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At least 271 records · Page 15Linked to original sources

Variational mixture of Bayesian independent component analyzers.

There has been growing interest in subspace data modeling over the past few years. Methods such as principal component analysis, factor analysis, and independent component analysis have gained in popularity and have found many applications in image modeling, signal processing, and data compression, to name just a few. As applications and computing power grow, more and more sophisticated analyses and meaningful representations are sought. Mixture modeling methods have been proposed for principal and factor analyzers that exploit local gaussian features in the subspace manifolds. Meaningful representations may be lost, however, if these local features are nongaussian or discontinuous. In this article, we propose extending the gaussian analyzers mixture model to an independent component analyzers mixture model. We employ recent developments in variational Bayesian inference and structure determination to construct a novel approach for modeling nongaussian, discontinuous manifolds. We automatically determine the local dimensionality of each manifold and use variational inference to calculate the optimum number of ICA components needed in our mixture model. We demonstrate our framework on complex synthetic data and illustrate its application to real data by decomposing functional magnetic resonance images into meaningful-and medically useful-features.

Bayes Theorem↗

Context-tree modeling of observed symbolic dynamics.

Modern techniques invented for data compression provide efficient automated algorithms for the modeling of the observed symbolic dynamics. We demonstrate the relationship between coding and modeling, motivating the well-known minimum description length (MDL) principle, and give concrete demonstrations of the "context-tree weighting" and "context-tree maximizing" algorithms. The predictive modeling technique obviates many of the technical difficulties traditionally associated with the correct MDL analyses. These symbolic models, representing the symbol generating process as a finite-state automaton with probabilistic emission probabilities, provide excellent and reliable entropy estimations. The resimulations of estimated tree models satisfying the MDL model-selection criterion are faithful to the original in a number of measures. The modeling suggests that the automated context-tree model construction could replace fixed-order word lengths in many traditional forms of empirical symbolic analysis of the data. We provide an explicit pseudocode for implementation of the context-tree weighting and maximizing algorithms, as well as for the conversion to an equivalent Markov chain.

Journal Article↗

Circular harmonic averaging of rotary-shadowed and negatively stained creatine kinase macromolecules.

The structure of mitochondrial creatine kinase is investigated by high-resolution shadowing at very low temperature and conventional negative staining. The electron microscopic images are analyzed with circular harmonic averaging, a method suited for the processing of single molecules. The rotational alignment and averaging is performed with the circular harmonic components, which allows data compression and several steps of noise reduction to be carried out within the averaging procedure. In addition, the symmetry can be deduced. For the mitochondrial creatine kinase, a fourfold symmetry is found that is compatible with the biochemical and biophysical characterization of the molecule.

Creatine Kinase↗

Reference deconvolution, phase correction, and line listing of NMR spectra by the 1D filter diagonalization method.

We describe a new way to attack the problem of identifying and quantifying the number of NMR transitions in a given NMR spectrum. The goal is to reduce the spectrum to a tabular line list of peak positions, widths, amplitudes, and phases, and to have this line list be of high fidelity. In this context "high fidelity" means that each true NMR transition is represented by a single entry, with no spurious entries and no missed peaks. A high fidelity line list allows the measurement of chemical shifts and coupling constants with good accuracy and precision and is the ultimate in data compression. There are two parts to the problem. The first is to overcome common imperfections: the non-Lorentzian lineshapes that can arise whenever the magnetic field inhomogeneity is less than perfect, and nonzero time delays that cause frequency-dependent phase errors. The second is to fit the spectral features to a model of Lorentzian lines. We use the recently developed filter diagonalization method (FDM) to accomplish the reference deconvolution, the phase correction, and the fitting, and show good progress toward the goal of obtaining a high fidelity line list.

Fourier Analysis↗

Structure of Lumbricus terrestris hemoglobin at 30 A resolution determined using angular reconstitution.

The three-dimensional (3D) structure of the giant hemoglobin of the common earthworm Lumbricus terrestris was determined from cryomicroscopical images of a vitrified molecular solution. From about 5000 molecular images, the best-fit 3D structure was calculated using recently developed analysis techniques. Multivariate statistical analysis data compression and automatic classification were used to find the characteristic projection images of the oligomer. The angular reconstitution approach was then applied to find the Euler angle orientations of these characteristic views. The Lumbricus hemoglobin molecule has an overall D6 (622) point-group symmetry and is found to have a local threefold symmetry axis within the 1/12th subunit. This additional symmetry appears to predict the presence of 36 abcd globin tetramers in the Lumbricus hemoglobin or a total of 144 heme chains for the whole oligomer. A distinct doughnut-shaped structure is elucidated in the center of the molecule. This central subunit, representing around 10% of the protein volume, may consist of non-heme-containing linker chains found generally in giant annelid hemoglobins.

Animals↗

Flexibility of globular proteins in water as revealed by compressibility.

In order to elucidate the flexibility-structure-function relationships of proteins, the adiabatic compressibility of about 30 globular proteins, including food proteins, was determined by means of sound velocity and density measurements in aqueous solutions. Most proteins studied showed positive compressibility, indicating the large internal flexibility of the molecules. The volume fluctuation was in the range of 30-200 ml/mol, which corresponded to about 0.3% of the total protein volume. From the statistical analyses of the compressibility data, it was found that the flexibility of proteins is closely related to structural factors such as hydrophobicity, helix element, and amino acid composition, and to functional properties such as digestibility and foaming capacity. These results indicate that the dynamics of protein structure should be taken into account in predicting precisely the functions and properties of a protein from its primary or tertiary structure.

Amino Acids↗

Auto-association by multilayer perceptrons and singular value decomposition.

The multilayer perceptron, when working in auto-association mode, is sometimes considered as an interesting candidate to perform data compression or dimensionality reduction of the feature space in information processing applications. The present paper shows that, for auto-association, the nonlinearities of the hidden units are useless and that the optimal parameter values can be derived directly by purely linear techniques relying on singular value decomposition and low rank matrix approximation, similar in spirit to the well-known Karhunen-Loève transform. This approach appears thus as an efficient alternative to the general error back-propagation algorithm commonly used for training multilayer perceptrons. Moreover, it also gives a clear interpretation of the rôle of the different parameters.

Mathematics↗

The application of delta modulation to EEG waveforms for database reduction and real-time signal processing.

The large volume of digital data and the demanding processing task involved in electroencephalogram (EEG) analysis place stringent requirements on computer resources in terms of data transfer, computation speed, and temporary or permanent storage. The reduction of the database to a manageable size is therefore necessary for economical use of transmission channels and the storage media. The two criteria, waveform reproducibility and processing applications, must be analyzed and optimized in terms of signal-to-noise ratio (SNR) using the various factors affecting the coding. This analysis and optimization can become cumbersome, and a specialized workstation has been developed specifically for analysis of digital coding. Our interest in data compression stems from the study of the feasibility of predicting pilots' acceleration (Gz) tolerance during flight by processing both their uncoded and coded EEG.

Aerospace Medicine↗

Management and clinical utilization of computed tomography, magnetic resonance imaging, and angiography in Hokkaido University Hospital picture archiving and communication system.

We made a preliminary assessment of the Hokkaido University picture archiving and communication system (HU-PACS). Data access time from either imaging machines or data base to workstations was 1.5 minutes, which is great benefit for data communication in routine examinations. Image quality of the work station was estimated in terms of brain computed tomography (CT) and digitized cerebral angiograms. Cerebral infarction was definitely observed on the cathode-ray tube (CRT) monitor of the work station. Although the picture quality of CRT was acceptable, we had to manipulate window level and width for CRT diagnosis of cerebral angiography. Data compression was routinely used without significant degradation of those image quality. Nevertheless, further improvement of maneuverability of the workstation should be considered.

Angiography, Digital Subtraction↗

Neural networks in higher levels of abstraction.

Existing artificial neural network models are not very successful in understanding or generating natural language texts. Therefore it is proposed to design novel neural network structures in higher levels of abstraction. This concept leads to a hierarchy of network layers which extract and store local details in every layer and transfer the remaining nonlocal context information to higher levels. At the same time data compression is provided from layer to layer. The use of the same network elements (meta-words) in higher levels for different word series in the basis level is introduced and discussed for grammatical identity or similarity. Thus text can be compressed to forms which are almost free of redundancy. Possible applications are storage, transmission, understanding, generating and translation of texts.

Cybernetics↗

High pressure volumetric measurements in dipalmitoylphosphatidylcholine bilayers.

The one previously reported high pressure volumetric experiment on a phospholipid bilayer investigated a region of pressure between 0 and 25 MPa and obtained isothermal compressibility values for the liquid crystal and intermediate phases which differed by more than a factor of ten. We report new volumetric measurements around the main transition in dipalmitoylphosphatidylcholine (DPPC) from 0 to 100 MPa. The isothermal compressibility data for the two phases are of the same order of magnitude, and the experimentally determined coexistence curve, specific volume dependence, and volume discontinuity values are compared with the predictions of the phenomenological theory according to Sugar and Tarjan ((1982) Sov. Phys. Crystallogr. 27, 4-5). Significant discrepancies between this theory and experiment are found. Finally, the data indicate that steric interactions play a more dominant role in the main transition of phospholipid bilayers than in transitions in most thermotropic liquid crystals.

Atmospheric Pressure↗

A computer feedback system for clinical research.

This paper presents a computerized data base management and information retrieval system for a heroin addiction research clinic, which has potential application for any type of clinical research. It describes data input checking programs, file structures, and output programs. The system contains several interesting features: built-in feedback error detection and correction; patient month matrix formatting and data compression; and a virtual blocking system to reduce the size of the files.

Computers↗

Pattern recognition and interpretation of electromyogram data from cat jaw muscle.

This study investigates the effect of emotional behavior on the masseteric muscle EMG response patterns. Two experimental protocols are utilized: (1) does not elicit emotional behavior (stick chewing) and (2) elicits emotional behavior (hypothalamic stimulation). The Karhunen-Loève transform is used to compute features which exactly represent the correlated patterns of mean-zero observations, with data compression and noise immunity. Using nonparametric tests, it is found that the populations of biting and hissing features are significantly different (p < 0.05), with increased statistical significance as the size of the training set is increased. No statistically significant difference is seen in a test of the two biting populations.

Animals↗

Power spectral analysis of normal and pathological brainstem auditory evoked potentials.

The brainstem auditory evoked potential (BAEP) recording has become a powerful investigational tool in neurological diagnosis. The BAEPs of patients have different latencies and morphologies when compared to those of normals. In this paper the power spectra (PS) of BAEPs of 21 normals, 17 patients with multiple sclerosis (MS) and 12 patients with head injury (HI) computed by Blackman-Tukey (BT) and Maximum Entropy (ME) methods are examined for their frequency composition. Three major peaks appear at approximately 170 Hz, 520 Hz and 950 Hz in PS of normal BAEPs. The average power contained in the frequency bands spread around these frequency bands for BAEPs of patients differed significantly (P less than 0.05) from those of normal BAEPs. The peaks observed in ME spectra were found to match those computed using BT method. The model order for representing both normal and patient BAEPs is greater than 40 and data compression afforded by modelling the BAEPs is of the order of 5:1.

Adolescent↗

The CODATA/IUIS Hybridoma Data Bank: development of a hybrid system to handle complex data relationships.

System design for the Hybridoma Data Bank, a database of comprehensive information on immunoreagents for use by scientists in diverse disciplines, is described. Unique problems include: use of nomenclature from diverse fields that is neither static nor standard; the need for two representations of the database--textual for readability and numeric for complex search capabilities, analysis and data compression; and a method of translating between the two representations of the database.

Animals↗

Assessing the evolution of the evoked potential average: a new color display method.

A new method to control the averaging process and to check the stability of evoked potential (EP) components is described. The principle of the method is based on the display of the consecutive averages of the EP after each stimulus in a color-coded picture. In this way the evolution of the process is visualised instead of only the last average. The colors are assigned according to the amplitudes. The resulting picture initially consists of erratic colors. However, with increasing numbers of stimuli, tracks of one color soon emerge, indicating stable components. The number of stimuli necessary to generate a stable peak and the duration of stability can easily be quantified. Details with regard to the methods of extraction of essential data and data compression to record the picture are described. The color display method was evaluated with the analysis of 18 somatosensory evoked potentials and 17 visual evoked potentials of controls and 33 EPs of 18 patients. It is shown that this method preserves essential information about the averaging process: the stability of the EP components can be quantified and consequently the optimum number of stimuli to be applied. Furthermore, 14 of the 33 patient recordings showed artifacts, which could be traced with the average-evolution method, but not from the final average alone.

Color↗

Clinical experience of Hokkaido University-PACS and FCR-angiography.

Three years' experience with Hokkaido University-PACS (HU-PACS) is reported. In particular, this paper describes the suitability of FCR-angiography for HU-PACS, which has been in clinical use since March 1991. Image quality of FCR-arteriograms was evaluated in the head-and-face region and the abdominal region independently. The image quality in both regions was excellent. Quality of transferred images to image workstation for HU-PACS with 10:1 data compression was also evaluated, and no appreciable image degradation or loss of information was found in the transferred images. There was no significant difference in the examination time required for one patient in abdominal angiography between conventional angiography and FCR-angiography. In summary, FCR-angiography is suitable for HU-PACS as its image acquisition modality.

Abdomen↗

Non-linear CT windows.

The display of computerized tomographic (CT) data requires data compression because of the limited shades of grey which the eye can differentiate. This may lead to information loss which can be minimized by a more efficient utilization of the available levels of grey than that afforded by conventional linear windows. Automated histogram equalization for grey level assignment has not been satisfactory because of the underlying assumption that the information content at any given CT level is proportional to the number of pixels at that level. For four different anatomic regions; the lumber spine, abdomen, brain and chest, an empiric graph of the clinical information content vs CT levels was integrated to yield the shape of a graph assigning shades of grey vs CT level i.e. a non-linear window. This non-linear window curve was utilized in the same manner as the linear window, namely the window center and width were under the direct control of the observer through the window center and width knobs. Each non-linear window was implemented on images of its anatomic region and interactively optimized on the screen till a maximal display of information was obtained. These optimal non-linear windows compared favorably with linear windows in most cases. This method provides the means to display more information on a CT image with no extra processing time, additional equipment or special training.

Brain↗