RCaller: A Software Library for Calling R from Java

Satman, Mehmet Hakan

doi:10.9734/bjmcs/2014/10902

Cited by 10 publications

(8 citation statements)

References 2 publications

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“…In Figure 2, the principle of CARD is displayed. A prototype software for these purposes was developed in our institute in the programming language JAVA (version 1.7), using the RCaller-class (version 2.0.7) 16 to enable the usage of the R-implementation Breimans' RF algorithm 10 to perform the classification.…”

Section: Rf Classifiers In Diagnosticsmentioning

confidence: 99%

Computer-aided radiological diagnostics improves the preoperative diagnoses of medulloblastoma, pilocytic astrocytoma, and ependymoma

Porz

Knecht

Sick

et al. 2018

Clinical and Translational Neuroscience

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Introduction: Imaging-based diagnosis of intra-axial contrast-enhancing brain tumors is frequently challenging. We show that the diagnosis of medulloblastoma (MDB) versus pilocytic astrocytoma (PA) and ependymoma (EPM) profit from computational analyses, based on quantitative image properties (i.e. textural features from apparent diffusion coefficient (ADC)-maps) and an automated machine learning classification (random forests (RF)). Methods: Forty patients who were diagnosed with three types of brain tumors were included in this study: 16 with MDB, 4 with PA, and 10 EPM. Based on the analysis of multi parametric preoperative magnetic resonance images, neuroradiologists gave a clear-cut diagnosis if they were sure of the diagnosis; however, most diagnoses comprise several possible tumor types. To distinguish between the named tumor types, a computer-based differential diagnosis (DD) tool was developed. Tumor lesion volumes were manually defined using ADC-maps only. From the demarked ADC-map, texture-parameters were extracted to train RF classifiers for pairwise DD. Performance of the RF models and reproducibility of the manual segmentation were evaluated. Results: Neuroradiologists gave correct and clear-cut diagnoses for 31% of MDB, 14.3% of PA, and 10% of EPM. Most diagnoses comprised several tumor types and altogether diagnoses containing the right tumor were given in 69% of true MDB, 64% of true PA, and 30% of true EPM. Ambiguous diagnoses could be improved by RF classifiers showing the following PA versus MDB performance: sensitivity 0.888 + 0.031, specificity 0.886 + 0.036; EPM versus MDB: sensitivity: 0.938 (95% CI ¼ (0.677, 0.997)) and specificity: 0.7 (95% CI ¼ (0.354, 0.919)); EPM versus PA: sensitivity: 0.786 (95% CI ¼ (0.488, 0.942) and specificity: 0.100 (95% CI ¼ (0.005, 0.458). An inter-and intra-rater analysis (three human raters) was performed and the Fleiss' kappa test revealed high inter-rater agreement of ¼ 0.821 (p value << 0.001) and an intra-rater agreement of ¼ 0.822 (p value << 0.001). Conclusion: In the frequent case of ambiguous neuroradiologist diagnoses, a subsequent differential RF classification improves the diagnoses in all cases. The largest benefit is gained for the discrimination PA versus MDB with an accuracy of 88.0 + 3.0% followed by EPM versus MDB with an accuracy of 84.6%.

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Section: Rf Classifiers In Diagnosticsmentioning

confidence: 99%

Computer-aided radiological diagnostics improves the preoperative diagnoses of medulloblastoma, pilocytic astrocytoma, and ependymoma

Porz

Knecht

Sick

et al. 2018

Clinical and Translational Neuroscience

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“…RCaller is a Java library for interfacing R from within Java (Satman, 2014). R is a popular programming language and a programming environment with hundreds of packages written in C, C++, Fortran, and R itself (R Core Team, 2020).…”

Section: Statement Of Needmentioning

confidence: 99%

“…Previous works showed that the performance of the library is suitable for more cases, and studies with moderate datasets can be handled in reasonable times (Satman & Curcean, 2016). Following its first publication (Satman, 2014), support for DataFrame objects, R start-up options, automatic Rscript executable locator, and Java Scripting API (JSR 223) have been implemented.…”

Section: Statement Of Needmentioning

confidence: 99%

RCaller: A Java package for interfacing R

Satman¹,

Aleksandr²

2020

JOSS

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“…The authors used the approach of RCaller that was proposed and described in Satman (2014). Experiments utilized RCaller v2.1.1 implemented by Satman (2013) as an R integration library for Java applications.…”

Section: Testbed Design and Experimentsmentioning

confidence: 99%

Evolutionary approaches to signal decomposition in an application service management system

Sikora

Magoulas

2015

Soft Comput

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The increased demand for autonomous control in enterprise information systems has generated interest on efficient global search methods for multivariate datasets in order to search for original elements in time-series patterns, and build causal models of systems interactions, utilization dependencies, and performance characteristics. In this context, activity signals deconvolution is a necessary step to achieve effective adaptive control in Application Service Management. The paper investigates the potential of population-based metaheuristic algorithms, particularly variants of particle swarm, genetic algorithms and differential evolution methods, for activity signals deconvolution when the application performance model is unknown a-priori. In our approach, the Application Service Management System is treated as a black-or grey-box, and the activity signals deconvolution is formulated as a search problem, decomposing time-series that outline relations between action signals and utilization-execution time of resources. Experiments are conducted using a queuebased computing system model as a test-bed under different load conditions and search configurations. Special attention was put on high-dimensional scenarios, testing effectiveness for large-scale multivariate data analyses that can obtain a near-optimal signal decomposition solution in a short time. The experimental results reveal benefits, qualities and drawbacks of the various metaheuristic strategies selected for a given signal deconvolution problem, and confirm the potential of evolutionary-type search to effectively explore the search space even in high-dimensional cases. The approach and the algorithms investigated can be useful in support of human administrators, or in enhancing the effectiveness of feature extraction schemes that feed decision blocks of autonomous controllers.

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RCaller: A Software Library for Calling R from Java

Cited by 10 publications

References 2 publications

Computer-aided radiological diagnostics improves the preoperative diagnoses of medulloblastoma, pilocytic astrocytoma, and ependymoma

Computer-aided radiological diagnostics improves the preoperative diagnoses of medulloblastoma, pilocytic astrocytoma, and ependymoma

RCaller: A Java package for interfacing R

Evolutionary approaches to signal decomposition in an application service management system

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