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A via-point time optimization algorithm for complex sequential trajectory formation.

In our previous research, we proposed a method for the reproduction of complex movement trajectories and robot arm control that could mimic fast, skilled human movements. That method is based on bi-directional theory and uses a representation of a set of via-points as boundary conditions or control variables to perform robot arm trajectory control. The via-points are extracted from human movement data and the resultant via-point representation is able to regenerate handwritten characters, control a Kendama toy, and perform a tennis serve. The via-point information contains both spatial and temporal information, that is, the position on the trajectory and the time of passing through the via-point position, respectively. Trajectory generation is performed using the trajectory formation model based on the optimal criterion, namely, the smoothness criterion, for which the boundary conditions are both the position and the timing of the via-point information. However, generating a smooth trajectory at different movement speeds is quite difficult if the time of passing through the via-point position is unknown or different from the extracted via-point time. In this paper, we therefore propose a new algorithm which can determine temporal via-point information. Our proposed algorithm can generate roughly the same trajectory as the measured human trajectory from only the spatial information of via-point locations. The optimality and the convergence of the new algorithm are investigated theoretically, and the trajectory generated by the algorithm is shown in numerical experiments. It is shown that starting from arbitrary temporal information the proposed algorithm can produce an appropriate trajectory.

Algorithms↗

Fast algorithm and implementation of dissimilarity self-organizing maps.

In many real-world applications, data cannot be accurately represented by vectors. In those situations, one possible solution is to rely on dissimilarity measures that enable a sensible comparison between observations. Kohonen's self-organizing map (SOM) has been adapted to data described only through their dissimilarity matrix. This algorithm provides both nonlinear projection and clustering of nonvector data. Unfortunately, the algorithm suffers from a high cost that makes it quite difficult to use with voluminous data sets. In this paper, we propose a new algorithm that provides an important reduction in the theoretical cost of the dissimilarity SOM without changing its outcome (the results are exactly the same as those obtained with the original algorithm). Moreover, we introduce implementation methods that result in very short running times. Improvements deduced from the theoretical cost model are validated on simulated and real-world data (a word list clustering problem). We also demonstrate that the proposed implementation methods reduce the running time of the fast algorithm by a factor up to three over a standard implementation.

Algorithms↗

A knowledge-driven algorithm for a rapid and automatic extraction of the human cerebral ventricular system from MR neuroimages.

A knowledge-driven algorithm for a rapid, robust, accurate, and automatic extraction of the human cerebral ventricular system from MR neuroimages is proposed. Its novelty is in combination of neuroanatomy, radiological properties, and variability of the ventricular system with image processing techniques. The ventricular system is divided into six 3D regions: bodies and inferior horns of the lateral ventricles, third ventricle, and fourth ventricle. Within each ventricular region, a 2D region of interest (ROI) is defined based on anatomy and variability. Each ventricular region is further subdivided into subregions, and conditions detecting and preventing leakage into the extra-ventricular space are specified for each subregion. The algorithm extracts the ventricular system by (1) processing each ROI (to calculate its local statistics, determine local intensity ranges of cerebrospinal fluid and gray and white matters, set a seed point within the ROI, grow region directionally in 3D, check anti-leakage conditions, and correct growing if leakage occurred) and (2) connecting all unconnected regions grown by relaxing growing conditions. The algorithm was validated qualitatively on 68 and quantitatively on 38 MRI normal and pathological cases (30 clinical, 20 MGH Brain Repository, and 18 MNI BrainWeb data sets). It runs successfully for normal and pathological cases provided that the slice thickness is less than 3.0 mm in axial and less than 2.0 mm in coronal directions, and the data do not have a high inter-slice intensity variability. The algorithm also works satisfactorily in the presence of up to 9% noise and up to 40% RF inhomogeneity for the BrainWeb data. The running time is less than 5 s on a Pentium 4, 2.0 GHz PC. The best overlap metric between the results of a radiology expert and the algorithm is 0.9879 and the worst 0.9527; the mean and standard deviation of the overlap metric are 0.9723 and 0.01087, respectively.

Adolescent↗

A meta-algorithm for brain extraction in MRI.

Accurate identification of brain tissue and cerebrospinal fluid (CSF) in a whole-head MRI is a critical first step in many neuroimaging studies. Automating this procedure can eliminate intra- and interrater variance and greatly increase throughput for a labor-intensive step. Many available procedures perform differently across anatomy and under different acquisition protocols. We developed the Brain Extraction Meta-Algorithm (BEMA) to address these concerns. It executes many extraction algorithms and a registration procedure in parallel to combine the results in an intelligent fashion and obtain improved results over any of the individual algorithms. Using an atlas space, BEMA performs a voxelwise analysis of training data to determine the optimal Boolean combination of extraction algorithms to produce the most accurate result for a given voxel. This allows the provided extractors to be used differentially across anatomy, increasing both the accuracy and robustness of the procedure. We tested BEMA using modified forms of BrainSuite's Brain Surface Extractor (BSE), FSL's Brain Extraction Tool (BET), AFNI's 3dIntracranial, and FreeSurfer's MRI Watershed as well as FSL's FLIRT for the registration procedure. Training was performed on T1-weighted scans of 136 subjects from five separate data sets with different acquisition parameters on separate scanners. Testing was performed on 135 separate subjects from the same data sets. BEMA outperformed the individual algorithms, as well as interrater results from a subset of the scans, when compared for the mean Dice coefficient, a rating of the similarity of output masks to the manually defined gold standards.

Adult↗

Evaluation of the GTRACT diffusion tensor tractography algorithm: a validation and reliability study.

Fiber tracking, based on diffusion tensor imaging (DTI), is the only approach available to non-invasively study the three-dimensional structure of white matter tracts. Two major obstacles to this technique are partial volume artifacts and tracking errors caused by image noise. In this paper, a novel fiber tracking algorithm called Guided Tensor Restore Anatomical Connectivity Tractography (GTRACT) is presented. This algorithm utilizes a multi-pass approach to fiber tracking. In the first pass, a 3D graph search algorithm is utilized. The second pass incorporates anatomical connectivity information generated in the first pass to guide the tracking in this stage. This approach improves the ability to reconstruct complex fiber paths as well as the tracking accuracy. Validation and reliability studies using this algorithm were performed on both synthetic phantom data and clinical human brain data. A method is also proposed for the evaluating reliability of fiber tract generation based both on the position of the fiber tracts, as well the anisotropy values along the path. The results demonstrate that the GTRACT algorithm is less sensitive to image noise and more capable of handling areas of complex fiber crossing, compared to conventional streamline methods.

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Case finding for population-based studies of rheumatoid arthritis: comparison of patient self-reported ACR criteria-based algorithms to physician-implicit review for diagnosis of rheumatoid arthritis.

OBJECTIVE: To evaluate the interrater reliability of rheumatologist diagnosis of rheumatoid arthritis (RA) and the concordance between rheumatologist and computer algorithms for assessing the accuracy of a diagnosis of RA. METHODS: Self-reported data regarding symptoms and signs for a diagnosis of RA were considered by a panel of rheumatologists and by computer algorithms to assess the probability of a diagnosis of RA for 90 patients. The rheumatologists' review was validated through medical record. RESULTS: The interrater reliability among rheumatologists regarding a diagnosis of RA was 84%; the chance-corrected agreement (kappa) was 0.66. Agreement between the rheumatologists' rating and the best-performing algorithm was 95%. Using rheumatologist's review as a standard, the sensitivity of the algorithm was 100%, specificity was 88%, and the positive predictive value was 91%. The validation of rheumatologist's review by medical record showed 81% sensitivity, 60% specificity, and 78% positive predictive value. CONCLUSION: Reliability of rheumatologists' assignment of a diagnosis of RA by using self-report data is good. Algorithms defining symptoms as either joint swelling or tenderness with symptom duration >or=4 weeks have a better agreement with rheumatologist's diagnosis than do ones relying on a longer symptom duration. RELEVANCE: These findings have important implications for health services research and quality improvement interventions pertinent to case finding for RA through self-report data.

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Comparative investigation of subjective image quality of digital intraoral radiographs processed with 3 image-processing algorithms.

OBJECTIVE: To evaluate the subjective diagnostic image quality of clinical digital intraoral radiographs processed with 3 different image-processing algorithms. STUDY DESIGN: One hundred digital intraoral radiographs were collected and subsequently processed in 3 sets. In the first set the radiographs were processed for correction for attenuation and visual response. In the second set the radiographs were processed with the same algorithms but with an additional shift in gray levels so that the average brightness of a region of interest was displayed with the mean brightness of the computer monitor. In the third, the radiographs were processed with the default gamma-correction in the Dimaxis program (Planmeca Oy, Helsinki, Finland). The 3 radiographs that were differently processed from the same original were displayed simultaneously on the computer monitor. Ten observers evaluated subjectively all the radiographs according to the portrayal of normal structures under the same viewing conditions. Five of them performed repeated evaluations of 20 of the 100 radiographs 2 months later. RESULTS: The best subjective diagnostic quality was found for the radiographs processed with the new algorithms plus an additional shift in gray levels. Radiographs processed with the new algorithms were preferred when compared with those processed with the default gamma-correction. The differences between the 3 types of radiographs were significant (P <.0001). No significant intraobserver differences were found (P=.5487). CONCLUSION: Radiographs processed for correction for attenuation and visual response might be beneficial in clinical work. Clinical radiographs processed with the new algorithms plus an additional shift in gray levels further improve the subjective impression of normal structures.

Adolescent↗

Clinical performance of a specific algorithm to reconfirm self-terminating ventricular arrhythmias in current implantable cardioverter-defibrillators.

Inappropriate shock therapy is a frequent problem in patients with implantable cardioverter-defibrillators (ICDs), caused mostly by supraventricular rhythms. Self-terminating ventricular arrhythmias (STVAs), however, may also lead to inappropriate shock discharges even in ICDs with abortive shock capabilities. The aim of this study was to evaluate the clinical performance of a specific ventricular tachycardia/ventricular fibrillation (VT/VF) reconfirmation algorithm implemented in current ICD devices from Medtronic to prevent inappropriate shock discharges due to STVAs. A total of 161 STVA episodes were documented in 59 of 150 patients (39%) within a mean follow-up of 30 +/- 20 months and resulted in 25 inappropriate shock discharges in 15 of 150 patients (10%) despite activation of the reconfirmation algorithm. The first synchronization interval of the algorithm was met in 92% of STVA episodes with and even 38% of STVA episodes without shock delivery. A reduced incidence of inappropriate shocks due to STVAs was found with tachycardia/fibrillation detection intervals (TDI/FDI) programmed to shorter cycle lengths < or =280 ms or the use of the first 2 cycles after the end of charging to be considered for reconfirmation only. Thus, inappropriate shocks due to STVAs still occur in 10% of patients with ICDs despite activation of a specific VT/VF reconfirmation algorithm, and are mainly caused by meeting the first synchronization interval that therefore should be shortened in cycle length. Moreover, to reduce the likelihood of inappropriate shocks, the VF reconfirmation algorithm should be optimized by basing the synchronization intervals exclusively on the FDI with short cycle lengths or using the first 2 cycles for reconfirmation only.

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A fast numerical algorithm for electron mean energy calculation in radiation therapy.

A numerical algorithm for calculating the mean energy of radiotherapy electron beams has been developed. This algorithm is fast and accurate which makes it suitable for routine clinical use. First, a Gaussian distribution of the electron energy spectrum is derived from the linear Boltzmann equation. Based on this Gaussian spectrum, and after introducing a correction to the CSDA mean energy, a recursive-iterative algorithm for the mean energy calculation is developed. The multiple-scattering correction is taken into account using Yang's pathlength distribution theory. Numerical results of the present algorithm are compared with the results obtained through Monte Carlo simulation as well as Harder's formula. Good agreement with Monte Carlo simulation is achieved. Also the new algorithm is much more accurate than the commonly-used empirical formula of Harder.

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Enhancing the detection of seizures with a clustering algorithm.

Automated detection algorithms of EEG seizures or similar clinical events typically analyze a finite epoch a given channel at a time, producing a probability or a weight estimating how likely it is for the event to resemble a clinical pattern. Epochs are normally shorter than the duration of a seizure, which may spread to more than one electrode. This may result in a weak correspondence between the seizure pattern in the record and its calculated detector event counterpart. As a result, such algorithms suffer from a high rate of false detections. We show that the weights/probabilities of a generic detector can be described as a weight function embedded in a directed graph (digraph). Extended objects such as seizures therefore correspond to the connected components of the digraph. We introduce a clustering algorithm that accounts for the shortcomings of a generic detector of the type described above. By correlating detector results with respect to both time and channel, we effectively extend the detection to an unlimited number of electrodes over an indefinite time. The algorithm is fast (linear - O(m)) and may be implemented in real time. We argue that the algorithm enhances the detection of seizure onset and lowers the rate of false detections. Preliminary results demonstrate a strong correlation between the seizure and the cluster's boundaries and over 50% reduction of false detection rate.

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Slope filtered pointwise correlation dimension algorithm and its evaluation with prefibrillation heart rate data.

Various studies have shown that a low variability in heart rate is associated with increased risk of ventricular fibrillation. Low chaotic (correlation) dimension in the heart rate also appears to predict fibrillation risk. However, these results have been based on intergroup comparisons and have not been found useful for predicting when a patient may fibrillate with any degree of sensitivity, specificity, or temporal accuracy. There are two primary limitations in using dimensional analysis to predict imminent fibrillation. The first is that the standard algorithms (for correlation dimension) assume stationarity of the system. The second limitation is that these algorithms require 10,000-50,000 data points to achieve good accuracy. Thus, even if stationarity were not an issue, there would be a lag of 2.4-12 hours to warn of impending fibrillation. An algorithm has been developed to calculate an accurate pointwise correlation dimension of heart rate data. The slope filtered pointwise correlation dimension algorithm requires as few as 1,000 points of data. Using this algorithm, it was found that the correlation dimension dropped from 2.50 +/- 0.81 to 1.07 +/- 0.18 in the minute before fibrillation in conscious pigs with an occluded coronary artery. In clinical studies, Holter tapes from patients that had suffered fatal fibrillation were also analyzed along with healthy controls and nonfibrillation ventricular patients. The fibrillation patients all had excursions of low dimension (less than 1.5), while the majority of the others did not. In the minutes before fibrillation, the correlation dimension dropped to a steady range of 0.8-1.3. Drops in the slope filtered pointwise correlation dimension appear to predict fibrillation in animals and patients.

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Prospective validation of an algorithm with systematic sextant biopsy to predict pelvic lymph node metastasis in patients with clinically localized prostatic carcinoma.

PURPOSE: We prospectively validate an algorithm to predict pelvic lymph node metastasis in patients with clinically localized prostatic carcinoma. MATERIAL AND METHODS: A total of 293 patients with prostatic cancer were identified before pelvic lymph node dissection according to an algorithm developed with the classification and regression tree analysis as high-greater than 3 sextant biopsies containing any Gleason grade 4 or 5 cancer, intermediate-at least 1 biopsy dominated by Gleason grade 4 or 5 cancer but not high risk and low risk-all other patients. Observed and predicted frequencies of pelvic lymph node metastasis were compared. RESULTS: The observed frequencies of lymph node metastasis were remarkably similar to the predicted frequencies, including 2.8% versus 2.2% in 85.7% of patients in the low risk group, 16.7% versus 19.4% in 10.2% intermediate and 41.7% versus 45.5% in 4.1% high, respectively. If patients in the low risk group were considered to have node negative disease the specificity and negative predictive value of the algorithm were 88.4% and 97.2%, respectively. CONCLUSIONS: Our algorithm is valid as a simple and accurate tool for the prediction of pelvic lymph node metastasis in patients with clinically localized prostatic cancer. Those 85.7% of patients classified by the algorithm to have a low risk of lymphatic spread should not undergo pelvic lymph node dissection before definitive local treatment.

Algorithms↗

Clinical detection of optic nerve damage: measuring changes in cup steepness with use of a new image alignment algorithm.

The purpose of this study was to study the effect of a subpixel image alignment algorithm on the standard deviation (SD) of mean topography images obtained by laser scanning tomography and to evaluate changes of the cup shape measure parameter (CSM) over time based upon the individual parameter variability using the new algorithm. Triple measurements from optic nerve heads of 132 eyes of 132 subjects were obtained using the Heidelberg Retina Tomograph HRT. To calculate a mean topography image from three single topography images, alignment of the raw optical section image data was performed with the standard software and again with a new subpixel-based image alignment algorithm. The effect on the averaged (SD) of the mean topography images was evaluated. CSM was evaluated in 15 eyes of 15 normal subjects (N) and 28 eyes of 14 glaucoma patients (G) over a period of 28.6 +/- 4.6 months (N) and 28.56 +/- 5.2 months (G) respectively. A change in the CSM value over time was considered significant if CSM measurements exceeded two standard deviations of this variable determined for the individual eye. Mean-topography image SD was 22.86 +/- 8.2 microns (min. 9.5 microm; max. 47.8 microm) with the standard alignment procedure and 15.46 +/- 6.8 microm (min. 6.8 microm; max. 42.8 microm) with the new algorithm. The average SD improvement was 7.46 +/- 3.9 microns (min. -8.1 microm; max. 28.7 microm). The coefficient of correlation of both methods was R(2) = 0.77 (p < 0.0001). No control group eye demonstrated significant changes of CSM in the follow-up period. The CSM indicated an increase in cup steepness in 4 eyes of 4 glaucoma patients. In one of these four eyes, a deterioration of the visual field was identified by white on white perimetry. The new image alignment algorithm significantly reduces the SD of mean topography images calculated from identical raw data. If topometric variables are evaluated over time, the individual variability of data should be taken into account.

Adult↗

A bayesian statistical algorithm for RNA secondary structure prediction.

A Bayesian approach for predicting RNA secondary structure that addresses the following three open issues is described: (1) the need for a representation of the full ensemble of probable structures; (2) the need to specify a fixed set of energy parameters; (3) the desire to make statistical inferences on all variables in the problem. It has recently been shown that Bayesian inference can be employed to relax or eliminate the need to specify the parameters of bioinformatics recursive algorithms and to give a statistical representation of the full ensemble of probable solutions with the incorporation of uncertainty in parameter values. In this paper, we make an initial exploration of these potential advantages of the Bayesian approach. We present a Bayesian algorithm that is based on stacking energy rules but relaxes the need to specify the parameters. The algorithm returns the exact posterior distribution of the number of destabilizing loops, stacking energy matrices, and secondary structures. The algorithm generates statistically representative structures from the full ensemble of probable secondary structures in exact proportion to the posterior probabilities. Once the forward recursions for the algorithm are completed, the backward recursive sampling executes in O(n) time, providing a very efficient approach for generating representative structures. We demonstrate the utility of the Bayesian approach with several tRNA sequences. The potential of the approach for predicting RNA secondary structures and presenting alternative structures is illustrated with applications to the Escherichia coli tRNA(Ala) sequence and the Xenopus laevis oocyte 5S rRNA sequence.

Algorithms↗

A treatment algorithm for neuropathic pain.

BACKGROUND: Neuropathic pain is a chronic pain syndrome caused by drug-, disease-, or injury-induced damage or destruction of sensory neurons within the dorsal root ganglia of the peripheral nervous system. Characteristic clinical symptoms include the feeling of pins and needles; burning, shooting, and/or stabbing pain with or without throbbing; and numbness. Neuronal hyperexcitability represents the hallmark cellular mechanism involved in the underlying pathophysiology of neuropathic pain. Although the primary goal is to alleviate pain, clinicians recognize that even the most appropriate treatment strategy may be, at best, only able to reduce pain to a more tolerable level. OBJECTIVE: The purpose of this review is to propose a treatment algorithm for neuropathic pain that health care professionals can logically follow and adapt to the specific needs of each patient. The algorithm is intended to serve as a general guide to assist clinicians in optimizing available therapeutic options. METHODS: A comprehensive review of the literature using the PubMed, MEDLINE, Cochrane, and Toxnet databases was conducted to design and develop a novel treatment algorithm for neuropathic pain that encompasses agents from several drug classes, including antidepressants, antiepileptic drugs, topical antineuralgic agents, narcotics, and analgesics, as well as various treatment options for refractory cases. RESULTS: Any of the agents in the first-line drug classes (tricyclic antidepressants, antiepileptic drugs, topical antineuralgics, analgesics) may be used as a starting point in the treatment of neuropathic pain. If a patient does not respond to treatment with at least 3 different agents within a drug class, agents from a second drug class may be tried. When all first-line options have been exhausted, narcotic analgesics or refractory treatment options may provide some benefit. Patients who do not respond to monotherapy with any of the first- or second-line agents may respond to combination therapy or may be candidates for referral to a pain clinic. Because the techniques used at pain clinics tend to be invasive, referrals to these clinics should be reserved for patients who are truly refractory to all forms of pharmacotherapy. CONCLUSIONS: Neuropathic pain continues to be one of the most difficult pain conditions to treat. With the proposed algorithm, clinicians will have a framework from which to design a pain treatment protocol appropriate for each patient. The algorithm will also help streamline referrals to specialized pain clinics, thereby reducing waiting list times for patients who are truly refractory to traditional pharmacotherapy.

Algorithms↗

Interactions with 3D isotropic and homogeneous radiation fields: a Monte Carlo simulation algorithm.

Monte Carlo techniques have become important tools for many biomedical applications. Many of these involve simulations of radiation fields that rely on the isotropy and homogeneity of the radiation source. The current study proposes a general algorithm to simulate such a radiation field around a fixed object. The idea is to surround the object with a sphere and to limit the source of radiation to the surface of that sphere. To insure the isotropy of the radiation source, each point on the sphere surface as seen from the object defines a direction at which a unidirectional field of particles is created. The combination of all unidirectional fields approaching from all points on the source sphere creates the effect of an isotropic and homogeneous radiation source. The algorithm is first presented without mathematical detail. Next, the expressions for the position and direction of the particles that compose the field are derived using analytical geometry. The radius of the source sphere is the only parameter needed for this algorithm. The randomness of each particle is simulated by the choice of four random numbers. Two algorithms using these analytical results are proposed, and an example of a C program is given for each. Both algorithms can be easily adapted to any situation that involves the Monte Carlo simulation of radiation interactions of a fixed object immersed within an isotropic and homogeneous radiation field.

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Autonomous evolutionary algorithm in medical data analysis.

An autonomous evolutionary algorithm for constructing decision trees is presented. The algorithm requires no or minimal human interaction and shows some interesting properties when used on different medical datasets. The algorithm uses a non-standard implicit fitness evaluation in the selection phase of a co-evolving environment. Together with self-adaptation of evolution parameters and with some other improvements it can monitor and adjust its own behavior. The algorithm's capability to self-adapt to a given problem is used as a measure to predict if some dataset is just difficult or impossible to analyze. The autonomous algorithm on average produces very general solutions or gives no solution if the dataset is prone to the overfitting problem.

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Generalized linear least squares algorithm for non-uniformly sampled biomedical system identification with possible repeated eigenvalues.

The recently developed generalized linear least squares (GLLS) algorithm has been found very useful in non-uniformly sampled biomedical signal processing and parameter estimation. However, the current version of the algorithm cannot deal with signals and systems containing repeated eigenvalues. In this paper, we extend the algorithm, so that it can be used for non-uniformly sampled signals and systems with/without repeated eigenvalues. The related theory and detailed derivation of the algorithm are given. A case study is presented, which demonstrates that the extended algorithm can provide more choices for system identification and is able to select the most suitable model for the system from the non-uniformly sampled noisy signal.

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