alfred-n/dIon-datasets

dIon paper datasets

Datasets used in dIon. See the paper for original source accessions, citations, and experiment definitions.

Dataset Cards

• pretraining/bacterial_ssl
• pretraining/metric_label_budgets
• probes/end_aa
• representation_benchmarks/bacterial
• representation_benchmarks/ninespecies
• representation_benchmarks/kingdoms
• representation_benchmarks/gleams_selection_metadata
• de_novo/corpora/MSKB-final
• de_novo/corpora/DNL-v1
• de_novo/kingdoms
• de_novo/online_mini_denovo_probe
• de_novo/dia_oracle_precursor_pilot
• auxiliary_spectrum_tasks/spectrum_quality
• auxiliary_spectrum_tasks/chimericity_hye
• auxiliary_spectrum_tasks/oxidized_methionine

Contents

• pretraining/: bacterial SSL corpus and used 1%/10% metric-learning subsets.
• probes/end_aa/: shared online end-AA monitor.
• representation_benchmarks/: full-charge and separately constructed charge-2-4 retrieval/pair benchmarks.
• de_novo/: MSKB-final, DNL-v1, capped Kingdoms, mini-de-novo probe, and DIA pilot.
• auxiliary_spectrum_tasks/: SQA, HYE chimericity, and oxidized-methionine tasks.

dataset_inventory.json lists the files included in this release.