README.md

metadata

language:
  - en
license: cc-by-4.0
task_categories:
  - text-generation
  - token-classification
  - question-answering
tags:
  - biology
  - kluyveromyces-marxianus
  - yeast
  - genomics
  - proteomics
  - bioinformatics
size_categories:
  - 10K<n<100K
dataset_info:
  features:
    - name: id
      dtype: string
    - name: source
      dtype: string
    - name: category
      dtype: string
    - name: gene_id
      dtype: string
    - name: gene_name
      dtype: string
    - name: gene_symbol
      dtype: string
    - name: protein_id
      dtype: string
    - name: protein_name
      dtype: string
    - name: sequence
      dtype: string
    - name: title
      dtype: string
    - name: abstract
      dtype: string
    - name: full_text
      dtype: string
    - name: pmid
      dtype: string
    - name: doi
      dtype: string
    - name: authors
      dtype: string
    - name: journal
      dtype: string
    - name: year
      dtype: string
    - name: timestamp
      dtype: string
  splits:
    - name: validation
      num_bytes: 50247
      num_examples: 50
    - name: test
      num_bytes: 26233
      num_examples: 25
    - name: train
      num_bytes: 181691
      num_examples: 98
  download_size: 778393
  dataset_size: 258171
configs:
  - config_name: default
    data_files:
      - split: train
        path: cell3_semantic/train-*
      - split: validation
        path: cell2_splits/validation-*
      - split: test
        path: cell2_splits/test-*

🧬 Kluyveromyces marxianus Quantum Dataset v10.0.0

Overview

Comprehensive multi-omics dataset for Kluyveromyces marxianus collected using quantum-grade async streaming pipeline, fully integrated with Cell 0's structured directory system.

Statistics

Metric	Value
Total Collected	3,836
Total Local Saved	3,836
Version	v10.0.0
Collection Date	2025-11-10

Data Categories & Local Storage

• Literature: 1,417 records (local: 1,417)
• Proteins: 1,001 records (local: 1,001)
• PMC Full-Text: 1,000 records (local: 1,000)
• SRA Sequencing: 352 records (local: 352)
• GEO Expression: 48 records (local: 48)
• Nucleotide Sequences: 18 records (local: 18)

Cell 0 Integration

This dataset strictly respects Cell 0's directory structure. Only folders actively used by collectors:

km_dataset/
├── genomic/          # Genes, nucleotide sequences
├── protein/          # Protein sequences
├── literature/       # PubMed, PMC articles
├── expression/       # GEO, SRA sequencing data
└── checkpoints/
    └── cell1_quantum/  # Collection checkpoints

Note: Cell 0 also creates pathway/, interaction/, structure/, repository/ folders, but current collectors don't produce data for these categories yet.

HuggingFace Organization

Data is organized by phase using data_dir to prevent overwrites:

• cell1_genes - Gene data
• cell1_proteins - Protein sequences
• cell1_literature - PubMed articles
• cell1_pmc - PMC full-text articles
• cell1_sequences - Nucleotide sequences
• cell1_geo - GEO expression data
• cell1_sra - SRA sequencing data
• cell1_splits - Train/validation/test splits

Usage

Load All Data

from datasets import load_dataset, concatenate_datasets

# Load all phases (FIXED: correct data_dir names)
all_data = []
for phase in ['cell1_genes', 'cell1_proteins', 'cell1_literature',
              'cell1_pmc', 'cell1_sequences', 'cell1_geo', 'cell1_sra']:
    try:
        ds = load_dataset("Milad96/Kluyveromyces-marxianus", split='train', data_dir=phase)
        all_data.append(ds)
    except:
        pass

combined = concatenate_datasets(all_data)

Load Specific Phase

# Load only genes
genes = load_dataset("Milad96/Kluyveromyces-marxianus", split='train', data_dir='cell1_genes')

# Load only literature
literature = load_dataset("Milad96/Kluyveromyces-marxianus", split='train', data_dir='cell1_literature')

Load Splits

dataset = load_dataset("Milad96/Kluyveromyces-marxianus", data_dir='cell1_splits')
train = dataset['train']
val = dataset.get('validation')
test = dataset.get('test')

Citation

@dataset{km_quantum_v10_0_0,
  title={Kluyveromyces marxianus Quantum Dataset},
  version={v10.0.0},
  year={2025},
  url={https://huggingface.co/datasets/Milad96/Kluyveromyces-marxianus}
}

Status: ✅ Production Ready Quality: 🌟 Quantum Grade Pipeline: Async Streaming v10.0 + Cell 0 Full Integration Local Storage: ✅ All records saved in structured folders Overwrite Protection: ✅ Phase-specific data_dirs