Data visualization with simultaneous feature selection

Data visualization algorithms and feature selection techniques are both widely used in bioinformatics but as distinct analytical approaches. Until now there has been no method of measuring feature saliency while training a data visualization model. We derive a generative topographic mapping (GTM) based data visualization approach which estimates feature saliency simultaneously with the training of the visualization model. The approach not only provides a better projection by modeling irrelevant features with a separate noise model but also gives feature saliency values which help the user to assess the significance of each feature. We compare the quality of projection obtained using the new approach with the projections from traditional GTM and self-organizing maps (SOM) algorithms. The results obtained on a synthetic and a real-life chemoinformatics dataset demonstrate that the proposed approach successfully identifies feature significance and provides coherent (compact) projections. © 2006 IEEE.

Hyperspectral Mineral Identification using SVM and SOM

Remote sensing techniques involving hyperspectral imagery have applications in a number of sciences that study some aspects of the surface of the planet. The analysis of hyperspectral images is complex because of the large amount of information involved and the noise within that data. Investigating images with regard to identify minerals, rocks, vegetation and other materials is an application of hyperspectral remote sensing in the earth sciences. This thesis evaluates the performance of two classification and clustering techniques on hyperspectral images for mineral identification. Support Vector Machines (SVM) and Self-Organizing Maps (SOM) are applied as classification and clustering techniques, respectively. Principal Component Analysis (PCA) is used to prepare the data to be analyzed. The purpose of using PCA is to reduce the amount of data that needs to be processed by identifying the most important components within the data. A well-studied dataset from Cuprite, Nevada and a dataset of more complex data from Baffin Island were used to assess the performance of these techniques. The main goal of this research study is to evaluate the advantage of training a classifier based on a small amount of data compared to an unsupervised method. Determining the effect of feature extraction on the accuracy of the clustering and classification method is another goal of this research. This thesis concludes that using PCA increases the learning accuracy, and especially so in classification. SVM classifies Cuprite data with a high precision and the SOM challenges SVM on datasets with high level of noise (like Baffin Island).

An Optimum-Path Forest framework for intrusion detection in computer networks

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Timed mind maps using MINDMANAGER & MS-PROJECT for educational innovation

The adaptation to the European Higher Education Area (EHEA) is becoming a great challenge for the University Community, especially for its teaching and research staff, which is involved actively in the teaching-learning process. It is also inducing a paradigm change for lecturers and students. Among the methodologies used for processes of teaching innovation, system thinking plays an important role when working mainly with mind maps, and is focused to highlighting the essence of the knowledge, allowing its visual representation. In this paper, a method for using these mind maps for organizing a particular subject is explained. This organization is completed with the definition of duration, precedence relationships and resources for each of these activities, as well as with their corresponding monitoring. Mind maps are generated by means of the MINDMANAGER package whilst Ms-PROJECT is used for establishing tasks relationships, durations, resources, and monitoring. Summarizing, a procedure and the necessary set of applications for self organizing and managing (timed) scheduled teaching tasks has been described in this paper.

Timed mind maps using mindmanager & msproject for educational innovation

The adaptation to the European Higher Education Area (EHEA) is becoming a great challenge for the University Community, especially for its teaching and research staff, which is involved actively in the teaching-learning process. It is also inducing a paradigm change for lecturers and students. Among the methodologies used for processes of teaching innovation, system thinking plays an important role when working mainly with mind maps, and is focused to highlighting the essence of the knowledge, allowing its visual representation. In this paper, a method for using these mind maps for organizing a particular subject is explained. This organization is completed with the definition of duration, precedence relationships and resources for each of these activities, as well as with their corresponding monitoring. Mind maps are generated by means of the MINDMANAGER package whilst Ms-PROJECT is used for establishing tasks relationships, durations, resources, and monitoring. Summarizing, a procedure and the necessary set of applications for self organizing and managing (timed) scheduled teaching tasks has been described in this paper

Knowledge-based analysis of microarray gene expression data by using support vector machines

We introduce a method of functionally classifying genes by using gene expression data from DNA microarray hybridization experiments. The method is based on the theory of support vector machines (SVMs). SVMs are considered a supervised computer learning method because they exploit prior knowledge of gene function to identify unknown genes of similar function from expression data. SVMs avoid several problems associated with unsupervised clustering methods, such as hierarchical clustering and self-organizing maps. SVMs have many mathematical features that make them attractive for gene expression analysis, including their flexibility in choosing a similarity function, sparseness of solution when dealing with large data sets, the ability to handle large feature spaces, and the ability to identify outliers. We test several SVMs that use different similarity metrics, as well as some other supervised learning methods, and find that the SVMs best identify sets of genes with a common function using expression data. Finally, we use SVMs to predict functional roles for uncharacterized yeast ORFs based on their expression data.

Representation of 2D objects with a topology preserving network

Comunicación presentada en el 2nd International Workshop on Pattern Recognition in Information Systems, Alicante, April, 2002.

Growing Neural Gas approach for obtaining homogeneous maps by restricting the insertion of new nodes

The Growing Neural Gas model is used widely in artificial neural networks. However, its application is limited in some contexts by the proliferation of nodes in dense areas of the input space. In this study, we introduce some modifications to address this problem by imposing three restrictions on the insertion of new nodes. Each restriction aims to maintain the homogeneous values of selected criteria. One criterion is related to the square error of classification and an alternative approach is proposed for avoiding additional computational costs. Three parameters are added that allow the regulation of the restriction criteria. The resulting algorithm allows models to be obtained that suit specific needs by specifying meaningful parameters.

A connectionist computational method for face recognition

In this work, a modified version of the elastic bunch graph matching (EBGM) algorithm for face recognition is introduced. First, faces are detected by using a fuzzy skin detector based on the RGB color space. Then, the fiducial points for the facial graph are extracted automatically by adjusting a grid of points to the result of an edge detector. After that, the position of the nodes, their relation with their neighbors and their Gabor jets are calculated in order to obtain the feature vector defining each face. A self-organizing map (SOM) framework is shown afterwards. Thus, the calculation of the winning neuron and the recognition process are performed by using a similarity function that takes into account both the geometric and texture information of the facial graph. The set of experiments carried out for our SOM-EBGM method shows the accuracy of our proposal when compared with other state-of the-art methods.

Magnification factors for the SOM and GTM algorithms

Magnification factors specify the extent to which the area of a small patch of the latent (or `feature') space of a topographic mapping is magnified on projection to the data space, and are of considerable interest in both neuro-biological and data analysis contexts. Previous attempts to consider magnification factors for the self-organizing map (SOM) algorithm have been hindered because the mapping is only defined at discrete points (given by the reference vectors). In this paper we consider the batch version of SOM, for which a continuous mapping can be defined, as well as the Generative Topographic Mapping (GTM) algorithm of Bishop et al. (1997) which has been introduced as a probabilistic formulation of the SOM. We show how the techniques of differential geometry can be used to determine magnification factors as continuous functions of the latent space coordinates. The results are illustrated here using a problem involving the identification of crab species from morphological data.

Neural Networks: A Diagnostic Tool for Gastric Electrical Uncoupling?

Neural Networks have been successfully employed in different biomedical settings. They have been useful for feature extractions from images and biomedical data in a variety of diagnostic applications. In this paper, they are applied as a diagnostic tool for classifying different levels of gastric electrical uncoupling in controlled acute experiments on dogs. Data was collected from 16 dogs using six bipolar electrodes inserted into the serosa of the antral wall. Each dog underwent three recordings under different conditions: (1) basal state, (2) mild surgically-induced uncoupling, and (3) severe surgically-induced uncoupling. For each condition half-hour recordings were made. The neural network was implemented according to the Learning Vector Quantization model. This is a supervised learning model of the Kohonen Self-Organizing Maps. Majority of the recordings collected from the dogs were used for network training. Remaining recordings served as a testing tool to examine the validity of the training procedure. Approximately 90% of the dogs from the neural network training set were classified properly. However, only 31% of the dogs not included in the training process were accurately diagnosed. The poor neural-network based diagnosis of recordings that did not participate in the training process might have been caused by inappropriate representation of input data. Previous research has suggested characterizing signals according to certain features of the recorded data. This method, if employed, would reduce the noise and possibly improve the diagnostic abilities of the neural network.

Self-adaptive probabilistic roadmap generation for intelligent virtual agents

Agents inhabiting large scale environments are faced with the problem of generating maps by which they can navigate. One solution to this problem is to use probabilistic roadmaps which rely on selecting and connecting a set of points that describe the interconnectivity of free space. However, the time required to generate these maps can be prohibitive, and agents do not typically know the environment in advance. In this paper we show that the optimal combination of different point selection methods used to create the map is dependent on the environment, no point selection method dominates. This motivates a novel self-adaptive approach for an agent to combine several point selection methods. The success rate of our approach is comparable to the state of the art and the generation cost is substantially reduced. Self-adaptation therefore enables a more efficient use of the agent's resources. Results are presented for both a set of archetypal scenarios and large scale virtual environments based in Second Life, representing real locations in London.

Network construction and graph theoretical analysis of functional language networks in pediatric epilepsy

This dissertation introduces a new approach for assessing the effects of pediatric epilepsy on the language connectome. Two novel data-driven network construction approaches are presented. These methods rely on connecting different brain regions using either extent or intensity of language related activations as identified by independent component analysis of fMRI data. An auditory description decision task (ADDT) paradigm was used to activate the language network for 29 patients and 30 controls recruited from three major pediatric hospitals. Empirical evaluations illustrated that pediatric epilepsy can cause, or is associated with, a network efficiency reduction. Patients showed a propensity to inefficiently employ the whole brain network to perform the ADDT language task; on the contrary, controls seemed to efficiently use smaller segregated network components to achieve the same task. To explain the causes of the decreased efficiency, graph theoretical analysis was carried out. The analysis revealed no substantial global network feature differences between the patient and control groups. It also showed that for both subject groups the language network exhibited small-world characteristics; however, the patient's extent of activation network showed a tendency towards more random networks. It was also shown that the intensity of activation network displayed ipsilateral hub reorganization on the local level. The left hemispheric hubs displayed greater centrality values for patients, whereas the right hemispheric hubs displayed greater centrality values for controls. This hub hemispheric disparity was not correlated with a right atypical language laterality found in six patients. Finally it was shown that a multi-level unsupervised clustering scheme based on self-organizing maps, a type of artificial neural network, and k-means was able to fairly and blindly separate the subjects into their respective patient or control groups. The clustering was initiated using the local nodal centrality measurements only. Compared to the extent of activation network, the intensity of activation network clustering demonstrated better precision. This outcome supports the assertion that the local centrality differences presented by the intensity of activation network can be associated with focal epilepsy.^

The influence of interhemispheric connections on ongoing and evoked orientation preference maps and spiking activity in the cat primary visual cortex

In the primary visual cortex, neurons with similar physiological features are clustered together in columns extending through all six cortical layers. These columns form modular orientation preference maps. Long-range lateral fibers are associated to the structure of orientation maps since they do not connect columns randomly; they rather cluster in regular intervals and interconnect predominantly columns of neurons responding to similar stimulus features. Single orientation preference maps – the joint activation of domains preferring the same orientation - were observed to emerge spontaneously and it was speculated whether this structured ongoing activation could be caused by the underlying patchy lateral connectivity. Since long-range lateral connections share many features, i.e. clustering, orientation selectivity, with visual inter-hemispheric connections (VIC) through the corpus callosum we used the latter as a model for long-range lateral connectivity. In order to address the question of how the lateral connectivity contributes to spontaneously generated maps of one hemisphere we investigated how these maps react to the deactivation of VICs originating from the contralateral hemisphere. To this end, we performed experiments in eight adult cats. We recorded voltage-sensitive dye (VSD) imaging and electrophysiological spiking activity in one brain hemisphere while reversible deactivating the other hemisphere with a cooling technique. In order to compare ongoing activity with evoked activity patterns we first presented oriented gratings as visual stimuli. Gratings had 8 different orientations distributed equally between 0º and 180º. VSD imaged frames obtained during ongoing activity conditions were then compared to the averaged evoked single orientation maps in three different states: baseline, cooling and recovery. Kohonen self-organizing maps were also used as a means of analysis without prior assumption (like the averaged single condition maps) on ongoing activity. We also evaluated if cooling had a differential effect on evoked and ongoing spiking activity of single units. We found that deactivating VICs caused no spatial disruption on the structure of either evoked or ongoing activity maps. The frequency with which a cardinally preferring (0º or 90º) map would emerge, however, decreased significantly for ongoing but not for evoked activity. The same result was found by training self-organizing maps with recorded data as input. Spiking activity of cardinally preferring units also decreased significantly for ongoing when compared to evoked activity. Based on our results we came to the following conclusions: 1) VICs are not a determinant factor of ongoing map structure. Maps continued to be spontaneously generated with the same quality, probably by a combination of ongoing activity from local recurrent connections, thalamocortical loop and feedback connections. 2) VICs account for a cardinal bias in the temporal sequence of ongoing activity patterns, i.e. deactivating VIC decreases the probability of cardinal maps to emerge spontaneously. 3) Inter- and intrahemispheric long-range connections might serve as a grid preparing primary visual cortex for likely junctions in a larger visual environment encompassing the two hemifields.

The influence of interhemispheric connections on ongoing and evoked orientation preference maps and spiking activity in the cat primary visual cortex

In the primary visual cortex, neurons with similar physiological features are clustered together in columns extending through all six cortical layers. These columns form modular orientation preference maps. Long-range lateral fibers are associated to the structure of orientation maps since they do not connect columns randomly; they rather cluster in regular intervals and interconnect predominantly columns of neurons responding to similar stimulus features. Single orientation preference maps – the joint activation of domains preferring the same orientation - were observed to emerge spontaneously and it was speculated whether this structured ongoing activation could be caused by the underlying patchy lateral connectivity. Since long-range lateral connections share many features, i.e. clustering, orientation selectivity, with visual inter-hemispheric connections (VIC) through the corpus callosum we used the latter as a model for long-range lateral connectivity. In order to address the question of how the lateral connectivity contributes to spontaneously generated maps of one hemisphere we investigated how these maps react to the deactivation of VICs originating from the contralateral hemisphere. To this end, we performed experiments in eight adult cats. We recorded voltage-sensitive dye (VSD) imaging and electrophysiological spiking activity in one brain hemisphere while reversible deactivating the other hemisphere with a cooling technique. In order to compare ongoing activity with evoked activity patterns we first presented oriented gratings as visual stimuli. Gratings had 8 different orientations distributed equally between 0º and 180º. VSD imaged frames obtained during ongoing activity conditions were then compared to the averaged evoked single orientation maps in three different states: baseline, cooling and recovery. Kohonen self-organizing maps were also used as a means of analysis without prior assumption (like the averaged single condition maps) on ongoing activity. We also evaluated if cooling had a differential effect on evoked and ongoing spiking activity of single units. We found that deactivating VICs caused no spatial disruption on the structure of either evoked or ongoing activity maps. The frequency with which a cardinally preferring (0º or 90º) map would emerge, however, decreased significantly for ongoing but not for evoked activity. The same result was found by training self-organizing maps with recorded data as input. Spiking activity of cardinally preferring units also decreased significantly for ongoing when compared to evoked activity. Based on our results we came to the following conclusions: 1) VICs are not a determinant factor of ongoing map structure. Maps continued to be spontaneously generated with the same quality, probably by a combination of ongoing activity from local recurrent connections, thalamocortical loop and feedback connections. 2) VICs account for a cardinal bias in the temporal sequence of ongoing activity patterns, i.e. deactivating VIC decreases the probability of cardinal maps to emerge spontaneously. 3) Inter- and intrahemispheric long-range connections might serve as a grid preparing primary visual cortex for likely junctions in a larger visual environment encompassing the two hemifields.