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Jacob dev #7

Merged
merged 106 commits into from
Sep 21, 2023
Merged

Jacob dev #7

merged 106 commits into from
Sep 21, 2023

Commits on Aug 29, 2022

  1. Add files via upload

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    TianyuCodings authored Aug 29, 2022
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  2. Update __init__.py

    @jaydu1
    jaydu1 committed Aug 29, 2022
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  3. Rename covariates.

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  4. Specify dtype for pi_cov.

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  5. Add condition encoding.

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Commits on Aug 30, 2022

  1. Change mmd encoder and rewrite mmd calculation.

    @TianyuCodings
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  2. fix bug for mmd loop.

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    TianyuCodings authored Aug 30, 2022
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Commits on Aug 31, 2022

  1. rewrite pi_cov part

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  2. rename c_score to covariates.

    @TianyuCodings
    TianyuCodings committed Aug 31, 2022
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Commits on Sep 1, 2022

  1. fix bug of dtype cast in conditions

    @TianyuCodings
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  2. fix bug for mmd calculation num partition.

    @TianyuCodings
    TianyuCodings committed Sep 1, 2022
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Commits on Sep 6, 2022

  1. Update simulation results

    @jaydu1
    jaydu1 committed Sep 6, 2022
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  2. fix but of recognizing str type of "root"

    @TianyuCodings
    TianyuCodings committed Sep 6, 2022
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  3. load_data return dict and anndata

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  4. load_data return dict and anndata

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  5. modify evaluate function.

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    TianyuCodings committed Sep 6, 2022
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Commits on Sep 7, 2022

  1. Add save_model and load_model function.

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  2. Fix bug about save and load model function.

    @TianyuCodings
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  3. Add save_fig param to backbone and trajectory.

    @TianyuCodings
    TianyuCodings committed Sep 7, 2022
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  4. Fix bug about saving model.

    @TianyuCodings
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  5. Fix bug about evaluation.

    @TianyuCodings
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  6. Fix bug about evaluation.

    @TianyuCodings
    TianyuCodings committed Sep 7, 2022
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  7. Fix bug about return anndata in load_data.

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  8. temporarily add w_base to edge score.

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    TianyuCodings committed Sep 7, 2022
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  9. fix bug of evaluation when existing merged clusters.

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    TianyuCodings committed Sep 7, 2022
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Commits on Sep 8, 2022

  1. fix bug of evaluation topology.

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  2. fix bug of evaluation topology.

    @TianyuCodings
    TianyuCodings committed Sep 8, 2022
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Commits on Sep 10, 2022

  1. fix bug of evaluation topology.

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  2. fix bug of pseudotime when states are not connected.

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    TianyuCodings committed Sep 10, 2022
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  3. fix infer_traj and evaluation bug caused by pseudotime when states ar… 

    …e not connected.
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    TianyuCodings committed Sep 10, 2022
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Commits on Sep 17, 2022

  1. Add random seed setting function

    @jaydu1
    jaydu1 committed Sep 17, 2022
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  2. Fix bug: import random.

    @jaydu1
    jaydu1 committed Sep 17, 2022
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  3. Add scJoint datasets.

    @jaydu1
    jaydu1 committed Sep 17, 2022
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  4. Update: encoding covariates.

    @jaydu1
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  5. Update: add conditions encoding

    @jaydu1
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  6. Updata: np.nan not participant in mmd_loss.

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  7. Updata: load_data if return dict.

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    TianyuCodings committed Sep 17, 2022
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  8. Fix bug of mmd calculation.

    @TianyuCodings
    TianyuCodings committed Sep 17, 2022
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  9. Fix bug of load_model.

    @TianyuCodings
    TianyuCodings committed Sep 17, 2022
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  10. Fix bug of plotting when directly load model.

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    TianyuCodings committed Sep 17, 2022
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  11. Command cov scaler.

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    TianyuCodings committed Sep 17, 2022
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Commits on Sep 18, 2022

  1. Fix bug of load_model when existing cov.

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  2. Fix bug: visualization after loading model

    @jaydu1
    jaydu1 committed Sep 18, 2022
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  3. Reformat code

    @jaydu1
    jaydu1 committed Sep 18, 2022
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  4. Update plotting function 

    For visualizing legend on data, supply "legend_loc = 'on data'" as an extra parameter to the functions  "plot_backbone" and "infer_trajectory".
    @jaydu1
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  5. Update default L in posterior_estimation.

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    TianyuCodings committed Sep 18, 2022
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  6. Update mouse brain weights.

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    TianyuCodings committed Sep 18, 2022
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  7. Init Commit: Nature Cortex weights.

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  8. Add files via upload

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    TianyuCodings authored Sep 18, 2022
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  9. Init Commit: Nature cortex and mouse brain merged data weights.

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  10. Merge branch 'JacobDev' of https://github.com/jaydu1/VITAE into JacobDev

    @TianyuCodings
    TianyuCodings committed Sep 18, 2022
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  11. Update run_VITAE designed for mouse_brain dataset.

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    TianyuCodings committed Sep 18, 2022
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  12. Remove mouse_brain.ipynb from weights file.

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    TianyuCodings committed Sep 18, 2022
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  13. Remove mouse.inferece from nature_cortex weights file.

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  14. Reformat file. 

    Add case_study dictionary to store code about mouse_brain_merge, nature_cortex and nature_cortex_mouse_brain_merge.
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  15. Init commit: load_model notebook for mouse_brain_merged.

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Commits on Sep 19, 2022

  1. Add **kwargs to backbone plot.

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Commits on Sep 21, 2022

  1. Add kword color to infer_backbone so that backbone can be plotted by … 

    …other label.
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Commits on Sep 24, 2022

  1. Update .gitignore

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Commits on Sep 26, 2022

  1. Update load_data for new simulated data.

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Commits on Sep 27, 2022

  1. Merge remote-tracking branch 'origin/JacobDev' into JacobDev 

    Update simulated data by our model.
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Commits on Sep 28, 2022

  1. Update load_data for new simulated data.

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  2. Add color kwd to trajectory.

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  3. Update data 

    Update simulated model by our model.
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  4. Update result_other_methods.csv

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  5. Fix data name error.

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    TianyuCodings committed Sep 28, 2022
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Commits on Sep 30, 2022

  1. Load covariates for human hematopoiesis data

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Commits on Oct 1, 2022

  1. Update: center colors ordered by categories.

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Commits on Oct 2, 2022

  1. Fix bug: human hematopoiesis covariate truncated

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Commits on Oct 4, 2022

  1. Rename dataset

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  2. Update simulation result

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    TianyuCodings committed Oct 4, 2022
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  3. Merge branch 'JacobDev' of https://github.com/jaydu1/VITAE into JacobDev

    @TianyuCodings
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  4. Update benchmarking.

    @jaydu1
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  5. Update simulation result

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  6. Merge branch 'JacobDev' of https://github.com/jaydu1/VITAE into JacobDev

    @TianyuCodings
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  7. Update results of other methods.

    @jaydu1
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  8. Remove pdf.

    @jaydu1
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  9. Update result_other_methods.csv

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Commits on Oct 11, 2022

  1. Update weights for mouse brain datasets.

    @jaydu1
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Commits on Oct 12, 2022

  1. Update: change colors of cluster centers

    @jaydu1
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  2. Fix bug about plotting.

    @TianyuCodings
    TianyuCodings committed Oct 12, 2022
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Commits on Oct 17, 2022

  1. Add plot_center function.

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  2. Add plot index.

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    TianyuCodings committed Oct 17, 2022
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  3. Add edge score.

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Commits on Oct 24, 2022

  1. Higher order regression for DE test.

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  2. Fix bug in DE test.

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Commits on Nov 4, 2022

  1. Remove the cortex-only case study

    @jaydu1
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  2. Update mouse brain case study

    @jaydu1
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  3. Update script name

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  4. Add human hematopoiesis case study

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Commits on Nov 5, 2022

  1. Update plotting benchmark.

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  2. Update README.md

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Commits on Nov 6, 2022

  1. Rename folder

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  2. Delete paper/Benchmarking with Real and Synthetic Datasets directory

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Commits on Sep 10, 2023

  1. Update README.md

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Commits on Sep 13, 2023

  1. Update plotting of human hema datasets

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Commits on Sep 18, 2023

  1. Update .gitignore

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  2. Remove pycache

    @jaydu1
    jaydu1 committed Sep 18, 2023
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  3. Update annotations.

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Commits on Sep 20, 2023

  1. Update .gitignore

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  2. Upload simulation code

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  3. Clean up benchmarking simulation

    @jaydu1
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  4. Remove unused functions.

    @jaydu1
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  5. Update README.md

    @jaydu1
    jaydu1 committed Sep 20, 2023
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  6. Update __init__.py

    @jaydu1
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  7. Update doc

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