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PubMedDate not supplied

Neural network method to analyze data compression in DNA and RNA sequences.

Neural network computations on RNA sequences are used to demonstrate that data compression is possible in these sequences. The result implies that a certain discrimination should be achievable between structured vs random regions. The technique is illustrated by computing the compressibility of short RNA sequences such as tRNA. The method should be valuable in measuring the information content of DNA, including noncoding DNA, which has been shown to display certain properties resembling natural language attributes.

Base Sequence↗
PubMed1998

Data compression and information retrieval via symbolization.

Converting a continuous signal into a multisymbol stream is a simple method of data compression which preserves much of the dynamical information present in the original signal. The retrieval of selected types of information from symbolic data involves binary operations and is therefore optimal for digital computers. For example, correlation time scales can be easily recovered, even at high noise levels, by varying the time delay for symbolization. Also, the presence of periodicity in the signal can be reliably detected even if it is weak and masked by a dominant chaotic/stochastic background. (c) 1998 American Institute of Physics.

Journal Article↗
PubMed1990

Quadtree-based data compression of abdominal CT images.

An ROC study was performed to evaluate the effect of quadtree-based data compression on the diagnostic yield of CT images. Seventy images were selected from a series of consecutive abdominal/pelvic CT scans. Following the application of quadtree-based compression, all images were reviewed independently by three radiologists. The images were analyzed at six decreasing irreversible compression ratios (30.6:1 to 7.4:1), as well as after reversible compression (2.9:1). ROC curves reveal a gradual decrease in clinical accuracy with increasing compression ratios. At a compression ratio of 7.4:1, sensitivity for all major abnormalities was 99% with a specificity of 93%. As the compression ratio was increased to 30.6:1, sensitivity and specificity dropped to 75% and 83% respectively. Execution times for compression and decompression of the CT images with a PC-AT based digital radiography system varied from 24.7 to 18.5 seconds and from 16.2 to 5.1 seconds respectively, decreasing with higher levels of compression. We conclude that quadtree-based compression of abdominal CT images may have practical applications for a PC based digital radiography system.

Algorithms↗
PubMed2004

High performance data compression method with pattern matching for biomedical ECG and arterial pulse waveforms.

Biomedical waveforms, such as electrocardiogram (ECG) and arterial pulse, always possess a lot of important clinical information in medicine and are usually recorded in a long period of time in the application of telemedicine. Due to the huge amount of data, to compress the biomedical waveform data is vital. By recognizing the strong similarity and correlation between successive beat patterns in biomedical waveform sequences, an efficient data compression scheme mainly based on pattern matching is introduced in this paper. The waveform codec consists mainly of four units: beat segmentation, beat normalization, two-stage pattern matching and template updating and residual beat coding. Three different residual beat coding methods, such as Huffman/run-length coding, Huffman/run-length coding in discrete cosine transform domain, and vector quantization, are employed. The simulation results show that our compression algorithms achieve a very significant improvement in the performances of compression ratio and error measurement for both ECG and pulse, as compared with some other compression methods.

Algorithms↗
PubMed2005

Detection of simulated lesions on data-compressed digital mammograms.

PURPOSE: To evaluate retrospectively the effect of a wavelet-based compression method on the detection of simulated masses of various sizes and clustered microcalcifications on data-compressed digital mammograms. MATERIALS AND METHODS: The images used in this study were acquired with institutional review board approval and patient informed consent, both of which allowed subsequent image data analysis. Patient identification was removed from images, and the study complied with requirements of the Health Insurance Portability and Accountability Act. Masses 3, 6, and 8 mm in diameter were analytically simulated and added to clinical mammographic backgrounds. In addition, microcalcifications were extracted from a clinical mammogram and hybridized with simulated microcalcifications for use in this study. Image compression conditions of 1:1, 15:1, and 30:1 were investigated. Observer responses were recorded with a six-point rating scale, and receiver operating characteristic (ROC) analysis was performed. In addition, two well-established numeric observer models were used to study the effect of image compression under the same compression conditions as were used with human observers. Analysis of variance was performed after observer adjustment to compare the mean values for area under the ROC curve (A(z)) across the three compression levels for the masses and microcalcification clusters. RESULTS: The results of the study indicated no significant differences in the A(z) values for masses with the compression conditions investigated. For images of microcalcifications, there were significant differences in A(z) values between compression ratios of 1:1 and 30:1 (P = .0005) and of 15:1 and 30:1 (P = .004); the difference between compression ratios of 1:1 and 15:1 was nonsignificant (P = .053). The observer models and human observers exhibited similar trends in detection of the masses investigated in this study. CONCLUSION: Detection of simulated masses was not affected by the compression method with the conditions used in this study, while the detection of microcalcifications was significantly reduced with a compression ratio of more than 15:1.

Analysis of Variance↗
PubMed2000

Applying computer-assisted detection schemes to digitized mammograms after JPEG data compression: an assessment.

RATIONALE AND OBJECTIVES: The authors' purpose was to assess the effects of Joint Photographic Experts Group (JPEG) image data compression on the performance of computer-assisted detection (CAD) schemes for the detection of masses and microcalcification clusters on digitized mammograms. MATERIALS AND METHODS: This study included 952 mammograms that were digitized and compressed with a JPEG-compatible image-compression scheme. A CAD scheme, previously developed in the authors' laboratory and optimized for noncompressed images, was applied to reconstructed images after compression at five levels. The performance was compared with that obtained with the original noncompressed digitized images. RESULTS: For mass detection, there were no significant differences in performance between noncompressed and compressed images for true-positive regions (P = .25) or false-positive regions (P = .40). In all six modes the scheme identified 80% of masses with less than one false-positive region per image. For the detection of microcalcification clusters, there was significant performance degradation (P < .001) at all compression levels. Detection sensitivity was reduced by 4%-10% as compression ratios increased from 17:1 to 62:1. At the same time, the false-positive detection rate was increased by 91%-140%. CONCLUSION: The JPEG algorithm did not adversely affect the performance of the CAD scheme for detecting masses, but it did significantly affect the detection of microcalcification clusters.

Algorithms↗
PubMed2001

Data compression for arterial pulse waveform.

The arterial pulse possesses important clinical information in traditional Chinese medicine. It is usually recorded for a long period of time in the applications of telemedicine and PACS systems. Due to the huge amount of data, by recognizing the strong correlation between successive beat patterns in arterial pulse waveform sequences, a novel and efficient data compression scheme based mainly on pattern matching is introduced. The simulation results show that our coding scheme can achieve a very high compression ratio and low distortion for arterial pulse waveform.

Computer Simulation↗
PubMedDate not supplied

ECG data compression for the emergency setting.

A low-cost system for digital transmission of the electrocardiogram (ECG) from a remote location to a medical facility under emergency conditions is developed. Delta threshold, Aztec and a hybrid combination of these two data compression techniques are evaluated to determine their ability to accomplish real time transmission of the ECG over a telephone system. The evaluations are performed using ten electrocardiograms representing arrhythmias commonly encountered in the emergency setting. It is shown that the delta threshold technique may cause data expansion under certain conditions. The hybrid technique is the optimum choice and real-time transmission can be accomplished over a 2400 BAUD system.

Data Display↗
PubMed1997

Wavelet transform in electrocardiography--data compression.

An application of the wavelet transform to electrocardiography is described in the paper. The transform is used as a first stage of a lossy compression algorithm for efficient coding of rest ECG signals. The proposed technique is based on the decomposition of the ECG signal into a set of basic functions covering the time-frequency domain. Thus, non-stationary character of ECG data is considered. Some of the time-frequency signal components are removed because of their low influence to signal characteristics. Resulting components are efficiently coded by quantization, composition into a sequence of coefficients and compression by a run-length coder and a entropic Huffman coder. The proposed wavelet-based compression algorithm can compress data to average code length about 1 bit/sample. The algorithm can be also implemented to a real-time processing system when wavelet transform is computed by fast linear filters described in the paper.

Acoustics↗
PubMed2005

Monte Carlo simulation of Li+ motion in polyethylene based on polarization energy calculations and informed by data compression analysis.

We present an n-fold way kinetic Monte Carlo simulation of the hopping motion of Li+ ions in polyethylene on a grid of mesh 0.36 A superimposed on the voids of the rigid polymer. The structure of the polymer is derived from a higher-order simulation, and the energy of the ion at each site is derived by the self-consistent polarization field method. The ion motion evolves in time from free flight through anomalous diffusion to normal diffusion, with the average energy tending to decrease with increasing temperature through thermal annealing. We compare the results with those of hopping models with probabilistic energy distributions of increasing complexity by analyzing the mean-square displacement and the average energy of an ensemble of ions. The Gumbel distribution describes the ion energy statistics in this system better than the usual Gaussian distribution does; including energy correlation greatly affects the ion dynamics. The analysis uses the standard data compression program GZIP, which proves to be a powerful tool for data analysis by giving a measure of recurrences in the ion path.

Journal Article↗
PubMed2003

Parallel stored-integral and semidirect Hartree-Fock and DFT methods with data compression.

Recent developments in magnetic disk technology have made stored-integral techniques competitive with the currently more widely used direct methods, which involve the recalculation of the basic two-electron integrals. We present efficient conventional (all integrals stored) and semidirect Hartree-Fock and DFT algorithms with data compression for single-processor and distributed memory parallel computers, and compare them with the corresponding direct algorithms. On inexpensive modern personal computer-based hardware, the stored integral method is up to three times more efficient than the direct method in terms of total elapsed job time.

Journal Article↗
PubMed2003

Traveling front solutions to directed diffusion-limited aggregation, digital search trees, and the Lempel-Ziv data compression algorithm.

We use the traveling front approach to derive exact asymptotic results for the statistics of the number of particles in a class of directed diffusion-limited aggregation models on a Cayley tree. We point out that some aspects of these models are closely connected to two different problems in computer science, namely, the digital search tree problem in data structures and the Lempel-Ziv algorithm for data compression. The statistics of the number of particles studied here is related to the statistics of height in digital search trees which, in turn, is related to the statistics of the length of the longest word formed by the Lempel-Ziv algorithm. Implications of our results to these computer science problems are pointed out.

Journal Article↗
PubMed1995

Effect of data compression on quantitative coronary measurements.

Digital coronary and left ventricular angiography demand high transfer rates and very large data storage if all the clinical data are to be achieved. If appropriate compression schemes were available without compromising the quality and resolution of the image data, such demands could be lessened. In this study we compared the influence of different compression factors of the Adaptive Real Time Image Compression (ARTIC) scheme used on the Philips DCI-SX systems on coronary measurements assessed with the Automated Coronary Analysis (ACA) package. Loss-free acquired images of size 512(2) x 8 bits, which had been stored digitally on tape, were reloaded into the DCI with compression factors of 2, 3, and 4; only the factor 2 is loss free. To evaluate the effect of the different data compressions on the accuracy of the measurements, the diameters of a vessel phantom (tube sizes ranging from 0.687 to 5.062 mm) were determined. To evaluate the reproducibility of the results, the intraobserver variability was determined for the different compression factors from 40 coronary obstructions. The differences in the reference diameter measurements of the vessel phantom were -0.03 +/- 0.06 mm, 0.01 +/- 0.07 mm, and 0.04 +/- 0.08 mm for the compression factors 2 (loss free), 3, and 4, respectively. The results were not statistically significantly different. The intraobserver variabilities in the obstruction diameter measurements of the coronary obstructions were -0.04 +/- 0.13 mm, 0.00 +/- 0.14 mm, and 0.02 +/- 0.13 mm for the compression factors 2, 3 and 4, respectively. The intraobserver variabilities in the reference diameter measurements were -0.02 +/- 0.12 mm, 0.01 +/- 0.09 mm, and 0.03 +/- 0.09 mm for the compression factors 2, 3, and 4, respectively. The intraobserver variabilities of the percent diameter stenosis were 0.96 +/- 4.19%, -0.01 +/- 4.88% and -0.04 +/- 4.68% for the compression factors 2, 3, and 4, respectively. None of these differences were statistically significant. Both from a qualitative and quantitative point of view, data compression factors 3 and 4 are acceptable in digital coronary arteriography.

Coronary Angiography↗
PubMed2005

Data compression for speckle correlation interferometry temporal fringe pattern analysis.

Temporal fringe pattern analysis is gaining prominence in speckle correlation interferometry, in particular for transient phenomena studies. This form of analysis, nevertheless, necessitates large data storage. Current compression schemes do not facilitate efficient data retrieval and may even result in important data loss. We describe a novel compression scheme that does not result in crucial data loss and allows for the efficient retrieval of data for temporal fringe analysis. In sample tests with digital speckle interferometry on fringe patterns of a plate and of a cantilever beam subjected to temporal phase and load evolution, respectively, we achieved a compression ratio of 1.6 without filtering out any data from discontinuous and low fringe modulation spatial points. By eliminating 38% of the data from discontinuous and low fringe modulation spatial points, we attained a significant compression ratio of 2.4.

Journal Article↗
PubMed2006

Efficient transmission of compressed data for remote volume visualization.

One of the goals of telemedicine is to enable remote visualization and browsing of medical volumes. There is a need to employ scalable compression schemes and efficient client-server models to obtain interactivity and an enhanced viewing experience. First, we present a scheme that uses JPEG2000 and JPIP (JPEG2000 Interactive Protocol) to transmit data in a multi-resolution and progressive fashion. The server exploits the spatial locality offered by the wavelet transform and packet indexing information to transmit, in so far as possible, compressed volume data relevant to the clients query. Once the client identifies its volume of interest (VOI), the volume is refined progressively within the VOI from an initial lossy to a final lossless representation. Contextual background information can also be made available having quality fading away from the VOI. Second, we present a prioritization that enables the client to progressively visualize scene content from a compressed file. In our specific example, the client is able to make requests to progressively receive data corresponding to any tissue type. The server is now capable of reordering the same compressed data file on the fly to serve data packets prioritized as per the client's request. Lastly, we describe the effect of compression parameters on compression ratio, decoding times and interactivity. We also present suggestions for optimizing JPEG2000 for remote volume visualization and volume browsing applications. The resulting system is ideally suited for client-server applications with the server maintaining the compressed volume data, to be browsed by a client with a low bandwidth constraint.

Algorithms↗
PubMed2005

Fourier-transform method of data compression and temporal fringe pattern analysis.

Temporal fringe pattern analysis is invaluable in studies of transient phenomena but necessitates large data storage for two essential sets of data, i.e., fringe pattern intensity and deformation phase. We describe a compression scheme based on the Fourier-transform method for temporal fringe data storage that permits retrieval of both the intensity and the deformation phase. When the scheme was used with simulated temporal wavefront interferometry intensity fringe patterns, a high compression ratio of 10.77 was achieved, with a significant useful data ratio of 0.859. The average root-mean-square error in phase value restored was a low 0.0015 rad. With simulated temporal speckle interferometry intensity fringe patterns, the important paremeters varied with the modulation cutoff value applied. For a zero modulation cutoff value, the ratio of data points and the compression ratio values obtained were roughly the same as in wavelength interferometry, albeit the average root-mean-square error in the phase value restored was far higher. By increasing the modulation cutoff value we attained significant reduction and increase in the ratio of data points and the compression ratio, respectively, whereas the average root-mean-square error in the restored phase values was reduced only slightly.

Algorithms↗
PubMed1999

[Studies on data compression of 1-D NMR spectra using wavelet transform].

The multiresolution signal decomposition (MRSD) algorithm based on wavelet transform was applied to the compression of 1-D NMR spectra. A NMR spectrum which was composed of 32768 data points was investigated and the spectrum can be completely reconstructed with the residual square deviation (RSD) being as small as 2.7769 x 10(-4) when the spectrum was compressed to 512 data points. The relationship among the RSD and the different wavelet function, number of decomposiion and the compression ratio was also discussed.

English Abstract↗
PubMed1999

Compression data on bovine bone confirms that a "stressed volume" principle explains the variability of fatigue strength results.

The literature contains many measurements of the fatigue properties of compact bone, but these experimental results have been difficult to interpret and use due to a large amount of apparent scatter: variation in the number of cycles to failure for a given cyclic stress or strain range. Recently Taylor (1998a, Journal of Orthopaedic Research, 16, 163-169) showed that much of this scatter could be explained using a statistical model which took into account specimen size, or more specifically stressed volume. The present paper describes an attempt to test this model by using it to predict some new data, for bovine bone tested in compressive loading at room temperature at physiological loading rates. Twenty specimens were tested at the same applied load range (100 MPa). The theory was able to predict the mean behaviour of the specimens very well, with an accuracy (expressed in terms of stress) of 2%. It was also able to predict the degree of scatter (i.e. the variation of Nf), which was shown to be similar to that measured by other workers.

Animals↗