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cdskit localize peroxisome head

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Kenji Fukushima edited this page Jul 21, 2026 · 2 revisions

cdskit localize peroxisome head

p_peroxisome is available in the experimental prerelease model cdskit-localize-targeting5-perox-deeploc21-et-v1.pt, registered under the alias targeting5-perox-deeploc21-et-v1. When that alias is used with cdskit localize --model, CDSKIT downloads the model from GitHub Releases into the local model cache if it is not already present and verifies its SHA-256 checksum.

cdskit localize \
  --seq_file proteins.faa \
  --seq_type protein \
  --model targeting5-perox-deeploc21-et-v1 \
  --organism_group non_plant \
  --report localize.tsv

The peroxisome head is a CPU-runtime scikit-learn ExtraTrees classifier trained on DeepLoc21 Swiss-Prot train/validation rows with sequence-level features, including C-terminal PTS-like features. Interpret it as a peroxisome sequence-label probability that is strongest for PTS-like targeting signals, not as a general peroxisome-associated localization detector.

Release asset

Fairness checks

  • External accession and exact-sequence overlap are excluded or reported.
  • A constant-zero baseline and a regex PTS baseline are reported.
  • MMseqs homology subsets and cluster out-of-fold evaluation are used to expose similarity-driven optimism.
  • HPA is kept as a difficult broad-localization stress test.

Candidate comparison

The current candidate uses ExtraTrees because it improved the independent external and cluster-OOF checks compared with the earlier HGB candidate, while keeping inference CPU-only.

Candidate UniProt external AUPRC UniProt external F1 Cluster OOF AUPRC Cluster OOF F1 HPA stress AUPRC HPA stress F1
HGB, perox_sequence_v1 0.239 0.293 0.191 0.212 0.007 0.000
HGB, broad_localize_v1 0.209 0.302 0.125 0.142 - -
ExtraTrees, perox_sequence_v1 0.256 0.370 0.246 0.277 0.149 0.250

Evaluation snapshot

Model / evaluation Rows Positives AUPRC AUROC F1 Notes
DeepLoc21 validation, perox head 5,462 53 0.482 0.895 0.583 threshold tuned on DeepLoc21 fold_id=4
DeepLoc21 validation, regex PTS 5,462 53 0.080 0.765 0.217 simple PTS1/PTS2 signal baseline
UniProt experimental CC external, perox head 11,395 138 0.256 0.847 0.370 no accession/exact-sequence overlap with DeepLoc21 training
UniProt experimental CC external, regex PTS 11,395 138 0.041 0.642 0.156 same external rows
UniProt experimental CC cluster OOF, perox head 11,395 138 0.246 0.854 0.277 MMseqs clusters at 30% identity / 80% coverage
HPA external stress test, DeepLoc21-trained perox head 1,717 7 0.149 0.665 0.250 broad peroxisome-associated task; no positive homology hits

These results support replacing the previous constant-zero p_peroxisome placeholder for signal-like use cases, but they do not yet support advertising the head as a broad peroxisome-localization model.

Reproduce

Main candidate model and UniProt experimental CC external benchmark:

python -m cdskit.perox_benchmark \
  --training_tsv data/localize_bench/deeploc21/deeploc21_localization_train_validation.tsv \
  --external_test_tsv data/localize_bench/eukaryota_full_with_lineage.tsv \
  --external_format uniprot_exp_cc \
  --feature_profile perox_sequence_v1 \
  --model_kind extra_trees \
  --base_model targeting5 \
  --model_out data/localize_bench/perox_deeploc21_et_v1/cdskit-localize-targeting5-perox-deeploc21-et-v1.pt \
  --out_json data/localize_bench/perox_deeploc21_et_v1/perox_benchmark_uniprot_exp_external.json \
  --out_md data/localize_bench/perox_deeploc21_et_v1/perox_benchmark_uniprot_exp_external.md \
  --predictions_prefix data/localize_bench/perox_deeploc21_et_v1/perox_predictions_uniprot_exp \
  --homology_check yes \
  --homology_threads 4 \
  --cluster_oof yes \
  --cluster_oof_source external \
  --cluster_oof_folds 5 \
  --cluster_oof_method mmseqs

HPA stress test for the same DeepLoc21-trained candidate:

python -m cdskit.perox_benchmark \
  --training_tsv data/localize_bench/deeploc21/deeploc21_localization_train_validation.tsv \
  --external_test_tsv data/localize_bench/deeploc21/deeploc21_hpa_test.tsv \
  --external_format prepared \
  --feature_profile perox_sequence_v1 \
  --model_kind extra_trees \
  --homology_check yes \
  --homology_threads 4 \
  --out_json data/localize_bench/perox_deeploc21_et_v1/perox_benchmark_hpa_external.json \
  --out_md data/localize_bench/perox_deeploc21_et_v1/perox_benchmark_hpa_external.md \
  --predictions_prefix data/localize_bench/perox_deeploc21_et_v1/perox_predictions_hpa

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