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matsen committed May 21, 2024
1 parent 0db8ea0 commit 9d3b814
Showing 1 changed file with 5 additions and 2 deletions.
7 changes: 5 additions & 2 deletions netam/framework.py
Original file line number Diff line number Diff line change
Expand Up @@ -649,8 +649,11 @@ def joint_train(self, epochs=100, cycle_count=2, training_method="full"):
If training_method is "yun", then we use Yun's approximation to the branch lengths.
If training_method is "fixed", then we fix the branch lengths and only optimize the model.
We reset the optimization after each cycle, and we use a learning rate schedule that
uses a weighted geometric mean of the current learning rate and the initial learning rate that progressively moves towards keeping the current learning rate as the cycles progress.
We reset the optimization after each cycle, and we use a learning rate
schedule that uses a weighted geometric mean of the current learning
rate and the initial learning rate that progressively moves towards
keeping the current learning rate as the cycles progress.
"""
if training_method == "full":
optimize_branch_lengths = self.standardize_and_optimize_branch_lengths
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