| { |
| "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" |
| ] |
| } |
| } |
