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Benchmark whichmut dense vs sparse formats for re-implementation decision

Status: Open.

#171 In matsengrp/netam;

· jaredgalloway opened on Oct 17, 2025

Feature: Fine-grained nucleotide-level masking for problematic sites in whichmut loss

enhancementNew feature or requestNew feature or request

Status: Open.

#170 In matsengrp/netam;

· jaredgalloway opened on Oct 15, 2025

Bug: SparseWhichmutCodonDataset.compute_neutral_rates_from_sequences produces incorrect tensor format

Status: Open.

#169 In matsengrp/netam;

· jaredgalloway opened on Oct 15, 2025

Enhancement: Add Early Stopping and Learning Rate Scheduling to WhichmutTrainer

Status: Open.

#160 In matsengrp/netam;

· jaredgalloway opened on Aug 12, 2025

Removed failing test_neutral_probs and test_selection_probs from test_simulation.py

Status: Open.

#153 In matsengrp/netam;

· jaredgalloway opened on Jul 28, 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

What is up with the right hand side of the SHM model predictions?

Status: Open.

#15 In matsengrp/netam;

· matsen opened on Mar 21, 2024