Automatic Detection and Uncertainty Quantification of Landmarks on Elastic Curves.
Ontology highlight
ABSTRACT:
SUBMITTER: Strait J
PROVIDER: S-EPMC6781625 | biostudies-literature | 2019
REPOSITORIES: biostudies-literature
Publications
Automatic Detection and Uncertainty Quantification of Landmarks on Elastic Curves.
Strait Justin J Chkrebtii Oksana O Kurtek Sebastian S
Journal of the American Statistical Association 20190320 527
A population quantity of interest in statistical shape analysis is the location of landmarks, which are points that aid in reconstructing and representing shapes of objects. We provide an automated, model-based approach to inferring landmarks given a sample of shape data. The model is formulated based on a linear reconstruction of the shape, passing through the specified points, and a Bayesian inferential approach is described for estimating unknown landmark locations. The question of how many l ...[more]
Similar Datasets
Project description:Real-time PCR is a highly sensitive and powerful technology for the quantification of DNA and has become the method of choice in microbiology, bioengineering, and molecular biology. Currently, the analysis of real-time PCR data is hampered by only considering a single feature of the amplification profile to generate a standard curve. The current "gold standard" is the cycle-threshold ( Ct) method which is known to provide poor quantification under inconsistent reaction efficiencies. Multiple single-feature methods have been developed to overcome the limitations of the Ct method; however, there is an unexplored area of combining multiple features in order to benefit from their joint information. Here, we propose a novel framework that combines existing standard curve methods into a multidimensional standard curve. This is achieved by considering multiple features together such that each amplification curve is viewed as a point in a multidimensional space. Contrary to only considering a single-feature, in the multidimensional space, data points do not fall exactly on the standard curve, which enables a similarity measure between amplification curves based on distances between data points. We show that this framework expands the capabilities of standard curves in order to optimize quantification performance, provide a measure of how suitable an amplification curve is for a standard, and thus automatically detect outliers and increase the reliability of quantification. Our aim is to provide an affordable solution to enhance existing diagnostic settings through maximizing the amount of information extracted from conventional instruments.
| S-EPMC6551572 | biostudies-literature
Project description:PURPOSE:Magnetic resonance imaging (MRI)-based cell tracking has emerged as a useful tool for identifying the location of transplanted cells, and even their migration. Magnetically labeled cells appear as dark contrast in T2*-weighted MRI, with sensitivities of individual cells. One key hurdle to the widespread use of MRI-based cell tracking is the inability to determine the number of transplanted cells based on this contrast feature. In the case of single cell detection, manual enumeration of spots in three-dimensional (3D) MRI in principle is possible; however, it is a tedious and time-consuming task that is prone to subjectivity and inaccuracy on a large scale. This research presents the first comprehensive study on how a computer-based intelligent, automatic, and accurate cell quantification approach can be designed for spot detection in MRI scans. METHODS:Magnetically labeled mesenchymal stem cells (MSCs) were transplanted into rats using an intracardiac injection, accomplishing single cell seeding in the brain. T2*-weighted MRI of these rat brains were performed where labeled MSCs appeared as spots. Using machine learning and computer vision paradigms, approaches were designed to systematically explore the possibility of automatic detection of these spots in MRI. Experiments were validated against known in vitro scenarios. RESULTS:Using the proposed deep convolutional neural network (CNN) architecture, an in vivo accuracy up to 97.3% and in vitro accuracy of up to 99.8% was achieved for automated spot detection in MRI data. CONCLUSION:The proposed approach for automatic quantification of MRI-based cell tracking will facilitate the use of MRI in large-scale cell therapy studies. Magn Reson Med 78:1991-2002, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
| S-EPMC5817897 | biostudies-literature
Project description:According to Mayr, polar organic synthesis can be rationalized by a simple empirical relationship linking bimolecular rate constants to as few as three reactivity parameters. Here, we propose an extension to Mayr's reactivity method that is rooted in uncertainty quantification and transforms the reactivity parameters into probability distributions. Through uncertainty propagation, these distributions can be transformed into uncertainty estimates for bimolecular rate constants. Chemists can exploit these virtual error bars to enhance synthesis planning and to decrease the ambiguity of conclusions drawn from experimental data. We demonstrate the above at the example of the reference data set released by Mayr and co-workers [J. Am. Chem. Soc. 2001, 123, 9500; J. Am. Chem. Soc. 2012, 134, 13902]. As by-product of the new approach, we obtain revised reactivity parameters for 36 π-nucleophiles and 32 benzhydrylium ions.
| S-EPMC9314972 | biostudies-literature
Project description:BACKGROUND:This pilot study was designed to develop a fully automatic and quantitative scoring system of B-lines (QLUSS: quantitative lung ultrasound score) involving the pleural line and to compare it with previously described semi-quantitative scores in the measurement of extravascular lung water as determined by standard thermo-dilution. METHODS:This was a prospective observational study of 12 patients admitted in the intensive care unit with acute respiratory distress and each provided with 12 lung ultrasound (LUS) frames. Data collected from each patient consisted in five different scores, four semi-quantitative (nLUSS, cLUSS, qLUSS, %LUSS) and quantitative scores (QLUSS). The association between LUS scores and extravascular lung water (EVLW) was determined by simple linear regression (SLR) and robust linear regression (RLR) methods. A correlation analysis between the LUS scores was performed by using the Spearman rank test. Inter-observer variability was tested by computing intraclass correlation coefficient (ICC) in two-way models for agreement, basing on scores obtained by different raters blinded to patients' conditions and clinical history. RESULTS:In the SLR, QLUSS showed a stronger association with EVLW (R2 = 0.57) than cLUSS (R2 = 0.45) and nLUSS (R2 = 0.000), while a lower association than qLUSS (R2 = 0.85) and %LUSS (R2 = 0.72) occurred. By applying RLR, QLUSS showed an association for EVLW (R2 = 0.86) comparable to qLUSS (R2 = 0.85) and stronger than %LUSS (R2 = 0.72). QLUSS was significantly correlated with qLUSS (r = 0.772; p = 0.003) and %LUSS (r = 0.757; p = 0.005), but not with cLUSS (r = 0.561; p = 0.058) and nLUSS (r = 0.105; p = 0.744). Moreover, QLUSS showed the highest ICC (0.998; 95%CI from 0.996 to 0.999) among the LUS scores. CONCLUSIONS:This study demonstrates that computer-aided scoring of the pleural line percentage affected by B-lines has the potential to assess EVLW. QLUSS may have a significant impact, once validated with a larger dataset composed by multiple real-time frames. This approach has the potentials to be advantageous in terms of faster data analysis and applicability to large sets of data without increased costs. On the contrary, it is not useful in pleural effusion or consolidations.
| S-EPMC6712728 | biostudies-other
Project description:Cephalometric tracing is a standard analysis tool for orthodontic diagnosis and treatment planning. The aim of this study was to develop and validate a fully automatic landmark annotation (FALA) system for finding cephalometric landmarks in lateral cephalograms and its application to the classification of skeletal malformations. Digital cephalograms of 400 subjects (age range: 7-76 years) were available. All cephalograms had been manually traced by two experienced orthodontists with 19 cephalometric landmarks, and eight clinical parameters had been calculated for each subject. A FALA system to locate the 19 landmarks in lateral cephalograms was developed. The system was evaluated via comparison to the manual tracings, and the automatically located landmarks were used for classification of the clinical parameters. The system achieved an average point-to-point error of 1.2 mm, and 84.7% of landmarks were located within the clinically accepted precision range of 2.0 mm. The automatic landmark localisation performance was within the inter-observer variability between two clinical experts. The automatic classification achieved an average classification accuracy of 83.4% which was comparable to an experienced orthodontist. The FALA system rapidly and accurately locates and analyses cephalometric landmarks in lateral cephalograms, and has the potential to significantly improve the clinical work flow in orthodontic treatment.
| S-EPMC5028843 | biostudies-literature
Project description:The recognition of bony landmarks of the pelvis is a required operation in patient-specific orthopedics, subject-specific biomechanics or morphometrics. A fully automatic detection is preferable to a subjective and time-consuming manual identification. In this paper, a new approach, called the iterative tangential plane (ITP) method, for fully automatic identification of landmarks on surface models of the pelvis is introduced. The method includes the landmarks to construct the two most established anatomical reference frames of the pelvis: the anterior pelvic plane (APP) coordinate system and superior inferior spine plane (SISP) coordinate system. The ITP method proved to be robust against the initial alignment of the pelvis in space. A comparison to a manual identification was performed that showed minor but significant (p < 0.05) median differences below 3 mm for the position of the landmarks and below 1° for the orientation of the APP coordinate system. Whether these differences are acceptable, has to be evaluated for each specific use case. There were no significant differences for the orientation of the SISP coordinate system recommended by the International Society of Biomechanics.
| S-EPMC6746744 | biostudies-literature
Project description:Alchemical free energy methods have gained much importance recently from several reports of improved ligand-protein binding affinity predictions based on their implementation using molecular dynamics simulations. A large number of variants of such methods implementing different accelerated sampling techniques and free energy estimators are available, each claimed to be better than the others in its own way. However, the key features of reproducibility and quantification of associated uncertainties in such methods have barely been discussed. Here, we apply a systematic protocol for uncertainty quantification to a number of popular alchemical free energy methods, covering both absolute and relative free energy predictions. We show that a reliable measure of error estimation is provided by ensemble simulation-an ensemble of independent MD simulations-which applies irrespective of the free energy method. The need to use ensemble methods is fundamental and holds regardless of the duration of time of the molecular dynamics simulations performed.
| S-EPMC6095638 | biostudies-literature
Project description:High throughput screening (HTS) projects like the U.S. Environmental Protection Agency's ToxCast program are required to address the large and rapidly increasing number of chemicals for which we have little to no toxicity measurements. Concentration-response parameters such as potency and efficacy are extracted from HTS data using nonlinear regression, and models and analyses built from these parameters are used to predict in vivo and in vitro toxicity of thousands of chemicals. How these predictions are impacted by uncertainties that stem from parameter estimation and propagated through the models and analyses has not been well explored. While data size and complexity makes uncertainty quantification computationally expensive for HTS datasets, continued advancements in computational resources have allowed these computational challenges to be met. This study uses nonparametric bootstrap resampling to calculate uncertainties in concentration-response parameters from a variety of HTS assays. Using the ToxCast estrogen receptor model for bioactivity as a case study, we highlight how these uncertainties can be propagated through models to quantify the uncertainty in model outputs. Uncertainty quantification in model outputs is used to identify potential false positives and false negatives and to determine the distribution of model values around semi-arbitrary activity cutoffs, increasing confidence in model predictions. At the individual chemical-assay level, curves with high variability are flagged for manual inspection or retesting, focusing subject-matter-expert time on results that need further input. This work improves the confidence of predictions made using HTS data, increasing the ability to use this data in risk assessment.
| S-EPMC6059398 | biostudies-other
Project description:Noisy matrix completion aims at estimating a low-rank matrix given only partial and corrupted entries. Despite remarkable progress in designing efficient estimation algorithms, it remains largely unclear how to assess the uncertainty of the obtained estimates and how to perform efficient statistical inference on the unknown matrix (e.g., constructing a valid and short confidence interval for an unseen entry). This paper takes a substantial step toward addressing such tasks. We develop a simple procedure to compensate for the bias of the widely used convex and nonconvex estimators. The resulting debiased estimators admit nearly precise nonasymptotic distributional characterizations, which in turn enable optimal construction of confidence intervals/regions for, say, the missing entries and the low-rank factors. Our inferential procedures do not require sample splitting, thus avoiding unnecessary loss of data efficiency. As a byproduct, we obtain a sharp characterization of the estimation accuracy of our debiased estimators in both rate and constant. Our debiased estimators are tractable algorithms that provably achieve full statistical efficiency.
| S-EPMC6859358 | biostudies-literature
Project description:MotivationQuantification estimates of gene expression from single-cell RNA-seq (scRNA-seq) data have inherent uncertainty due to reads that map to multiple genes. Many existing scRNA-seq quantification pipelines ignore multi-mapping reads and therefore underestimate expected read counts for many genes. alevin accounts for multi-mapping reads and allows for the generation of "inferential replicates", which reflect quantification uncertainty. Previous methods have shown improved performance when incorporating these replicates into statistical analyses, but storage and use of these replicates increases computation time and memory requirements.ResultsWe demonstrate that storing only the mean and variance from a set of inferential replicates ("compression") is sufficient to capture gene-level quantification uncertainty, while reducing disk storage to as low as 9% of original storage and memory usage when loading data to as low as 6%. Using these values, we generate "pseudo-inferential" replicates from a negative binomial distribution and propose a general procedure for incorporating these replicates into a proposed statistical testing framework. When applying this procedure to trajectory-based differential expression analyses, we show false positives are reduced by more than a third for genes with high levels of quantification uncertainty. We additionally extend the Swish method to incorporate pseudo-inferential replicates and demonstrate improvements in computation time and memory usage without any loss in performance. Lastly, we show that discarding multi-mapping reads can result in significant underestimation of counts for functionally important genes in a real dataset.Availability and implementationmakeInfReps and splitSwish are implemented in the R/Bioconductor fishpond package available at https://bioconductor.org/packages/fishpond.Supplementary informationSupplementary results are available in the corresponding Supplement file.
| S-EPMC8289386 | biostudies-literature