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CASCADE-HLCA

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CASCADE-HLCA
File size: 2,352 Bytes
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{
  "dataset": "HLCA",
  "architecture": "TransformerGenerator",
  "d_model": 384,
  "nhead": 6,
  "nlayers": 12,
  "dim_embedding": 384,
  "dropout": 0.1,
  "nclass": 2,
  "pad_token": "<pad>",
  "cell_emb_style": "avg-pool",
  "context_specific_projections": true,
  "constant_ctx": false,
  "only_contrastive": true,
  "DA": true,
  "lambda_sinkhorn": 0.005,
  "contexts": [
    "disease",
    "cell_type",
    "tissue"
  ],
  "merged_contexts": "disease_cell_type_tissue",
  "vocab_size": 18711,
  "max_length_up": 1024,
  "max_length_down": 1024,
  "temperature": 0.1,
  "seed": 20,
  "training_epoch": 2,
  "training_global_step": 3682000,
  "data_composition": {
    "diseases": [
      "COVID-19",
      "chronic obstructive pulmonary disease",
      "chronic rhinitis",
      "cystic fibrosis",
      "hypersensitivity pneumonitis",
      "interstitial lung disease",
      "lung adenocarcinoma",
      "lung large cell carcinoma",
      "lymphangioleiomyomatosis",
      "non-specific interstitial pneumonia",
      "normal",
      "pleomorphic carcinoma",
      "pneumonia",
      "pulmonary fibrosis",
      "pulmonary sarcoidosis",
      "squamous cell lung carcinoma"
    ],
    "tissues": [
      "lung",
      "lung parenchyma",
      "nose",
      "respiratory airway"
    ],
    "cell_type_ontology_ids": [
      "CL:0000037",
      "CL:0000057",
      "CL:0000077",
      "CL:0000084",
      "CL:0000097",
      "CL:0000158",
      "CL:0000186",
      "CL:0000192",
      "CL:0000236",
      "CL:0000313",
      "CL:0000319",
      "CL:0000451",
      "CL:0000499",
      "CL:0000583",
      "CL:0000622",
      "CL:0000623",
      "CL:0000624",
      "CL:0000625",
      "CL:0000784",
      "CL:0000786",
      "CL:0000860",
      "CL:0000861",
      "CL:0000875",
      "CL:0000990",
      "CL:0002062",
      "CL:0002063",
      "CL:0002075",
      "CL:0002138",
      "CL:0002144",
      "CL:0002145",
      "CL:0002399",
      "CL:0002480",
      "CL:0002543",
      "CL:0002632",
      "CL:0002633",
      "CL:0005006",
      "CL:0005012",
      "CL:0009089",
      "CL:0010003",
      "CL:0019001",
      "CL:0019003",
      "CL:0019019",
      "CL:1000223",
      "CL:1000312",
      "CL:1001568",
      "CL:1001603",
      "CL:2000093",
      "CL:4028004",
      "CL:4028006",
      "CL:4030023",
      "unknown"
    ]
  }
}