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29.0 1.0 8.0 22.71 MB

๐Ÿงช ๐Ÿ–ฅ Transparent exploration of machine learning for biomarker discovery from proteomics and omics data

Home Page: https://ol-v14.streamlit.app

License: Other

Python 94.11% Shell 3.57% HTML 0.62% Inno Setup 1.70%
proteomics bioinformatics biomarker-discovery machine-learning omics transcriptomics

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omiclearn's Issues

Error running app

Hi, I was doing an analysis it stopped working. Error running app

OmicLearn v1.4 Updates

OmicLearn v1.4 Updates

  • Fix reqs.txt for some packages
  • Black formatting and isort
  • Text fixes on GUI
  • Replace all omic_learn with OmicLearn
  • Update Streamlit
  • FEATURE: Add download txt for summary text
  • FEATURE: Exclude features file upload should not need header/title row.
  • Code refactoring
  • FEATURE: Add file-uploader for "Additional features" like "Exclude features"
  • ???? FEATURE: Add StratifiedGroupKFold ????
  • NOT NEEDED FEATURE: Add file-uploader for "Manual features" like "Exclude features"

VERY CRITICAL BUGS

@straussmaximilian , I newly realized those issues . It would be nice if you can also check maybe you might encounter few other issues.

  • BUG: Summary text --> Even though there are missing values in the data, if the user selects Imputation method as None, the summary text says "There was no missing value"..
  • BUG: Feature selection methods other than "ExtraTrees" DO NOT WORK
  • BUG: LinearSVC classifier DOES NOT WORK
  • BUG: In one-click installer (v1.3, mac-os), when you run LogisticRegression, it opens several tabs on the browser and LogisticRegression DOES NOT WORK.
    • NOT A CONCERN FOR NOW AFTER MY TESTS IN LATEST VERSON BUT THIS STILL EXISTS IN V1.3 ONE-CLICK INSTALLATION MAC-OS)

  • Add XGBoost version to summary text
  • BUG: Fix summary text with model parameters , there is no comma in between them (example: we used a XGBoost-Classifier (random_state = 23 learning_rate = 0.1 min_split_loss = 0 max_depth = 6 min_child_weight = 1))
  • Upgrade python version
  • DISABLE target leakages that user can lead
  • Change the theme in docs to Material --> https://bashtage.github.io/sphinx-material/#getting-started OR Book --> https://sphinx-book-theme.readthedocs.io/en/latest/index.html
  • Update all docs and README
  • Check reproducibility
  • Add some unit/integration tests
  • Check one-click installer
  • Release the new v1.4 PROD version
  • Update logo | Add white borderline to fix the appearance in dark mode
    Screenshot 2023-03-25 at 22 38 47
  • Add multiclass classification support FUTURE RELEASES

new version

I downloaded the new version 1.4 (the old 1.3 was perfect, OS windows server 2019 ) and after the installation when I launched for the first time the app this was what I read on the screen:

ImportError: DLL load failed while importing iterative: The specified module could not be found.
Traceback:
File "streamlit\runtime\scriptrunner\script_runner.py", line 565, in run_script
exec(code, module.dict)
File "C:\Users\Administrator\AppData\Local\Programs\OmicLearn\omiclearn\omiclearn.py", line 17, in
from utils.ui_components import (
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "omiclearn\utils\ui_components.py", line 9, in
import sklearn
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "sklearn_init
.py", line 82, in
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "sklearn\base.py", line 17, in
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "sklearn\utils_init
.py", line 17, in
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse_init_.py", line 283, in
from . import csgraph
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\csgraph_init_.py", line 185, in
from .laplacian import laplacian
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\csgraph_laplacian.py", line 7, in
from scipy.sparse.linalg import LinearOperator
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\linalg_init
.py", line 120, in
from .isolve import *
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\linalg_isolve_init
.py", line 4, in
from .iterative import *
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\linalg_isolve\iterative.py", line 9, in
from . import _iterative

ImportError

Dear OmicLearn developers,
The software installed on my windows machine but I am getting the following error. Any help will be greatly appreciate.
Thanks

ImportError: DLL load failed while importing iterative: The specified module could not be found.
Traceback:
File "streamlit\runtime\scriptrunner\script_runner.py", line 565, in run_script
exec(code, module.dict)
File "C:\Users\fazeliniah\AppData\Local\Programs\OmicLearn\omiclearn\omiclearn.py", line 17, in
from utils.ui_components import (
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "omiclearn\utils\ui_components.py", line 9, in
import sklearn
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "sklearn_init
.py", line 82, in
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "sklearn\base.py", line 17, in
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "sklearn\utils_init
.py", line 17, in
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse_init_.py", line 283, in
from . import csgraph
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\csgraph_init_.py", line 185, in
from .laplacian import laplacian
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\csgraph_laplacian.py", line 7, in
from scipy.sparse.linalg import LinearOperator
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\linalg_init
.py", line 120, in
from .isolve import *
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\linalg_isolve_init
.py", line 4, in
from .iterative import *
File "PyInstaller\loader\pyimod03_importers.py", line 495, in exec_module
File "scipy\sparse\linalg_isolve\iterative.py", line 9, in
from . import _iterative

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