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CASCADE-LUCA

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CASCADE-LUCA
File size: 1,701 Bytes
177024c
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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{
  "dataset": "LUCA",
  "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": 14847,
  "max_length_up": 1024,
  "max_length_down": 1024,
  "temperature": 0.1,
  "seed": 20,
  "training_epoch": 1,
  "training_global_step": 400000,
  "data_composition": {
    "diseases": [
      "chronic obstructive pulmonary disease",
      "lung adenocarcinoma",
      "non-small cell lung carcinoma",
      "normal",
      "squamous cell lung carcinoma"
    ],
    "tissues": [
      "adrenal tissue",
      "brain",
      "liver",
      "lung",
      "lymph node",
      "pleural effusion"
    ],
    "cell_type_ontology_ids": [
      "CL:0000077",
      "CL:0000082",
      "CL:0000097",
      "CL:0000158",
      "CL:0000192",
      "CL:0000235",
      "CL:0000236",
      "CL:0000451",
      "CL:0000499",
      "CL:0000583",
      "CL:0000623",
      "CL:0000624",
      "CL:0000625",
      "CL:0000669",
      "CL:0000763",
      "CL:0000775",
      "CL:0000784",
      "CL:0000786",
      "CL:0000815",
      "CL:0000860",
      "CL:0000875",
      "CL:0000990",
      "CL:0001064",
      "CL:0002062",
      "CL:0002063",
      "CL:0002138",
      "CL:0002144",
      "CL:0002399",
      "CL:0002543",
      "CL:0002553",
      "CL:0005012",
      "CL:1001568",
      "CL:2000093"
    ]
  }
}