Enrique Fernández-Blanco

Random Forest classification based on star graph topological indices for antioxidant proteins.

Aging and life quality is an important research topic nowadays in areas such as life sciences, chemistry, pharmacology, etc. People live longer, and, thus, they want to spend that extra time with a better quality of life. At this regard, there exists a tiny subset of molecules in nature, named antioxidant proteins that may influence the aging process. However, testing every single protein in order to identify its properties is quite expensive and inefficient. For this reason, this work proposes a model, in which the primary structure of the protein is represented using complex network graphs that can be used to reduce the number of proteins to be tested for antioxidant biological activity. The graph obtained as a representation will help us describe the complex system by using topological indices. More specifically, in this work, Randićs Star Networks have been used as well as the associated indices, calculated with the S2SNet tool. In order to simulate the existing proportion of antioxidant proteins in nature, a dataset containing 1999 proteins, of which 324 are antioxidant proteins, was created. Using this data as input, Star Graph Topological Indices were calculated with the S2SNet tool. These indices were then used as input to several classification techniques. Among the techniques utilised, the Random Forest has shown the best performance, achieving a score of 94% correctly classified instances. Although the target class (antioxidant proteins) represents a tiny subset inside the dataset, the proposed model is able to achieve a percentage of 81.8% correctly classified instances for this class, with a precision of 81.3%.

Drug Discovery and Design for Complex Diseases through QSAR Computational Methods

There is a need for a study of the complex diseases due to their important impact on our society. One of the solutions involves the theoretical methods which are fast and efficient tools that can lead to the discovery of new active drugs specially designed for these diseases. The Quantitative Structure - Activity Relationship models (QSAR) and the complex network theory become important solutions for screening and designing efficient pharmaceuticals by coding the chemical information of the molecules into molecular descriptors. This review presents the most recent studies on drug discovery and design using QSAR of several complex diseases in the fields of Neurology, Cardiology and Oncology.

Artificial neuron–glia networks learning approach based on cooperative coevolution

Artificial Neuron-Glia Networks (ANGNs) are a novel bio-inspired machine learning approach. They extend classical Artificial Neural Networks (ANNs) by incorporating recent findings and suppositions about the way information is processed by neural and astrocytic networks in the most evolved living organisms. Although ANGNs are not a consolidated method, their performance against the traditional approach, i.e. without artificial astrocytes, was already demonstrated on classification problems. However, the corresponding learning algorithms developed so far strongly depends on a set of glial parameters which are manually tuned for each specific problem. As a consequence, previous experimental tests have to be done in order to determine an adequate set of values, making such manual parameter configuration time-consuming, error-prone, biased and problem dependent. Thus, in this paper, we propose a novel learning approach for ANGNs that fully automates the learning process, and gives the possibility of testing any kind of reasonable parameter configuration for each specific problem. This new learning algorithm, based on coevolutionary genetic algorithms, is able to properly learn all the ANGNs parameters. Its performance is tested on five classification problems achieving significantly better results than ANGN and competitive results with ANN approaches.

Naïve Bayes QSDR classification based on spiral-graph Shannon entropies for protein biomarkers in human colon cancer.

Fast cancer diagnosis represents a real necessity in applied medicine due to the importance of this disease. Thus, theoretical models can help as prediction tools. Graph theory representation is one option because it permits us to numerically describe any real system such as the protein macromolecules by transforming real properties into molecular graph topological indices. This study proposes a new classification model for proteins linked with human colon cancer by using spiral graph topological indices of protein amino acid sequences. The best quantitative structure-disease relationship model is based on eleven Shannon entropy indices. It was obtained with the Naïve Bayes method and shows excellent predictive ability (90.92%) for new proteins linked with this type of cancer. The statistical analysis confirms that this model allows diagnosing the absence of human colon cancer obtaining an area under receiver operating characteristic of 0.91. The methodology presented can be used for any type of sequential information such as any protein and nucleic acid sequence.

Automatic seizure detection based on star graph topological indices

The recognition of seizures is very important for the diagnosis of patients with epilepsy. The seizure is a process of rhythmic discharge in brain and occurs rarely and unpredictably. This behavior generates a need of an automatic detection of seizures by using the signals of long-term electroencephalographic (EEG) recordings. Due to the non-stationary character of EEG signals, the conventional methods of frequency analysis are not the best alternative to obtain good results in diagnostic purpose. The present work proposes a method of EEG signal analysis based on star graph topological indices (SGTIs) for the first time. The signal information, such as amplitude and time occurrence, is codified into invariant SGTIs which are the basis for the classification models that can discriminate the epileptic EEG records from the non-epileptic ones. The method with SGTIs and the simplest linear discriminant methods provide similar results to those previously published, which are based on the time-frequency analysis and artificial neural networks. Thus, this work proposes a simpler and faster alternative for automatic detection of seizures from the EEG recordings.

Classification of signals by means of Genetic Programming

This paper describes a new technique for signal classification by means of Genetic Programming (GP). The novelty of this technique is that no prior knowledge of the signals is needed to extract the features. Instead of it, GP is able to extract the most relevant features needed for classification. This technique has been applied for the solution of a well-known problem: the classification of EEG signals in epileptic and healthy patients. In this problem, signals obtained from EEG recordings must be correctly classified into their corresponding class. The aim is to show that the technique described here, with the automatic extraction of features, can return better results than the classical techniques based on manual extraction of features. For this purpose, a final comparison between the results obtained with this technique and other results found in the literature with the same database can be found. This comparison shows how this technique can improve the ones found.

A Genetic Algorithm for ANN Design, Training and Simplification

This paper proposes a new evolutionary method for generating ANNs. In this method, a simple real-number string is used to codify both architecture and weights of the networks. Therefore, a simple GA can be used to evolve ANNs. One of the most interesting features of the technique presented here is that the networks obtained have been optimised, and they have a low number of neurons and connections. This technique has been applied to solve one of the most used benchmark problems, and results show that this technique can obtain better results than other automatic ANN development techniques.

Classification of signaling proteins based on molecular star graph descriptors using Machine Learning models

Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein structure hinders the direct association of the signaling activity with the molecular structure. Therefore, the proposed solution involves the use of protein star graphs for the peptide sequence information encoding into specific topological indices calculated with S2SNet tool. The Quantitative Structure-Activity Relationship classification model obtained with Machine Learning techniques is able to predict new signaling peptides. The best classification model is the first signaling prediction model, which is based on eleven descriptors and it was obtained using the Support Vector Machines-Recursive Feature Elimination (SVM-RFE) technique with the Laplacian kernel (RFE-LAP) and an AUROC of 0.961. Testing a set of 3114 proteins of unknown function from the PDB database assessed the prediction performance of the model. Important signaling pathways are presented for three UniprotIDs (34 PDBs) with a signaling prediction greater than 98.0%.

A new signal classification technique by means of Genetic Algorithms and kNN

Signal classification is based on the extraction of several features that will be used as inputs of a classifier. The selection of these features is one of the most crucial parts, because they will design the search space, and, therefore, will determine the difficulty of the classification. Usually, these features are selected by using some prior knowledge about the signals, but there is no method that can determine that they are the most appropriate to solve the problem. This paper proposes a new technique for signal classification in which a Genetic Algorithm is used in order to automatically select the best feature set for signal classification, in combination with a kNN as classifier system. This method was used in a well known problem and its results improve those already published in other works.

Using genetic algorithms for automatic recurrent ANN development: an application to EEG signal classification

ANNs are one of the most successful learning systems. For this reason, many techniques have been published that allow the obtaining of feed-forward networks. However, few works describe techniques for developing recurrent networks. This work uses a genetic algorithm for automatic recurrent ANN development. This system has been applied to solve a well-known problem: classification of EEG signals from epileptic patients. Results show the high performance of this system, and its ability to develop simple networks, with a low number of neurons and connections.