Issues

• Step 2b/2c: reviewed member and non-member controls and specificity tests for the 15 Pfam families (task 04)

  stajichlab/adhesionPred#69 · Filter by author hyphaltip opened on Oct 7, 2026

• Repo hygiene: untracked scratch data and stray files in the working tree

  documentation
  stajichlab/adhesionPred#26 · Filter by author hyphaltip opened on Sep 30, 2026
  1

• Future category: fungal allergen sub-database (Alternaria and relatives)

  enhancement
  stajichlab/adhesionPred#19 · Filter by author hyphaltip opened on Sep 27, 2026

• NRP Nautilus: Nextflow k8s GPU pipeline to embed all Fungi_5k proteomes once -> S3

  enhancement
  stajichlab/adhesionPred#16 · Filter by author hyphaltip opened on Sep 27, 2026
  1

• Model v2: frozen ESM C / ESM-2 embeddings + architecture features (SignalP6, GPI, S/T, repeats, disorder, domains), calibrated; fine-tuning gated

  enhancement
  stajichlab/adhesionPred#15 · Filter by author hyphaltip opened on Sep 27, 2026
  2

• Curate hard negatives: non-adhesive GPI-CWPs, mucin-like sensors, S/T-rich secreted enzymes, laccases

  enhancement
  stajichlab/adhesionPred#14 · Filter by author hyphaltip opened on Sep 27, 2026
  4

• Curate an expanded fungal adhesin reference set with evidence levels (positives)

  enhancement
  stajichlab/adhesionPred#13 · Filter by author hyphaltip opened on Sep 27, 2026
  2

• Step 1 validation gaps: hard-negative FPR, per-genome precision vs curated inventories, calibration checks (tiers T0-T6)

  enhancement
  stajichlab/adhesionPred#12 · Filter by author hyphaltip opened on Sep 27, 2026
  3

• Handle proteins >1022 aa: sliding-window embeddings + N-terminal-domain embedding

  enhancement
  stajichlab/adhesionPred#10 · Filter by author hyphaltip opened on Sep 27, 2026
  1

• Save model bundle + model card (ESM model, layer, pooling, truncation, scaler, data hash); stop hard-coding repr layer 6

  enhancement
  stajichlab/adhesionPred#9 · Filter by author hyphaltip opened on Sep 27, 2026
  3