Large reduction in singular value calculation time using Savitzsky-Golay data precompression.
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Animals↗
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Self-organizing neural networks for pharmacophore mapping.
We have shown that the SOM network can be a useful tool in pharmacophore mapping strategy. A possibility for the generation of fuzzy molecular representations together with its ability for discovering such aspects of molecular similarity that can be easily overlooked by a human chemist is an important advantage. The reduction in complexity resulting from the data compression is another one. The main disadvantage of SOM usage is the need for the application of special software packages not usually organized in user friendly toolboxes that can be applied easily. Instead, it needs some experience and time to optimize the parameters controlling the performance of the network.
Fuzzy Logic↗
Recurrent fractal neural networks: a strategy for the exchange of local and global information processing in the brain.
The regulation of biological networks relies significantly on convergent feedback signaling loops that render a global output locally accessible. Ideally, the recurrent connectivity within these systems is self-organized by a time-dependent phase-locking mechanism. This study analyzes recurrent fractal neural networks (RFNNs), which utilize a self-similar or fractal branching structure of dendrites and downstream networks for phase-locking of reciprocal feedback loops: output from outer branch nodes of the network tree enters inner branch nodes of the dendritic tree in single neurons. This structural organization enables RFNNs to amplify re-entrant input by over-the-threshold signal summation from feedback loops with equivalent signal traveling times. The columnar organization of pyramidal neurons in the neocortical layers V and III is discussed as the structural substrate for this network architecture. RFNNs self-organize spike trains and render the entire neural network output accessible to the dendritic tree of each neuron within this network. As the result of a contraction mapping operation, the local dendritic input pattern contains a downscaled version of the network output coding structure. RFNNs perform robust, fractal data compression, thus coping with a limited number of feedback loops for signal transport in convergent neural networks. This property is discussed as a significant step toward the solution of a fundamental problem in neuroscience: how is neuronal computation in separate neurons and remote brain areas unified as an instance of experience in consciousness? RFNNs are promising candidates for engaging neural networks into a coherent activity and provide a strategy for the exchange of global and local information processing in the human brain, thereby ensuring the completeness of a transformation from neuronal computation into conscious experience.
Brain↗
Digital imaging in remote diagnosis of burns.
Images are capable of giving an accurate representation of skin color and have been used extensively in teaching about and researching burn therapy. The advance from analogue to digital imaging allows the remote transmission of the clinical information contained in the digital image of a burn, using a suitable system. The large size of these image files reduces transmission speed and makes data compression desirable. Compression, by means of the JPEG algorithm, of up to 50 times the original size of 38 digital images of burns suffered by 22 consecutive patients did not lessen its great usefulness in determining the depth of burn injuries, according to a group of experts in burn care. The success rate was close to 90%, both for non-compressed images in original BMP format (mean size:1500 Kb) and for compressed images with a Q index of 50 (30 Kb files), when compared with the clinical diagnoses confirmed one week after the accident.
Adult↗
Optimal image resolution for digital storage of radiotherapy-planning images.
PURPOSE: To evaluate the quality of digitized radiation-planning images at different resolution and to determine the optimal resolution for digital storage. METHODS AND MATERIALS: Twenty-five planning films were scanned and digitized using a film scanner at a resolution of 72 dots per inch (dpi) with 8-bit depth. The resolution of scanned images was reduced to 48, 36, 24, and 18 dpi using computer software. Image qualities of these five images (72, 48, 36, 24, and 18 dpi) were evaluated and given scores (4 = excellent; 3 = good; 2 = fair; and 1 = poor) by three radiation oncologists. An image data compression algorithm by the Joint Photographic Experts Group (JPEG) (not reversible and some information will be lost) was also evaluated. RESULTS: The scores of digitized images with 72, 48, 36, 24, and 17 dpi resolution were 3.8 +/- 0.3, 3.5 +/- 0.3, 3.3 +/- 0.5, 2.7 +/- 0.5, and 1.6 +/- 0.3, respectively. The quality of 36-dpi images were definitely worse compared to 72-dpi images, but were good enough as planning films. Digitized planning images with 72- and 36-dpi resolution requires about 800 and 200 KBytes, respectively. The JPEG compression algorithm produces little degradation in 36-dpi images at compression ratios of 5:1. CONCLUSION: The quality of digitized images with 36-dpi resolution was good enough as radiation-planning images and required 200 KBytes/image.
Humans↗
NMR and Bayesian regularized neural network regression for impurity determination of 4-aminophenol.
A method for the determination of 4-aminophenol as an impurity in paracetamol (N-(4-hydroxyphenyl)-acetamide) by proton nuclear magnetic resonance ((1)H-NMR) spectroscopy has been developed. The (13)C-satellite from the protons in the ortho position from the hydroxyl group in paracetamol was used as an internal standard, although these peaks interfered with the peaks from the protons in 4-aminophenol. Because of interference in the spectra and non-linearity over a wide calibration range, a Bayesian regularized neural network model was used for calibration. Various kinds of data preprocessing were examined: zero filling, multiplication by a negative exponential function (line broadening), followed by Fourier transformation of the free induction decay (FID). The NMR spectral data were automatically phased and shift-adjusted by means of a genetic algorithm. Multiplicative scatter correction and data compression by wavelets and sequential zeroing of weights variable selection were performed to obtain an optimal calibration model. Neither zero filling of the FID nor line broadening improved the calibration models with regard to error of prediction, so these processes were excluded in the final model. The generated Bayesian regularized network model was evaluated with an independent test set. Four different models with different test sets were constructed to explore the quality of the calibration. The mean error of the optimal calibration model was 25.3 x 10(-6) weight of 4-aminophenol per weight paracetamol. The method is characterized by being relative fast, simple and sufficient sensitive for typical pharmaceutical impurity determinations.
Acetaminophen↗
Data preprocessing by wavelets and genetic algorithms for enhanced multivariate analysis of LC peptide mapping.
Peptide mapping by means of liquid chromatography is a powerful technique used for the characterisation and analysis of the primary structure of proteins. Subtle changes in the covalent structure of the protein can be detected by means of the chromatographic profile (fingerprint). Chromatographic methods, however, display variations in the chromatographic profile even at identical instrumental settings and sample conditions. These variations may be due to changes of the chromatographic conditions, e.g. slight shifts in column temperature, and degradation or alterations of the stationary phase or small changes in the trifluoroacetic acid (TFA) concentration. Such variations may result in varying retention times and peak shapes of the analytes and differences in the chromatographic baseline, thereby having a detrimental impact on the results obtained on multivariate analysis of peptide maps. In order to reduce the non-sample-related variations and to be able to more fully extract the information in peptide mapping, approaches for achieving this objective are outlined in the present study. These methods are denoising and data compression of the chromatograms by wavelets, baseline corrections by linear interpolation, and peak shift alignments towards a target chromatogram by means of a genetic algorithm. Visual inspections of preprocessed chromatograms and principal component analysis (PCA) score plots demonstrate the efficiency of the methodology used. Furthermore, deliberately added changes, e.g. insertions of small Gaussian peaks (outliers), are more easily detected by the proposed methods than from the original chromatograms by multivariate analysis.
Algorithms↗
Suitability of minidisc (MD) recordings for voice perturbation analysis.
A new digital recording format, Minidisc (MD), shows promise for high-quality voice recordings. It is available in a portable size and uses magneto-optical recording techniques on a miniature compact disc. The disc can be recorded an unlimited number of times with essentially the same playback life span: however, the digital recording technique uses a data compression algorithm that may interfere with acoustic voice perturbation analysis. This study investigated what effects this compression may have and whether the MD format is viable for use in this application. The MD format was evaluated by traditional synthetic test signals used on recording devices. In addition, human phonation recorded on Digital Audio Tape (DAT) was used as the input to the MD. The output of the MD was then compared to the original DAT recording. The two signals were analyzed for long- and short-term perturbation measures, and their waveforms were visually inspected. The results indicated that the MD format performed as well as the DAT format in all areas of standard tests, with the exception of signal-to-noise (S/N) ratio. S/N ratio for the MD was approximately 10 dB less than for the DAT under normal operating conditions; however, in comparing perturbation measures on normal human vowels, there were no significant differences between the two formats, i.e., no distortions in voice perturbation were introduced by the MD record/playback process.
Female↗
The enhanced LBG algorithm.
Clustering applications cover several fields such as audio and video data compression, pattern recognition, computer vision, medical image recognition, etc. In this paper, we present a new clustering algorithm called Enhanced LBG (ELBG). It belongs to the hard and K-means vector quantization groups and derives directly from the simpler LBG. The basic idea we have developed is the concept of utility of a codeword, a powerful instrument to overcome one of the main drawbacks of clustering algorithms: generally, the results achieved are not good in the case of a bad choice of the initial codebook. We will present our experimental results showing the ELBG is able to find better codebooks than previous clustering techniques and the computational complexity is virtually the same as the simpler LBG.
Algorithms↗
The eigenspace separation transform for neural-network classifiers.
This paper presents a linear transform that compresses data in a manner designed to improve the performance of a neural network used as a binary classifier. The classifier is intended to accommodate data distributions that may be non-normal, may have equal class means, may be multimodal, and have unknown a priori probabilities for the two classes. The transform, which is called the eigenspace separation transform, allows the reduction of the size of a neural network while enhancing its generalization accuracy as a binary classifier.
Journal Article↗
A measure of folding complexity for d-dimensional polymers.
A measure of folding characterizes aspects of the instantaneous organization of a polymer chain in space. For three-dimensional polymers (D = 3), one such measure is the mean overcrossing number. An intuitively similar property, the radial intersection number, has been proposed as a tool to characterize "folding features" in two-dimensional polymers (D = 2). In this work, we show rigorously that these measures are indeed related and that they can be derived as particular cases within a single, unified formulation. The present approach provides an analytical expression for a measure of folding complexity that can be applied to generic D-dimensional polymers. In the case D = 2, we show results for models derived from experimental structures by using optimized multidimensional scaling transformations for data compression.
Journal Article↗
Comparative molecular surface analysis: a novel tool for drug design and molecular diversity studies.
The application of the SOM network in drug design and molecular diversity is discussed. In particular, examples of the applications of the Comparative Molecular Surface Analysis (CoMSA) are reviewed. Molecular surface is a fuzzy category, inspired by the macroscopic world, which has no unique equivalent in the molecular scale. However, it is somewhere near the area where the molecular recognition processes are taking place. Consequently, the methods that analyze this region promise better efficiency than procedures that are based on uniform grids. An important advantage of the CoMSA method is the possibility for the generation of fuzzy molecular representations together with its ability to discover such aspects of molecular similarity that can be easily overlooked by a chemist. The ability for data compression is a further advantage. It has also been shown that the fast processing of the comparative Kohonen mapping enables one to implement this method in the field of molecular diversity.
Anti-HIV Agents↗
Image Storage Requirements for Treatment Planning and Verification.
Digital imaging techniques are becoming increasingly accepted in radiation therapy, and they bring significant advantages when compared with film, especially the ease of storage and retrieval. A simple model is proposed for the estimation of digital data storage requirements in a typical department of radiation therapy. The model assumes that 100 patients are undergoing treatment at any given time, and their computed tomography (CT) images, treatment plans, digitized simulator films, and portal images are to be available at short notice ("on-line"). Off-line archival image storage is required after the completion of treatment, for 1,000 patients per year. Reasonable assumptions are postulated regarding image sizes and acquisition rates, and on-line storage requirements are estimated to be up to 300 megabytes (MB) for CT data, 170 MB for treatment plans, 200 MB for digitized simulator films, and 500 MB for digitized port films. If electronic portal imaging is used instead of port films, the on-line requirement becomes about 2 gigabytes (GB) for verification images, and 20 GB if portal movies are to be archived. Off-line storage requirements are a factor of ten larger. It is suggested that data compression may reduce these requirements by up to a factor of 20.
Journal Article↗
[Wavelet representation of corneal topography data after nonmechanical penetrating keratoplasty--a clinical study].
BACKGROUND: Corneal surface irregularities may limit the visual outcome after penetrating keratoplasty (PK). Corneal topographers mainly render empirically derived and system-specific statistical indices for characterization of superficial inhomogeneities which may lack clinical evidence and make inter-system comparisons difficult. The purpose of this study was to detect and quantify focal surface irregularities of the cornea after nonmechanical PK by 2-dimensional wavelet decomposition based on corneal topography data. PATIENTS AND METHODS: Our study included 15 patients with keratoconus and 10 patients with Fuchs' dystrophy with all-sutures-out after penetrating keratoplasty. For trephination we used the excimer laser MEL60 (Aesculap-Meditec, Germany) (7.5/7.6 mm diameter in dystrophies, 8.0/8.1 mm in keratoconus, double-running 10-0 nylon suture). After suture removal a complete ophthalmological examination including OrbScan topography analysis (Orbtec, USA) was performed. The refraction data were extracted via "data recorder" and decomposed using 2-dimensional wavelet analysis methods (Daubechies-4-wavelets on five scales of resolution). Corneal irregularities were quantified (scale 1 = fine details to scale 5 = coarse details). RESULTS: All detail coefficients (horizontal, vertical and diagonal) correlated statistically significant with the "Irregular Astigmatism" provided by the OrbScan-system (p < 0.05). In scale 3 and 4 a relative maximum of the wavelet detail coefficients occurred, whereas the coefficients at scale 2 and 5 were significantly smaller. The horizontal and vertical detail coefficients correlated significantly inversely with the best-corrected visual acuity (p < 0.04). All detail coefficients were significantly lower in the patient group with keratoconus compared to Fuchs' dystrophy. CONCLUSIONS: Wavelet decomposition of corneal topography refraction data allows an analytical isolation and quantification of focal corneal superficial irregularities. This algorithm is independent of the currently used topography system and allows a smoothing of the raw data set adapted to scale of resolution and data compression.
Adult↗
Image manipulation: digital versus analog.
A conceptual difference between "analog" and "digital" digitizing is reviewed. Analog and digital type image filing systems are discussed from a comparative point of view: The analog type is advantageous in the number of recordable images, the recording and reproducing speed, and the ability to record a moving picture, while the digital type, in which images are digitized when recorded, is capable of reproducing a higher quality image that does not deteriorate when copied repeatedly. It has the advantage that it easily interfaces with computer systems. As technology developed to compensate for the drawbacks of the digital type systems, image data compression was introduced. Finally, the possibility for recording a moving picture in a digital type system is discussed.
Image Processing, Computer-Assisted↗
High-resolution facial feature saliency mapping.
For recognition of a target there must be some form of comparison process between the image of that target and a stored representation of that target. In the case of faces there must be a very large number of such stored representations, yet human beings seem able to perform comparisons at phenomenal speed. It is possible that faces are memorized by fitting unusual features or combinations of features onto a bland prototypical face, and such a data-compression technique would help to explain our computational speed. If humans do indeed function in this fashion, it is necessary to ask just what are the features that distinguish one face from another, and also, what are the features that form the basic set of the prototypical face. The distributed apertures technique was further developed in an attempt to answer both questions. Four target faces, stored in an image-processing computer, were each divided up into 162 contiguous squares that could be displayed in their correct positions in any combination of 24 or fewer squares. Each observer was required to judge which of the four target faces was displayed during a 1 s presentation, and the proportion of correct responses for each individual square was computed. The resultant response distributions, displayed as brightness maps, give a vivid impression of the relative saliency of each feature square, both for the individual targets and for all of them combined. The results, while broadly confirming previous work, contain some very interesting and surprising details about the differences between the target faces.
Adult↗
Algorithmic cooling and scalable NMR quantum computers.
We present here algorithmic cooling (via polarization heat bath)-a powerful method for obtaining a large number of highly polarized spins in liquid nuclear-spin systems at finite temperature. Given that spin-half states represent (quantum) bits, algorithmic cooling cleans dirty bits beyond the Shannon's bound on data compression, by using a set of rapidly thermal-relaxing bits. Such auxiliary bits could be implemented by using spins that rapidly get into thermal equilibrium with the environment, e.g., electron spins. Interestingly, the interaction with the environment, usually a most undesired interaction, is used here to our benefit, allowing a cooling mechanism. Cooling spins to a very low temperature without cooling the environment could lead to a breakthrough in NMR experiments, and our "spin-refrigerating" method suggests that this is possible. The scaling of NMR ensemble computers is currently one of the main obstacles to building larger-scale quantum computing devices, and our spin-refrigerating method suggests that this problem can be resolved.
Journal Article↗
Increase in apparent compressibility of cytochrome c upon oxidation.
The apparent molal adiabatic compressibilities of ferri- and ferrocytochrome c have been determined from measurements of density and sound velocity. The values found were +2.99 X 10(-8) and -2.40 X 10(-8) cm5 mol-1 dyne-1 for the ferri and ferro forms, respectively. Experiments were performed on identical solutions containing either the oxidized or reduced form of protein. Solutions of ferricytochrome c were found to have significantly greater adiabatic compressibility than equivalent solutions of ferrocytochrome c at 25 degrees C and pH 7.15. The remarkable similarity of the three-dimensional structures of the ferri and ferro proteins [Takano, T. & Dickerson, R.E. (1980) Proc. Natl. Acad. Sci. USA 77, 6371-6375] strongly suggests that this difference in compressibility is due to an increase in volume fluctuations within ferricytochrome c relative to the ferro form rather than a change in equilibrium structure or hydration. Such a difference in the dynamic properties of the structures is consistent with both the crystallographic thermal B factors and the observed increase in amide hydrogen exchange kinetics when ferrocytochrome c is oxidized. The relative magnitude of the root mean square volume fluctuations is approximated from an ideal solution treatment of the compressibility data and yields a ratio of delta Vrms (ferri cyt c)/ delta Vrms (ferro cyt c) = 1.3.
Animals↗