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Commits on Apr 25, 2024

• Update README.

  dnbaker

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Commits on Sep 28, 2023

• Skip first softplus, allowing negative off-diagonal covariances.

  PB-DB

  committed
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Commits on Sep 26, 2023

• Correct mean/variance for negative binomial. Small cleanups.

  PB-DB

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• Cleanup.

  dnbaker

  committed
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Commits on Sep 24, 2023

• Simplify some aspects, plan future ones.

  dnbaker

  committed
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• Relative variance-scaled reconstruction (higher-variance genes more important). Try to simplify encoding.

  dnbaker

  committed
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Commits on Aug 18, 2023

• Some rust cleanup.

  dnbaker

  committed
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• Track classification loss with -C even if not trained. TODO: classification loss, mean covariance matrix, and outputting trained model evaluations, not just the model.

  dnbaker

  committed
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Commits on Jul 7, 2023

• Correction to labeled_unpack. Fleshed-out examples.

  dnbaker

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Commits on Jul 6, 2023

• Clean up + docs.

  dnbaker

  committed
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Commits on Jun 7, 2023

• Update README

  dnbaker

  committed
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Commits on Jun 6, 2023

• Update readme.md

  dnbaker

  committed
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• Working classification loss incorporation. Supporting both binary cross entropy and cross entropy with logits.

  dnbaker

  committed
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Commits on May 27, 2023

• Merge pull request #1 from dnbaker/cat

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  dnbaker

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• Updates:

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  dnbaker

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Commits on May 20, 2023

• Save work: mostly plugged in for categorical variables for batch correction.

  dnbaker

  committed
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• Reorganize, rename to scavenger. Still working to understand how to define and dispatch the equivariant ND model.

  dnbaker

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Commits on May 13, 2023

• Save

  dnbaker

  committed
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• Working full-covariance latent gaussian. Yields substantally better reconstruction. Can deploy in rust thanks to tch::CModule.

  dnbaker

  committed
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• Add code for parsing data from aquiladb for spatial tx

  dnbaker

  committed
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Commits on May 11, 2023

• Add pt convert code + spatial parsing code.

  dnbaker

  committed
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Commits on May 4, 2023

• Update for new tch version, and add program (from-cmodule-zinb) which uses a jit-compiled CModule.

  dnbaker

  committed
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Commits on Apr 29, 2023

• Start experiment sweeping parameters.

  dnbaker

  committed
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Commits on Apr 28, 2023

• Finishedfull cov in python

  dnbaker

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• Save: refactor that does covar, at last in no covar branch.

  dnbaker

  committed
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• Added KL divergence for full gaussian. Nearly complete; need to handle unpacking for the full diag case.

  dnbaker

  committed
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Commits on Apr 27, 2023

• Simplify, work to generalize to full cov.

  dnbaker

  committed
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• UNet

  dnbaker

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Commits on Apr 26, 2023

• mean/var for nb

  dnbaker

  committed
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Commits on Apr 25, 2023

• Save changes. 1: successful jit trace save (needed to freeze the VariantStore)

  dnbaker

  committed
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• Remove logging.

  dnbaker

  committed
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• Add csr mode.

  dnbaker

  committed
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• Trainable module that can be shared with pytorch!

  dnbaker

  committed
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Commits on Apr 20, 2023

• Add loader for sparse matrix! Now we can lazily expand sparse submatrices.

  dnbaker

  committed
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• save

  dnbaker

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