Automated pipeline for evaluating pre-computed fingerprints#2

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blazejba wants to merge 48 commits intomainfrom bb/finetuning-on-fingerprints

+4,493-24

Commits on Dec 11, 2023

download LargeMix datasets in a single command
Blazej Banaszewski
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Commits on Dec 21, 2023

add a script for finetuning on fingerprints on cpu
Blazej Banaszewski
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fix target types for regression
Blazej Banaszewski
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Commits on Dec 22, 2023

add lr scheduling
Blazej Banaszewski
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sweeping script ready
Blazej Banaszewski
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Delete sweep_finetunning_on_fingerprints.sh
blazejba
authored
various fixes
Blazej Banaszewski
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Merge branch 'bb/finetuning-on-fingerprints' of github.com:graphcore-research/graphium-smg into bb/finetuning-on-fingerprints
Blazej Banaszewski
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full TDC eval for a checkpoint implemented
Blazej Banaszewski
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Commits on Jan 3, 2024

add config + small fixes
Blazej Banaszewski
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allow disabling wandb + drop last batch if not full
Blazej Banaszewski
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log number of trainable params to wandb
Blazej Banaszewski
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add spearmanr metric to regression tasks
Blazej Banaszewski
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add fingerprint extraction
Blazej Banaszewski
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Commits on Jan 4, 2024

small bug fix + allow to add a suffix to the fingerprint filenames
Blazej Banaszewski
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refactoring
Blazej Banaszewski
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auto extraction of scores from the fingerprinting sweeps
Blazej Banaszewski
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fix a bug with regression eval + add worker to unfinished sweeps instead of always creating a new one
Blazej Banaszewski
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use args instead of consts for the sweeping script
Blazej Banaszewski
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fix small bugs
Blazej Banaszewski
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analyze_results now produces a table in a csv file that can be copied to excel
Blazej Banaszewski
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Commits on Jan 5, 2024

simplify the script by removing repeating stuff
Blazej Banaszewski
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fix a bug in the sweeper
Blazej Banaszewski
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Commits on Jan 6, 2024

dump a csv with extracted scores from the sweeps
Blazej Banaszewski
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add weight decay + filter out nans
Blazej Banaszewski
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combine all results correctly
Blazej Banaszewski
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randomly choose with dataset to sweep to avoid workers collision
Blazej Banaszewski
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Commits on Jan 8, 2024

filter out samples with NaNs in training
Blazej Banaszewski
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order the csv table and include empty rows to match the excel template
Blazej Banaszewski
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a bug with casting targets
Blazej Banaszewski
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run finetuning with 5-fold scaffold split and report min,max,mean and std
Blazej Banaszewski
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Commits on Jan 9, 2024

analzye 5-fold cross validation results
Blazej Banaszewski
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Commits on Jan 11, 2024

script for analyzing the best hparams
Blazej Banaszewski
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fixing the metric for the metabolism datasets
Blazej Banaszewski
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Commits on Jan 16, 2024

load mup in validation/fingerprint extraction
Blazej Banaszewski
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Commits on Jan 17, 2024

extract node and edge level features
Blazej Banaszewski
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yolo.py extends fingerprint training with node and edge level features
Blazej Banaszewski
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Commits on Jan 25, 2024

data analysis
Blazej Banaszewski
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Commits on Jan 28, 2024

smaller sweeps + improved analytics
Blazej Banaszewski
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Commits on Jan 30, 2024

add "fair" test score selection
Blazej Banaszewski
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ensemble evaluation
Blazej Banaszewski
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allow extracting node features as fingerprints
Blazej Banaszewski
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change program name
Blazej Banaszewski
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Commits on Mar 12, 2024

remove Gradient link from README
kerstink-GC
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Commits on Mar 26, 2024

update
Blazej Banaszewski
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Commits on Apr 8, 2024

cleaning
Blazej Banaszewski
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move files
Blazej Banaszewski
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Merge branch 'bb/finetuning-on-fingerprints' of github.com:graphcore-research/graphium-smg into bb/finetuning-on-fingerprints
Blazej Banaszewski
committed