Software Pipeline Research Articles

Automatic Diagnosis of Alzheimer’s Disease Using Deep Learning Techniques

Neuroimaging data analysis has attracted a great deal of attention with respect to the accurate diagnosis of Alzheimer’s disease (AD). Magnetic Resonance Imaging (MRI) scanners have thus been commonly used to study AD-related brain structural variations, providing images that demonstrate both morphometric and anatomical changes in the human brain. Deep learning algorithms have already been effectively exploited in other medical image processing applications to identify features and recognise patterns for many diseases that affect the brain and other organs; this paper extends on this to describe a novel computer aided software pipeline for the classification and early diagnosis of AD. The proposed method uses two types of three-dimensional Convolutional Neural Networks (3D CNN) to facilitate brain MRI data analysis and automatic feature extraction and classification, so that pre-processing and post-processing are utilised to normalise the MRI data and facilitate pattern recognition. The experimental results show that the proposed approach achieves 97.5%, 82.5%, and 83.75% accuracy in terms of binary classification AD vs. cognitively normal (CN), CN vs. mild cognitive impairment (MCI) and MCI vs. AD, respectively, as well as 85% accuracy for multi class-classification, based on publicly available data sets from the Alzheimer’s disease Neuroimaging Initiative (ADNI).

LTD064402+245919: A Subgiant with a 1–3 M ⊙ Undetected Companion Identified from LAMOST-TD Data

Abstract Single-line spectroscopic binaries have recently contributed to stellar-mass black hole discovery, independently of the X-ray transient method. We report the identification of a single-line binary system, LTD064402+245919, with an orbital period of 14.50 days. The observed component is a subgiant with a mass of 2.77 ± 0.68 M ⊙, radius 15.5 ± 2.5 R ⊙, effective temperature T eff 4500 ± 200 K, and surface gravity log g 2.5 ± 0.25 dex. The discovery makes use of the Large Sky Area Multi-Object fiber Spectroscopic Telescope time-domain and Zwicky Transient Facility survey. Our general-purpose software pipeline applies a Lomb–Scargle periodogram to determine the orbital period and uses machine learning to classify the variable type from the folded light curves. We apply a combined model to estimate the orbital parameters from both the light and radial velocity curves, taking constraints on the primary star mass, mass function, and detection limit of secondary luminosity into consideration. We obtain a radial velocity semiamplitude of 44.6 ± 1.5 km s−1, mass ratio of 0.73 ± 0.07, and an undetected component mass of 2.02 ± 0.49 M ⊙ when the type of the undetected component is not set. We conclude that the inclination is not well constrained, and that the secondary mass is larger than 1 M ⊙ when the undetected component is modeled as a compact object. According to our investigations using a Monte Carlo Markov Chain simulation, increasing the spectra signal-to-noise ratio by a factor of 3 would enable the secondary light to be distinguished (if present). The algorithm and software in this work are able to serve as general-purpose tools for the identification of compact objects quiescent in X-rays.

The Mouse Action Recognition System (MARS) software pipeline for automated analysis of social behaviors in mice.

The study of naturalistic social behavior requires quantification of animals' interactions. This is generally done through manual annotation-a highly time-consuming and tedious process. Recent advances in computer vision enable tracking the pose (posture) of freely behaving animals. However, automatically and accurately classifying complex social behaviors remains technically challenging. We introduce the Mouse Action Recognition System (MARS), an automated pipeline for pose estimation and behavior quantification in pairs of freely interacting mice. We compare MARS's annotations to human annotations and find that MARS's pose estimation and behavior classification achieve human-level performance. We also release the pose and annotation datasets used to train MARS to serve as community benchmarks and resources. Finally, we introduce the Behavior Ensemble and Neural Trajectory Observatory (BENTO), a graphical user interface for analysis of multimodal neuroscience datasets. Together, MARS and BENTO provide an end-to-end pipeline for behavior data extraction and analysis in a package that is user-friendly and easily modifiable.

SnpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data.

Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of different bioinformatics tools. Software incompatibilities, and inconsistencies across computing environments, are recurrent challenges, leading to poor reproducibility. Existing semi-automated or automated solutions lack comprehensive quality checks, flexible workflow architecture, and user control. To address these challenges, we have developed snpQT: a scalable, stand-alone software pipeline using nextflow and BioContainers, for comprehensive, reproducible and interactive quality control of human genomic data. snpQT offers some 36 discrete quality filters or correction steps in a complete standardised pipeline, producing graphical reports to demonstrate the state of data before and after each quality control procedure. This includes human genome build conversion, population stratification against data from the 1,000 Genomes Project, automated population outlier removal, and built-in imputation with its own pre- and post- quality controls. Common input formats are used, and a synthetic dataset and comprehensive online tutorial are provided for testing, educational purposes, and demonstration. The snpQT pipeline is designed to run with minimal user input and coding experience; quality control steps are implemented with numerous user-modifiable thresholds, and workflows can be flexibly combined in custom combinations. snpQT is open source and freely available at https://github.com/nebfield/snpQT. A comprehensive online tutorial and installation guide is provided through to GWAS (https://snpqt.readthedocs.io/en/latest/), introducing snpQT using a synthetic demonstration dataset and a real-world Amyotrophic Lateral Sclerosis SNP-array dataset.

Predicting the performance of automated crystallographic model-building pipelines.

Proteins are macromolecules that perform essential biological functions which depend on their three-dimensional structure. Determining this structure involves complex laboratory and computational work. For the computational work, multiple software pipelines have been developed to build models of the protein structure from crystallographic data. Each of these pipelines performs differently depending on the characteristics of the electron-density map received as input. Identifying the best pipeline to use for a protein structure is difficult, as the pipeline performance differs significantly from one protein structure to another. As such, researchers often select pipelines that do not produce the best possible protein models from the available data. Here, a software tool is introduced which predicts key quality measures of the protein structures that a range of pipelines would generate if supplied with a given crystallographic data set. These measures are crystallographic quality-of-fit indicators based on included and withheld observations, and structure completeness. Extensive experiments carried out using over 2500 data sets show that the tool yields accurate predictions for both experimental phasing data sets (at resolutions between 1.2 and 4.0 Å) and molecular-replacement data sets (at resolutions between 1.0 and 3.5 Å). The tool can therefore provide a recommendation to the user concerning the pipelines that should be run in order to proceed most efficiently to a depositable model.

Participant followup rate can bias structural imaging measures in longitudinal studies

Longitudinal MRI analysis is essential to accurately describe neuroanatomical changes over time. Loss of participants to followup (dropout) in longitudinal studies is inevitable and can lead to great difficulty in interpretation of statistical results if dropout is correlated with a study outcome or exposure. Beyond this, technical aspects of longitudinal MRI analysis require specialised processing pipelines to improve reliability while avoiding bias towards individual timepoints. In this article we test whether there is an additional problem that must be considered in longitudinal imaging studies, namely whether dropout has an impact on the function of FreeSurfer, a popular software pipeline used to estimate important structural brain metrics.We find that the number of acquisitions available per individual can impact the estimation of cortical thickness and brain volume using the FreeSurfer longitudinal pipeline, and can induce group differences in brain metrics. The effect on trajectories of brain metrics is smaller than the effect on brain metrics.

MeTiS: A Modular Pipeline for Extracting 3D-Printable Brain-Surface Models from Conventional and Ultra-High Field MRI

Aim: To develop a modular software pipeline for robustly extracting 3D brain-surface models from MRIs for visualization or printing. No other end-to-end pipeline specialized for neuroimaging does this directly with an interchangeable combination of methods. Materials & methods: A software application was developed to dynamically generate Nipype workflows using interfaces from the Analysis of Functional NeuroImages, Advanced Normalization Tools, FreeSurfer, BrainSuite, Nighres and the FMRIB Software Library suites. The application was deployed for public use via the LONI pipeline environment. Results: In a small, head-to-head comparison test, a pipeline using FreeSurfer for both the skull stripping and cortical-mesh extraction stages earned the highest subjective quality scores. Conclusion: We have deployed a publicly available and modular software tool for extracting 3D models from brain MRIs to use in medical education.

ICompare: A Package for Automated Comparison of Solar System Integrators*

Abstract We present a tool for the comparison and validation of the integration packages suitable for Solar System dynamics. iCompare, written in Python, compares the ephemeris prediction accuracy of a suite of commonly-used integration packages (JPL/HORIZONS, OpenOrb, OrbFit at present). It integrates a set of test particles with orbits picked to explore both usual and unusual regions in Solar System phase space and compares the computed to reference ephemerides. The results are visualized in an intuitive dashboard. This allows for the assessment of integrator suitability as a function of population, as well as monitoring their performance from version to version (a capability needed for the Rubin Observatory’s software pipeline construction efforts). We provide the code on GitHub with a readily runnable version in Binder (https://github.com/dirac-institute/iCompare).

Insights from Initial Variant Detection by Sequencing Single Sperm in Cattle

Meiotic de novo mutation (DNM) is one of the important phenomena contributing to gamete genome diversity. However, except for humans and a few model organisms, they are not well studied in livestock, including cattle. Moreover, bulk sperm samples have been routinely utilized in experiments, which include millions of single sperm cells and only report high-frequency variants. In this study, we isolated and sequenced 143 single sperms from two Holstein bulls and identified hundreds of candidate DNM events in ten sperms with deep sequencing coverage. We estimated DNM rates ranging from 1.08 × 10−8 to 3.78 × 10−8 per nucleotide per generation. We further validated 12 out of 14 selected DNM events using Sanger sequencing. To our knowledge, this is the first single sperm whole-genome sequencing effort in livestock, which provided useful information for future studies of point mutations and male fertility. Our preliminary results pointed out future research directions and highlighted the importance of uniform whole genome amplification, deep sequence coverage, and dedicated software pipelines for genetic variant detection using single-cell sequencing data.

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification.

Command-line annotation software tools have continuously gained popularity compared to centralized online services due to the worldwide increase of sequenced bacterial genomes. However, results of existing command-line software pipelines heavily depend on taxon-specific databases or sufficiently well annotated reference genomes. Here, we introduce Bakta, a new command-line software tool for the robust, taxon-independent, thorough and, nonetheless, fast annotation of bacterial genomes. Bakta conducts a comprehensive annotation workflow including the detection of small proteins taking into account replicon metadata. The annotation of coding sequences is accelerated via an alignment-free sequence identification approach that in addition facilitates the precise assignment of public database cross-references. Annotation results are exported in GFF3 and International Nucleotide Sequence Database Collaboration (INSDC)-compliant flat files, as well as comprehensive JSON files, facilitating automated downstream analysis. We compared Bakta to other rapid contemporary command-line annotation software tools in both targeted and taxonomically broad benchmarks including isolates and metagenomic-assembled genomes. We demonstrated that Bakta outperforms other tools in terms of functional annotations, the assignment of functional categories and database cross-references, whilst providing comparable wall-clock runtimes. Bakta is implemented in Python 3 and runs on MacOS and Linux systems. It is freely available under a GPLv3 license at https://github.com/oschwengers/bakta. An accompanying web version is available at https://bakta.computational.bio.

SnpQT: flexible, reproducible, and comprehensive quality control and imputation of genomic data

Quality control of genomic data is an essential but complicated multi-step procedure, often requiring separate installation and expert familiarity with a combination of different bioinformatics tools. Software incompatibilities, and inconsistencies across computing environments, are recurrent challenges, leading to poor reproducibility. Existing semi-automated or automated solutions lack comprehensive quality checks, flexible workflow architecture, and user control. To address these challenges, we have developed snpQT: a scalable, stand-alone software pipeline using nextflow and BioContainers, for comprehensive, reproducible and interactive quality control of human genomic data. snpQT offers some 36 discrete quality filters or correction steps in a complete standardised pipeline, producing graphical reports to demonstrate the state of data before and after each quality control procedure. This includes human genome build conversion, population stratification against data from the 1,000 Genomes Project, automated population outlier removal, and built-in imputation with its own pre- and post- quality controls. Common input formats are used, and a synthetic dataset and comprehensive online tutorial are provided for testing, educational purposes, and demonstration. The snpQT pipeline is designed to run with minimal user input and coding experience; quality control steps are implemented with numerous user-modifiable thresholds, and workflows can be flexibly combined in custom combinations. snpQT is open source and freely available at https://github.com/nebfield/snpQT. A comprehensive online tutorial and installation guide is provided through to GWAS (https://snpqt.readthedocs.io/en/latest/), introducing snpQT using a synthetic demonstration dataset and a real-world Amyotrophic Lateral Sclerosis SNP-array dataset.

WebTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study.

The development of transcriptome-wide association studies (TWAS) has enabled researchers to better identify and interpret causal genes in many diseases. However, there are currently no resources providing a comprehensive listing of gene-disease associations discovered by TWAS from published GWAS summary statistics. TWAS analyses are also difficult to conduct due to the complexity of TWAS software pipelines. To address these issues, we introduce a new resource called webTWAS, which integrates a database of the most comprehensive disease GWAS datasets currently available with credible sets of potential causal genes identified by multiple TWAS software packages. Specifically, a total of 235 064 gene-diseases associations for a wide range of human diseases are prioritized from 1298 high-quality downloadable European GWAS summary statistics. Associations are calculated with seven different statistical models based on three popular and representative TWAS software packages. Users can explore associations at the gene or disease level, and easily search for related studies or diseases using the MeSH disease tree. Since the effects of diseases are highly tissue-specific, webTWAS applies tissue-specific enrichment analysis to identify significant tissues. A user-friendly web server is also available to run custom TWAS analyses on user-provided GWAS summary statistics data. webTWAS is freely available at http://www.webtwas.net.

Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding

SummaryMolecular interactions at identical transcriptomic locations or at proximal but non-overlapping sites can mediate RNA modification and regulation, necessitating tools to uncover these spatial relationships. We present nearBynding, a flexible algorithm and software pipeline that models spatial correlation between transcriptome-wide tracks from diverse data types. nearBynding can process and correlate interval as well as continuous data and incorporate experimentally derived or in silico predicted transcriptomic tracks. nearBynding offers visualization functions for its statistics to identify colocalizations and adjacent features. We demonstrate the application of nearBynding to correlate RNA-binding protein (RBP) binding preferences with other RBPs, RNA structure, or RNA modification. By cross-correlating RBP binding and RNA structure data, we demonstrate that nearBynding recapitulates known RBP binding to structural motifs and provides biological insights into RBP binding preference of G-quadruplexes. nearBynding is available as an R/Bioconductor package and can run on a personal computer, making correlation of transcriptomic features broadly accessible.

Parakeet: a digital twin software pipeline to assess the impact of experimental parameters on tomographic reconstructions for cryo-electron tomography.

In cryo-electron tomography (cryo-ET) of biological samples, the quality of tomographic reconstructions can vary depending on the transmission electron microscope (TEM) instrument and data acquisition parameters. In this paper, we present Parakeet, a 'digital twin' software pipeline for the assessment of the impact of various TEM experiment parameters on the quality of three-dimensional tomographic reconstructions. The Parakeet digital twin is a digital model that can be used to optimize the performance and utilization of a physical instrument to enable in silico optimization of sample geometries, data acquisition schemes and instrument parameters. The digital twin performs virtual sample generation, TEM image simulation, and tilt series reconstruction and analysis within a convenient software framework. As well as being able to produce physically realistic simulated cryo-ET datasets to aid the development of tomographic reconstruction and subtomogram averaging programs, Parakeet aims to enable convenient assessment of the effects of different microscope parameters and data acquisition parameters on reconstruction quality. To illustrate the use of the software, we present the example of a quantitative analysis of missing wedge artefacts on simulated planar and cylindrical biological samples and discuss how data collection parameters can be modified for cylindrical samples where a full 180° tilt range might be measured.

Chauffeur: Benchmark Suite for Design and End-to-End Analysis of Self-Driving Vehicles on Embedded Systems

Self-driving systems execute an ensemble of different self-driving workloads on embedded systems in an end-to-end manner, subject to functional and performance requirements. To enable exploration, optimization, and end-to-end evaluation on different embedded platforms, system designers critically need a benchmark suite that enables flexible and seamless configuration of self-driving scenarios, which realistically reflects real-world self-driving workloads’ unique characteristics. Existing CPU and GPU embedded benchmark suites typically (1) consider isolated applications, (2) are not sensor-driven, and (3) are unable to support emerging self-driving applications that simultaneously utilize CPUs and GPUs with stringent timing requirements. On the other hand, full-system self-driving simulators (e.g., AUTOWARE, APOLLO) focus on functional simulation, but lack the ability to evaluate the self-driving software stack on various embedded platforms. To address design needs, we present Chauffeur, the first open-source end-to-end benchmark suite for self-driving vehicles with configurable representative workloads. Chauffeur is easy to configure and run, enabling researchers to evaluate different platform configurations and explore alternative instantiations of the self-driving software pipeline. Chauffeur runs on diverse emerging platforms and exploits heterogeneous onboard resources. Our initial characterization of Chauffeur on different embedded platforms – NVIDIA Jetson TX2 and Drive PX2 – enables comparative evaluation of these GPU platforms in executing an end-to-end self-driving computational pipeline to assess the end-to-end response times on these emerging embedded platforms while also creating opportunities to create application gangs for better response times. Chauffeur enables researchers to benchmark representative self-driving workloads and flexibly compose them for different self-driving scenarios to explore end-to-end tradeoffs between design constraints, power budget, real-time performance requirements, and accuracy of applications.

Optimization of pipeline lifecycle cost using alternatives with different life spans

Abstract This paper suggests a pipeline project optimization approach that compares alternatives with different life spans. The average inflation rate is used to project the future maintenance, operation and replacement costs. The average interest rate is used to express all the costs in Equivalent Real Annual Cost (ERAC), which is the correct cost form to compare alternatives with different life spans. The pipe diameter, material, pressure rating, surge tank size, and inlet/outlet resistances are the decision variables. A software was compiled with a commercial pipeline software to generate all the possible design alternatives based on the decision variables. Pipe initial cost as well as operation and maintenance costs are computed for each design alternative. The alternative with the least ERAC value is the optimum one. It was found that the approach can lead to substantial savings in pipeline projects cost. For pipes 800 mm in diameter or larger, and when selecting the optimum diameter, savings are between 23 and 27% in the total project cost. When imposing certain pipe material savings in overall cost will be 8.5, 16.3 and 31.3% for ductile iron, GRP and mild steel pipe material, respectively.

A standardized analytics pipeline for reliable and rapid development and validation of prediction models using observational health data

Background and objectiveAs a response to the ongoing COVID-19 pandemic, several prediction models in the existing literature were rapidly developed, with the aim of providing evidence-based guidance. However, none of these COVID-19 prediction models have been found to be reliable. Models are commonly assessed to have a risk of bias, often due to insufficient reporting, use of non-representative data, and lack of large-scale external validation. In this paper, we present the Observational Health Data Sciences and Informatics (OHDSI) analytics pipeline for patient-level prediction modeling as a standardized approach for rapid yet reliable development and validation of prediction models. We demonstrate how our analytics pipeline and open-source software tools can be used to answer important prediction questions while limiting potential causes of bias (e.g., by validating phenotypes, specifying the target population, performing large-scale external validation, and publicly providing all analytical source code). MethodsWe show step-by-step how to implement the analytics pipeline for the question: ‘In patients hospitalized with COVID-19, what is the risk of death 0 to 30 days after hospitalization?’. We develop models using six different machine learning methods in a USA claims database containing over 20,000 COVID-19 hospitalizations and externally validate the models using data containing over 45,000 COVID-19 hospitalizations from South Korea, Spain, and the USA. ResultsOur open-source software tools enabled us to efficiently go end-to-end from problem design to reliable Model Development and evaluation. When predicting death in patients hospitalized with COVID-19, AdaBoost, random forest, gradient boosting machine, and decision tree yielded similar or lower internal and external validation discrimination performance compared to L1-regularized logistic regression, whereas the MLP neural network consistently resulted in lower discrimination. L1-regularized logistic regression models were well calibrated. ConclusionOur results show that following the OHDSI analytics pipeline for patient-level prediction modelling can enable the rapid development towards reliable prediction models. The OHDSI software tools and pipeline are open source and available to researchers from all around the world.

Neuroimaging Guided Transcranial Electrical Stimulation in Enhancing Surgical Skill Acquisition. Comment on Hung et al. The Efficacy of Transcranial Direct Current Stimulation in Enhancing Surgical Skill Acquisition: A Preliminary Meta-Analysis of Randomized Controlled Trials. Brain Sci. 2021, 11, 707.

Surgical skill acquisition may be facilitated with a safe application of transcranial direct current stimulation (tDCS). A preliminary meta-analysis of randomized control trials showed that tDCS was associated with significantly better improvement in surgical performance than the sham control; however, meta-analysis does not address the mechanistic understanding. It is known from skill learning studies that the hierarchy of cognitive control shows a rostrocaudal axis in the frontal lobe where a shift from posterior to anterior is postulated to mediate progressively abstract, higher-order control. Therefore, optimizing the transcranial electrical stimulation to target surgical task-related brain activation at different stages of motor learning may provide the causal link to the learning behavior. This comment paper presents the computational approach for neuroimaging guided tDCS based on open-source software pipelines and an open-data of functional near-infrared spectroscopy (fNIRS) for complex motor tasks. We performed an fNIRS-based cortical activation analysis using AtlasViewer software that was used as the target for tDCS of the motor complexity-related brain regions using ROAST software. For future studies on surgical skill training, it is postulated that the higher complexity laparoscopic suturing with intracorporeal knot tying task may result in more robust activation of the motor complexity-related brain areas when compared to the lower complexity laparoscopic tasks.

Industrial robot programming by demonstration using stereoscopic vision and inertial sensing

PurposeThe purpose of this paper is to present a programming by demonstration (PbD) system based on 3D stereoscopic vision and inertial sensing that provides a cost-effective pose tracking system, even during error-prone situations, such as camera occlusions.Design/methodology/approachThe proposed PbD system is based on the 6D Mimic innovative solution, whose six degrees of freedom marker hardware had to be revised and restructured to accommodate an IMU sensor. Additionally, a new software pipeline was designed to include this new sensing device, seeking the improvement of the overall system’s robustness in stereoscopic vision occlusion situations.FindingsThe IMU component and the new software pipeline allow the 6D Mimic system to successfully maintain the pose tracking when the main tracking tool, i.e. the stereoscopic vision, fails. Therefore, the system improves in terms of reliability, robustness, and accuracy which were verified by real experiments.Practical implicationsBased on this proposal, the 6D Mimic system reaches a reliable and low-cost PbD methodology. Therefore, the robot can accurately replicate, on an industrial scale, the artisan level performance of highly skilled shop-floor operators.Originality/valueTo the best of the authors’ knowledge, the sensor fusion between stereoscopic images and IMU applied to robot PbD is a novel approach. The system is entirely designed aiming to reduce costs and taking advantage of an offline processing step for data analysis, filtering and fusion, enhancing the reliability of the PbD system.

From mathematics to medicine: A practical primer on topological data analysis (TDA) and the development of related analytic tools for the functional discovery of latent structure in fMRI data.

fMRI is the preeminent method for collecting signals from the human brain in vivo, for using these signals in the service of functional discovery, and relating these discoveries to anatomical structure. Numerous computational and mathematical techniques have been deployed to extract information from the fMRI signal. Yet, the application of Topological Data Analyses (TDA) remain limited to certain sub-areas such as connectomics (that is, with summarized versions of fMRI data). While connectomics is a natural and important area of application of TDA, applications of TDA in the service of extracting structure from the (non-summarized) fMRI data itself are heretofore nonexistent. “Structure” within fMRI data is determined by dynamic fluctuations in spatially distributed signals over time, and TDA is well positioned to help researchers better characterize mass dynamics of the signal by rigorously capturing shape within it. To accurately motivate this idea, we a) survey an established method in TDA (“persistent homology”) to reveal and describe how complex structures can be extracted from data sets generally, and b) describe how persistent homology can be applied specifically to fMRI data. We provide explanations for some of the mathematical underpinnings of TDA (with expository figures), building ideas in the following sequence: a) fMRI researchers can and should use TDA to extract structure from their data; b) this extraction serves an important role in the endeavor of functional discovery, and c) TDA approaches can complement other established approaches toward fMRI analyses (for which we provide examples). We also provide detailed applications of TDA to fMRI data collected using established paradigms, and offer our software pipeline for readers interested in emulating our methods. This working overview is both an inter-disciplinary synthesis of ideas (to draw researchers in TDA and fMRI toward each other) and a detailed description of methods that can motivate collaborative research.