Supplementary files for "Constraining classifiers in molecular analysis: invariance and robustness"
ReadMe file for the supplementary material.
This provides the code used for training the (invariant) SVMs and predicting the class labels of a new matrix in R.
The code is bundled as the R package invariantSVM_1.0.tar.gz. It can be installed from command line by using the command:
R CMD INSTALL invariantSVM_1.0.tar.gz
After the package is loaded into the workspace (by using library(invariantSVM)), automatic parameter tuning in a multi-objective setting can be performed as shown in the following example:
#calculate 10x10 Accuracy on iris dataset over all invariances and R = 2library(TunePareto)print(tunePareto(data = as.matrix(iris[1:100, -ncol(iris)]),labels = iris[1:100,ncol(iris)],classifier = tunePareto.invariantSVM(), C=1, R = 2,invariance = c("lin","off","con","off&con","mon"),objectiveFunctions = list(cvAccuracy(10, 10))))
Collection of the analysed artificial datasets.
Artificial dataset (with noise)
Collection of the fold lists used for the 10x10 cross-validation experiments.
This file provides the results of the experiments on artificial and transcriptome datasets. The accuracies and the selected number of features (R1-SVM) are given.
Wissenschaftlicher Mitarbeiter (m/w/d)
Our paper "Sparse keypoint segmentation of lung fissures: efficient geometric deep learning for abstracting volumetric images" has been published in the International Journal of Computer Assisted Radiology and Surgery. Please find electronical supplementary material here.
Our paper "Boolean network modeling and its integration with experimental read-outs: An interdiscipliary presentation using a leukemia model" has been published online first in Pathologie.
"Combined analysis of a serum mRNA/miRNA marker signature and CA 19-9 for timely and accurate diagnosis of recurrence after resection of pancreatic ductal adenocarcinoma: A prospective multicenter cohort study" has been published online first in the United European Gastroenterology Journal.
"Identifications of Similarity Metrics for Patients With Cancer: Protocol for a Scoping Review" has been published in JMIR Research Protocols.
"Recent Trends and Future Challenges in Learning from Data" has been published with Springer.
Our paper "Permutation-invariant linear classifiers" has been published in Machine Learning.
Our paper "Prediction of resistance to bevacizumab plus FOLFOX in metastatic colorectal cancer-Results of the prospective multicenter PERMAD trial" has been published in PLoS One.
Our paper "Segmentation-based cardiomegaly detection based on semi-supervised estimation of cardiothoracic ratio" has been published in Scientific Reports.
"Prospective study validating a multidimensional treatment decision score predicting the 24-month outcome in untreated patients with clinically isolated syndrome and early relapsing–remitting multiple sclerosis, the ProVal-MS study" has been published in Neurological Research and Practice.
Our paper "GatekeepR: an R shiny application for the identification of nodes with high dynamic impact in boolean networks" has been published online first in Bioinformatics.
Our paper "The Necessity of Interoperability to Uncover the Full Potential of Digital Health Devices" has been published in JMIR Medical Informatics.
"Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients" has been published in npj Precision Oncology.
Our paper "AMBAR-interactive alteration annotations for molecular tumor boards" has been published in Computer Methods and Programs in Biomedicine.
"A protocol for the use of cloud-based quantum computers for logical network analysis of biological systems" has been published in STAR Protocols.
Our paper "A systems biology approach to define mechanisms, phenotypes, and drivers in PanNETs with a personalized perspective" has been published in npj systems biology and applications.
"Supporting SURgery with GEriatric Co-Management and AI (SURGE-Ahead): A study protocol for the development of a digital geriatrician" has been published in PLoS One.
"Self-Assessment of Having COVID-19 With the Corona Check Mhealth App" has been published in IEEE Journal of Biomedical and Health Informatics.
Our first quantum computing paper "Leveraging quantum computing for dynamic analyses of logical networks in systems biology" has been published in Patterns.