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Merged
Vghxv merged 81 commits into from
Apr 20, 2025
Merged

Orange Pipeline #84

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101c99e
[add] re-split lung datasets
Vghxv Nov 3, 2024
922985d
[add] preprocessing 📩
Vghxv Nov 3, 2024
26b477b
[add] add terms count and dbeta TSS data files for lung tissue analysis
Vghxv Nov 3, 2024
a14bde8
[add] add toml package dependency and update poetry.lock
Vghxv Nov 30, 2024
93ba08e
[add] add plotly and nbformat package dependencies
Vghxv Dec 2, 2024
450ba7f
add new analysis scripts for lung tissue data processing
Vghxv Dec 2, 2024
5344b9c
add configuration file for lung tissue analysis preprocessing parameters
Vghxv Dec 2, 2024
547142f
add google authentication package dependencies
Vghxv Dec 4, 2024
6fd7622
add .gitignore entries for pickle files and credentials
Vghxv Dec 4, 2024
55189ef
add utility functions for Google Drive authentication and file uploads
Vghxv Dec 4, 2024
c4e43ae
[update] result updates
Vghxv Dec 4, 2024
cb5de73
add global CONFIG_PATH variable to store configuration path
Vghxv Dec 4, 2024
a6e2cef
add gdown and related dependencies for Google Drive file downloads
Vghxv Dec 4, 2024
26ac01e
add error handling for Google Drive file operations
Vghxv Dec 4, 2024
36e8c8d
add configuration files for prostate, rectal, and stomach tissue data…
Vghxv Dec 4, 2024
6aa0cdb
[add] rectal GDC tissue 450K dbeta
xzh0623 Nov 14, 2024
3e16cbc
[add] rectal GDC tissue 450K filtering by TSS and threshold
xzh0623 Nov 14, 2024
1415760
[update] rectal GDC tissue 450K dbeta and filtering by TSS and threshold
xzh0623 Dec 11, 2024
0422c24
[update] adjust training and testing sample sizes and class distribut…
Vghxv Dec 14, 2024
6f0252b
rewrite RFE
Vghxv Dec 15, 2024
f684c46
[add] add FPR, TPR, and results CSV files for lung tissue model evalu…
Vghxv Dec 15, 2024
937c52d
update RFE
Vghxv Dec 16, 2024
36191e5
[update] adjust training and testing sample sizes and class distribut…
Vghxv Dec 16, 2024
7a57d7a
improve function clearity, fix typos
Vghxv Dec 17, 2024
8e57de1
[update] lung with oversampling results
Vghxv Dec 17, 2024
5d6b4bf
fix dbeta calculation
Vghxv Dec 22, 2024
881d41e
[update] adjust lung configuration parameters for preprocessing and c…
Vghxv Dec 22, 2024
3c7cfbd
[update] update selected feature names for lung tissue models
Vghxv Dec 22, 2024
adc1eb8
[update] add clustering and training utility functions, update lung c…
Vghxv Dec 23, 2024
03be337
[update] add new dbeta calculation results and selected feature names…
Vghxv Dec 23, 2024
f9e4c86
[update] enhance lung configuration and add combination utility funct…
Vghxv Dec 23, 2024
5b8128b
[update] ROC curve on testing
Vghxv Dec 24, 2024
881e316
update: handle division by zero in specificity calculation with warni…
Vghxv Jan 4, 2025
391d58b
fix: correct spelling of 'specificity' in record function
Vghxv Jan 4, 2025
d73985c
feat: add ROC curve and performance difference plotting functions
Vghxv Jan 4, 2025
76e4172
delete outdated results
Vghxv Jan 4, 2025
d5e71ae
feat: enhance hierarchical clustering functions to save plots and acc…
Vghxv Jan 4, 2025
73c91f2
lung no oversample metrics and results
Vghxv Jan 4, 2025
227da3d
feat: stucked
Vghxv Jan 4, 2025
27722bc
remove garbge
Vghxv Jan 5, 2025
9537732
feat: enhance function signatures with type hints and improve perform…
Vghxv Jan 5, 2025
51fef21
feat: add performance metrics and selected features for lung tissue m…
Vghxv Jan 5, 2025
7b481ea
general pipeline
Vghxv Jan 5, 2025
a799c66
combination
Vghxv Jan 6, 2025
5dfadb5
feat: add consensus selected features for lung tissue models, clean up
Vghxv Jan 6, 2025
fd3e8fa
feat: remove
Vghxv Jan 11, 2025
8110c38
fix: update type hints for hierarchical_clustering_compare function
Vghxv Jan 13, 2025
78473a7
feat: modules
Vghxv Jan 13, 2025
e39d9d1
rfe
Vghxv Jan 13, 2025
7523158
feat: rfe seleted feature names
Vghxv Jan 13, 2025
4318832
update modules
Vghxv Jan 14, 2025
8b996ab
feat: sfs pipeline
Vghxv Jan 14, 2025
e438252
sfs results
Vghxv Jan 14, 2025
33879b0
ignore log
Vghxv Jan 14, 2025
b5ee87f
feat: update selected feature names and add voting metrics
Vghxv Jan 15, 2025
d95f425
feat: selected gene cleaning
Vghxv Jan 17, 2025
5fe2118
fix naming
Vghxv Jan 17, 2025
b586fa3
feat: add training parameters for machine learning models
Vghxv Jan 18, 2025
930adb1
fix: create logs dir
Vghxv Jan 18, 2025
c444856
fix confusion
Vghxv Jan 18, 2025
3240377
fix stupid logic
Vghxv Jan 18, 2025
2e6da13
workflow done
Vghxv Feb 3, 2025
856379d
new rfe sfs results
Vghxv Feb 3, 2025
c27b6bd
lung results
Vghxv Feb 6, 2025
e41903b
final polish
Vghxv Feb 6, 2025
2fc0dcd
remove old files
Vghxv Feb 6, 2025
a712d22
add cat
Vghxv Feb 6, 2025
54b6e5e
update lock file
Vghxv Feb 6, 2025
834c69a
Revert "update lock file"
Vghxv Feb 6, 2025
37ed86b
refactor configuration and notebook to streamline data file references
Vghxv Feb 6, 2025
0651ec0
remove unused function to clean up dataset processing code
Vghxv Feb 6, 2025
31413a3
add README.md for configuration details and data processing parameters
Vghxv Feb 6, 2025
d72536d
some cool updates with plan A
Vghxv Feb 17, 2025
b5fabe1
typo
Vghxv Feb 18, 2025
fc2259a
some updates
Vghxv Feb 20, 2025
cbf816a
set the index of the last row as "label" in split_dataset function
Vghxv Feb 22, 2025
4daff7e
[add] Orange-pipeline plan A result
xzh0623 Feb 22, 2025
7bd4820
add new images and CSV files for hierarchical clustering and feature …
Vghxv Feb 20, 2025
1b66d42
breast-RFE
OuChiaYun Feb 21, 2025
2123a4e
RFE planA
OuChiaYun Feb 21, 2025
6aa91fa
no smote
pizza6inch Feb 23, 2025
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -18,3 +18,6 @@
**/champ_result/
**/data/
all_beta_normalized*
*.pickle
notebooks/credentials.json
/notebooks/logs
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