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Timeline & Changelog


Timeline

2023
January 5

Identification of Mycobacterium abscessus Subspecies by MALDI-TOF Mass Spectrometry and Machine Learning

https://doi.org/10.1128/jcm.01110-22

2022
November 28

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.
September 7

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.

 

August 28

Ultrasensitive and rapid identification of ESRI developer- and piperacillin/tazobactam-resistant Escherichia coli by the MALDIpiptaz test

July 7

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
January 10

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
2021
October 18

Minor version v0.4.5

  • ROC curves added in all modules
  • Precision-Recall curves added in all modules
July 19

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

June 18

An Improved Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Data Analysis Pipeline for the Identification of Carbapenemase-Producing Klebsiella pneumoniae

June 3

Detection of azole resistance in Aspergillus fumigatus complex isolates using MALDI-TOF mass spectrometry

June 1

Multicenter Performance Evaluation of MALDI-TOF MS for Rapid Detection of Carbapenemase Activity in Enterobacterales: The Future of Networking Data Analysis With Online Software

May 7

Video Tutorials Release

 

February 15

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
January 24

Rapid and Reproducible MALDI-TOF-Based Method for the Detection of Vancomycin-Resistant Enterococcus faecium Using Classifying Algorithms

2020
December 2

Implementation of MALDI-TOF Mass Spectrometry and Peak Analysis: Application to the Discrimination of Cryptococcus neoformans Species Complex and Their Interspecies Hybrids

September 28

Minor version v0.3.5 K-Nearest Neighbors

  • K- Nearest Neighbors (KNN) added
  • Neighborhood Components Analysis (NCA) added in KNN module
March 24

Minor version v0.3.5 Carbapenemases detection

  • Carbapenemases detection module added for specific institutions
  • FAQ´s section added
2019
September 16

Major version v0.3 Random Forest Analysis

  • Random Forest (RF) Analysis added
  • Module for blind sample identification added
February 18

Minor version v0.2.5

  • Biomarker analysis module added
  • Reproducibility analysis improvements
  • Metrics for K-Fold validation added
    • F1 score
    • Clinical scores
    • Classification scores
  • Feature importances added in all analysis
2018
November 12

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