Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

feat: improvements for federated learning and QoL #137

Open
wants to merge 74 commits into
base: master
Choose a base branch
from
Open

feat: improvements for federated learning and QoL #137

wants to merge 74 commits into from

Commits on Nov 18, 2023

  1. ci: add .gitignore

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    8799bba View commit details
    Browse the repository at this point in the history

  2. ci: add pre-commit with black

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    239aec0 View commit details
    Browse the repository at this point in the history

  3. style: reformat with black

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    2912fb2 View commit details
    Browse the repository at this point in the history

  4. test: correct test_dsm.py indentation

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    b5a764b View commit details
    Browse the repository at this point in the history

  5. style: use tqdm.auto for better rendering

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    a3f0ea8 View commit details
    Browse the repository at this point in the history

  6. refactor: remove unused code

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    bf6fb01 View commit details
    Browse the repository at this point in the history

  7. refactor: add distinct init phase for dcph

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    20d3444 View commit details
    Browse the repository at this point in the history

  8. style: remove dead code

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    4a4e0e6 View commit details
    Browse the repository at this point in the history

  9. fix: tentative fix for early stopping

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    b4ad53f View commit details
    Browse the repository at this point in the history

  10. fix: revert fix for early stopping

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    905fa5d View commit details
    Browse the repository at this point in the history

  11. feat: add patience param to DeepCoxPH::fit

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    e768f91 View commit details
    Browse the repository at this point in the history

  12. refactor: set-up logging

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    80f028a View commit details
    Browse the repository at this point in the history

  13. style: fix tqdm label

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    37d70f3 View commit details
    Browse the repository at this point in the history

  14. style: fix logs and warnings

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    b123535 View commit details
    Browse the repository at this point in the history

  15. style: fix assert messages

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    72d5eab View commit details
    Browse the repository at this point in the history

  16. style: tentative fix for warnings.warn misprint

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    87337a7 View commit details
    Browse the repository at this point in the history

  17. style: revert tentative fix for warnings.warn misprint

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    d3e6f0c View commit details
    Browse the repository at this point in the history

  18. style: redirect warnings to logger

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    e79186d View commit details
    Browse the repository at this point in the history

  19. style: fix warnings

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    32dc810 View commit details
    Browse the repository at this point in the history

  20. style: revert warnings fix

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    f9d4d21 View commit details
    Browse the repository at this point in the history

  21. style: replace warnings with logs

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    2cd1769 View commit details
    Browse the repository at this point in the history

  22. style: add proper logging

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    15637b5 View commit details
    Browse the repository at this point in the history

  23. style: add log config

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    5743635 View commit details
    Browse the repository at this point in the history

  24. style: remove log config

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    abb9705 View commit details
    Browse the repository at this point in the history

  25. style: more log config

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    925ad01 View commit details
    Browse the repository at this point in the history

  26. style: add colored logs

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    768d401 View commit details
    Browse the repository at this point in the history

  27. style: fix invasive logs

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    63c92ef View commit details
    Browse the repository at this point in the history

  28. style: fix invasive logs

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    447c64c View commit details
    Browse the repository at this point in the history

  29. style: fix logger

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    265172a View commit details
    Browse the repository at this point in the history

  30. style: fix logger

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    5d03707 View commit details
    Browse the repository at this point in the history

  31. style: fix logger

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    e2a3963 View commit details
    Browse the repository at this point in the history

  32. style: fix logger

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    b169f06 View commit details
    Browse the repository at this point in the history

  33. style: configure loguru

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    3c96047 View commit details
    Browse the repository at this point in the history

  34. style: configure loguru

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    cc031b6 View commit details
    Browse the repository at this point in the history

  35. refactor: move duplicate and shared functions to models.utils package

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    5f01830 View commit details
    Browse the repository at this point in the history

  36. Add debug logs to metrics::survival_regression_metric

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    650c53f View commit details
    Browse the repository at this point in the history

  37. style: refine loguru config

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    368ac2a View commit details
    Browse the repository at this point in the history

  38. style: loguru levels

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    18b3b53 View commit details
    Browse the repository at this point in the history

  39. style: remove debug logging

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    e172cfd View commit details
    Browse the repository at this point in the history

  40. style: disable loguru as per best practices

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    61f0f63 View commit details
    Browse the repository at this point in the history

  41. style: modular logging

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    318b152 View commit details
    Browse the repository at this point in the history

  42. style: custom log levels

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    836d6a3 View commit details
    Browse the repository at this point in the history

  43. style: use warnings.warn for user warnings and defer to loguru

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    4667c49 View commit details
    Browse the repository at this point in the history

  44. refactor: remove duplicated code for patience early returns

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    c590a7e View commit details
    Browse the repository at this point in the history

  45. feat(dcph): add predict_raw_risk and metrics.concordance_index_censored

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    5416836 View commit details
    Browse the repository at this point in the history

  46. feat(dcph): add predict_time_independent_risk and predict_time_indepe… 

    …ndent_survival
    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    b3ab0d1 View commit details
    Browse the repository at this point in the history

  47. refactor(dcph)

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    4e172e3 View commit details
    Browse the repository at this point in the history

  48. fix(dcph): preprocess test data in predict_time_independent_risk

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    405f6b2 View commit details
    Browse the repository at this point in the history

  49. fix(dcph): add inference_mode to predict methods

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    e56e788 View commit details
    Browse the repository at this point in the history

  50. feat(datasets): optionally return feature dict when loading support

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    7a0af3c View commit details
    Browse the repository at this point in the history

  51. feat(dpch): add torch_module @Property

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    37b8a52 View commit details
    Browse the repository at this point in the history

  52. fix(dcph): assign default to optimizer in init_torch_model

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    2bdee98 View commit details
    Browse the repository at this point in the history

  53. fix(dcph): don't raise exception when calling predict_time_independen… 

    …t before fix
    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    89ddad6 View commit details
    Browse the repository at this point in the history

  54. fix(dcph): add default optimizer to init_torch_model

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    b8f1ad9 View commit details
    Browse the repository at this point in the history

  55. fix(dcph): predict_time_independent_risk fails on no torch module

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    a0ec736 View commit details
    Browse the repository at this point in the history

  56. fix(utils._dataframe_to_array): copy array if not writable

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    9066fa7 View commit details
    Browse the repository at this point in the history

  57. fix(utils._dataframe_to_array): copy array if not writable

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    e008bde View commit details
    Browse the repository at this point in the history

  58. feat(dcph): add weight decay

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    cca0c0b View commit details
    Browse the repository at this point in the history

  59. feat(dcph): add activation param

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    690bc47 View commit details
    Browse the repository at this point in the history

  60. fix(dcph): correct activation

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    1f42c82 View commit details
    Browse the repository at this point in the history

  61. feat(dcph): configurable dropout, activation, weight decay, bias

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    2d1eac3 View commit details
    Browse the repository at this point in the history

  62. docs(dcph): document new features

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    4fab724 View commit details
    Browse the repository at this point in the history

  63. ci(tests): add -v flag to unittest cmd

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    af2792c View commit details
    Browse the repository at this point in the history

  64. refactor(logs): revert to standard python logs

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    dae6c25 View commit details
    Browse the repository at this point in the history

  65. refactore(logs): add logging.basicConfig() to __init__

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    37dadf9 View commit details
    Browse the repository at this point in the history

  66. refactor(logs): add better log config

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    bd069ce View commit details
    Browse the repository at this point in the history

  67. refactor(logs): add 'autonlab' root logger

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    721096f View commit details
    Browse the repository at this point in the history

  68. refactor(logs): revert custom root logger

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    fff591c View commit details
    Browse the repository at this point in the history

  69. refactor(logs): add single logger

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    0e8fe99 View commit details
    Browse the repository at this point in the history

  70. refactor(logs): add nullhandler

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    8f8df71 View commit details
    Browse the repository at this point in the history

  71. refactor(logs): basicConfig for logs

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    58b568a View commit details
    Browse the repository at this point in the history

  72. refactor(logs): remove basicConfig for logs

    @matteo4diani
    matteo4diani committed Nov 18, 2023
    Configuration menu
    Copy the full SHA
    df45ead View commit details
    Browse the repository at this point in the history

Commits on Nov 19, 2023

  1. refactor(dcph): use torch_module instead of torch_model[0]

    @matteo4diani
    matteo4diani committed Nov 19, 2023
    Configuration menu
    Copy the full SHA
    b83ddab View commit details
    Browse the repository at this point in the history

  2. test(dcph): add tests for early initialization

    @matteo4diani
    matteo4diani committed Nov 19, 2023
    Configuration menu
    Copy the full SHA
    05bdd31 View commit details
    Browse the repository at this point in the history