merge codebase changes on main into default#92
Merged
cameronraysmith merged 104 commits intodna-diffusionfrom Mar 7, 2023
Merged
merge codebase changes on main into default#92cameronraysmith merged 104 commits intodna-diffusionfrom
cameronraysmith merged 104 commits intodna-diffusionfrom
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Added a bunch of directories with (mostly) empty/dummy .py files for now, so that everyone can see what the project will be structured like. On top of the present directories, there will also be a datasets and a logs directory, the latter being dynamically created at traintime or validation time.
wip: dataloader first draft
Revert "wip: dataloader first draft"
Deleting metrics directory as it was decided we'll have only one file with all metrics.
Refactored Lucas's DDPM, UNet and units and added them as PL modules.
Added "instantiate_from_config" import.
Added nucleotides as a parameter with a default of 4 to the sample method.
Added default function import.
Designed config template mainly for PL-related parameters. Keeping multiprocessing arguments for multi-GPU for the first test, which we'll change to multi-node. Diffusion and UNet parameters can easily vary.
Dataloader Draft
Adding test folder and dummy files
Deprecated.
Deprecated.
Codebase Update via Noah's Refactored DDPM Notebook
Changed default number of timesteps from 1000 to 200.
Moved unet_config params inside the diffusion models params, so it mirrors the hierarchical relationship between the diffusion class and the unet class.
Minor dict property name changes.
Update the unit tests
for more information, see https://pre-commit.ci
cameronraysmith
changed the title
* WIP new folder structure * ema parameter fix * Base dataloader instantiation with full hydraconfig succesful, missing full params * Update sequence_dataloader.py * Remove outputs folder, update .gitignore * Update network.py * Update sequence_datamodule.py * Update sequence_datamodule.py --------- Co-authored-by: cmvcordova <cmvcordova@github.com> Co-authored-by: cmvcordova <cmvcordova@pm.me> Co-authored-by: Matei Bejan <24592776+mateibejan1@users.noreply.github.com>
cameronraysmith
requested review from
LucasSilvaFerreira,
cmvcordova,
mateibejan1 and
ssenan
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at this time the default branch is pinellolab/dna-diffusion:dna-diffusion at 73cf225