Issues

• Threshold minimum precision is not configurable

  feature
  LadnerLab/PepSeqPred#88 · Filter by author jeffreyHoelzel opened on May 22, 2026

• --use-pos-weight in Optuna appears misleading

  bug
  LadnerLab/PepSeqPred#87 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Optuna best checkpoint copy path mismatch

  bug
  LadnerLab/PepSeqPred#86 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Raw protein sequence length is appended as an unnormalized feature

  mayberefactor
  LadnerLab/PepSeqPred#85 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Model has no local sequence modeling beyond ESM embeddings

  featurerefactor
  LadnerLab/PepSeqPred#84 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Grouped splits prevent family leakage but are not label-stratified

  refactor
  LadnerLab/PepSeqPred#83 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Threshold policy is hard-coded and can be overly conservative

  refactor
  LadnerLab/PepSeqPred#82 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Positive class weight is stale or fold-inappropriate

  refactor
  LadnerLab/PepSeqPred#81 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Training uses overlapping windows while evaluation uses full proteins

  bug
  LadnerLab/PepSeqPred#80 · Filter by author jeffreyHoelzel opened on May 22, 2026

• DDP and batch loss weighting are likely biased by local valid-residue counts

  bug
  LadnerLab/PepSeqPred#79 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Sparse or zero-valid windows still participate in training

  bug
  LadnerLab/PepSeqPred#78 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Label/objective mismatch for residue-level prediction

  mayberefactor
  LadnerLab/PepSeqPred#77 · Filter by author jeffreyHoelzel opened on May 22, 2026

• Figure out how to improve multi-dataset training

  bugfeature
  LadnerLab/PepSeqPred#74 · Filter by author jeffreyHoelzel opened on May 18, 2026
  

• docs: update webpage with results from new training

  choredocumentation
  LadnerLab/PepSeqPred#64 · Filter by author jeffreyHoelzel opened on May 3, 2026