neuralbioinfo/all-nr-plasmid-training-public

All-NR Clean Plasmid 50Mbp 1:4 Top50-Switchable Dataset actL4000

This public all-NR plasmid-vs-host training dataset is freshly sampled from the clean NR profile skani_minaf80_ani99_afsym97p5_affull99_afpart95. It is not derived from a curr1 dataset. Plasmid sampling uses a 50Mbp host-genus budget and the strict training_clean config targets four clean host negatives per sampleable plasmid-positive segment after minimap2 filtering.

This upload was produced with config group switchable_top50_pool_only. In the default training_clean_only group, only the strict training dataset is published as a Hugging Face config. Summary and audit tables are kept locally beside the generated dataset rather than uploaded as public configs.

Generated: 2026-06-15 13:30:41 CEST

Repository: neuralbioinfo/all-nr-plasmid-training-public

Contents

Config Semantics

Loading

from datasets import load_dataset

dataset = load_dataset(
    "neuralbioinfo/all-nr-plasmid-training-public",
    name="allnr_nr97p5_l200k_tsh50m_up5_down0p25_hc2p5_mm_p1h4_top50tag_actL4000_training_switchable_top50_pool",
    split="train",
)

For top50-driver ablation with training_switchable_top50_pool, drop positive rows where top50_host_hit_driver_positive=True, keep host rows where filtered_by_non_top50_plasmid=False, and then sample the requested host:plasmid ratio for training.

Local Summaries Not Uploaded As Configs

The following local outputs are retained under /project/c_evolm/training_datasets/phage_db/plasmids/ncbi/TrainingSamples/plasmid_allnr_nr97p5_l200k_tsh50m_up5_down0p25_hc2p5_mm_p1h4_top50tag for audit and debugging:

• —manifests/dataset_manifest.json
• —checks/minimap_filtering_summary.*
• —checks/final_dataset_summary.feather
• —checks/genus_balance_summary.feather
• —checks/top50_host_hit_driver_plasmids.feather
• —checks/top50_switchable_summary.feather
• —hf_upload/upload_summary.json

Key Counts

Sampling Parameters

Validation