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Enhancement: Add Early Stopping and Learning Rate Scheduling to WhichmutTrainer

Status: Open.

#160 In matsengrp/netam;

· jgallowa07 opened on Aug 12, 2025

Optimize whichmut loss computation with vectorized implementation

Status: Open.

#158 In matsengrp/netam;

· jgallowa07 opened on Jul 30, 2025

Migrate from flake8/black/docformatter to ruff for improved linting and formatting

Status: Open.

#155 In matsengrp/netam;

· matsen opened on Jul 29, 2025

Removed failing test_neutral_probs and test_selection_probs from test_simulation.py

Status: Open.

#153 In matsengrp/netam;

· jgallowa07 opened on Jul 28, 2025

Implement Whichmut Trainer and Loss Function

Status: Open.

#152 In matsengrp/netam;

· matsen opened on Jul 13, 2025

src_key_padding_mask and ambiguities at 4-fold degenerate sites

Status: Open.

#139 In matsengrp/netam;

· willdumm opened on May 29, 2025

Assertion message when checking pcp's

Status: Open.

#136 In matsengrp/netam;

· jgallowa07 opened on May 22, 2025

Independent code paths for codon probability computations

Status: Open.

#134 In matsengrp/netam;

· willdumm opened on Apr 23, 2025

Learning rate and stopping criterion

Status: Open.

#101 In matsengrp/netam;

· matsen opened on Dec 18, 2024

Cleanup

Status: Open.

#97 In matsengrp/netam;

· matsen opened on Dec 13, 2024

Try rotary positional embedding

Status: Open.

#37 In matsengrp/netam;

· matsen opened on Jun 12, 2024

Consider having a separate parent and a child mask

Status: Open.

#16 In matsengrp/netam;

· matsen opened on Apr 18, 2024