension of the SOM. This extension proceeds until the total number of training patterns that are mapped to neurons with high entropy (and therefore with ambiguous classification) reduces to a size manageable numerically with a capable supervised model. The second learning phase (the supervised training) has the objective of constructing better decision boundaries at the ambiguous regions. At this phase, a special supervised network is trained for the computationally reduced task of performing the classification at the ambiguous regions only. The performance of the SNet-SOM has been evaluated on both synthetic data and on an ischemia detection application with data extracted from the European ST-T database. In all cases, the utilization of SNet-SOM with supervised learning based on both Radial Basis Functions and Support Vector Machines has improved the results significantly related to those obtained with the unsupervised SOM and has enhanced the scalability of the supervised learning schemes. The highly disciplined design of the generalization performance of the Support Vector Machine allows to design the proper model for the particular training set.

Predicting protein complexes from weighted protein-protein interaction graphs with a novel unsupervised methodology

OBJECTIVE Proteins are considered to be the most important individual components of biological systems and they combine to form physical protein complexes which are responsible for certain molecular functions. Despite the large availability of protein-protein interaction (PPI) information, not much information is available about protein complexes. Experimental methods are limited in terms of time, efficiency, cost and performance constraints. Existing computational methods have provided encouraging preliminary results, but they phase certain disadvantages as they require parameter tuning, some of them cannot handle weighted PPI data and others do not allow a protein to participate in more than one protein complex. In the present paper, we propose a new fully unsupervised methodology for predicting protein complexes from weighted PPI graphs. METHODS AND MATERIALS The proposed methodology is called evolutionary enhanced Markov clustering (EE-MC) and it is a hybrid combination of an adaptive evolutionary algorithm and a state-of-the-art clustering algorithm named enhanced Markov clustering. EE-MC was compared with state-of-the-art methodologies when applied to datasets from the human and the yeast Saccharomyces cerevisiae organisms. RESULTS Using public available datasets, EE-MC outperformed existing methodologies (in some datasets the separation metric was increased by 10-20%). Moreover, when applied to new human datasets its performance was encouraging in the prediction of protein complexes which consist of proteins with high functional similarity. In specific, 5737 protein complexes were predicted and 72.58% of them are enriched for at least one gene ontology (GO) function term. CONCLUSIONS EE-MC is by design able to overcome intrinsic limitations of existing methodologies such as their inability to handle weighted PPI networks, their constraint to assign every protein in exactly one cluster and the difficulties they face concerning the parameter tuning. This fact was experimentally validated and moreover, new potentially true human protein complexes were suggested as candidates for further validation using experimental techniques.

EnsembleGASVR: a novel ensemble method for classifying missense single nucleotide polymorphisms

MOTIVATION Single nucleotide polymorphisms (SNPs) are considered the most frequently occurring DNA sequence variations. Several computational methods have been proposed for the classification of missense SNPs to neutral and disease associated. However, existing computational approaches fail to select relevant features by choosing them arbitrarily without sufficient documentation. Moreover, they are limited to the problem of missing values, imbalance between the learning datasets and most of them do not support their predictions with confidence scores. RESULTS To overcome these limitations, a novel ensemble computational methodology is proposed. EnsembleGASVR facilitates a two-step algorithm, which in its first step applies a novel evolutionary embedded algorithm to locate close to optimal Support Vector Regression models. In its second step, these models are combined to extract a universal predictor, which is less prone to overfitting issues, systematizes the rebalancing of the learning sets and uses an internal approach for solving the missing values problem without loss of information. Confidence scores support all the predictions and the model becomes tunable by modifying the classification thresholds. An extensive study was performed for collecting the most relevant features for the problem of classifying SNPs, and a superset of 88 features was constructed. Experimental results show that the proposed framework outperforms well-known algorithms in terms of classification performance in the examined datasets. Finally, the proposed algorithmic framework was able to uncover the significant role of certain features such as the solvent accessibility feature, and the top-scored predictions were further validated by linking them with disease phenotypes. AVAILABILITY AND IMPLEMENTATION Datasets and codes are freely available on the Web at http://prlab.ceid.upatras.gr/EnsembleGASVR/dataset-codes.zip. All the required information about the article is available through http://prlab.ceid.upatras.gr/EnsembleGASVR/site.html.