Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Feature selection”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources
PubMed1985

Biological factors predisposing to traumatic posterior dislocation of the hip. A selection process in the mechanism of injury.

The factors involved in the mechanism leading to traumatic posterior dislocation of the hip are examined. In 47 adult patients who had previously suffered such a dislocation, ultrasound scans were used to measure femoral anteversion on both the affected and the uninjured side. In 36 normal adult volunteers, used as controls, similar measurements were made. Femoral anteversion on both the injured and uninjured side was significantly reduced in the patients compared with the volunteers. These findings are discussed in the light of previous work which indicates that medial rotation is a factor in the mechanism of posterior dislocation of the hip. It is suggested that reduced anteversion acts like medial rotation to make the hip more susceptible to posterior dislocation, and that the less the anteversion the more likely is the injury to be a dislocation rather than a fracture-dislocation. It is concluded that patients who suffer such dislocated hips belong at one extreme of the normal population, having either reduced femoral anteversion or even retroversion, and that this anatomical feature selects towards hip dislocation rather than to injury of the femoral shaft, knee or tibia during the appropriate type of accident.

Adult↗
PubMed1992

Acoustic-phonetic contrasts and intelligibility in the dysarthria associated with mixed cerebral palsy.

This study evaluated the relationship between specific acoustic features of speech and perceptual judgments of word intelligibility of adults with cerebral palsy-dysarthria. Use of a contrasting word task allowed for intelligibility analysis and correlated acoustic analysis according to specified spectral and temporal features. Selected phonemic contrasts included syllable-initial voicing; syllable-final voicing; stop-nasal; fricative-affricate; front-back, high-low, and tense-lax vowels. Speech materials included a set of CVC stimulus words. Acoustic data are reported on vowel duration, formant frequency locations, voice onset times, amplitude rise times, and frication durations. Listeners' perceptual assessment of intelligibility of the 16 dysarthric adults by transcription and rating tasks is also presented. All but one acoustic contrast was successfully made as evidenced by measured acoustic differences between contrast pairs. However, the generally successful acoustic contrasts stood in marked contrast to the poorly rated intelligibility scores and high error percentages that were ascribed to the opposite pair members. A second analysis examined the contribution of these acoustic features towards estimates and prediction of intelligibility deficits in speakers with dysarthria. The scaled intelligibility was predicted by multiple regression analysis with 62.6% accuracy by acoustic measures related to one consonant contrast (fricative-affricate) and three vowel contrasts (front-back, high-low, and tense-lax). Other measured contrasts, such as those related to contrast voicing effects and stop-nasal distinctions, did not seem to contribute in a significant way to variability in the intelligibility estimates. These findings are discussed in relation to specific areas of production deficiency that are consistent across different types of dysarthria with cerebral palsy as the etiology.

Adult↗
PubMed1998

Evaluation of a statistically derived decision tree for the cytodiagnosis of fine needle aspirates of the breast (FNAB).

A decision tree for the diagnosis of FNAB was derived from defined human observations using a rule induction method, C4.5 (a derivative of the ID3 algorithm). This algorithm is an implementation of the top-down induction method where the tree is determined iteratively by adding those nodes and branches which maximize the information gain at each step. The tree was derived from a training set of 200 FNAB with known outcome using 10 defined features (from one observer) and patient age. The tree contained a total of seven nodes (six observable features and patient age) with eight endpoints (four benign, four malignant). The tree was applied to a test set of 400 further FNAB with observations from the training observer and produced a sensitivity of 95%, specificity of 93% and a positive predictive value (PPV) of a malignant result of 89%. Four trainee pathologists were given a training session on the observable features and then used the tree to determine outcome in a further 50 FNAB. The observers were blind to clinical details apart from age and the endpoints were coded with letters and not labelled benign or malignant. The results from these observers produced ranges of sensitivity 80-96%, specificity 64-92%, PPV 73-92% and kappa statistics (with known outcome) 0.6-0.8. Reported difficulties in using the tree included estimation of nuclear size. These results were worse than the performance of the observers on a further 50 cases without using the decision tree (sensitivity 80-100%, specificity 72-100%, PPV 78-100%, kappa 0.72-0.92). The original 50 case test set was rerandomized and the four trainee observers made all 10 defined observations on each specimen without using the decision tree; these observations were then used to derive decisions from the tree. The performance from this method was similar to that using selected features from the tree, suggesting that observation of all features together does not improve the reliability of each specific observation. The poor performance of this tree suggests that this methodology may be unsuitable for producing decision support aids for diagnostic or training purposes in this domain.

Biopsy, Needle↗
PubMed1998

Association of prognosis in surgically treated lung cancer patients with cytometric, histometric and ligand histochemical properties: with an emphasis on structural entropy.

OBJECTIVE: To explore new tumor features for refined category formation that permits the tailoring of individualized treatment schemes in lung cancer. STUDY DESIGN: Survival data on patients from six independent studies on cases with surgically treated lung cancer, primary lung carcinoids or metastasizing breast carcinoma (including data on primary breast carcinoma) were analyzed by nonhierarchic multivariant discriminant analysis with respect to a set of cytometric/histometric and immunohistochemical/ligand histochemical parameters. The number of stem lines, S-phase-related tumor cell fraction and the extent of structural entropy and its current were measured. In addition, the expression of binding capacities for histo-blood group trisacharides, galectins, the alpha/beta-interferon antagonist sarcolectin, the lymphokine macrophage migration inhibitory factor and a monoclonal antibody to the Le(y) epitope was monitored for insight into aspects of immunologic and biologic behavior. RESULTS: In all studies, a correlation between tumor parameters, according to TNM stage and survival, was seen. In order to refine this category formation, at least certain selected features should provide an even more stringent association than TNM stages. Indeed, statistical correlation of the cytometric and histometric parameters as well as the expression of receptors for the two histo-blood group trisaccharides, ligands for the galectins (CL-16, CL-14) and macrophage migration inhibitory factor was stronger than that of TNM stage. A large amount of the current of structural entropy was especially highly significantly associated with poor survival. This observation could be verified in each of the different studies. CONCLUSION: The obtained data strongly support the notion that thermodynamic evaluation of tumor growth focusing on the "entropy distance" of the tumor from its environment is a promising perspective warranting extended studies. Additionally, glycohistochemical features, including binding capacities for histo-blood group trisaccharides, have the potential to aid in establishment of a biologic marker set for tumor staging.

Biomarkers, Tumor↗
PubMed2026

Transfer Learning across Material Properties Using Center-Environment Features: From Energetics to Mechanical Properties in Multicomponent Mo Alloys.

Transfer learning (TL) provides a viable approach to mitigate data scarcity in materials informatics. While conventional TL focuses on predicting identical properties across different systems, this work demonstrates a cross-property extension of TL from energy to mechanical properties via end-to-end model weight pre-training and fine-tuning: knowledge learned from predicting substitution energies is transferred to predict distinctly different mechanical properties, substantially improving computational efficiency given the typically higher cost of acquiring target-domain data. To accelerate computational alloy design, machine learning models using center-environment (CE) features were first developed to predict substitution energies of alloying elements in molybdenum (Mo)-based alloys. The Random Forest models achieved the optimal performance and transferability-R2 = 0.97, 〈MAE〉 = 0.11 eV, and 〈RMSE〉 = 0.16 eV-against the density functional theory (DFT) benchmark. The model dependency of feature selection and importance analysis was discussed. The transferability of the energy models was validated on unknown systems with new elements. Subsequently, the energy models were fine-tuned using limited mechanical property data to construct energy-to-property (E2P) TL models capable of predicting elastic properties, including bulk modulus, Young's modulus, shear modulus, and elastic constants, achieving an improved accuracy over the non-transferred ML by ∼10-30%, with its transferability verified by additional DFT calculations. This cross-property E2P transfer learning framework opens a new avenue for accelerating computational materials discovery and may be extended to other multiproperty predictions governed by similar physical principles.

center-environment feature↗
PubMed1996

Differential distribution of Fos-like immunoreactivity in the spinal trigeminal nucleus after noxious and innocuous thermal and chemical stimulation of rat cornea.

Corneal afferent nerves project to two spatially distinct sites within the spinal trigeminal nucleus: the subnucleus interpolaris/caudalis transition and the subnucleus caudalis/upper cervical spinal cord transition. The role of these two regions in processing corneal input is uncertain. To determine if neurons in these regions encode different features of an applied corneal stimulus, immunoreactivity for the immediate early gene protein product, Fos, was quantified in barbiturate-anesthetized rats. Intensity was varied across thermal (thermal probe 5, 35, 42, 52 degrees C; radiant heat of approximately 45 degrees C) stimuli and compared with that seen after mustard oil (5 microliters, 20%) or mineral oil application. All stimuli increased the number of Fos-positive neurons located at the ventrolateral pole of the subnucleus interpolaris/caudalis transition compared with unstimulated controls. By contrast, only 52 degrees C thermal probe and mustard oil produced an additional peak of Fos-positive neurons within the superficial laminae at the subnucleus caudalis/cervical cord transition. Further, the magnitudes of the bimodal peaks of Fos produced by 52 degrees C thermal probe and mustard oil stimuli were different quantitatively. Mustard oil caused a greater Fos response at the subnucleus interpolaris/caudalis transition than 52 degrees C thermal probe stimulation, whereas the opposite was true at the subnucleus caudalis/cervical cord transition. Double-labeling revealed that Fos immunoreactive neurons within the spinal trigeminal nucleus were restricted to regions densely labeled for calcitonin gene-related peptide. These results indicate that select features of corneal stimuli such as modality are encoded differently by neurons in the trigeminal subnucleus interpolaris/caudalis transition compared with those located in the subnucleus caudalis/cervical cord transition. It is likely that neurons in these two brainstem regions subserve different aspects of corneal sensation.

Animals↗
PubMed2002

Detecting genomic features under weak selective pressure: the example of codon usage in animals and plants.

Large scale experiments of gene inactivation in yeast have shown that 50% of genes have no detectable impact on the phenotype, and similar observations have been made in other model organisms. This apparent paradox is probably due to the fact that many genes only have a marginal contribution to the fitness of organisms. Because of the size of populations and the number of generations that can be studied in laboratories, experimental approaches only permit to detect functional elements that have a strong phenotypic impact. Comparative sequence analysis can help to solve this problem: the analysis of sequences evolution permits to detect the action of selection, and hence to reveal functional features of genomes. This approach will be illustrated by the study of synonymous codon usage in animals and plants.

Animals↗
PubMed1991

Three-dimensional reconstruction of temporal bone from computed tomographic scans on a personal computer.

The advantages of computer reconstruction of anatomical structures from computed tomographic scans are common knowledge by now. Unfortunately, to date most reconstructions have required the use of large computers and/or have entailed tedious manual contour tracing. The system described here allows largely automatic detection of surfaces in computed tomographic scans plus the usual display capabilities including feature selection, magnification, rotation, shading, and slicing as well as measurement of lengths and angles. It runs on a normal International Business Machines AT-compatible computer with a medium-resolution video card.

Child↗
PubMed1980

Discontinuing therapy in childhood acute lymphocytic leukemia. A multicentric survey in Italy.

The results of discontinuing therapy in children with acute lymphocytic leukemia observed at four associated institutions are presented. Of the 247 patients who achieved complete remission, 122 (49.3%) reached the point of discontinuing therapy after 2-4 years of continuous remission. The median period off therapy was 13 months with a range of 1-69 months. Of the 122 children removed from therapy, 27 (22.1%) relapsed, mainly in the bone marrow; relapses occurred 1-32 months after cessation of therapy (median ten months) with only two relapses occurring later than two years. By actuarial analysis, 57% of the patients are projected in continuous remission after five years from cessation of therapy. Neither selected features at diagnosis nor single modalities of treatment were found to predict whether relapse would occur after discontinuing therapy. Long-term remission and possibly cure can be expected in over one-third of newly diagnosed children with ALL after 2-4 years of antileukemic treatment.

Adolescent↗
PubMed2001

Multiresolution image registration for two-dimensional gel electrophoresis.

In proteomic research, two-dimensional electrophoresis (2-D) is an important tool for investigating differential patterns of qualitative and quantitative protein expression. The strength of the technique is due to its unrivalled power of being able to separate simultaneously thousands of proteins. The key to the comparison of 2-D protein profiles, however, lies in the use of a fast and robust image matching process which is essential to the subsequent quantification procedure. To satisfy the growing demand for a robust and fully automatic method of matching 2-D gel protein separation profiles, we describe in this paper a novel registration technique based on image intensity distribution rather than selected features. The method uses a multiresolution representation of the gel profiles and exploits the fact that coarse approximations to the optimal matching can be extracted efficiently from low-resolution images. This permits the removal of misalignments at different scales in a systematic manner and the strength of the new method has been confirmed by a double blind trial of 111 2-D gel pairs. The proposed method requires neither landmarks nor an a priori image alignment, and takes about five seconds for processing a typical gel pair on a standard personal computer.

Algorithms↗
PubMed1983

The functional significance of tumour-associated cell surface alterations of embryonic and unknown origin.

The study of the phenotype of tumours aims to elucidate cell surface alterations that could be used for diagnostic, prognostic or therapeutic purposes. As tumours tend to escape the homeostatic growth control mechanisms of the host, it can be assumed that plasma membrane alterations are also responsible for the antisocial behaviour of tumour cells. Selected features of the transformed phenotype, of fetal or unknown origin, namely tumour-associated antigens, isozymes and growth factors, are discussed in relation to the altered growth pattern of the tumour cell. It is concluded that definitive structure-function relationships have not yet been established, but areas for future investigation are suggested.

Animals↗
PubMed1989

On fully automatic feature measurement for banded chromosome classification.

Procedures for fully automatic location of chromosome axis and centromere in metaphase chromosomes are described for a practical interactive chromosome analysis system that omits the usual stages of interactive axis and centromere correction. Accuracy of centromere finding and consequential determination of a chromosome's polarity, i.e., which end is which, is measured experimentally. The saving in interaction by not correcting centromeres is compared to the increase in errors at the classification stage and the consequent increase in interaction needed to correct these errors. Some previously unreported features for banded chromosome classification are described, and in particular a set of global shape features is introduced. The discrimination capability of the feature measurements is evaluated by use of simple statistics and by reference to the performance of classifiers trained with various feature subsets. Class discrimination capability of the global shape feature set is shown to be comparable to that of centromere position, a widely used local shape feature. The variability of feature measurements that might occur in data from different laboratories on account of differing tissue, preparation methods, and digitiser hardware is assessed using three data bases of G-banded human metaphase cells. It is shown that the differences can be considerable and that appropriate feature selection and classifier training substantially improve classification performance.

Chromosomes↗
PubMed2002

Automated diagnosis of pigmented skin lesions.

Since advanced melanoma remains practically incurable, early detection is an important step toward a reduction in mortality. High expectations are entertained for a technique known as dermoscopy or epiluminescence light microscopy; however, evaluation of pigmented skin lesions by this method is often extremely complex and subjective. To obviate the problem of qualitative interpretation, methods based on mathematical analysis of pigmented skin lesions, such as digital dermoscopy analysis, have been developed. In the present study, we used a digital dermoscopy analyzer (DBDermo-Mips system) to evaluate a series of 588 excised, clinically atypical, flat pigmented skin lesions (371 benign, 217 malignant). The analyzer evaluated 48 parameters grouped into 4 categories (geometries, colors, textures and islands of color), which were used to train an artificial neural network. To evaluate the diagnostic performance of the neural network and to check it during the training process, we used the error area over the receiver operating characteristic curve. The discriminating power of the digital dermoscopy analyzer plus artificial neural network was compared with histologic diagnosis. A feature selection procedure indicated that as few as 13 of the variables were sufficient to discriminate the 2 groups of lesions, and this also ensured high generalization power. The artificial neural network designed with these variables enabled a diagnostic accuracy of about 94%. In conclusion, the good diagnostic performance and high speed in reading and analyzing lesions (real time) of our method constitute an important step in the direction of automated diagnosis of pigmented skin lesions.

Automation↗
PubMed1978

Structure-activity studies of barbiturates using pattern recognition techniques.

The relationship between molecular structure and duration of depressant effect for barbiturates was investigated. A data set of 160 5,5'-disubstituted barbiturates with various acyclic substituents was coded using 47 numerical descriptors including fragments, substructures, environmental descriptors, and molecular connectivity indexes. All descriptors were derived directly from the connection tables of the barbiturates. Using an interactive error-correction feedback algorithm, linear discriminant functions were developed that could dichotomize the data set with respect to several thresholds separating longer from shorter acting compounds. Feature selection was used to focus on the relatively few structural descriptors sufficient to support linear separability. For three specific thresholds, nine, 11, and nine descriptors were sufficient. The importance of these descriptors and the utility of the technique are discussed. Predictive abilities of approximately 94% were obtained for known barbiturates of the same general molecular types.

Animals↗
PubMed1987

A comparison of the chemical analyses of cell lipids with their complete proton NMR spectrum.

Whole cells are made up of molecules in different environments to which NMR spectroscopy is sensitive. In particular, malignant and transformed cells contain lipids not only in bilayers but in isotropically tumbling domains which give rise to high-resolution spectra. We have recently developed a technique for simultaneously analyzing broadline and high-resolution signals (M. Bloom, K. T. Holmes, C. E. Mountford, and P. G. Williams, J. Magn. Reson., in press) and we report here its application to a range of rat, mouse, and human cell lines. Some selected features of the NMR spectra were compared with the chemical analysis of the whole-cell lipid. We found that in general the proportion of protons in the narrow methylene resonance at 1.3 ppm increased with the neutral lipid content of the cells. This peak was chosen because its T2 relaxation behavior correlates with metastatic potential in a rat model system. This new technique could be applied to other high-resolution components both in healthy and in diseased states.

Animals↗
PubMed1989

Eigenimage filtering in MR imaging: an application in the abnormal chest wall.

A postprocessing linear filter was applied to spin-echo images on 10 patients with known or suspected chest wall invasion due to bronchogenic carcinoma. This technique known as eigenimage filtering allows selective feature extraction of suspected abnormalities from conventional MR images. The final result is an image with marked increased contrast range through enhancement of a desired process (tumor) with suppression of an interfering process (e.g., normal surrounding tissue). This preliminary work demonstrates the ease with which the technique may be implemented, the contrast enhancement obtained between the desired and the interfering feature in the final eigenimage, and its ability to correct for partial volume averaging effects. Also demonstrated are artifacts that can interfere with the interpretation of the eigenimage and a method for minimizing these artifacts in the final eigenimage.

Carcinoma, Bronchogenic↗
PubMed2002

Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic.

We investigated protein motions using normal modes within a database framework, determining on a large sample the degree to which normal modes anticipate the direction of the observed motion and were useful for motions classification. As a starting point for our analysis, we identified a large number of examples of protein flexibility from a comprehensive set of structural alignments of the proteins in the PDB. Each example consisted of a pair of proteins that were considerably different in structure given their sequence similarity. On each pair, we performed geometric comparisons and adiabatic-mapping interpolations in a high-throughput pipeline, arriving at a final list of 3,814 putative motions and standardized statistics for each. We then computed the normal modes of each motion in this list, determining the linear combination of modes that best approximated the direction of the observed motion. We integrated our new motions and normal mode calculations in the Macromolecular Motions Database, through a new ranking interface at http://molmovdb.org. Based on the normal mode calculations and the interpolations, we identified a new statistic, mode concentration, related to the mathematical concept of information content, which describes the degree to which the direction of the observed motion can be summarized by a few modes. Using this statistic, we were able to determine the fraction of the 3,814 motions where one could anticipate the direction of the actual motion from only a few modes. We also investigated mode concentration in comparison to related statistics on combinations of normal modes and correlated it with quantities characterizing protein flexibility (e.g., maximum backbone displacement or number of mobile atoms). Finally, we evaluated the ability of mode concentration to automatically classify motions into a variety of simple categories (e.g., whether or not they are "fragment-like"), in comparison to motion statistics. This involved the application of decision trees and feature selection (particular machine-learning techniques) to training and testing sets derived from merging the "list" of motions with manually classified ones.

Databases, Protein↗