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Results for “Classification Algorithms”

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PubMed1990

System for flow sorting chromosomes on the basis of pulse shape.

Sorting on the basis of the complex features resolved by chromosome slit-scan analysis requires rapid and flexible pulse shape acquisition and processing for determining sort decisions before droplet breakoff. Fluorescence scans of chromosome morphology contain centromeric index and banding information suitable for chromosome classification, but these scans are often characterized by variability in length and height and require sophisticated data processing procedures for identification. Setting sort criteria on such complex morphological data requires digitization and subsequent computation by an algorithm tolerant of variations in overall pulse shape. We demonstrate here the capability to sort individual chromosomes based on their morphological features measured by slit-scan flow cytometry. To do this we have constructed a sort controller capable of acquiring an 128 byte chromosome waveform and executing a series of numerical computations resulting in an area-based centromeric index sort decision in less than 2 ms. The system is configured in a NOVIX microprocessor, programmed in FORTH, and interfaced to a slit-scan flow cytometer data acquisition system. An advantage of this configuration is direct control over the machine state during program execution for minimal processing time. Examples of flow sorted chromosomes are shown with their corresponding fluorescence pulse shapes.

Animals↗

PubMedDate not supplied

Image processing for the rest of us: the potential utility of inexpensive computerized image analysis in clinical pathology and radiology.

Recent progress in computer technology in both hardware and software, combined with marked cost reductions, have placed quantitatively accurate video densitometry systems within the reach of the individual clinician, biomedical researcher, and community hospital. While much of the attention generated by advances in image processing has focussed on larger scale procedures, such as CAT, chemical shift, and positron emission tomography, important applications can be found for considerably more modest systems. In this article, we discuss three such applications of DUMAS, a personal computer-based imaging system developed by the Image Processing Center at Drexel University. A potential technique for quantifying numbers of estrogen receptors in tumorous breast tissue samples as a predictor of patient responsiveness to hormonal therapy is described first, along with possible sources of error. The second application, also related to clinical pathology and cancer, outlines methods for relating changes in nuclear and cell morphology to the diagnosis of Sezary Cell Syndrome. The utility of binary image filtering methods in the classification of cell types is discussed. The third application involves the development of a semi-automatic procedure for the determination of vessel diameter in arteriograms. A detailed description of the optimization and curve-fitting algorithms is provided along with preliminary test results comparing various approaches. The need for user demand to fuel research and development in small-scale imaging systems is also discussed.

Algorithms↗

PubMed1992

Histopathological prediction of liver metastasis after curative resection of colorectal cancer.

To estimate the risk of liver metastasis after curative resection of colorectal cancer, resected specimens from 290 patients (45 with metachronous liver metastasis) were examined and the relationships between 10 histopathological variables and liver metastasis were analysed using our application of the Akaike information criterion (AIC). Of the 10 variables examined, the depth of venous invasion (Vd) had the greatest prognostic value for metastasis, followed by the number of venous invasions, the number of lymphovascular invasions, lymph node metastasis and type of infiltration. The prediction of liver metastasis was further improved by combining Vd with lymphocyte infiltration, mucinous production, interstitial fibrosis or depth of penetration, although these four variables per se were minimally informative for metastasis. We conclude that the prediction of liver metastasis is best achieved by combining Vd with other variables. Our risk group classification, and the estimated probability of liver metastasis for each group, are shown.

Adenocarcinoma↗

PubMedDate not supplied

Staging of maxillary cancer. Which classification?

Of the many proposed classifications for staging maxillary sinus cancer, none has been adopted universally and none is known to be superior to the others. This study identified the best of six currently used classifications using data from 53 previously untreated patients with squamous cell carcinoma of the maxillary sinus. Analysis of each classification's ability to stage the majority of patients, produce a balanced distribution of T stages, and correlate T stage with treatment and prognosis revealed Harrison's classification to be the best. Harrison's classification should be adopted worldwide as the classification of choice for staging squamous cell carcinoma of the maxillary sinus.

Algorithms↗

PubMed1994

DNA sequence analysis using hierarchical ART-based Classification Networks.

Adaptive resonance theory (ART) describes a class of artificial neural network architectures that act as classification tools which self-organize, work in realtime, and require no retraining to classify novel sequences. We have adapted ART networks to provide support to scientists attempting to categorize tandem repeat DNA fragments from Onchocerca volvulus. In this approach, sequences of DNA fragments are presented to multiple ART-based networks which are linked together into two (or more) tiers; the first provides coarse sequence classification while the subsequent tiers refine the classifications as needed. The overall rating of the resulting classification of fragments is measured using statistical techniques based on those introduced by Zimmerman, et al. (1994) to validate results from traditional phylogenetic analysis. Tests of the Hierarchical ART-based Classification Network, or HABclass network, indicate its value as a fast, easy-to-use classification tool which adapts to new data without retraining on previously classified data.

Algorithms↗

PubMed1989

Classification and evaluation of the obesities.

Obesity is a condition of multifactorial etiology that can be associated with important health and functional consequences. Suggestions for the proper evaluation of obese patients have been presented along with brief descriptions of the rationales for their use. The evaluation protocol has been summarized in two algorithms to aid in the performance of a complete and organized work-up.

Adipose Tissue↗

PubMed1982

Numerical classification of some Rhodococci, Corynebacteria and related organisms.

Nineteen strains of Corynebacterium sensu stricto, 23 received as Corynebacterium equi or Rhodococcus equi, marker cultures of Arthrobacter, Brevibacterium, Bacterionema matruchotii, Cellulomonas flavigena, Kurthia zopfii, Listeria denitrificans, Microbacterium lacticum, Rhodococcus rubropertinctus and 88 representatives of Mycobacterium, Nocardia, Rhodococcus and the 'aurantiaca' taxon were the subject of numerical phenetic analyses using 92 characters. The data were examined using the simple matching (SSM) and Jaccard (SJ) coefficients and clustering was achieved using the average linkage algorithm. With a single exception, strains containing meso-diaminopimelic acid, arabinose, galactose and mycolic acids were recovered in five aggregate clusters corresponding to Corynebacterium sensu stricto, Mycobacterium, Nocardia, Rhodococcus and the 'aurantiaca' taxon. Most of the Corynebacterium (Rhodococcus) equi strains formed a good taxospecies which included the type strain of Corynebacterium hoagii. The numerical data, and the results of earlier chemical and genetical studies, also provide sufficient evidence for the transfer of Bacterionema matruchotii to Corynebacterium sensu stricto as Corynebacterium matruchotii comb.nov. and for the recognition of Rhodococcus globerulus sp.nov. for some strains previously classified as Rhodococcus rubropertinctus (Hefferan) Goodfellow & Alderson. The classification of the remaining marker strains correlates well with other major developments in coryneform taxonomy.

Actinomycetales↗

PubMed1991

Speaker normalization of static and dynamic vowel spectral features.

Two methods are described for speaker normalizing vowel spectral features: one is a multivariable linear transformation of the features and the other is a polynomial warping of the frequency scale. Both normalization algorithms minimize the mean-square error between the transformed data of each speaker and vowel target values obtained from a "typical speaker." These normalization techniques were evaluated both for formants and a form of cepstral coefficients (DCTCs) as spectral parameters, for both static and dynamic features, and with and without fundamental frequency (F0) as an additional feature. The normalizations were tested with a series of automatic classification experiments for vowels. For all conditions, automatic vowel classification rates increased for speaker-normalized data compared to rates obtained for nonnormalized parameters. Typical classification rates for vowel test data for nonnormalized and normalized features respectively are as follows: static formants--69%/79%; formant trajectories--76%/84%; static DCTCs 75%/84%; DCTC trajectories--84%/91%. The linear transformation methods increased the classification rates slightly more than the polynomial frequency warping. The addition of F0 improved the automatic recognition results for nonnormalized vowel spectral features as much as 5.8%. However, the addition of F0 to speaker-normalized spectral features resulted in much smaller increases in automatic recognition rates.

Adult↗

PubMed1991

Echographic differentiation of histological types of intraocular melanoma.

The aim of this study was to assess the differentiation of histologically different types of choroidal melanomas by means of clinical and quantitative acoustic/texture parameters of echograms. Clinical parameters were graded by morphological, kinetic and quantitative statements about the A- and B-mode echograms by a skilled diagnostician. Acoustic/texture parameters were obtained by processing and analysing radio frequency, AM-demodulated and FM-demodulated echograms. The data were preprocessed to remove influences induced by beam diffraction and focusing. The correlations between the clinical parameters were lower than 0.5 but significant in a few cases. The best set of four clinical echographic parameters enabled a retrospective classification of spindle type melanomas vs. mixed + epithelioid type melanomas with an accuracy of 77% (area under the ROC-curve of 86%). These figures do not enable, however, a prospective diagnosis. The correlations of the clinical parameters with the acoustic/texture parameters were investigated. The mutual correlations between the latter parameters were also assessed, the most significant (0.70) being between the speckle size and the slope of the linearized backscattering spectrum. The discriminant analysis performed with the best four acoustic/texture parameters (n = 30) yielded a sensitivity of 89%, a specificity of 92% and an area under the ROC-curve corresponding to a probability of correct classification of 96.6%. When using these data prospectively to classify tumours of unknown cell type (n = 21), this classification could be performed in 86% of cases.

Algorithms↗

PubMed1992

Echographic differentiation of intraocular melanomas by computer analysis.

The aim of this study was to assess the differentiation of histologically different types of choroidal melanomas by means of clinical and quantitative acoustic/texture parameters of echograms. Clinical parameters were graded by morphological, kinetic and quantitative statements about the A- and B-mode echograms by a skilled diagnostician. Acoustic/texture parameters were obtained by processing and analysing radio frequency, AM-demodulated and FM-demodulated echograms. The latter data were preprocessed to remove influence induced by beam diffraction and focusing. The best set of four clinical echographic parameters enabled a retrospective classification of spindle type melanomas vs. mixed+epithelioid type melanomas with an accuracy of 77% (area under the ROC-curve of 86%). The discriminant analysis performed with the best four acoustic/texture parameters (n = 30) yielded a sensitivity of 89%, a specificity of 92%, and an area under the ROC-curve which corresponds to a probability of correct classification of 96.6%. When using these data prospectively to classify tumours of unknown cell type (n = 21), this classification could be performed in 86% of cases.

Algorithms↗

PubMed1991

Flow phenomena, classification, and clinical aspects of magnetic resonance angiography.

Both time-of-flight and phase-contrast techniques are currently being employed in producing angiographic MR images of arteries and veins. Both two-dimensional and three-dimensional acquisition methods can be used to display projective vascular images with the maximum intensity projection algorithm, eliminating the need for image subtraction. MR angiography has expanded the armamentarium of MR imaging, especially in the head and neck, and should in some organ systems reduce the need for conventional x-ray catheter angiography.

Blood Flow Velocity↗

PubMed1989

Adapting best linear unbiased prediction (BLUP) for timely genetic evaluation: II. Progeny traits in multiple contemporary groups within a herd.

The second step of a procedure to partially circumvent the voluminous calculations for some BLUP (Best Linear Unbiased Prediction) computing algorithms for genetic evaluation is presented. In addition, the procedure allows timely evaluations of each contemporary group. This procedure is pertinent especially for polytocous species such as swine and poultry, for which the occurrence of full-sib families makes the inclusion of dam effects in the model necessary and tests are completed throughout the year. Formulas are developed for a model including sires, dams, individuals within full-sib families and records within individuals. This model has a fundamentally hierarchical structure but includes some cross-classification. The formulas for predictors combine information across contemporary groups within a herd and incorporate relationships between sires and(or) dams in that herd. Formulas to approximate prediction error variances also are developed.

Algorithms↗

PubMed1988

A numerical classification of the genus Bacillus.

Three hundred and sixty-eight strains of aerobic, endospore-forming bacteria which included type and reference cultures of Bacillus and environmental isolates were studied. Overall similarities of these strains for 118 unit characters were determined by the SSM, SJ and DP coefficients and clustering achieved using the UPGMA algorithm. Test error was within acceptable limits. Six cluster-groups were defined at 70% SSM, which corresponded to 69% SP and 48-57% SJ. Groupings obtained with the three coefficients were generally similar but there were some changes in the definition and membership of cluster-groups and clusters, particularly with the SJ coefficient. The Bacillus strains were distributed among 31 major (4 or more strains), 18 minor (2 or 3 strains) and 30 single-member clusters at the 83% SSM level. Most of these clusters can be regarded as taxospecies. The heterogeneity of several species, including Bacillus brevis, B. circulans, B. coagulans, B. megateriun, B. sphaericus and B. stearothermophilus, has been indicated and the species status of several taxa of hitherto uncertain validity confirmed. Thus on the basis of the numerical phenetic and appropriate (published) molecular genetic data, it is proposed that the following names be recognized; Bacillus flexus (Batchelor) nom. rev., Bacillus fusiformis (Smith et al.) comb. nov., Bacillus kaustophilus (Prickett) nom. rev., Bacillus psychrosaccharolyticus (Larkin & Stokes) nom. rev. and Bacillus simplex (Gottheil) nom. rev. Other phenetically well-defined taxospecies included 'B. aneurinolyticus', 'B. apiarius', 'B. cascainensis', 'B. thiaminolyticus' and three clusters of environmental isolates related to B. firmus and previously described as 'B. firmus-B. lentus intermediates'. Future developments in the light of the numerical phenetic data are discussed.

Bacillus↗

PubMed1991

Molecular modeling of antibody combining sites.

Each of the six CDRs of Gloop2 is shown with the modeled structure in. Overall, the results obtained using the combined algorithm are similar in accuracy to those achieved using the canonical method of Chothia et al. However, the canonical method is limited to those loops where the key residues identified by Chothia are present. With the number of antibody structures currently available, it is not possible to classify CDR-H3 into canonical ensembles. Additionally, a small percentage of examples in the remaining CDRs do not match the current canonical classifications and the protein engineer may well wish to mutate the key residues, precluding the use of Chothia's method for modeling the resulting conformation. Thus the best approach appears to be to use Chothia's method (at least to model the backbone conformation) when the loop to be modeled is represented in the database of canonical structures. Any other loops, either unrepresented among the known canonicals (including CDR-H3), or where mutations have been made to the key residues, may then be modeled by the combined algorithm presented here.

Algorithms↗

PubMed1990

An introduction to Anatomical Image Digitizing System (AIDS).

We designed, constructed, and evaluated a prototype of a digital data management system for anatomical studies and education, named AIDS (Anatomical Image Digitizing System). By implementing the prototype systems, we intended to determine the technical and anatomical parameters required for such a system, and to attempt digital imaging analysis of morphology. We demonstrated that such systems can be used as a new morphological tool on a macroscopic level, particularly in mathematical image analysis, in comparative anatomy by organizing a database and by modifying images with graphic techniques, and in statistical discussions by manipulating large numbers of illustrations quickly. A 512 X 512 X 8 bit matrix is judged to be satisfactory for analyzing images mathematically and producing illustrations of bones, but higher quality tools are required to store anatomical figures with halftones in a good condition, and to prepare fine anatomical illustrations. Classifications of figures and formats of figure legends are necessary to standardize the storage of figures in the form of a database.

Algorithms↗

PubMedDate not supplied

A conversational program for hierarchic and non-hierarchic cluster analysis.

The theoretical basis and the features of some cluster analysis programs are described in this paper. These programs use as input data an N x M matrix. For the N' less than or equal to N set of individuals, the cross-correlation matrix, R = (rij), is then calculated. The dissimilarity matrix, D = (dhk), and the distribution histogram of the distances between each pair is worked out. Hierarchic and non-hierarchic clustering techniques are allowed. Using the non-hierarchic strategy, the non-overlapping clusters are then separated into different groups. The distances between these groups are calculated and statistical tests of significance are performed. In the hierarchic case, a dendrogram is drawn using an agglomerative algorithm. As an example the programs (written in FORTRAN, batch or TSS version) were used to classify human mitotic chromosomes.

Classification↗

PubMed1990

Rough sets approach to the analysis of the structure-activity relationship of quaternary imidazolium compounds.

The relationship between chemical structure and antimicrobial activity of 201 quaternary imidazolium compounds is analysed using the theory of rough sets. The compounds are described by 8 attributes concerning structure and are divided into 5 classes of activity. The description builds up on information system. Using the rough sets approach, first a minimum set of 4 attributes significant for a high quality of classification has been found. The analysis of distribution of values of significant attributes in the best and worst class led to the definition of typical representatives of best and worst compounds in terms of significant attributes. Finally, a decision algorithm has been driven from information system, showing important relations between structure and activity. It may be helpful in supporting decisions concerning the synthesis of new antimicrobial compounds.

Algorithms↗

PubMedDate not supplied

[Informatics in mental sciences: clinical data management and "expert systems"].

The role of information systems and particularly that of expert systems in medicine is analysed in brief. It is pointed out that, unlike other branches of medicine, in mental sciences the role of expert systems has so far been more limited because of certain intrinsic problems of programming on the one hand, and the scientific models of the psychiatrist on the other. An improvement in information technology and programming languages and better empirical classification of mental disturbances could provide useful bases for the realisation of computerised consultancy systems in mental sciences.

Algorithms↗