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

Automated pipeline for evaluating pre-computed fingerprints #2

Open
wants to merge 48 commits into
base: main
Choose a base branch
from
Open

Automated pipeline for evaluating pre-computed fingerprints #2

wants to merge 48 commits into from

Commits on Dec 11, 2023

  1. download LargeMix datasets in a single command

    @blazejba
    blazejba committed Dec 11, 2023
    Configuration menu
    Copy the full SHA
    884f98e View commit details
    Browse the repository at this point in the history

Commits on Dec 21, 2023

  1. add a script for finetuning on fingerprints on cpu

    @blazejba
    blazejba committed Dec 21, 2023
    Configuration menu
    Copy the full SHA
    8a35f54 View commit details
    Browse the repository at this point in the history

  2. fix target types for regression

    @blazejba
    blazejba committed Dec 21, 2023
    Configuration menu
    Copy the full SHA
    1c80129 View commit details
    Browse the repository at this point in the history

Commits on Dec 22, 2023

  1. add lr scheduling

    @blazejba
    blazejba committed Dec 22, 2023
    Configuration menu
    Copy the full SHA
    63e54ad View commit details
    Browse the repository at this point in the history

  2. sweeping script ready

    @blazejba
    blazejba committed Dec 22, 2023
    Configuration menu
    Copy the full SHA
    8ab2887 View commit details
    Browse the repository at this point in the history

  3. Delete sweep_finetunning_on_fingerprints.sh

    @blazejba
    blazejba committed Dec 22, 2023
    Configuration menu
    Copy the full SHA
    e521b52 View commit details
    Browse the repository at this point in the history

  4. various fixes

    @blazejba
    blazejba committed Dec 22, 2023
    Configuration menu
    Copy the full SHA
    e4fc5fa View commit details
    Browse the repository at this point in the history

  5. Merge branch 'bb/finetuning-on-fingerprints' of github.com:graphcore-… 

    …research/graphium-smg into bb/finetuning-on-fingerprints
    @blazejba
    blazejba committed Dec 22, 2023
    Configuration menu
    Copy the full SHA
    43495d8 View commit details
    Browse the repository at this point in the history

  6. full TDC eval for a checkpoint implemented

    @blazejba
    blazejba committed Dec 22, 2023
    Configuration menu
    Copy the full SHA
    a501ad2 View commit details
    Browse the repository at this point in the history

Commits on Jan 3, 2024

  1. add config + small fixes

    @blazejba
    blazejba committed Jan 3, 2024
    Configuration menu
    Copy the full SHA
    b5d0fb6 View commit details
    Browse the repository at this point in the history

  2. allow disabling wandb + drop last batch if not full

    @blazejba
    blazejba committed Jan 3, 2024
    Configuration menu
    Copy the full SHA
    20485bd View commit details
    Browse the repository at this point in the history

  3. log number of trainable params to wandb

    @blazejba
    blazejba committed Jan 3, 2024
    Configuration menu
    Copy the full SHA
    65cc2da View commit details
    Browse the repository at this point in the history

  4. add spearmanr metric to regression tasks

    @blazejba
    blazejba committed Jan 3, 2024
    Configuration menu
    Copy the full SHA
    dee7d2e View commit details
    Browse the repository at this point in the history

  5. add fingerprint extraction

    @blazejba
    blazejba committed Jan 3, 2024
    Configuration menu
    Copy the full SHA
    cbf847f View commit details
    Browse the repository at this point in the history

Commits on Jan 4, 2024

  1. small bug fix + allow to add a suffix to the fingerprint filenames

    @blazejba
    blazejba committed Jan 4, 2024
    Configuration menu
    Copy the full SHA
    71dfc69 View commit details
    Browse the repository at this point in the history

  2. refactoring

    @blazejba
    blazejba committed Jan 4, 2024
    Configuration menu
    Copy the full SHA
    a1e8e45 View commit details
    Browse the repository at this point in the history

  3. auto extraction of scores from the fingerprinting sweeps

    @blazejba
    blazejba committed Jan 4, 2024
    Configuration menu
    Copy the full SHA
    5722964 View commit details
    Browse the repository at this point in the history

  4. fix a bug with regression eval + add worker to unfinished sweeps inst… 

    …ead of always creating a new one
    @blazejba
    blazejba committed Jan 4, 2024
    Configuration menu
    Copy the full SHA
    30b0a0f View commit details
    Browse the repository at this point in the history

  5. use args instead of consts for the sweeping script

    @blazejba
    blazejba committed Jan 4, 2024
    Configuration menu
    Copy the full SHA
    c3733f2 View commit details
    Browse the repository at this point in the history

  6. fix small bugs

    @blazejba
    blazejba committed Jan 4, 2024
    Configuration menu
    Copy the full SHA
    e0fc687 View commit details
    Browse the repository at this point in the history

  7. analyze_results now produces a table in a csv file that can be copied… 

    … to excel
    @blazejba
    blazejba committed Jan 4, 2024
    Configuration menu
    Copy the full SHA
    16c0b71 View commit details
    Browse the repository at this point in the history

Commits on Jan 5, 2024

  1. simplify the script by removing repeating stuff

    @blazejba
    blazejba committed Jan 5, 2024
    Configuration menu
    Copy the full SHA
    656410b View commit details
    Browse the repository at this point in the history

  2. fix a bug in the sweeper

    @blazejba
    blazejba committed Jan 5, 2024
    Configuration menu
    Copy the full SHA
    9ba63c9 View commit details
    Browse the repository at this point in the history

Commits on Jan 6, 2024

  1. dump a csv with extracted scores from the sweeps

    @blazejba
    blazejba committed Jan 6, 2024
    Configuration menu
    Copy the full SHA
    c4d2109 View commit details
    Browse the repository at this point in the history

  2. add weight decay + filter out nans

    @blazejba
    blazejba committed Jan 6, 2024
    Configuration menu
    Copy the full SHA
    4237502 View commit details
    Browse the repository at this point in the history

  3. combine all results correctly

    @blazejba
    blazejba committed Jan 6, 2024
    Configuration menu
    Copy the full SHA
    d5163cb View commit details
    Browse the repository at this point in the history

  4. randomly choose with dataset to sweep to avoid workers collision

    @blazejba
    blazejba committed Jan 6, 2024
    Configuration menu
    Copy the full SHA
    7a2fcdc View commit details
    Browse the repository at this point in the history

Commits on Jan 8, 2024

  1. filter out samples with NaNs in training

    @blazejba
    blazejba committed Jan 8, 2024
    Configuration menu
    Copy the full SHA
    98fb812 View commit details
    Browse the repository at this point in the history

  2. order the csv table and include empty rows to match the excel template

    @blazejba
    blazejba committed Jan 8, 2024
    Configuration menu
    Copy the full SHA
    f9451ba View commit details
    Browse the repository at this point in the history

  3. a bug with casting targets

    @blazejba
    blazejba committed Jan 8, 2024
    Configuration menu
    Copy the full SHA
    d2e14d0 View commit details
    Browse the repository at this point in the history

  4. run finetuning with 5-fold scaffold split and report min,max,mean and… 

    … std
    @blazejba
    blazejba committed Jan 8, 2024
    Configuration menu
    Copy the full SHA
    c41a606 View commit details
    Browse the repository at this point in the history

Commits on Jan 9, 2024

  1. analzye 5-fold cross validation results

    @blazejba
    blazejba committed Jan 9, 2024
    Configuration menu
    Copy the full SHA
    6e54218 View commit details
    Browse the repository at this point in the history

Commits on Jan 11, 2024

  1. script for analyzing the best hparams

    @blazejba
    blazejba committed Jan 11, 2024
    Configuration menu
    Copy the full SHA
    a8f5876 View commit details
    Browse the repository at this point in the history

  2. fixing the metric for the metabolism datasets

    @blazejba
    blazejba committed Jan 11, 2024
    Configuration menu
    Copy the full SHA
    282a944 View commit details
    Browse the repository at this point in the history

Commits on Jan 16, 2024

  1. load mup in validation/fingerprint extraction

    @blazejba
    blazejba committed Jan 16, 2024
    Configuration menu
    Copy the full SHA
    0352b96 View commit details
    Browse the repository at this point in the history

Commits on Jan 17, 2024

  1. extract node and edge level features

    @blazejba
    blazejba committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    8880d0d View commit details
    Browse the repository at this point in the history

  2. yolo.py extends fingerprint training with node and edge level features

    @blazejba
    blazejba committed Jan 17, 2024
    Configuration menu
    Copy the full SHA
    41afd4e View commit details
    Browse the repository at this point in the history

Commits on Jan 25, 2024

  1. data analysis

    @blazejba
    blazejba committed Jan 25, 2024
    Configuration menu
    Copy the full SHA
    69a0a2c View commit details
    Browse the repository at this point in the history

Commits on Jan 28, 2024

  1. smaller sweeps + improved analytics

    @blazejba
    blazejba committed Jan 28, 2024
    Configuration menu
    Copy the full SHA
    8b5c2a6 View commit details
    Browse the repository at this point in the history

Commits on Jan 30, 2024

  1. add "fair" test score selection

    @blazejba
    blazejba committed Jan 30, 2024
    Configuration menu
    Copy the full SHA
    69f1fc1 View commit details
    Browse the repository at this point in the history

  2. ensemble evaluation

    @blazejba
    blazejba committed Jan 30, 2024
    Configuration menu
    Copy the full SHA
    074e009 View commit details
    Browse the repository at this point in the history

  3. allow extracting node features as fingerprints

    @blazejba
    blazejba committed Jan 30, 2024
    Configuration menu
    Copy the full SHA
    051e5a1 View commit details
    Browse the repository at this point in the history

  4. change program name

    @blazejba
    blazejba committed Jan 30, 2024
    Configuration menu
    Copy the full SHA
    c5cbf5f View commit details
    Browse the repository at this point in the history

Commits on Mar 12, 2024

  1. remove Gradient link from README

    @kerstink-GC
    kerstink-GC committed Mar 12, 2024
    Configuration menu
    Copy the full SHA
    a06c802 View commit details
    Browse the repository at this point in the history

Commits on Mar 26, 2024

  1. update

    @blazejba
    blazejba committed Mar 26, 2024
    Configuration menu
    Copy the full SHA
    3fabe6f View commit details
    Browse the repository at this point in the history

Commits on Apr 8, 2024

  1. cleaning

    @blazejba
    blazejba committed Apr 8, 2024
    Configuration menu
    Copy the full SHA
    b2cbe3d View commit details
    Browse the repository at this point in the history

  2. move files

    @blazejba
    blazejba committed Apr 8, 2024
    Configuration menu
    Copy the full SHA
    76aa26d View commit details
    Browse the repository at this point in the history

  3. Merge branch 'bb/finetuning-on-fingerprints' of github.com:graphcore-… 

    …research/graphium-smg into bb/finetuning-on-fingerprints
    @blazejba
    blazejba committed Apr 8, 2024
    Configuration menu
    Copy the full SHA
    abc4a4b View commit details
    Browse the repository at this point in the history