Ana Maria Tomé

Brain connectivity analysis: a short survey

This short survey the reviews recent literature on brain connectivity studies. It encompasses all forms of static and dynamic connectivity whether anatomical, functional, or effective. The last decade has seen an ever increasing number of studies devoted to deduce functional or effective connectivity, mostly from functional neuroimaging experiments. Resting state conditions have become a dominant experimental paradigm, and a number of resting state networks, among them the prominent default mode network, have been identified. Graphical models represent a convenient vehicle to formalize experimental findings and to closely and quantitatively characterize the various networks identified. Underlying these abstract concepts are anatomical networks, the so-called connectome, which can be investigated by functional imaging techniques as well. Future studies have to bridge the gap between anatomical neuronal connections and related functional or effective connectivities.

KPCA denoising and the pre-image problem revisited

Kernel principal component analysis (KPCA) is widely used in classification, feature extraction and denoising applications. In the latter it is unavoidable to deal with the pre-image problem which constitutes the most complex step in the whole processing chain. One of the methods to tackle this problem is an iterative solution based on a fixed-point algorithm. An alternative strategy considers an algebraic approach that relies on the solution of an under-determined system of equations. In this work we present a method that uses this algebraic approach to estimate a good starting point to the fixed-point iteration. We will demonstrate that this hybrid solution for the pre-image shows better performance than the other two methods. Further we extend the applicability of KPCA to one-dimensional signals which occur in many signal processing applications. We show that artefact removal from such data can be treated on the same footing as denoising. We finally apply the algorithm to denoise the famous USPS data set and to extract EOG interferences from single channel EEG recordings.

Knowledge-based gene expression classification via matrix factorization

Motivation: Modern machine learning methods based on matrix decomposition techniques, like independent component analysis (ICA) or non-negative matrix factorization (NMF), provide new and efficient analysis tools which are currently explored to analyze gene expression profiles. These exploratory feature extraction techniques yield expression modes (ICA) or metagenes (NMF). These extracted features are considered indicative of underlying regulatory processes. They can as well be applied to the classification of gene expression datasets by grouping samples into different categories for diagnostic purposes or group genes into functional categories for further investigation of related metabolic pathways and regulatory networks. Results: In this study we focus on unsupervised matrix factorization techniques and apply ICA and sparse NMF to microarray datasets. The latter monitor the gene expression levels of human peripheral blood cells during differentiation from monocytes to macrophages. We show that these tools are able to identify relevant signatures in the deduced component matrices and extract informative sets of marker genes from these gene expression profiles. The methods rely on the joint discriminative power of a set of marker genes rather than on single marker genes. With these sets of marker genes, corroborated by leave-one-out or random forest cross-validation, the datasets could easily be classified into related diagnostic categories. The latter correspond to either monocytes versus macrophages or healthy vs Niemann Pick C disease patients. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: elmar.lang@biologie.uni-regensburg.de

How to Apply Nonlinear Subspace Techniques to Univariate Biomedical Time Series

In this paper, we propose an embedding technique for univariate single-channel biomedical signals to apply projective subspace techniques. Biomedical signals are often recorded as 1-D time series; hence, they need to be transformed to multidimensional signal vectors for subspace techniques to be applicable. The transformation can be achieved by embedding an observed signal in its delayed coordinates. We propose the application of two nonlinear subspace techniques to embedded multidimensional signals and discuss their relation. The techniques consist of modified versions of singular-spectrum analysis (SSA) and kernel principal component analysis (KPCA). For illustrative purposes, both nonlinear subspace projection techniques are applied to an electroencephalogram (EEG) signal recorded in the frontal channel to extract its dominant electrooculogram (EOG) interference. Furthermore, to evaluate the performance of the algorithms, an experimental study with artificially mixed signals is presented and discussed.

Automatic Generation of Biped Walk Behavior Using Genetic Algorithms

Controlling a biped robot with several degrees of freedom is a challenging task that takes the attention of several researchers in the fields of biology, physics, electronics, computer science and mechanics. For a humanoid robot to perform in complex environments, fast, stable and adaptive behaviors are required. This paper proposes a solution for automatic generation of a walking gait using genetic algorithms (GA). A method based on partial Fourier series was developed for joint trajectory planning. GAs were then used for offline generation of the parameters that define the gait. GAs proved to be a powerful method for automatic generation of humanoid behaviors resulting on a walk forward velocity of 0.51m/s which is a good result considering the results of the three best teams of RoboCup 3D simulation league for the same movement.

The generalized eigendecomposition approach to the blind source separation problem

This paper proposes a novel formulation of the generalized eigendecomposition (GED) approach to blind source separation (BSS) problems. The generalized eigendecomposition algorithms consider the estimation of a pair of correlation matrices (a matrix pencil) using observed sensor signals. Each of various algorithms proposed in the literature uses a different approach to form the pencil. This study proposes a linear algebra formulation which exploits the definition of congruent matrix pencils and shows that the solution and its constraints are independent of the way the matrix pencil is computed. Also an iterative eigendecomposition algorithm, that updates separation parameters on a sample-by-sample basis, is developed. It comprises of: (1) performing standard eigendecompositions based on power and deflation techniques; (2) computing a transformation matrix using spectral factorization. Another issue discussed in this work is the influence of the length of the data segment used to estimate the pencil. The algorithm is applied to artificially mixed audio data and it is shown that the separation performance depends on the eigenvalue spread. The latter varies with the number of samples used to estimate the eigenvalues.

Ensemble Empirical Mode Decomposition Analysis of EEG Data Collected during a Contour Integration Task

We discuss a data-driven analysis of EEG data recorded during a combined EEG/fMRI study of visual processing during a contour integration task. The analysis is based on an ensemble empirical mode decomposition (EEMD) and discusses characteristic features of event related modes (ERMs) resulting from the decomposition. We identify clear differences in certain ERMs in response to contour vs noncontour Gabor stimuli mainly for response amplitudes peaking around 100 [ms] (called P100) and 200 [ms] (called N200) after stimulus onset, respectively. We observe early P100 and N200 responses at electrodes located in the occipital area of the brain, while late P100 and N200 responses appear at electrodes located in frontal brain areas. Signals at electrodes in central brain areas show bimodal early/late response signatures in certain ERMs. Head topographies clearly localize statistically significant response differences to both stimulus conditions. Our findings provide an independent proof of recent models which suggest that contour integration depends on distributed network activity within the brain.

EMDLAB: A toolbox for analysis of single-trial {EEG} dynamics using empirical mode decomposition

BACKGROUND Empirical mode decomposition (EMD) is an empirical data decomposition technique. Recently there is growing interest in applying EMD in the biomedical field. NEW METHOD EMDLAB is an extensible plug-in for the EEGLAB toolbox, which is an open software environment for electrophysiological data analysis. RESULTS EMDLAB can be used to perform, easily and effectively, four common types of EMD: plain EMD, ensemble EMD (EEMD), weighted sliding EMD (wSEMD) and multivariate EMD (MEMD) on EEG data. In addition, EMDLAB is a user-friendly toolbox and closely implemented in the EEGLAB toolbox. COMPARISON WITH EXISTING METHODS EMDLAB gains an advantage over other open-source toolboxes by exploiting the advantageous visualization capabilities of EEGLAB for extracted intrinsic mode functions (IMFs) and Event-Related Modes (ERMs) of the signal. CONCLUSIONS EMDLAB is a reliable, efficient, and automated solution for extracting and visualizing the extracted IMFs and ERMs by EMD algorithms in EEG study.

A perceptual memory system for grounding semantic representations in intelligent service robots

This paper addresses the problem of grounding semantic representations in intelligent service robots. In particular, this work contributes to addressing two important aspects, namely the anchoring of object symbols into the perception of the objects and the grounding of object category symbols into the perception of known instances of the categories. The paper discusses memory requirements for storing both semantic and perceptual data and, based on the analysis of these requirements, proposes an approach based on two memory components, namely a semantic memory and a perceptual memory. The perception, memory, learning and interaction capabilities, and the perceptual memory, are the main focus of the paper. Three main design options address the key computational issues involved in processing and storing perception data: a lightweight, NoSQL database, is used to implement the perceptual memory; a thread-based approach with zero copy transport of messages is used in implementing the modules; and a multiplexing scheme, for the processing of the different objects in the scene, enables parallelization. The system is designed to acquire new object categories in an incremental and open-ended way based on user-mediated experiences. The system is fully integrated in a broader robot system comprising low-level control and reactivity to high-level reasoning and learning.

Hybridizing sparse component analysis with genetic algorithms for microarray analysis

Nonnegative matrix factorization (NMF) has proven to be a useful tool for the analysis of nonnegative multivariate data. However, it is known not to lead to unique results when applied to blind source separation (BSS) problems. In this paper we present an extension of NMF capable of solving the BSS problem when the underlying sources are sufficiently sparse. In contrast to most well-established BSS methods, the devised algorithm is capable of solving the BSS problem in cases where the underlying sources are not independent or uncorrelated. As the proposed fitness function is discontinuous and possesses many local minima, we use a genetic algorithm for its minimization. Finally, we apply the devised algorithm to real world microarray data.