Evolutionarily Tuned Generalized Pseudo-Inverse in Linear Discriminant Analysis

Linear Discriminant Analysis (LDA) and the related Fisher's linear discriminant are very important techniques used for classification and for dimensionality reduction. A certain complication occurs in applying these methods to real data. We have to estimate the class means and common covariance matrix, which are not known. A problem arises if the number of features exceeds the number of observations. In this case the estimate of the covariance matrix does not have full rank, and so cannot be inverted. There are a number of ways to deal with this problem. In our previous paper, we proposed improving LDA in this area, and we presented a new approach which uses a generalization of the Moore-Penrose (MP) pseudo-inverse to remove this weakness. However, for data sets with a larger number of features, our method was computationally too slow to achieve good results. Now we propose a model selection method with a genetic algorithm to solve this problem. Experimental results on different data sets demonstrate that the improvement is efficient

Statistical Analysis of Protein Sequences: A Coevolutionary Study of Molecular Chaperones

Recent advances in DNA sequencing technologies led to the accumulation of enormous quantities of genetic information available in public databases. This rapid growth of available biological datasets calls for quantitative analysis tools and concomitantly opens the doors for new analysis paradigms. Particularly, the analysis of correlated mutations and their structural interpretation have witnessed a second youth in the last years. A natural formulation for such approaches is provided by the statistical physics of disordered systems. This thesis is articulated around different projects aimed at studying particular biological systems of interests, the Hsp70 molecular chaperones, through the lens provided by methods rooted in statistical physics. In a first project, we focus on correlated mutations within the Hsp70 family. Our analysis reveals the existence of a biologically important macro-molecular arrangement of these chaperones and we investigate its phylogenetic origin. A second project investigates the interactions between the Hsp70 chaperones and one of their main co-chaperones, J-proteins. Through the combined use of coevolutionary analysis and molecular simulations at both coarse-grained and atomistic levels, we construct a structural and dynamical model of this interaction which rationalizes previous experimental evidence. In a subsequent study, we specifically focus on the J-protein co-chaperones. Through phylogenetic and coevolutionary methods, we investigate the origin of recently discovered interactions which form the basis of the disaggregation machinery in higher eukaryotes. Finally, in a fourth project, we shift our attention to the analysis of proteins involved in the iron-sulfur cluster assembly pathway. Analysis of residue coevolution in the different proteins composing this pathway reveals multiple structural insights at several scales

Review of the BCI Competition IV

The BCI competition IV stands in the tradition of prior BCI competitions that aim to provide high quality neuroscientific data for open access to the scientific community. As experienced already in prior competitions not only scientists from the narrow field of BCI compete, but scholars with a broad variety of backgrounds and nationalities. They include high specialists as well as students. The goals of all BCI competitions have always been to challenge with respect to novel paradigms and complex data. We report on the following challenges: (1) asynchronous data, (2) synthetic, (3) multi-class continuous data, (4) session-to-session transfer, (5) directionally modulated MEG, (6) finger movements recorded by ECoG. As after past competitions, our hope is that winning entries may enhance the analysis methods of future BCIs.BMBF, 01IB001A, LOKI - Lernen zur Organisation komplexer Systeme der Informationsverarbeitung - Lernen im Kontext der SzenenanalyseBMBF, 01GQ0850, Bernstein Fokus Neurotechnologie - Nichtinvasive Neurotechnologie für Mensch-Maschine InteraktionEC/FP7/224631/EU/Tools for Brain-Computer Interaction/TOBIEC/FP7/216886/EU/Pattern Analysis, Statistical Modelling and Computational Learning 2/PASCAL2BMBF, 01GQ0420, Verbundprojekt: Bernstein-Zentrum für Neural Dynamics, Freiburg - CNDFBMBF, 01GQ0761, Bewegungsassoziierte Aktivierung - Dekodierung bewegungsassoziierter GehirnsignaleBMBF, 01GQ0762, Bewegungsassoziierte Aktivierung - Gehirn- und Maschinenlerne

Use of Pattern Classification Algorithms to Interpret Passive and Active Data Streams from a Walking-Speed Robotic Sensor Platform

In order to perform useful tasks for us, robots must have the ability to notice, recognize, and respond to objects and events in their environment. This requires the acquisition and synthesis of information from a variety of sensors. Here we investigate the performance of a number of sensor modalities in an unstructured outdoor environment, including the Microsoft Kinect, thermal infrared camera, and coffee can radar. Special attention is given to acoustic echolocation measurements of approaching vehicles, where an acoustic parametric array propagates an audible signal to the oncoming target and the Kinect microphone array records the reflected backscattered signal. Although useful information about the target is hidden inside the noisy time domain measurements, the Dynamic Wavelet Fingerprint process (DWFP) is used to create a time-frequency representation of the data. A small-dimensional feature vector is created for each measurement using an intelligent feature selection process for use in statistical pattern classification routines. Using our experimentally measured data from real vehicles at 50 m, this process is able to correctly classify vehicles into one of five classes with 94% accuracy. Fully three-dimensional simulations allow us to study the nonlinear beam propagation and interaction with real-world targets to improve classification results

A novel EEG based linguistic BCI

While a human being can think coherently, physical limitations no matter how severe, should never become disabling. Thinking and cognition are performed and expressed through language, which is the most natural form of human communication. The use of covert speech tasks for BCIs has been successfully achieved for invasive and non-invasive systems. In this work, by incorporating the most recent discoveries on the spatial, temporal, and spectral signatures of word production, a novel system is designed, which is custom-build for linguistic tasks. Other than paying attention and waiting for the onset cue, this BCI requires absolutely no cognitive effort from the user and operates using automatic linguistic functions of the brain in the first 312ms post onset, which is also completely out of the control of the user and immune from inconsistencies. With four classes, this online BCI achieves classification accuracy of 82.5%. Each word produces a signature as unique as its phonetic structure, and the number of covert speech tasks used in this work is limited by computational power. We demonstrated that this BCI can successfully use wireless dry electrode EEG systems, which are becoming as capable as traditional laboratory grade systems. This frees the potential user from the confounds of the lab, facilitating real-world application. Considering that the number of words used in daily life does not exceed 2000, the number of words used by this type of novel BCI may indeed reach this number in the future, with no need to change the current system design or experimental protocol. As a promising step towards noninvasive synthetic telepathy, this system has the potential to not only help those in desperate need, but to completely change the way we communicate with our computers in the future as covert speech is much easier than any form of manual communication and control

Transcriptome and Genome Analyses Applied to Aquaculture Research

Aquaculture is an important economic activity for food production all around the world that has experienced an exponential growth during the last few decades. However, several weaknesses and bottlenecks still need to be addressed in order to improve the aquaculture productive system. The recent fast development of the omics technologies has provided scientists with meaningful tools to elucidate the molecular basis of their research interests. This reprint compiles different works about the use of transcriptomics and genomics technologies in different aspects of the aquaculture research, such as immunity, stress response, development, sexual dimorphism, among others, in a variety of fish and shellfish, and even in turtles. Different transcriptome (mRNAs and non-coding RNAs (ncRNAs)), genome (Single Nucleotide Polymorphisms (SNPs)), and metatranscriptome analyses were conducted to unravel those different aspects of interest