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Commits on Dec 4, 2024

first commit
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new: add bib and html
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fix(onboarding): citations work; update html
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change(bib): update bibliography using hardlink
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change(onboarding): delegate setup to monorepo
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add ref
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use local-bib
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change bib file
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Adding image.png

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Add plan description

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extracting a sub dataset

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push code

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push code again

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Add first classifier pipeline on features

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update flake

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Add splitter and fixing environment

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Add custom splitter

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Updating flake and adding custom split

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Custom split consistent over kernel and server

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Flake, req solved. classifier done, portrait start

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Add image classifier, update flake torch

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MultiGPU training fixed

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Jamboree day - moa distribution

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Add receptive field calculation

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Including loss save in training loop

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Evaluation loop multi GPU

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Add visualisation of result from training

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start working with lightning

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update requirement.txt with lightning

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Update lightning script

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Parallel training fixed in script

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Model VGG trained

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Start generative part on Diane example

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Organisation of GANs notebook

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Add captum package

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MLP classfier and start of GANs profiles

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lightning V2 better handling of metric and GAN

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Finish GANs lightning module

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Fix GAN training, add accuracy

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GANs trained and overfitting

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Plan update

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Update image processing: clip, rotation, flip

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Fix the save image dataset

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Adding confusion matrix

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mAP calculation for better subsampling of dataset

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sub subset target2 created based on phen activity

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Fix the round step of data split for single moa

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Start GAN pipeline on images

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Fixing multi-GPU GAN training

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Start working on UNetAdaIN

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Finish building UNetAdaIN

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Fixing AdaIN bug and start training

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Start working on the lightning StarGANV2

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Add draft.org

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Create a reference dataset

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dataloaders finished

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Training loop done in StarGANv2

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Training loop update

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Update logging in training loop

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Add StarGANv2 model

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Update training script

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Debug StarGANv2 Training, update plot img

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Add test step

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Test step for vgg classifier

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Implemented generation for validation purposes

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Almost finish generate dataset from stargan

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Fix bug in generate fake dataset

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Create plot fake img

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Creating dataset to handle fake images storage

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Add a mask for fake dataset and start fid metric

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Finish FID and LPIPS score

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Debug Fid and Lpips

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FID and LPIPS final debugging

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Create Dataset to access real and fake img at once

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Test of attribution methods updated

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Update attribution techniques

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Finished implementing D-GradCam and D-INGRAD

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Correct bug with DeepLift and ReLU module

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Update attribution visualisation method

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Update of the mask techniques

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Update attribution visual with mask

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Update FID plot and finished DAC curve plot

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Update acc for dac computation

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update plot of dac

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Speeding up DAC computation

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Update parallelization

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Updating comment and function definition

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Finished attribution score computation

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Update plotting method

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Compute DAC score

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Plot min_mask

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update plot dac curve per transition

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Add plot dac curve per transition

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Adding option to choose baseline for attribution

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Update smallest mask

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Update custom_dataset & start filter image

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Debug custom_dataset

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Debut custom_dataset

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feat(filter_image): plot mapping moa_id to pert

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feat(flake): add isort

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refactor(filter_image): ordering code

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feat(filter_image): add channel to rgb and crop

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fix(filter_image): update rgb normalisation

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feat(filter_image): otsu and blob detector filter

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refactor(filter_img): clarity and update filter

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Refactor(filter_image): Update code

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feat(conv_model): add max channel to VGG_ch

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refactor: debugging, running pipeline, new ideas

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update: refactor code and start interactive viz

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feat(image_classifier): add enbedding generator

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Update: file permission executable

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deps: update polars; add altair
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feat(viz): add csv->parquet; add marimo viz
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Fix(csv_to_parquet): use PCA and UMAP on embedding

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actions: add duplicate-code-detection
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chore: run ruff autofixes
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fix(gans_profiles_script): match triple quoting
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fix(custom_dataset): use valid unpacking
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deps: have nix provide pyright and ruff
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actions: fix root dir
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