biocore / biocore/mmvec

Better summaries

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Python
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Description

In the old version of mmvec, we stored histograms of the parameters - this has not been added into pytorch yet.

I'm thinking this maybe a good time to refine what sort of summaries should be stored.
We can easily enable anything listed on this [tutorial](https://tensorboardx.readthedocs.io/en/latest/tutorial.html), for example

- [ ] Histograms of all model parameters
- [ ] Histograms of all gradients
- [ ] Tensorboard embeddings - this would a cheap way to enable search-ability across points / metadata (see here: https://github.com/biocore/emperor/issues/710 @ElDeveloper )
- [ ] Display images of molecular structures - should be possible to tack on top of embeddings provided we have a mapping from images to ms2 ids @lfnothias @mwang87

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Research direction

The issue names no files or tests; start by reviewing the current PyTorch summary or logging integration and the linked TensorBoard tutorial. First agree which summaries are in scope, then verify that the selected parameter, gradient, embedding, or molecular-image summaries appear in TensorBoard with the needed metadata.

Written by the indexing model from the issue text.

Assessment

Tech stack
python, pytorch
Domain
data-visualization, machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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