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Results for “Feature selection”

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PubMed2005

Computer aided characterization of the solitary pulmonary nodule using volumetric and contrast enhancement features.

RATIONALE AND OBJECTIVES: To investigate the utility of a computer-aided diagnosis (CAD) in the task of differentiating malignant nodules from benign nodules based on quantitative features extracted from volumetric thin section CT image data acquired before and after the injection of contrast media. MATERIALS AND METHODS: 35 volumetric CT datasets of solitary pulmonary nodules (SPN) with proven diagnoses (19 malignant/16 benign) were contoured by a thoracic radiologist. All studies had at least a baseline series obtained without contrast media and at least one series following an intravenous contrast injection at 45, 90, 180, and 360 seconds. Two separate contours were created for each nodule: one including only the solid portion and another including the ground-glass component, if any, of the nodule. For each contour 31 features were calculated that measured the attenuation, shape, and enhancement of the nodule due to the injection of contrast. These features were input into a feature selection step and three different classifiers to determine if the diagnosis could be predicted from the resulting feature vector. In addition, observer input was introduced to two of the classifiers as an a priori probability of malignancy and the resulting performance was compared. Training and testing was conducted in a resubstitution and leave-one-out fashion and performance was evaluated using ROC analysis. RESULTS: In a leave-one-out testing methodology, the classifiers achieved areas under the ROC curves AZ that ranged from 0.69 to 0.92. A classifier based on logistic regression performed the best with an AZ of 0.92 while a classifier based on quadratic discriminant analysis performed the poorest (AZ, 0.69). The AZ increased when using a priori observer input in most cases reaching a maximum of 0.95. CONCLUSION: Based on this initial work with a limited number of nodules in our dataset, it appears that CAD using volumetric and contrast-enhanced data has the potential to assist radiologists in the task of differentiating solitary pulmonary nodules and in the management of these patients. Further studies with an increased number of patients are required to validate these results.

Adult↗

PubMed2026

Essence: A benchmarking-validated transformer framework for early diagnosis of Parkinson's disease using cerebrospinal fluid protein biomarkers.

Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by motor and non-motor symptoms. The lack of objective molecular biomarkers limits early diagnosis and personalized treatment. Here, we propose Essence, a benchmarking-validated framework integrating cerebrospinal fluid (CSF) proteomics with traditional and deep learning models to identify robust protein signatures for PD. Using data from two independent cohorts, 1266 high-confidence proteins are quantified, among which 178 exhibit differential abundance between PD and healthy controls (HC). Through systematic benchmarking of ten machine learning algorithms and four neural architectures, the Transformer model consistently outperforms alternatives across multiple feature selection strategies, achieving an area under the receiver operating characteristic curve (AUC) of 1.0000 with only 35 features. Functional analyses of the top-ranked 35 proteins reveal enrichment in neuroinflammatory, synaptic, and oxidative stress-related pathways. Importantly, spatial transcriptomic profiling based on the Allen Brain Atlas shows region-specific expression of these biomarkers in PD-relevant brain structures, including the striatum, subthalamic nucleus, hippocampus, and white matter tracts. This anatomical alignment supports the functional relevance of the identified markers and highlights their potential utility in early-stage diagnosis and mechanistic understanding of PD.

Benchmarking↗

PubMed2003

Differential brain responses when applying criterion attribute versus family resemblance rule learning.

Subsystems of category learning have been identified on the basis of general domains of content (e.g., tools, faces). The present study examined categories from the standpoint of internal structure and determined brain topography associated with expressing two fundamentally different category rule structures (criterion attribute, CA, and family resemblance, FR). CA category learning involves processing stimuli by isolated features and classifying by properties held by all members. FR learning involves processing stimuli by integral wholes and classifying on overall similarity among members without sharing identical features. fMRI BOLD response to CA and FR categorization was measured with pseudowords as stimuli. Category knowledge for both tasks was mastered prior to brain imaging. Areas of activation emerged unique to the structure of each category and followed from the nature of the rule abstraction procedure. CA categorization was implemented by strong target monitoring and expectation (medial parietal), rule maintenance in working memory, feature selection processes (inferior frontal), and a sensitivity to high frequency components of the stimulus such as isolated features (anterior temporal). FR categorization, consistent with its multi-featural nature, involved word-level processing (left extrastriate) that evoked articulatory rehearsal (medial cerebellar). The data suggest category structure is an important determinant of brain response during categorization. For instance, anterior temporal structures may help attune visual processing systems to high frequency components to support the learning of criterial, highly predictive rules.

Adolescent↗

PubMed2004

Accurate identification of alternatively spliced exons using support vector machine.

MOTIVATION: Alternative splicing is a major component of the regulatory action on mammalian transcriptomes. It is estimated that over half of all human genes have more than one splice variant. Previous studies have shown that alternatively spliced exons possess several features that distinguish them from constitutively spliced ones. Recently, we have demonstrated that such features can be used to distinguish alternative from constitutive exons. In the current study, we used advanced machine learning methods to generate robust classifier of alternative exons. RESULTS: We extracted several hundred local sequence features of constitutive as well as alternative exons. Using feature selection methods we find seven attributes that are dominant for the task of classification. Several less informative features help to slightly increase the performance of the classifier. The classifier achieves a true positive rate of 50% for a false positive rate of 0.5%. This result enables one to reliably identify alternatively spliced exons in exon databases that are believed to be dominated by constitutive exons.

Algorithms↗

PubMedDate not supplied

[The crisis in psychiatry and the protection of the civil rights of mentally ill patients].

In Poland a basic opinion of the mental health care system is that it considers that mental disorders are illnesses and that an ill person is weaker (worse) and less useful in the social distribution of roles and tasks. Consequently, the ill are excluded from the main-stream of social life: they are deprived of jobs by an easy and early recognition of disability, and the granting of disability pensions, by civil law prohibition of marriage, criminal law ban on sexual contacts etc. A person has little chance for a just life if he/she is deprived of the possibility of working, founding a family, if he/she receives an inadequate pension, remains sexually isolated and on the margin of public life. This medical model of care includes a lot of discriminatory features in the area of human and civil rights of the mentally ill. The discussion concentrated on selected features of the crisis in world psychiatry as well as the practical, ideological, clinical, institutional and organizational difficulties of Polish psychiatry. The main goal of this paper is the raising of psychiatry's awareness of its faults, in order to induce the creation of a new system of mental health care, free of the discriminatory stigmas of the ill and more adequately adapted the ideas of a contemporary democratic state.

Civil Rights↗

PubMed1983

Computer applications in hospital pharmacy practice. I. Computer expectations/applications.

Following vendor selection of a pharmacy computer system, attention must be directed toward which computerized functions to include. Although most features are uniform among the various systems, a discussion is presented listing those applications considered the minimum acceptable for any hospital pharmacy computer system. The descriptions focus on computerization of those labor-intensive activities necessary to support drug distribution services. Computerized support of an intravenous (I.V.) admixture and unit dose program centers around label production and charging/crediting functions. Label production is used to generate a manual backup profile and unit dose cart fill list. The scope of information to include on I.V. and unit dose labels is described. Charging/crediting functions via computer are also discussed, with mention of free-form capabilities. Other computer applications mentioned include: medication profiling, drug interaction flagging, data confidentiality, census support, and hard copy reports. Feature selection depends on the aspects and unique needs that benefit most from computerization.

Accounting↗

PubMed2002

Personality features of children treated due to vocal nodules.

There were estimated 14 features of personality of the children treated for vocal nodules. The purpose of study was definition of the selected features, which are typical of the examined group. The conclusion drawn from the conducted studies was: the children cured of the vocal nodules are more excitable, nervous, independent and often--individualists. They are inclined to leading and dominating. The results of the study suggest that psychotherapy can be completion of traditional treatment for vocal nodules in children.

Anxiety↗

PubMed2006

Reducing multiclass cancer classification to binary by output coding and SVM.

Multiclass cancer classification based on microarray data is presented. The binary classifiers used combine support vector machines with a generalized output-coding scheme. Different coding strategies, decoding functions and feature selection methods are incorporated and validated on two cancer datasets: GCM and ALL. Using random coding strategy and recursive feature elimination, the testing accuracy achieved is as high as 83% on GCM data with 14 classes. Comparing with other classification methods, our method is superior in classificatory performance.

Artificial Intelligence↗

PubMed1998

Optimizing sound features for cortical neurons.

The brain's cerebral cortex decomposes visual images into information about oriented edges, direction and velocity information, and color. How does the cortex decompose perceived sounds? A reverse correlation technique demonstrates that neurons in the primary auditory cortex of the awake primate have complex patterns of sound-feature selectivity that indicate sensitivity to stimulus edges in frequency or in time, stimulus transitions in frequency or intensity, and feature conjunctions. This allows the creation of classes of stimuli matched to the processing characteristics of auditory cortical neurons. Stimuli designed for a particular neuron's preferred feature pattern can drive that neuron with higher sustained firing rates than have typically been recorded with simple stimuli. These data suggest that the cortex decomposes an auditory scene into component parts using a feature-processing system reminiscent of that used for the cortical decomposition of visual images.

Acoustic Stimulation↗

PubMedDate not supplied

Fine needle aspiration biopsy diagnosis of mucoepidermoid carcinoma. Statistical analysis.

Fine needle aspiration (FNA) biopsy is an increasingly popular method for the evaluation of salivary gland tumors. Of the common salivary gland tumors, mucoepidermoid carcinoma is probably the most difficult to diagnose accurately by this means. A series of 96 FNA biopsy specimens of salivary gland masses, including 34 mucoepidermoid carcinomas, 51 other benign and malignant neoplasms, 7 nonneoplastic lesions and 4 normal salivary glands, were analyzed in order to identify the most useful criteria for diagnosing mucoepidermoid carcinoma. Thirteen cytologic criteria were evaluated in the FNA specimens, and a stepwise logistic regression analysis was performed. The three cytologic features selected as most predictive of mucoepidermoid carcinoma were intermediate cells, squamous cells and overlapping epithelial groups. Using these three features together, the sensitivity and specificity of accurately diagnosing mucoepidermoid carcinoma were 97% and 100%, respectively.

Biopsy, Needle↗

PubMed2006

Monitoring of heavy metal partitioning in reef corals of Lakshadweep Archipelago, Indian Ocean.

This paper focuses on the partitioning of trace metals in five selected coral species from Lakshadweep Archipelago, which remains as one of the least studied areas in the Indian Ocean. Based on the morphological features, selected coral species are classified as massive (Porites andrewsi), ramose or branching (Lobophyllia corymbosa, Acropora formosa and Psammocora contigua) and foliaceous (Montipora digitata). Relating trace metal concentrations with morphological features in skeleton, highest concentrations of all the trace metals (except Zn) were reported for the ramose type corals. In tissue, all the metals (essential as well as non essential) showed highest concentrations within the branching type corals. Irrespective of their growth characteristics/pattern, all species except P. contigua displayed higher concentrations of Pb, Ni, Mn and Cd within their skeleton compared to tissue which may exemplify a regulatory mechanism to avoid the build up of the concentrations of these metals in their bio-part, strikingly toxic metals like Cd and Pb. The concentrations of trace metals in the skeleton and tissues of these coral species were subjected to 3 way ANOVA based on non standardized original data and the results showed significant differences between metals and between species leading to high skeleton/ tissue - species interaction as well as skeleton/tissue - metal interaction. The significant values of student's t calculated are depicted in the form of Trellis diagrams.

Animals↗

PubMed1984

Use of logistic regression analysis to improve prediction of prognosis in acute myeloid leukaemia.

The prognostic usefulness of a range of factors has been examined for patients with acute myeloid leukaemia. Although there was a statistical association between some of these factors and remission rate, the association was only partial. To improve the usefulness of the data, multiple logistic regressional analysis was used. The features selected for use in the analysis were age, blood blast count, FAB classification and colony growth pattern. The last three features could be used as categorical variables, since blood blast counts of greater than 100 X 10(9)/1, FAB group 1 and a prolific pattern of colony growth were associated with a low remission rate. Age was used as a continuous variable. Using these features, eight regression groups were defined. Thus when this data for an individual patient is analysed, it is possible to obtain a value for the probability of that patient achieving remission.

Adult↗

PubMedDate not supplied

[Reproducibility of radiologic diagnosis in gonarthrosis].

AIM OF STUDY: Ongoing efforts of the "German Society of Orthopaedic Surgery and Traumatology" (DGOT) to standardize diagnosis and therapy of osteoarthritis, necessitated this study, where the reproducibility of different radiographic features of knee-OA was assessed. METHODS: Three readers graded 100 antero-posterior and lateral knee radiographs for selected features (femorotibial osteophytes, joint space narrowing, sclerosis and chondrocalcinosis; patellofemoral osteophytes) and an overall-score (Kellgren and Lawrence, 1963) at two time points 3 months apart. Intra- and inter-observer-reliability were calculated by intra-class correlation-coefficient (ICC). RESULTS: Osteophytes in the femorotibial as well as in the patellofemoral joint could be assessed with a high intra- and inter-observer-reliability. While for joint space narrowing intra-observer-reliability is excellent, the inter-observer-reliability is less satisfactory, and subchondral sclerosis as well as chondrocalcinosis showed even less reproducibility. The Kellgren-Lawrence global score proofed to be highly reproducible. CONCLUSION: Based on the results of this examination, we can recommend a reliable radiographic classification of knee osteoarthritis by grading of relevant individual features (osteophytes and joint space narrowing) and overall assessment.

Follow-Up Studies↗

PubMed2026

BaGGLS: a Bayesian shrinkage framework for interpretable modeling of interactions in high-dimensional biological data.

MOTIVATION: Biological data is often high dimensional, noisy, and governed by complex interactions among sparse signals. This poses major challenges for interpretability and reliable feature selection. Tasks such as identifying motif interactions in genomics exemplify these difficulties, as only a small subset of biologically relevant features (e.g. motifs) are typically active, and their effects are often non-linear and context-dependent. While statistical approaches often result in more interpretable models, deep learning models have proven effective in modeling complex interactions and prediction accuracy, yet their black-box nature limits interpretability. RESULTS: We introduce BaGGLS, a flexible and interpretable probabilistic binary regression model designed for high-dimensional biological inference involving feature interactions. BaGGLS incorporates a Bayesian group global-local shrinkage prior, aligned with the group structure introduced by interaction terms. This prior encourages sparsity while retaining interpretability, helping to isolate meaningful signals and suppress noise. To enable scalable inference, we employ a partially factorized variational approximation that captures posterior skewness and supports efficient learning even in large feature spaces. In extensive simulations, we compare BaGGLS to frequentist probit regressions (unconstrained and with L1-penalty) as well as a probit model with Markov Chain Monte Carlo (MCMC) sampling under a horseshoe prior. We can show that BaGGLS outperforms the other methods with regard to interaction detection and is many times faster than MCMC sampling under the horseshoe prior. We also demonstrate the usefulness of BaGGLS in the context of interaction discovery from motif scanner outputs (e.g. Find Individual Motif Occurrences (FIMO)) and noisy attribution scores from deep learning models. This shows that BaGGLS is a promising approach for uncovering biologically relevant interaction patterns, with potential applicability across a range of high-dimensional tasks in computational biology. AVAILABILITY: Code is available at gitlab.com/dacs-hpi/baggls.

Bayes Theorem↗

PubMed2004

Cell culture modeling of specialized tissue: identification of genes expressed specifically by follicle-associated epithelium of Peyer's patch by expression profiling of Caco-2/Raji co-cultures.

Peyer's patch follicle-associated epithelium (FAE) regulates intestinal antigen access to the immune system in part through the action of microfold (M) cells which mediate transcytosis of antigens and microorganisms. Studies on M cells have been limited by the difficulties in isolating purified cells, so we applied TOGA mRNA expression profiling to identify genes associated with the in vitro induction of M cell-like features in Caco-2 cells and tested them against normal Peyer's patch tissue for their expression in FAE. Among the genes identified by this method, laminin beta3, a matrix metalloproteinase and a tetraspan family member, showed enriched expression in FAE of mouse Peyer's patches. Moreover, the C. perfringens enterotoxin receptor (CPE-R) appeared to be expressed more strongly by UEA-1(+) M cells relative to neighboring FAE. Expression of the tetraspan TM4SF3 gene and CPE-R was also confirmed in human Peyer's patch FAE. Our results suggest that while the Caco-2 differentiation model is associated with some functional features of M cells, the genes induced may instead reflect the acquisition of a more general FAE phenotype, sharing only select features with the M cell subset.

Animals↗

PubMed2005

Cortical sensitivity to visual features in natural scenes.

A central hypothesis concerning sensory processing is that the neuronal circuits are specifically adapted to represent natural stimuli efficiently. Here we show a novel effect in cortical coding of natural images. Using spike-triggered average or spike-triggered covariance analyses, we first identified the visual features selectively represented by each cortical neuron from its responses to natural images. We then measured the neuronal sensitivity to these features when they were present in either natural images or random stimuli. We found that in the responses of complex cells, but not of simple cells, the sensitivity was markedly higher for natural images than for random stimuli. Such elevated sensitivity leads to increased detectability of the visual features and thus an improved cortical representation of natural scenes. Interestingly, this effect is due not to the spatial power spectra of natural images, but to their phase regularities. These results point to a distinct visual-coding strategy that is mediated by contextual modulation of cortical responses tuned to the spatial-phase structure of natural scenes.

Animals↗

PubMed1990

Molecular conformational space analysis using computer graphics: going beyond FRODO.

The molecular graphics program FRODO has been modified to support analytical animation of molecular dynamics trajectories. The enhanced program, mdFRODO, supports all features available in FRODO and is interfaced to GROMOS. A variety of analytical animation modes is included. Extensive coloring and atom selection features are implemented to aid the user in distinguishing features of interest in a set of conformations. Molecular conformational space can be analyzed efficiently and comprehended. Animations may be viewed in stereo, and the animated object can be overlaid with any of the standard FRODO objects. The mdFRODO program is of wide use in molecular dynamics, X-ray crystallography and two-dimensional NMR work. Examples illustrating various aspects of collective motion in protein molecules are given and discussed.

Computer Graphics↗

PubMed1991

The development of perceived structure and attention: evidence from divided and selective attention tasks.

Three experiments provide converging evidence for the view that both perceived structure and attention change during the elementary school years. Kindergarteners, second graders, and adults performed three speeded tasks: divided attention to conjunctions of features, selective attention to orthogonal dimensions and selective attention to correlated dimensions. The tasks were performed with sizes and shapes that were either spatially integrated or spatially separated. In the divided attention task, conjunctions were identified as quickly as single features with integrated stimuli at all ages, but conjunctions were identified more slowly than single features with separated stimuli by all age group. In the orthogonal dimensions task, interference was observed with integrated stimuli across ages, but the interference in adult performance was asymmetric. With separated stimuli, interference was gradually eliminated with increasing age. In correlated dimensions tasks, younger children showed a redundancy gain with integrated stimuli, but no gain was observed in the performances of the older subjects. With separated stimuli there was no redundancy gain at any age. These results were interpreted to mean that integrated stimuli are initially perceived as wholes by all subjects, but that features become more accessible with increasing age. Even so, attention remains constrained by stimulus structure. In contrast, separated stimuli are initially perceived as features at all ages, and the improvement in performance with increasing age is attributable to the increasing command of attentional resources that accompanies development. Our discussion of these findings focuses on three issues: multiple trends in perceptual development, the characteristics of an adequate theory of perceptual representation and processing, and a comparison of the separability hypothesis and other developmental accounts of perceptual development.

Adult↗