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A detailed comparison of analysis processes for MCC-IMS data in disease classification-Automated methods can replace manual peak annotations.

ABSTRACT: Disease classification from molecular measurements typically requires an analysis pipeline from raw noisy measurements to final classification results. Multi capillary column-ion mobility spectrometry (MCC-IMS) is a promising technology for the detection of volatile organic compounds in the air of exhaled breath. From raw measurements, the peak regions representing the compounds have to be identified, quantified, and clustered across different experiments. Currently, several steps of this analysis process require manual intervention of human experts. Our goal is to identify a fully automatic pipeline that yields competitive disease classification results compared to an established but subjective and tedious semi-manual process.We combine a large number of modern methods for peak detection, peak clustering, and multivariate classification into analysis pipelines for raw MCC-IMS data. We evaluate all combinations on three different real datasets in an unbiased cross-validation setting. We determine which specific algorithmic combinations lead to high AUC values in disease classifications across the different medical application scenarios.The best fully automated analysis process achieves even better classification results than the established manual process. The best algorithms for the three analysis steps are (i) SGLTR (Savitzky-Golay Laplace-operator filter thresholding regions) and LM (Local Maxima) for automated peak identification, (ii) EM clustering (Expectation Maximization) and DBSCAN (Density-Based Spatial Clustering of Applications with Noise) for the clustering step and (iii) RF (Random Forest) for multivariate classification. Thus, automated methods can replace the manual steps in the analysis process to enable an unbiased high throughput use of the technology.

SUBMITTER: Horsch S

PROVIDER: S-EPMC5598980 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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A detailed comparison of analysis processes for MCC-IMS data in disease classification-Automated methods can replace manual peak annotations.

Horsch Salome S Kopczynski Dominik D Kuthe Elias E Baumbach Jörg Ingo JI Rahmann Sven S Rahnenführer Jörg J

PloS one 20170914 9

<h4>Motivation</h4>Disease classification from molecular measurements typically requires an analysis pipeline from raw noisy measurements to final classification results. Multi capillary column-ion mobility spectrometry (MCC-IMS) is a promising technology for the detection of volatile organic compounds in the air of exhaled breath. From raw measurements, the peak regions representing the compounds have to be identified, quantified, and clustered across different experiments. Currently, several s ...[more]

PMID: 28910313

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Project description:New chest compression detection technology allows for the recording and graphical depiction of clinical cardiopulmonary resuscitation (CPR) chest compressions. The authors sought to determine the inter-rater reliability of chest compression pattern classifications by human raters. Agreement with automated chest compression classification was also evaluated by computer analysis.This was an analysis of chest compression patterns from cardiac arrest patients enrolled in the ongoing Resuscitation Outcomes Consortium (ROC) Continuous Chest Compressions Trial. Thirty CPR process files from patients in the trial were selected. Using written guidelines, research coordinators from each of eight participating ROC sites classified each chest compression pattern as 30:2 chest compressions, continuous chest compressions (CCC), or indeterminate. A computer algorithm for automated chest compression classification was also developed for each case. Inter-rater agreement between manual classifications was tested using Fleiss's kappa. The criterion standard was defined as the classification assigned by the majority of manual raters. Agreement between the automated classification and the criterion standard manual classifications was also tested.The majority of the eight raters classified 12 chest compression patterns as 30:2, 12 as CCC, and six as indeterminate. Inter-rater agreement between manual classifications of chest compression patterns was ? = 0.62 (95% confidence interval [CI] = 0.49 to 0.74). The automated computer algorithm classified chest compression patterns as 30:2 (n = 15), CCC (n = 12), and indeterminate (n = 3). Agreement between automated and criterion standard manual classifications was ? = 0.84 (95% CI = 0.59 to 0.95).In this study, good inter-rater agreement in the manual classification of CPR chest compression patterns was observed. Automated classification showed strong agreement with human ratings. These observations support the consistency of manual CPR pattern classification as well as the use of automated approaches to chest compression pattern analysis.

Project description:BackgroundCross-mapping establishes equivalence between terms from different terminology systems, which is useful for interoperability, updated terminological versions, and reuse of terms. Due to the number of terms to be mapped, this work can be extensive, tedious, and thorough, and it is susceptible to errors; this can be minimized by automated processes, which use computational tools.ObjectiveThe aim of this study was to compare the results of manual and automated term mapping processes.MethodsIn this descriptive, quantitative study, we used the results of two mapping processes as an empirical basis: manual, which used 2638 terms of nurses' records from a university hospital in southern Brazil and the International Classification for Nursing Practice (ICNP); and automated, which used the same university hospital terms and the primitive terms of the ICNP through MappICNP, an algorithm based on rules of natural language processing. The two processes were compared via equality and exclusivity assessments of new terms of the automated process and of candidate terms.ResultsThe automated process mapped 569/2638 (21.56%) of the source bank's terms as identical, and the manual process mapped 650/2638 (24.63%) as identical. Regarding new terms, the automated process mapped 1031/2638 (39.08%) of the source bank's terms as new, while the manual process mapped 1251 (47.42%). In particular, manual mapping identified 101/2638 (3.82%) terms as identical and 429 (16.26%) as new, whereas the automated process identified 20 (0.75%) terms as identical and 209 (7.92%) as new. Of the 209 terms mapped as new by the automated process, it was possible to establish an equivalence with ICNP terms in 48 (23.0%) cases. An analysis of the candidate terms offered by the automated process to the 429 new terms mapped exclusively by the manual process resulted in 100 (23.3%) candidates that had a semantic relationship with the source term.ConclusionsThe automated and manual processes map identical and new terms in similar ways and can be considered complementary. Direct identification of identical terms and the offering of candidate terms through the automated process facilitate and enhance the results of the mapping; confirmation of the precision of the automated mapping requires further analysis by researchers.

Project description:MotivationSingle-cell time-lapse microscopy is a ubiquitous tool for studying the dynamics of complex cellular processes. While imaging can be automated to generate very large volumes of data, the processing of the resulting movies to extract high-quality single-cell information remains a challenging task. The development of software tools that automatically identify and track cells is essential for realizing the full potential of time-lapse microscopy data. Convolutional neural networks (CNNs) are ideally suited for such applications, but require great amounts of manually annotated data for training, a time-consuming and tedious process.ResultsWe developed a new approach to CNN training for yeast cell segmentation based on synthetic data and present (i) a software tool for the generation of synthetic images mimicking brightfield images of budding yeast cells and (ii) a convolutional neural network (Mask R-CNN) for yeast segmentation that was trained on a fully synthetic dataset. The Mask R-CNN performed excellently on segmenting actual microscopy images of budding yeast cells, and a density-based spatial clustering algorithm (DBSCAN) was able to track the detected cells across the frames of microscopy movies. Our synthetic data creation tool completely bypassed the laborious generation of manually annotated training datasets, and can be easily adjusted to produce images with many different features. The incorporation of synthetic data creation into the development pipeline of CNN-based tools for budding yeast microscopy is a critical step toward the generation of more powerful, widely applicable and user-friendly image processing tools for this microorganism.Availability and implementationThe synthetic data generation code can be found at https://github.com/prhbrt/synthetic-yeast-cells. The Mask R-CNN as well as the tuning and benchmarking scripts can be found at https://github.com/ymzayek/yeastcells-detection-maskrcnn. We also provide Google Colab scripts that reproduce all the results of this work.Supplementary informationSupplementary data are available at Bioinformatics online.

Dataset Information

A detailed comparison of analysis processes for MCC-IMS data in disease classification-Automated methods can replace manual peak annotations.

Publications

A detailed comparison of analysis processes for MCC-IMS data in disease classification-Automated methods can replace manual peak annotations.

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