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PubMed2004

Analysis of 3-D myocardial motion in tagged MR images using nonrigid image registration.

Tagged magnetic resonance imaging (MRI) is unique in its ability to noninvasively image the motion and deformation of the heart in vivo, but one of the fundamental reasons limiting its use in the clinical environment is the absence of automated tools to derive clinically useful information from tagged MR images. In this paper, we present a novel and fully automated technique based on nonrigid image registration using multilevel free-form deformations (MFFDs) for the analysis of myocardial motion using tagged MRI. The novel aspect of our technique is its integrated nature for tag localization and deformation field reconstruction using image registration and voxel based similarity measures. To extract the motion field within the myocardium during systole we register a sequence of images taken during systole to a set of reference images taken at end-diastole, maximizing the normalized mutual information between the images. We use both short-axis and long-axis images of the heart to estimate the full four-dimensional motion field within the myocardium. We also present validation results from data acquired from twelve volunteers.

Algorithms↗
PubMed2005

Fast fourier transform-based support vector machine for prediction of G-protein coupled receptor subfamilies.

Although the sequence information on G-protein coupled receptors (GPCRs) continues to grow, many GPCRs remain orphaned (i.e. ligand specificity unknown) or poorly characterized with little structural information available, so an automated and reliable method is badly needed to facilitate the identification of novel receptors. In this study, a method of fast Fourier transform-based support vector machine has been developed for predicting GPCR subfamilies according to protein's hydrophobicity. In classifying Class B, C, D and F subfamilies, the method achieved an overall Matthe's correlation coefficient and accuracy of 0.95 and 93.3%, respectively, when evaluated using the jackknife test. The method achieved an accuracy of 100% on the Class B independent dataset. The results show that this method can classify GPCR subfamilies as well as their functional classification with high accuracy. A web server implementing the prediction is available at http://chem.scu.edu.cn/blast/Pred-GPCR.

Algorithms↗
PubMed2004

An automated method for lumen and media-adventitia border detection in a sequence of IVUS frames.

In this paper, we present a method for the automated detection of lumen and media-adventitia border in sequential intravascular ultrasound (IVUS) frames. The method is based on the use of deformable models. The energy function is appropriately modified and minimized using a Hopfield neural network. Proper modifications in the definition of the bias of the neurons have been introduced to incorporate image characteristics. A simulated annealing scheme is included to ensure convergence at a global minimum. The method overcomes distortions in the expected image pattern, due to the presence of calcium, employing a specialized structure of the neural network and boundary correction schemas which are based on a priori knowledge about the vessel geometry. The proposed method is evaluated using sequences of IVUS frames from 18 arterial segments, some of them indicating calcified regions. The obtained results demonstrate that our method is statistically accurate, reproducible, and capable to identify the regions of interest in sequences of IVUS frames.

Algorithms↗
PubMed2003

Three-dimensional guide-wire reconstruction from biplane image sequences for integrated display in 3-D vasculature.

Using three-dimensional rotational X-ray angiography (3DRA), three-dimensional (3-D) information of the vasculature can be obtained prior to endovascular interventions. However, during interventions, the radiologist has to rely on fluoroscopy images to manipulate the guide wire. In order to take full advantage of the 3-D information from 3DRA data during endovascular interventions, a method is presented that yields an integrated display of the position of the guide wire and vasculature in 3-D. The method relies on an automated method that tracks the guide wire simultaneously in biplane fluoroscopy images. Based on the calibrated geometry of the C-arm, the 3-D guide-wire position is determined and visualized in the 3-D coordinate system of the vasculature. The method is evaluated in an intracranial anthropomorphic vascular phantom. The influence of the angle between projections, distortion correction of the projection images, and accuracy of geometry knowledge on the accuracy of 3-D guide-wire reconstruction from biplane images is determined. If the calibrated geometry information is used and the images are corrected for distortion, a mean distance to the reference standard of 0.42 mm and a tip distance of 0.65 mm is found, which means that accurate guide-wire reconstruction from biplane images can be performed.

Algorithms↗
PubMed2002

Assessment of neuropsychological function through use of the Cambridge Neuropsychological Testing Automated Battery: performance in 4- to 12-year-old children.

In this article, children's performance on subtasks from the Cambridge Neuropsychological Testing Automated Battery (CANTAB) is described. Two samples were recruited, one of which included children who spoke English as a second language. Children in this group also completed subtests from the Wechsler Intelligence Scale for Children-Third Revision (WISC-III). Despite the fact that ESL children scored over 1 SD below the norm on the WISC-III Vocabulary subtest, there were no CANTAB performance distinctions between primary versus secondary English-language speakers. In addition, several aspects of CANTAB performance were significantly correlated with verbal and nonverbal IQ. When developmental trends were examined, findings indicated that several aspects of frontal lobe function (memory span, working memory, and planning skills) are not functionally mature, by the age of 12 years. Implications for use of the CANTAB in clinical studies are discussed.

Attention↗
PubMed2005

A novel method for automated EMG decomposition and MUAP classification.

OBJECTIVE: This paper proposes a novel method for the extraction and classification of individual motor unit action potentials (MUAPs) from intramuscular electromyographic signals. METHODOLOGY: The proposed method automatically detects the number of template MUAP clusters and classifies them into normal, neuropathic or myopathic. It consists of three steps: (i) preprocessing of electromyogram (EMG) recordings, (ii) MUAP detection and clustering and (iii) MUAP classification. RESULTS: The approach has been validated using a dataset of EMG recordings and an annotated collection of MUAPs. The correct identification rate for MUAP clustering is 93, 95 and 92% for normal, myopathic and neuropathic, respectively. Ninety-one percent of the superimposed MUAPs were correctly identified. The obtained accuracy for MUAP classification is about 86%. CONCLUSION: The proposed method, apart from efficient EMG decomposition addresses automatic MUAP classification to neuropathic, myopathic or normal classes directly from raw EMG signals.

Action Potentials↗
PubMed2006

A graph-search framework for associating gene identifiers with documents.

BACKGROUND: One step in the model organism database curation process is to find, for each article, the identifier of every gene discussed in the article. We consider a relaxation of this problem suitable for semi-automated systems, in which each article is associated with a ranked list of possible gene identifiers, and experimentally compare methods for solving this geneId ranking problem. In addition to baseline approaches based on combining named entity recognition (NER) systems with a "soft dictionary" of gene synonyms, we evaluate a graph-based method which combines the outputs of multiple NER systems, as well as other sources of information, and a learning method for reranking the output of the graph-based method. RESULTS: We show that named entity recognition (NER) systems with similar F-measure performance can have significantly different performance when used with a soft dictionary for geneId-ranking. The graph-based approach can outperform any of its component NER systems, even without learning, and learning can further improve the performance of the graph-based ranking approach. CONCLUSION: The utility of a named entity recognition (NER) system for geneId-finding may not be accurately predicted by its entity-level F1 performance, the most common performance measure. GeneId-ranking systems are best implemented by combining several NER systems. With appropriate combination methods, usefully accurate geneId-ranking systems can be constructed based on easily-available resources, without resorting to problem-specific, engineered components.

Animals↗
PubMed2006

OrthologID: automation of genome-scale ortholog identification within a parsimony framework.

MOTIVATION: The determination of gene orthology is a prerequisite for mining and utilizing the rapidly increasing amount of sequence data for genome-scale phylogenetics and comparative genomic studies. Until now, most researchers use pairwise distance comparisons algorithms, such as BLAST, COG, RBH, RSD and INPARANOID, to determine gene orthology. In contrast, orthology determination within a character-based phylogenetic framework has not been utilized on a genomic scale owing to the lack of efficiency and automation. RESULTS: We have developed OrthologID, a Web application that automates the labor-intensive procedures of gene orthology determination within a character-based phylogenetic framework, thus making character-based orthology determination on a genomic scale possible. In addition to generating gene family trees and determining orthologous gene sets for complete genomes, OrthologID can also identify diagnostic characters that define each orthologous gene set, as well as diagnostic characters that are responsible for classifying query sequences from other genomes into specific orthology groups. The OrthologID database currently includes several complete plant genomes, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, as well as a unicellular outgroup, Chlamydomonas reinhardtii. To improve the general utility of OrthologID beyond plant species, we plan to expand our sequence database to include the fully sequenced genomes of prokaryotes and other non-plant eukaryotes. AVAILABILITY: http://nypg.bio.nyu.edu/orthologid/

Algorithms↗
PubMed2005

Model-based analysis of local shape for lesion detection in CT scans.

Thin-slice computer tomography provides high-resolution images that facilitate the diagnosis of early-stage lung cancer. However, the sheer size of the CT volumes introduces variability in radiological readings, driving the need for automated detection systems. The main contribution of this paper is a technique for combining geometric and intensity models with the analysis of local curvature for detecting pulmonary lesions in CT. The local shape at each voxel is represented via the principal curvatures of its associated isosurface without explicitly extracting the isosurface. The comparison of these curvatures to values derived from analytical shape models is then used to label the voxel as belonging to particular anatomical structures, e.g., nodules or vessels. The algorithm was evaluated on 242 CT exams with expert-determined ground truth. The performance of the algorithm is quantified by free-response receiver-operator characteristic curves, as well as by its potential for improvement in radiologist sensitivity.

Algorithms↗
PubMed2005

Accurate image registration for quadrature tomographic microscopy.

This paper presents a robust and fully automated registration algorithm for registration of images of Quadrature Tomographic Microscopy (QTM), which is an optical interferometer. The need for registration of such images is to recognize distinguishing features of viable embryos to advance the technique for In Vitro Fertilization. QTM images a sample (live embryo) multiple times with different hardware configurations, each in turn producing 4 images taken by 4 CCD cameras simultaneously. Embryo movement is often present between imaging. Our algorithm handles camera calibration of multiple cameras using a variant of ICP, and elimination of embryo movement using a hybrid of feature- and intensity-based methods. The algorithm is tested on 20 live mouse embryos containing various cell numbers between 8 and 26. No failure thus far, and the average alignment error is 0.09 pixels, corresponding to the range of 639 and 675 nanometers.

Algorithms↗
PubMed2006

A reversible jump Markov chain Monte Carlo algorithm for bacterial promoter motifs discovery.

Effective probabilistic modeling approaches have been developed to find motifs of biological function in DNA sequences. However, the problem of automated model choice remains largely open and becomes more essential as the number of sequences to be analyzed is constantly increasing. Here we propose a reversible jump Markov chain Monte Carlo algorithm for estimating both parameters and model dimension of a Bayesian hidden semi-Markov model dedicated to bacterial promoter motif discovery. Bacterial promoters are complex motifs composed of two boxes separated by a spacer of variable but constrained length and occurring close to the protein translation start site. The algorithm allows simultaneous estimations of the width of the boxes, of the support size of the spacer length distribution, and of the order of the Markovian model used for the "background" nucleotide composition. The application of this method on three sequence sets points out the good behavior of the algorithm and the biological relevance of the estimated promoter motifs.

Algorithms↗
PubMed2003

Multiwavelet grading of pathological images of prostate.

Histological grading of pathological images is used to determine level of malignancy of cancerous tissues. This is a very important task in prostate cancer prognosis, since it is used for treatment planning. If infection of cancer is not rejected by non-invasive diagnostic techniques like magnetic resonance imaging, computed tomography scan, and ultrasound, then biopsy specimens of tissue are tested. For prostate, biopsied tissue is stained by hematoxyline and eosine method and viewed by pathologists under a microscope to determine its histological grade. Human grading is very subjective due to interobserver and intraobserver variations and in some cases difficult and time-consuming. Thus, an automatic and repeatable technique is needed for grading. Gleason grading system is the most common method for histological grading of prostate tissue samples. According to this system, each cancerous specimen is assigned one of five grades. Although some automatic systems have been developed for analysis of pathological images, Gleason grading has not yet been automated; the goal of this research is to automate it. To this end, we calculate energy and entropy features of multiwavelet coefficients of the image. Then, we select most discriminative features by simulated annealing and use a k-nearest neighbor classifier to classify each image to appropriate grade (class). The leaving-one-out technique is used for error rate estimation. We also obtain the results using features extracted by wavelet packets and co-occurrence matrices and compare them with the multiwavelet method. Experimental results show the superiority of the multiwavelet transforms compared with other techniques. For multiwavelets, critically sampled preprocessing outperforms repeated-row preprocessing and has less sensitivity to noise for second level of decomposition. The first level of decomposition is very sensitive to noise and, thus, should not be used for feature extraction. The best multiwavelet method grades prostate pathological images correctly 97% of the time.

Algorithms↗
PubMed1992

The role of automated speech recognition in endoscopic data collection.

Speech recognition technology has developed substantially in the past half decade. Currently, large vocabulary, speaker independent, discrete recognizers are the state-of-the-art. This will change. Moderate sized, continuous recognition systems now exist in research settings. However, it is unlikely that such systems will be widely available until the mid to late 1990's. The accuracy rates of current speech recognition systems are high. Consequently, speech accuracy is not the current limiting aspect of using ASR. The limiting aspect of using ASR technology is the approach to integrating speech functionality into applications. One approach is to use ATNs as models of natural language to support both an input strategy and a text generation system. ATNs provide approaches to both syntactical correctness and semantic richness. This is an approach which plays to the strengths of the discrete nature of current speech technology and also provides a methodology for the capture and archiving of highly detailed information. The ATN approach avoids the natural language parsing problem created by a fully free form dictation interface. Evolving along with the underlying speech technology are standards in the definitions and criteria used in endoscopic practice. There are clear benefits from standards in this area. However, it is likely that this will also take several years and may never yield a universally accepted lexicon. Furthermore, there will be user interface barriers to surmount in any system attempting to use speech as an input modality. Because of the relatively large vocabularies used in medical discourse, the user interface will need to be carefully crafted.(ABSTRACT TRUNCATED AT 250 WORDS)

Data Collection↗
PubMed2006

Automated discovery of 3D motifs for protein function annotation.

MOTIVATION: Function inference from structure is facilitated by the use of patterns of residues (3D motifs), normally identified by expert knowledge, that correlate with function. As an alternative to often limited expert knowledge, we use machine-learning techniques to identify patterns of 3-10 residues that maximize function prediction. This approach allows us to test the assumption that residues that provide function are the most informative for predicting function. RESULTS: We apply our method, GASPS, to the haloacid dehalogenase, enolase, amidohydrolase and crotonase superfamilies and to the serine proteases. The motifs found by GASPS are as good at function prediction as 3D motifs based on expert knowledge. The GASPS motifs with the greatest ability to predict protein function consist mainly of known functional residues. However, several residues with no known functional role are equally predictive. For four groups, we show that the predictive power of our 3D motifs is comparable with or better than approaches that use the entire fold (Combinatorial-Extension) or sequence profiles (PSI-BLAST). AVAILABILITY: Source code is freely available for academic use by contacting the authors. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Algorithms↗
PubMed2004

Automated feature extraction in color retinal images by a model based approach.

Color retinal photography is an important tool to detect the evidence of various eye diseases. Novel methods to extract the main features in color retinal images have been developed in this paper. Principal component analysis is employed to locate optic disk; A modified active shape model is proposed in the shape detection of optic disk; A fundus coordinate system is established to provide a better description of the features in the retinal images; An approach to detect exudates by the combined region growing and edge detection is proposed. The success rates of disk localization, disk boundary detection, and fovea localization are 99%, 94%, and 100%, respectively. The sensitivity and specificity of exudate detection are 100% and 71%, correspondingly. The success of the proposed algorithms can be attributed to the utilization of the model-based methods. The detection and analysis could be applied to automatic mass screening and diagnosis of the retinal diseases.

Algorithms↗
PubMed2006

Automated validation of polymerase chain reaction amplicon melting curves.

The polymerase chain reaction (PCR) is a fundamental tool of molecular biology. Quantitative PCR is the gold-standard methodology for determination of DNA copy numbers, quantitating transcription, and numerous other applications. A major barrier to large-scale application of PCR for quantitative genomic analyses is the current requirement for manual validation of individual PCRs to ensure generation of a single product. This typically requires visual inspection either of gel electrophoreses or temperature dissociation ("melting") curves of individual PCRs--a time-consuming and costly process. Here we describe a robust computational solution to this fundamental problem. Using a training set of 10 080 reactions comprising multiple quantitative PCRs from each of 1728 unique human genomic amplicons, we developed a support vector machine classifier capable of discriminating single-product PCRs with better than 99% accuracy. This approach has broad utility, and eliminates a major bottleneck to widespread application of PCR for high-throughput genomic applications.

Algorithms↗
PubMed2004

Tooth segmentation of dental study models using range images.

The accurate segmentation of the teeth from the digitized representation of a dental study model is an important component in computer-based algorithms for orthodontic feature detection and measurement and in the simulation of orthodontic procedures such as tooth rearrangement. This paper presents an automated method for tooth segmentation from the three-dimensional (3-D) digitized image captured by a laser scanner. We avoid the complexity of directly processing 3-D mesh data by proposing the innovative idea of detecting features on two range images computed from the 3-D image. The dental arch is first obtained from the plan-view range image. Using the arch as the reference, a panoramic range image of the dental model can be computed. The interstices between the teeth are detected separately in the two range images, and results from both views are combined for a determination of interstice locations and orientations. Finally, the teeth are separated from the gums by delineating the gum margin. The algorithm was tested on 34 dental models representing a variety of malocclusions and was found to be robust and accurate.

Algorithms↗
PubMed2003

Testing and optimization of a semiautomatic prostate boundary segmentation algorithm using virtual operators.

Image analysis tasks such as size measurement and landmark-based registration require the user to select control points in an image. The output of such algorithms depends on the choice of control points. Since the choice of points varies from one user to the next, the requirement for user input introduces variability into the output of the algorithm. In order to test and/or optimize such algorithms, it is necessary to assess the multiplicity of outputs generated by the algorithm in response to a large set of inputs; however, the input of data requires substantial time and effort from multiple users. In this paper we describe a method to automate the testing and optimization of algorithms using "virtual operators," which consist of a set of spatial distributions describing how actual users select control points in an image. In order to construct the virtual operator, multiple users must repeatedly select control points in the image on which testing is to be performed. Once virtual operators are generated, control points for initializing the algorithm can be generated from them using a random number generator. Although an initial investment of time is required from the users in order to construct the virtual operator, testing and optimization of the algorithm can be done without further user interaction. We illustrate the construction and use of virtual operators by testing and optimizing our prostate boundary segmentation algorithm. The algorithm requires the user to select four control points on the prostate as input.

Algorithms↗