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DLMBL 2023 excercise #36
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@ziw-liu I've tested the whole exercise on dlmbl1 node. In addition to prototyping 3 solutions above, can you suggest how to log all validation samples? At this point, the subsample of validation set comes out empty in multiple runs. With solutions in hand, I'll write the exercise prompt. Earlier exercise prompts are commented out so that you can just run the script by clicking |
I think I know what's happening here. The validation samples are the first sample of the first Edit: see f7229a8 |
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We now look at some metrics of performance. Loss is a differentiable metric. But, several non-differentiable metrics are useful to assess the performance of the model. We typically evaluate the model performance on a held out test data. We will use the following metrics to evaluate the accuracy of regression of the model: |
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Minor language edit: these 3 metrics are actually differentiable because the developers of torchmetrics
has made sure that all the operators used in the implementation are differentiable.
@ziw-liu the conflicts in
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* pixelshuffle decoder * Allow sampling multiple patches from the same stack (#35) * sample multiple patches from one stack * do not use type annotations from future it breaks jsonargparse * fix channel stacking for non-training samples * remove batch size from model the metrics will be automatically reduced by lightning * add flop counting script * 3d ouput head * add datamodule target dims mode * remove unused argument and configure drop path * move architecture argument to model level * DLMBL 2023 excercise (#36) * updated intro and paths * updated figures, tested data loader * setup.sh fetches correct dataset * finalized the exercise outline * semi-final exercise * parts 1 and 2 tested, part 3 outline ready * clearer variables, train with larger patch size * fix typo * clarify variable names * trying to log graph * match example size with training * reuse globals * fix reference * log sample images from the first batch * wider model * low LR solution * fix path * seed everything * fix test dataset without masks * metrics solution this needs a new test dataset * fetch test data, compute metrics * byass cellpose import error due to numpy version conflicts * final exercise * moved files * fixed formatting - ready for review * viscy -> VisCy (#34) (#39) Introducing capitalization to highlight vision and single-cell aspects of the pipeline. * trying to log graph * log graph * black --------- Co-authored-by: Shalin Mehta <shalin.mehta@gmail.com> Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org> * fix channel dimension size for example input #40 * fix argument linking * 3D prediction writer sliding windows are blended with uniform average * update network diagram * upgrade flop counting * shallow 3D (2.5D) SSIM metric * ms-ssim * mixed loss * fix arguments * fix inheritance * fix weight checking * squeeze metric * aggregate metrics * optinal clamp to stabilize gradient of MS-SSIM * fix calling * increase epsilon * disable autocast for loss * restore relu for clamping * plot all architectures with network_diagram script --------- Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
* pixelshuffle decoder * Allow sampling multiple patches from the same stack (#35) * sample multiple patches from one stack * do not use type annotations from future it breaks jsonargparse * fix channel stacking for non-training samples * remove batch size from model the metrics will be automatically reduced by lightning * add flop counting script * 3d ouput head * add datamodule target dims mode * remove unused argument and configure drop path * move architecture argument to model level * DLMBL 2023 excercise (#36) * updated intro and paths * updated figures, tested data loader * setup.sh fetches correct dataset * finalized the exercise outline * semi-final exercise * parts 1 and 2 tested, part 3 outline ready * clearer variables, train with larger patch size * fix typo * clarify variable names * trying to log graph * match example size with training * reuse globals * fix reference * log sample images from the first batch * wider model * low LR solution * fix path * seed everything * fix test dataset without masks * metrics solution this needs a new test dataset * fetch test data, compute metrics * byass cellpose import error due to numpy version conflicts * final exercise * moved files * fixed formatting - ready for review * viscy -> VisCy (#34) (#39) Introducing capitalization to highlight vision and single-cell aspects of the pipeline. * trying to log graph * log graph * black --------- Co-authored-by: Shalin Mehta <shalin.mehta@gmail.com> Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org> * fix channel dimension size for example input #40 * fix argument linking * 3D prediction writer sliding windows are blended with uniform average * update network diagram * upgrade flop counting * shallow 3D (2.5D) SSIM metric * ms-ssim * mixed loss * fix arguments * fix inheritance * fix weight checking * squeeze metric * aggregate metrics * optinal clamp to stabilize gradient of MS-SSIM * fix calling * increase epsilon * disable autocast for loss * shuffle validation data for logging this hurts cache hit rate, but can avoid logging neighboring windows * simplify decoder structure * pop-head * fix head expansion * init conv weights * update diagnostic scripts * fix center slice metrics for 3D output (#51) * Configure the number of image samples logged at each epoch and batch (#49) * log sample size at epoch and batch levels * update example configs * do not shuffle validation dataset * fix upsampling weight initialization * fix merge * fix merge error * fix formatting --------- Co-authored-by: Shalin Mehta <shalin.mehta@gmail.com> Co-authored-by: Shalin Mehta <shalin.mehta@czbiohub.org>
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