Julian Dorado

Automatic epileptic seizure detection in EEGs based on line length feature and artificial neural networks

About 1% of the people in the world suffer from epilepsy. The main characteristic of epilepsy is the recurrent seizures. Careful analysis of the electroencephalogram (EEG) recordings can provide valuable information for understanding the mechanisms behind epileptic disorders. Since epileptic seizures occur irregularly and unpredictably, automatic seizure detection in EEG recordings is highly required. Wavelet transform (WT) is an effective analysis tool for non-stationary signals, such as EEGs. The line length feature reflects the waveform dimensionality changes and is a measure sensitive to variation of the signal amplitude and frequency. This paper presents a novel method for automatic epileptic seizure detection, which uses line length features based on wavelet transform multiresolution decomposition and combines with an artificial neural network (ANN) to classify the EEG signals regarding the existence of seizure or not. To the knowledge of the authors, there exists no similar work in the literature. A famous public dataset was used to evaluate the proposed method. The high accuracy obtained for three different classification problems testified the great success of the method.

Automatic feature extraction using genetic programming: An application to epileptic EEG classification

This paper applies genetic programming (GP) to perform automatic feature extraction from original feature database with the aim of improving the discriminatory performance of a classifier and reducing the input feature dimensionality at the same time. The tree structure of GP naturally represents the features, and a new function generated in this work automatically decides the number of the features extracted. In experiments on two common epileptic EEG detection problems, the classification accuracy on the GP-based features is significant higher than on the original features. Simultaneously, the dimension of the input features for the classifier is much smaller than that of the original features.

Artificial neural networks in real-life applications

Part I: Biological Modelization, Part II: Time Series Forecasting, Part III: Data mining, Part IV: Civil Engineering, Part V: Financial Analysis, Part VI: Other applications.

Prediction and modeling of the rainfall-runoff transformation of a typical urban basin using ann and gp

This paper proposes an application of Genetic Programming (GP) and Artificial Neural Networks (ANN) in hydrology, showing how these two techniques can work together to solve a problem, namely for modeling the effect of rain on the runoff flow in a typical urban basin. The ultimate goal of this research is to design a real-time alarm system to warn of floods or subsidence in various types of urban basins. Results look promising and appear to offer some improvement for analyzing river basin systems over stochastic methods such as unitary hydrographs.

Trypano-PPI: a web server for prediction of unique targets in trypanosome proteome by using electrostatic parameters of protein-protein interactions.

Trypanosoma brucei causes African trypanosomiasis in humans (HAT or African sleeping sickness) and Nagana in cattle. The disease threatens over 60 million people and uncounted numbers of cattle in 36 countries of sub-Saharan Africa and has a devastating impact on human health and the economy. On the other hand, Trypanosoma cruzi is responsible in South America for Chagas disease, which can cause acute illness and death, especially in young children. In this context, the discovery of novel drug targets in Trypanosome proteome is a major focus for the scientific community. Recently, many researchers have spent important efforts on the study of protein-protein interactions (PPIs) in pathogen Trypanosome species concluding that the low sequence identities between some parasite proteins and their human host render these PPIs as highly promising drug targets. To the best of our knowledge, there are no general models to predict Unique PPIs in Trypanosome (TPPIs). On the other hand, the 3D structure of an increasing number of Trypanosome proteins is reported in databases. In this regard, the introduction of a new model to predict TPPIs from the 3D structure of proteins involved in PPI is very important. For this purpose, we introduced new protein-protein complex invariants based on the Markov average electrostatic potential xi(k)(R(i)) for amino acids located in different regions (R(i)) of i-th protein and placed at a distance k one from each other. We calculated more than 30 different types of parameters for 7866 pairs of proteins (1023 TPPIs and 6823 non-TPPIs) from more than 20 organisms, including parasites and human or cattle hosts. We found a very simple linear model that predicts above 90% of TPPIs and non-TPPIs both in training and independent test subsets using only two parameters. The parameters were (d)xi(k)(s) = |xi(k)(s(1)) - xi(k)(s(2))|, the absolute difference between the xi(k)(s(i)) values on the surface of the two proteins of the pairs. We also tested nonlinear ANN models for comparison purposes but the linear model gives the best results. We implemented this predictor in the web server named TrypanoPPI freely available to public at http://miaja.tic.udc.es/Bio-AIMS/TrypanoPPI.php. This is the first model that predicts how unique a protein-protein complex in Trypanosome proteome is with respect to other parasites and hosts, opening new opportunities for antitrypanosome drug target discovery.

A new approach to the extraction of ANN rules and to their generalization capacity through GP

Various techniques for the extraction of ANN rules have been used, but most of them have focused on certain types of networks and their training. There are very few methods that deal with ANN rule extraction as systems that are independent of their architecture, training, and internal distribution of weights, connections, and activation functions. This article proposes a methodology for the extraction of ANN rules, regardless of their architecture, and based on genetic programming. The strategy is based on the previous algorithm and aims at achieving the generalization capacity that is characteristic of ANNs by means of symbolic rules that are understandable to human beings.

Generalized lattice graphs for 2D-visualization of biological information

Abstract Several graph representations have been introduced for different data in theoretical biology. For instance, complex networks based on Graph theory are used to represent the structure and/or dynamics of different large biological systems such as protein–protein interaction networks. In addition, Randic, Liao, Nandy, Basak, and many others developed some special types of graph-based representations. This special type of graph includes geometrical constrains to node positioning in space and adopts final geometrical shapes that resemble lattice-like patterns. Lattice networks have been used to visually depict DNA and protein sequences but they are very flexible. However, despite the proved efficacy of new lattice-like graph/networks to represent diverse systems, most works focus on only one specific type of biological data. This work proposes a generalized type of lattice and illustrates how to use it in order to represent and compare biological data from different sources. We exemplify the following cases: protein sequence; mass spectra (MS) of protein peptide mass fingerprints (PMF); molecular dynamic trajectory (MDTs) from structural studies; mRNA microarray data; single nucleotide polymorphisms (SNPs); 1D or 2D-Electrophoresis study of protein polymorphisms and protein-research patent and/or copyright information. We used data available from public sources for some examples but for other, we used experimental results reported herein for the first time. This work may break new ground for the application of Graph theory in theoretical biology and other areas of biomedical sciences.

Complex Network Spectral Moments for ATCUN Motif DNA Cleavage: First Predictive Study on Proteins of Human Pathogen Parasites

The development of methods that can predict the metal-mediated biological activity based only on the 3D structure of metal-unbound proteins has become a goal of major importance. This work is dedicated to the amino terminal Cu(II)- and Ni(II)-binding (ATCUN) motifs that participate in the DNA cleavage and have antitumor activity. We have calculated herein, for the first time, the 3D electrostatic spectral moments for 415 different proteins, including 133 potential ATCUN antitumor proteins. Using these parameters as input for Linear Discriminant Analysis, we have found a model that discriminates between ATCUN-DNA cleavage proteins and nonactive proteins with 91.32% Accuracy (379 out of 415 of proteins including both training and external validation series). Finally, the model has predicted for the first time the DNA cleavage function of proteins from the pathogen parasites. We have predicted possible ATCUN-like proteins with a probability higher than 99% in nine parasite families such as Trypanosoma, Plasmodium, Leishmania, or Toxoplasma. The distribution by biological function of the ATCUN proteins predicted has been the following: oxidoreductases 70.5%, signaling proteins 62.5%, lyases 58.2%, membrane proteins 45.5%, ligases 44.4%, hydrolases 41.3%, transferases 39.2%, cell adhesion proteins 34.5%, metal binders 33.5%, translation proteins 25.0%, transporters 16.7%, structural proteins 9.1%, and isomerases 8.2%. The model is implemented at http://miaja.tic.udc.es/Bio-AIMS/ATCUNPred.php.

An artificial neural network improves the non-invasive diagnosis of significant fibrosis in HIV/HCV coinfected patients

OBJECTIVE To develop an artificial neural network to predict significant fibrosis (F≥2) (ANN-SF) in HIV/Hepatitis C (HCV) coinfected patients using clinical data derived from peripheral blood. METHODS Patients were randomly divided into an estimation group (217 cases) used to generate the ANN and a test group (145 cases) used to confirm its power to predict F≥2. Liver fibrosis was estimated according to the METAVIR score. RESULTS The values of the area under the receiver operating characteristic curve (AUC-ROC) of the ANN-SF were 0.868 in the estimation set and 0.846 in the test set. In the estimation set, with a cut-off value of <0.35 to predict the absence of F≥2, the sensitivity (Se), specificity (Sp), and positive (PPV) and negative predictive values (NPV) were 94.1%, 41.8%, 66.3% and 85.4% respectively. Furthermore, with a cut-off value of >0.75 to predict the presence of F≥2, the ANN-SF provided Se, Sp, PPV and NPV of 53.8%, 94.9%, 92.8% and 62.8% respectively. In the test set, with a cut-off value of <0.35 to predict the absence of F≥2, the Se, Sp, PPV and NPV were 91.8%, 51.7%, 72.9% and 81.6% respectively. Furthermore, with a cut-off value of >0.75 to predict the presence of F≥2, the ANN-SF provided Se, Sp, PPV and NPV of 43.5%, 96.7%, 94.9% and 54.7% respectively. CONCLUSION The ANN-SF accurately predicted significant fibrosis and outperformed other simple non-invasive indices for HIV/HCV coinfected patients. Our data suggest that ANN may be a helpful tool for guiding therapeutic decisions in clinical practice concerning HIV/HCV coinfection.

Optical Fish Trajectory Measurement in Fishways through Computer Vision and Artificial Neural Networks

Vertical slot fishways are hydraulic structures that allow the upstream migration of fish through obstructions in rivers. The appropriate design of a vertical slot fishway depends on the interplay between hydraulic and biological variables because the hydrodynamic properties of the fishway must match the requirements of the fish species for which it is intended. One of the primary difficulties associated with studies of real fish behavior in fishway models is that the existing mechanisms to measure the behavior of the fish in these assays, such as direct observation or placement of sensors on the specimens, are impractical or unduly affect the animal behavior. This paper proposes a new procedure for measuring the behavior of the fish. The proposed technique uses artificial neural networks and computer vision techniques to analyze images obtained from the assays by means of a camera system designed for fishway integration. It is expected that this technique will provide detailed information about the fish behavior, and it will help to improve fish passage devices, which is currently a subject of interest in the area of civil engineering. A series of assays has been performed to validate this new approach in a full-scale fishway model with living fish. We have obtained very promising results that allow accurate reconstruction of the movements of the fish within the fishway.