Autotune with Ray Tune

[adamgayoso]

It should be relatively straightforward to create a new autotune module with Ray tune.

[adamgayoso]

@mjayasur and I discussed this on slack, but an acceptable initial API might do the following

auto = Autotune(adata, scvi.model.SCVI, name=name)
# set config
auto.set_hyperparam_space(dict(lr=...))
# set callback
auto.track_metrics(metrics_dict)
auto.add_scheduler(scheduler)
auto.add_reporter(reporter)
# runs tune.run
auto()

which could then be wrapped with functions like

# wraps code snippet above
best_model_instance = autotune_scvi(adata, hyperparm_space: Optional[dict] = None, scheduler=None, reporter=None)

[mjayasur]

dummy metric function:

• do something dumb

silhouette metric function:

• get latent representation from model
• scanpy neighbors
• scanpy leiden cluster
• get the leiden, then compute the silhouette with respect to the latent representation

[martinkim0]

Closing issue because of #1565.