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Ftr peak ml#1361

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Commits on Apr 28, 2021

• Export peak information for classification

  

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• Set-up for MOI based classification

  

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• Remove old ML logic from TableDockWidget

  

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• Remove libsvm, predictor and classifier

  

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• Basic set-up for communicating with MLB

  

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• Display probability value in peak table

  

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• Add logic for inferences from PeakML output

  

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• Add SHAP-style classification inference

  

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• Give peak group labels their own column

  

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• Allow re-classifying ML-labelled peak groups

  

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• Fix crash due to invalidated lambda contexts

  

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• [Travis] Development package for Qt Charts module

  

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• Save PeakML results in emDB

  

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• Add a new multi-selection combo box widget

  

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• Allow hiding different classes of ML prediction

  

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• Load prediction information only if available

  

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• Fix rebase error @ setLabel/setUserLabel

  

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• Fix show/hide mechanism for PeakML classes

  

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• Export classification label and probablity

  

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• Disable classification disagreement

  

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• Update PeakML icons

  

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• Enable reading in correlation information

  

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• Add correlation information to peak tables

  

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• Add table widget for correlated PeakML groups

  

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• [Fix] Assign prediction to C12 PARENT group

  

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• [UI] Hide correlation widget on table destroy

  

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• [UI] Link correlation & peak table selections

  

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• [UI] Highlight reference peak-group in correlation table

  

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• [ftr] Added feature of undo for changing peakgroup labels

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• [ftr] Added a feature of selecting whether to run peakMl or not

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• [ftr] Added the login feature for polly users

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• [ftr] Modified peaktable to show peakMl related column to authorized users

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• [ftr] Added a feature of dropdown to select peakMl model Type

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• [fix] Fixed a bug in undo function

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• [ftr] Removed "Explain Classification" option from context menu of peaks

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• [ui] Made changes to the SHAP plot that explained classification of peaks

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• [fix] Fixed visualization bugs of peakgroups due to rebasing

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• [fix] Fix label column in peaktable when previously saved emdb is loaded

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• [fix] Fix display of peakgroups when peak curation is done after deletion an existing peakTable

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• [ftr] Add correlated group information while saving session

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• [ftr] Download binary and model automatically from s3 bucket

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• [ftr] Download peak ml files using polly cli

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• [ftr] Add peakML documentation in support dialog

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• [ref] Remove qt chart modules required

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• [ref] Improve force plot

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• [ftr] Write cookie.json file while authenticating user to polly

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• [ftr] Classify isotopes along with parent peakgroup in peakML

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• [fix] Fix Group validation in status bar for good and bad peaks

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• [ref] Refactor csv export options for peakgroups

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• [fix] Fix bugs for peakML after rebasing to version-12(with ghost peakgroups)

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• [ref] Remove 'unique id' from peakgroup

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• [fix] Fix filtering labels and exporting peakgroups to csv

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• [ftr] Add feature for 'may be good' peakgroup curation

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• [ui] UI changes to range slider in peak detection dialog

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• [ui] Add icon for may be good peakgroups

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• [ui] UI fixes

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• [fix] Fix different exports of peakgroups

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• [ftr] Add legend to classification widget

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• [fix] Fix crash on uploading cohort

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• [ftr] Add a feature to relabel already classified groups

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• [ui] Add distribution of classification percentage in the legend

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• [ui] UI changes related to relabel dialog

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• [ui] Add PeakML parameters in setting log

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• [ref] Refactored moi download mechanism to include download from signed URL

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• [ref] Changes after monday meeting

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• [fix] Small fixes and ui changes

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• [fix] Fix the execution of model and binary in windows

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• [fix] Fix closing of relabel widget on windows

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• [fix] Disable removeFiles for changed API endpoint

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• [fix] Fix issues occurred due to deleting commit

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• [ui] Warning for no internet connection while downloading files

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• [ui] Reducing the size of peak detection dialog

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• [ftr] Added the list of models for organisation in peak detection dialog

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• [fix] Fix crash in El-MAVEN due to cookie file

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• [ref] Refactor shap figure and invert colors for signals and noise

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• [ref] Accomodate the changes of output file exported through moi

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• [ref] Add base value and output value in classification widget

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• [ref] Save output and basevalue in project DB

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• [Fix] Fix the crash when cookie file is read

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• [ref] Classify child adducts along with the child isotopes

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• [ref] Changes after review1

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• [ref] Rename 'superSlider' class name to 'rangeSlider'

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• [ref] Made changes after review2

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• [ui] Fix peakdetection and relabel dialog

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• [ref] Renaming peakML attributes in maven parameters

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• [ref] Make 'noActiveInternet' of main window generic

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• [ref] Store maven paramenters specific to peak curation in emdb

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• [fix] Fix crash when edited peaks session is reloaded to El-MAVEN

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• [ref] Made changes after review 3

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• [fix] Made changes after usability review

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• [ref] Preparation of implementing license for peakML

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• [fix] Divide 'Preparing inputs for peakML' in 3 small steps

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• [fix] Fix Polly-phi working in peakML version

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• [ftr] Add event tracker to peakML checkbox in peakdetectin dialog

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• [fix] update the peakML range in setting logs after relabeling

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• [ref] Change the predicted_label column name and add extra column

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• [ref] Refactored the logic for downloading model files including license check

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• [ftr] Add version check for binary file 'moi'

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• [fix] Fix json check on Api response

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• [fix] Fix losing information of infenece plot while loading emdb

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• [ref] Change the name of the columns in emdb schema for peakML

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• [ftr] Export peakML related attributes in csv both in group and peak report

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• [ref] Change variable names of baseValue and outputValue in peakgroup class

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• [fix] Fix unauthorized error message for fetching models

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• [ftr] Add an input dialog for user input to save EIC in raw data emDB

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• [ftr] Integrate the logic of setting rtMin and rtMax for storing EIC in raw data emDB

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• [ftr] Add an option on EPI to export emDB with raw data

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• [ftr] Cohort file made necessity for accessing peakML

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• [ref] Change export raw data options in input dialog

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• [ftr] Allow user to choose uploading sliced or complete EIC using EPI

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• [ref] Make 'complete-rangeEIC' option on EPI by default checked

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• [ref] Change the integration of test polly to prod polly

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• [Fix] Fix crash on peak detection using SRM database

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• [fix] Fix issues after rebasing

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Commits on Jun 9, 2021

• [ref] Add Parallelization in curation

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Commits on Feb 13, 2022

• [fix] Label legend on classified peak table doesnt maintain its filtered state

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Commits on Feb 14, 2022

• [fix] Marking peak group good or bad pushes the group down

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