Clover MSDAS v1.3 Features & Improvements
- Outliers Detection Module first version release. PCA Reconstruction and Spectra Correlation analysis have been implemented.
- Shapley Values plot includes now a bar plot to show the shapley values mean.
- New file size upload limit is upgrade to 300MB.
- Validation & Identification modules run now asynchronously. You can leave the screen and recover the result later.
- Hyperparameters at classification can be now choosen manually or calculated via autotune algorithm.
- ROC and Precision-Recall curves displayed up to 4 decimals for AUC values and can be downloaded in CSV format.
- Error Rate have been added as a metric.
- LightGBM have been adjusted on how hyperparameters are optimized.
- In the ROC curve table at Biomarker Analysis module, you can click now on the table rows for selecting masses. Once they are selected, a peak matrix can be automatically generated by using those masses.
Stable version v1.0 of Clover MS Data Analysis Software
Major updates
- Multitask mode: Now supervised classifiers run in asynchronous mode. Therefore, the user can leave or close the page/tab safely or work in other tasks, because the result will be there next time the classifier page is accessed.
- Performance improvements: Algorithms now work in dedicated processes.
- Random Forest: Newly optimized hyperparameters are: number of estimators, max features, max tree depth, min split size, min number of samples per leaf.
- LightGBM: Adjustments on hyperparameters optimization. Shapley feature importances optimization.
- Biomarker Analysis: In the ROC curve table, the user can click on the table rows for selecting masses. Once they are selected, a peak matrix can be automatically generated by using those masses as biomarkers.
Minor updates
- TIC normalization: is now performed using the area under the entire spectrum.
- Find Peaks Graph: The user can click on a detected peak for displaying a label with the mass value.
- Biomarker Analysis: When a row is clicked in the ROC curve table, now it is also filtered in the Peak Distribution table.
Ultrasensitive and rapid identification of ESRI developer- and piperacillin/tazobactam-resistant Escherichia coli by the MALDIpiptaz test
Major version v0.6 LightGBM Algorithm
- Light Gradient Boosting Machine (LightGBM) algorithm added
- Shapley Values analysis section added in Random Forest and LightGMB algorithms
- Confidence ellipses now can be displayed at PCA Analysis
- SVG vector image format added. Now plots and charts can be downloaded as .svg
Major version v0.5 FTIR support
- Fourier transform infrared (FTIR) format is now supported
- The platform now allows work with infrared spectroscopy data in all modules
- FTIR Specific preprocessing steps added
Occurrence of the p019 Gene in the blaKPC-Harboring Plasmids: Adverse Clinical Impact for Direct Tracking of KPC-Producing Klebsiella pneumoniae by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
An Improved Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Data Analysis Pipeline for the Identification of Carbapenemase-Producing Klebsiella pneumoniae
Detection of azole resistance in Aspergillus fumigatus complex isolates using MALDI-TOF mass spectrometry
Multicenter Performance Evaluation of MALDI-TOF MS for Rapid Detection of Carbapenemase Activity in Enterobacterales: The Future of Networking Data Analysis With Online Software
Major version v0.4 Validation Module
- Validation Module added
- Now all models can be validated easily
- Results can be downloaded as .csv
- Resulting plots can be download as images
Rapid and Reproducible MALDI-TOF-Based Method for the Detection of Vancomycin-Resistant Enterococcus faecium Using Classifying Algorithms
Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids
Minor version v0.3.5 K-Nearest Neighbors
- K- Nearest Neighbors (KNN) added
- Neighborhood Components Analysis (NCA) added in KNN module
Minor version v0.3.5 Carbapenemases detection
- Carbapenemases detection module added for specific institutions
- FAQ´s section added
Major version v0.3 Random Forest Analysis
- Random Forest (RF) Analysis added
- Module for blind sample identification added
Major Version v2 Support Vector Machine Analysis
- Support Vector Machine (SVM) Analysis added
- MALDI-TOF Bruker© format support added
- K-fold cross validation added
- Categories section added for studies
