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Add case study notebooks #20

Merged
merged 85 commits into from
Jan 26, 2024
Merged

Add case study notebooks #20

merged 85 commits into from
Jan 26, 2024

Commits on Oct 27, 2023

  1. build skeleton of case studies in paper

    @srtaheri
    srtaheri committed Oct 27, 2023
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Commits on Oct 30, 2023

  1. build initial skeleton of large sars case study data generation

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    srtaheri committed Oct 30, 2023
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Commits on Nov 1, 2023

  1. data generation for large sars cov example

    @srtaheri
    srtaheri committed Nov 1, 2023
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  2. build initial skeleton for the case studies in the paper

    @srtaheri
    srtaheri committed Nov 1, 2023
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  3. added discriptioon to the example

    @srtaheri
    srtaheri committed Nov 1, 2023
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Commits on Nov 6, 2023

  1. worked on the skeleton of case studies

    @srtaheri
    srtaheri committed Nov 6, 2023
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  2. added necessary function names to init

    @srtaheri
    srtaheri committed Nov 6, 2023
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  3. changed data to discretized data

    @srtaheri
    srtaheri committed Nov 6, 2023
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Commits on Nov 7, 2023

  1. filled out steps of the workflow for case studies

    @srtaheri
    srtaheri committed Nov 7, 2023
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  2. added steps of the workflow to sars cov example

    @srtaheri
    srtaheri committed Nov 7, 2023
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  3. added steps of the workflow to covid case study

    @srtaheri
    srtaheri committed Nov 7, 2023
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Commits on Nov 8, 2023

  1. worked on CI tests for case studies

    @srtaheri
    srtaheri committed Nov 8, 2023
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  2. added sars discrete data generator

    @srtaheri
    srtaheri committed Nov 8, 2023
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  3. worked on case studies notebook

    @srtaheri
    srtaheri committed Nov 8, 2023
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  4. create discrete data for Sars case study

    @srtaheri
    srtaheri committed Nov 8, 2023
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Commits on Nov 10, 2023

  1. ran and got results from all case studies, all steps of workflow

    @srtaheri
    srtaheri committed Nov 10, 2023
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Commits on Nov 13, 2023

  1. added relevant data and images

    @srtaheri
    srtaheri committed Nov 13, 2023
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Commits on Nov 14, 2023

  1. convert single long line into multiple shorter ones for Tsignaling ca… 

    …se study
    @srtaheri
    srtaheri committed Nov 14, 2023
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Commits on Nov 22, 2023

  1. small changes

    @srtaheri
    srtaheri committed Nov 22, 2023
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Commits on Dec 5, 2023

  1. Adding sars_cov2 data

    @pnavada
    pnavada committed Dec 5, 2023
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Commits on Dec 6, 2023

  1. small changes

    @srtaheri
    srtaheri committed Dec 6, 2023
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  2. Merge branch 'notebooks' of https://github.com/y0-causal-inference/el… 

    …iater into notebooks
    @srtaheri
    srtaheri committed Dec 6, 2023
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Commits on Jan 11, 2024

  1. Modified notebooks to import functions from eliater

    @pnavada
    pnavada committed Jan 11, 2024
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Commits on Jan 13, 2024

  1. modified notebooks

    @srtaheri
    srtaheri committed Jan 13, 2024
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Commits on Jan 14, 2024

  1. Resolving conflict from origin

    @pnavada
    pnavada committed Jan 14, 2024
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  2. notebook changes

    @pnavada
    pnavada committed Jan 14, 2024
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Commits on Jan 16, 2024

  1. add evaluation criterion to SARS case study

    @srtaheri
    srtaheri committed Jan 16, 2024
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  2. verfied the results in EColi case study

    @srtaheri
    srtaheri committed Jan 16, 2024
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Commits on Jan 17, 2024

  1. added evaluation criterion

    @srtaheri
    srtaheri committed Jan 17, 2024
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  2. added evaluation to the motivating example

    @srtaheri
    srtaheri committed Jan 17, 2024
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Commits on Jan 18, 2024

  1. Reorganize

    @cthoyt
    cthoyt committed Jan 18, 2024
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  2. Merge branch 'main' into notebooks

    @cthoyt
    cthoyt committed Jan 18, 2024
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  3. Reuse graph

    @cthoyt
    cthoyt committed Jan 18, 2024
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  4. Lint

    @cthoyt
    cthoyt committed Jan 18, 2024
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  5. Merge branch 'main' into notebooks

    @cthoyt
    cthoyt committed Jan 18, 2024
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  6. Clean up T signaling notebook

    @cthoyt
    cthoyt committed Jan 18, 2024
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  7. Update motivating_example.ipynb

    @cthoyt
    cthoyt committed Jan 18, 2024
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  8. Update motivating_example.ipynb

    @cthoyt
    cthoyt committed Jan 18, 2024
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  9. Update motivating example notebook

    @cthoyt
    cthoyt committed Jan 18, 2024
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  10. Adding boxplot for ecoli and refactoring

    @pnavada
    pnavada committed Jan 18, 2024
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Commits on Jan 19, 2024

  1. Merge branch 'main' into notebooks

    @cthoyt
    cthoyt committed Jan 19, 2024
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  2. Reorg data

    @cthoyt
    cthoyt committed Jan 19, 2024
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  3. Improve output in motiviating example and t cell signalling

    @cthoyt
    cthoyt committed Jan 19, 2024
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  4. Update printing and reorganize notebooks

    @cthoyt
    cthoyt committed Jan 19, 2024
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  5. Pass flake8 and add progress bar option for long ecoli notebook

    @cthoyt
    cthoyt committed Jan 19, 2024
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  6. Update Case_study3_The_EColi.ipynb

    @cthoyt
    cthoyt committed Jan 19, 2024
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  7. Finish rerunning ecoli case study

    @cthoyt
    cthoyt committed Jan 19, 2024
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  8. Update network_validation.py

    @cthoyt
    cthoyt committed Jan 19, 2024
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Commits on Jan 20, 2024

  1. Adding images of networks

    @pnavada
    pnavada committed Jan 20, 2024
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  2. Adding network images to notebooks

    @pnavada
    pnavada committed Jan 20, 2024
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  3. modified case studies

    @srtaheri
    srtaheri committed Jan 20, 2024
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  4. Revert "Adding network images to notebooks" 

    This reverts commit 3020e06.
    @pnavada
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  5. merged

    @srtaheri
    srtaheri committed Jan 20, 2024
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  6. added sars continuous

    @srtaheri
    srtaheri committed Jan 20, 2024
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  7. testing continuous data for sars

    @pnavada
    pnavada committed Jan 20, 2024
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Commits on Jan 21, 2024

  1. tetsing case studies

    @srtaheri
    srtaheri committed Jan 21, 2024
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  2. discretized sars data

    @srtaheri
    srtaheri committed Jan 21, 2024
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Commits on Jan 23, 2024

  1. changed SARS data from binary to continuous

    @srtaheri
    srtaheri committed Jan 23, 2024
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  2. finalized sars case study

    @srtaheri
    srtaheri committed Jan 23, 2024
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Commits on Jan 24, 2024

  1. Adding images to notebooks

    @pnavada
    pnavada committed Jan 24, 2024
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  2. executed all the cells

    @pnavada
    pnavada committed Jan 24, 2024
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  3. changed a parameter in data generation process to avoid creating many… 

    … zeros for EGFR
    @srtaheri
    srtaheri committed Jan 24, 2024
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  4. added motivating example data generation

    @srtaheri
    srtaheri committed Jan 24, 2024
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  5. added motivating example to init

    @srtaheri
    srtaheri committed Jan 24, 2024
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  6. add motivating example

    @srtaheri
    srtaheri committed Jan 24, 2024
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  7. added distribution of ATEs

    @srtaheri
    srtaheri committed Jan 24, 2024
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  8. modified case studies

    @srtaheri
    srtaheri committed Jan 24, 2024
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  9. added sars ATE boxplot

    @srtaheri
    srtaheri committed Jan 24, 2024
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  10. added datasets given by Karen

    @srtaheri
    srtaheri committed Jan 24, 2024
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  11. reading sachs test data and random sampling evaluation

    @pnavada
    pnavada committed Jan 24, 2024
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  12. added quantile ranges

    @srtaheri
    srtaheri committed Jan 24, 2024
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  13. try to solve conflict

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    srtaheri committed Jan 24, 2024
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Commits on Jan 25, 2024

  1. motivating example was checked against text in paper

    @srtaheri
    srtaheri committed Jan 25, 2024
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  2. made sure results in the notebook align with text in paper

    @srtaheri
    srtaheri committed Jan 25, 2024
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  3. Resizing image

    @pnavada
    pnavada committed Jan 25, 2024
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  4. Resizing images to 500X500

    @pnavada
    pnavada committed Jan 25, 2024
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Commits on Jan 26, 2024

  1. added sachs continuous data

    @srtaheri
    srtaheri committed Jan 26, 2024
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  2. Adding method for loading sachs continuous data and regression plot f… 

    …or ecoli
    @pnavada
    pnavada committed Jan 26, 2024
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  3. loading sachs data fix

    @pnavada
    pnavada committed Jan 26, 2024
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  4. Reran notebooks and cleaned up imports

    @cthoyt
    cthoyt committed Jan 26, 2024
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  5. Run lint

    @cthoyt
    cthoyt committed Jan 26, 2024
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  6. Update MANIFEST.in

    @cthoyt
    cthoyt committed Jan 26, 2024
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  7. Update __init__.py

    @cthoyt
    cthoyt committed Jan 26, 2024
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  8. Update

    @cthoyt
    cthoyt committed Jan 26, 2024
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  9. Merge branch 'main' into notebooks

    @cthoyt
    cthoyt authored Jan 26, 2024
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