DRAFT: Preprocess the IMPROVE way for our Uno model by rajeeja · Pull Request #1 · JDACS4C-IMPROVE/Benchmarks

Commits on Oct 19, 2023

Commits on Oct 20, 2023

test branch push permissions

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cleanup

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Draft uno_preprocess2.py
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Commits on Dec 19, 2023

preprocess and train sh files standardized for cuda devices and etc...

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IMPROVE_DATA_DIR instead of CANDLE_DATA_DIR

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Commits on Dec 20, 2023

Update uno_preprocess_improve.py
wilke
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Merge pull request #4 from JDACS4C-IMPROVE/wilke-patch-1
wilke
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Updated preprocess, check for config file, removed CUDA
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Merge branch 'preprocess_improve' of github.com:JDACS4C-IMPROVE/Benchmarks into preprocess_improve
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Check for config file, removed CUDA
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Check for config file, removed CUDA
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Debugging and simplifywq
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Added missing option
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Reverse any changes to original Uno

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Revert "Reverse any changes to original Uno"

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Had to revert VS Code formatting... making the original uno have no changes

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Commits on Jan 10, 2024

Create conda_env.sh
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Commits on Jan 11, 2024

Commits on Jan 12, 2024

CANDLE_DATA_DIR is deprecated. Use IMPROVE_DATA_DIR

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Rough preprocess call in train.sh and preprocess python file formatting

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Fix pathing looking for processed data inside IMPROVE_DATA_DIR

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tweak parameter file

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Path fix for preprocess call

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Commits on Jan 16, 2024

add test inferral

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Commits on Jan 19, 2024

unnecessary IMPROVE_DATA_DIR check

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adding hyperparameter functionality with number of layers

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warmup type hyperparameter functionality

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better naming and updating txt file for new hyperparameters

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txt file for num layers hyperparameter functionality

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Commits on Jan 20, 2024

parquet reading and smaller dataset debug setting

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Better debug setting

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parquet reading in infer

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Revise debug setting to work (can't load only n rows)

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Commits on Jan 22, 2024

Update README.md
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update train_params definitions

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fix test split naming

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update default model and fix train debug param name

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Commits on Jan 23, 2024

update train_params definitions and polish preprocessing / add debug option

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polish preprocessing / add debug option

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refine compose_data_arrays and make prints cleaner

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make prints cleaner

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times

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times

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subset data functionality

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Commits on Jan 24, 2024

save and load one data file

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slight hyperparameter change

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slight hyperparameter change

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update defaults and remove old prints

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fix test set read

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Commits on Jan 25, 2024

merge differenlt and create common samples function

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improve subsetting

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preprocess debug false by default
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gene symbol to solve multilevel dataframe issue
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debug accidentally set default true
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train data batching

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update infer and polish others to use auc param
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flatten to accomodate store predictions
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Commits on Jan 26, 2024

better ntime keeping
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import timekeeping instead of multiple functions
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deal with memory issues. data loaders, r2 callback adjustment, and gpu configuration
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update params for batching
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more for dealing with large datasets
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Commits on Jan 27, 2024

optimizer for HPO add

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Commits on Jan 28, 2024

Update infer to work with large datasets and put common functions in utils
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GPU check

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Update README.md
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update def file and instructions
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take preprocess out of train.sh
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default params and preprocess in train.sh
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protobuf version fix
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preprocess.sh
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clone Uno_IMPROVE not original
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update def file
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cross study add
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singularity testing
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optimizer and missing interaction activation defaults
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move src location
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not in use for now
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restore defaults
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can't have singularity in here when trying to build with cloning this directory
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make robust preprocess in train.sh
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Update train.sh
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directory to execute preprocess in container
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fix variable
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Commits on Jan 29, 2024

fix index error with data generation
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better early stopping default and no warmup option
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Commits on Jan 30, 2024

data generator factory for r2 callback. additional definitions fix for HPO, and one data generation batch size
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fix definitions list error
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verbosity to tell indices
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Commits on Jan 31, 2024

soft debugging and subsetting. training batch size and validating batch size same
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use generator batch size
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load preprocess_param into train
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make train debug and subset CL passable
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missing comma
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Commits on Feb 1, 2024

update sh scripts to say IMPROVE and preprocess list allowed datasets
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stick with CANDLE_MODEL because models are candleized, datasets are IMPROVE
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slight cchanges for using generator
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update README
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punctuation
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unintentional added line
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Commits on Feb 2, 2024

make preprocess have train params
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move definitions for hpo compatibility
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move parameters
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Commits on Feb 6, 2024

Update README.md data downloading
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Commits on Feb 7, 2024

Data Shuffling and regression hyperparameter
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Merge branch 'preprocess_improve' of github.com:JDACS4C-IMPROVE/Benchmarks into preprocess_improve
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simple comment fix
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better early stopping parameter
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Commits on Feb 8, 2024

activation function note
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Commits on Feb 9, 2024

regression activation
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Commits on Feb 12, 2024

comment uneccessary gpu memory growth
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Commits on Feb 18, 2024

Take out lr_log_10_range hyperparameter and improve compliance with train.sh
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standardize train.sh
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Commits on Feb 21, 2024

debug power_yj scaling
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exploring different hp-spaces functionality
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Commits on Feb 22, 2024

update to new params
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fix typo in params type
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Update README.md
RylieWeaver
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Update README.md
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better pathing defaults
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Merge branch 'preprocess_improve' of github.com:JDACS4C-IMPROVE/Benchmarks into preprocess_improve
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Commits on Feb 23, 2024

cleaning up
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clean
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Commits on Feb 25, 2024

comment test prediction
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clean up gpu detection
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take test prediction out of train
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Commits on Feb 28, 2024

update parameters
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Commits on Mar 19, 2024

different scheme for larger datasets (merging during batch yielding)
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Commits on Mar 27, 2024

cleanup given addition of new model
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Commits on Mar 30, 2024

combine utils
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Commits on Mar 31, 2024

put more functions in utils
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have batch merging as default
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better naming
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update infer
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revise back to original
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Commits

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