Add files using upload-large-folder tool

README.md

@@ -30,12 +30,12 @@ Model files are stored under `models/`:
 
 * `models/sfm_config.json`
 * `models/sfm_model.safetensors`
+* `models/cond_dict.json`
 * `models/vocab.json`
 * `models/vocab.safetensors`
 
-Supporting CSV resources such as `cond_dict.csv`, `human_tfs.csv`, `mouse_tfs.csv`, `OmniPath.csv`, and `homologous.csv` stay at the repository root.
+Supporting CSV resources such as `human_tfs.csv`, `mouse_tfs.csv`, `OmniPath.csv`, and `homologous.csv` stay at the repository root.
 
 The source code, training pipeline, and full documentation are maintained in the GitHub repository:
 
 * https://github.com/Catchxu/scCAFM
-

models/cond_dict.json

@@ -0,0 +1,710 @@
+[
+  {
+    "cond_value": "<unk>",
+    "token_index": 0
+  },
+  {
+    "cond_value": "10x 3' v3",
+    "token_index": 1
+  },
+  {
+    "cond_value": "10x 3' v2",
+    "token_index": 2
+  },
+  {
+    "cond_value": "seq-well",
+    "token_index": 3
+  },
+  {
+    "cond_value": "10x 5' v2",
+    "token_index": 4
+  },
+  {
+    "cond_value": "10x 5' v1",
+    "token_index": 5
+  },
+  {
+    "cond_value": "human",
+    "token_index": 6
+  },
+  {
+    "cond_value": "blood",
+    "token_index": 7
+  },
+  {
+    "cond_value": "umbilical cord blood",
+    "token_index": 8
+  },
+  {
+    "cond_value": "normal",
+    "token_index": 9
+  },
+  {
+    "cond_value": "drop-seq",
+    "token_index": 10
+  },
+  {
+    "cond_value": "brain",
+    "token_index": 11
+  },
+  {
+    "cond_value": "left frontal lobe",
+    "token_index": 12
+  },
+  {
+    "cond_value": "left temporal lobe",
+    "token_index": 13
+  },
+  {
+    "cond_value": "right temporal lobe",
+    "token_index": 14
+  },
+  {
+    "cond_value": "forebrain",
+    "token_index": 15
+  },
+  {
+    "cond_value": "right frontal lobe",
+    "token_index": 16
+  },
+  {
+    "cond_value": "frontal lobe",
+    "token_index": 17
+  },
+  {
+    "cond_value": "parietal lobe",
+    "token_index": 18
+  },
+  {
+    "cond_value": "temporal lobe",
+    "token_index": 19
+  },
+  {
+    "cond_value": "occipital lobe",
+    "token_index": 20
+  },
+  {
+    "cond_value": "glioblastoma",
+    "token_index": 21
+  },
+  {
+    "cond_value": "cerebral nuclei",
+    "token_index": 22
+  },
+  {
+    "cond_value": "cerebral cortex",
+    "token_index": 23
+  },
+  {
+    "cond_value": "dorsolateral prefrontal cortex",
+    "token_index": 24
+  },
+  {
+    "cond_value": "thalamic complex",
+    "token_index": 25
+  },
+  {
+    "cond_value": "primary motor cortex",
+    "token_index": 26
+  },
+  {
+    "cond_value": "hypothalamus",
+    "token_index": 27
+  },
+  {
+    "cond_value": "hippocampal formation",
+    "token_index": 28
+  },
+  {
+    "cond_value": "midbrain",
+    "token_index": 29
+  },
+  {
+    "cond_value": "pons",
+    "token_index": 30
+  },
+  {
+    "cond_value": "myelencephalon",
+    "token_index": 31
+  },
+  {
+    "cond_value": "cerebellum",
+    "token_index": 32
+  },
+  {
+    "cond_value": "gexscope technology",
+    "token_index": 33
+  },
+  {
+    "cond_value": "indrop",
+    "token_index": 34
+  },
+  {
+    "cond_value": "bd rhapsody whole transcriptome analysis",
+    "token_index": 35
+  },
+  {
+    "cond_value": "lung",
+    "token_index": 36
+  },
+  {
+    "cond_value": "squamous cell lung carcinoma",
+    "token_index": 37
+  },
+  {
+    "cond_value": "lung adenocarcinoma",
+    "token_index": 38
+  },
+  {
+    "cond_value": "non-small cell lung carcinoma",
+    "token_index": 39
+  },
+  {
+    "cond_value": "middle temporal gyrus",
+    "token_index": 40
+  },
+  {
+    "cond_value": "substantia nigra pars compacta",
+    "token_index": 41
+  },
+  {
+    "cond_value": "breast",
+    "token_index": 42
+  },
+  {
+    "cond_value": "10x 5' transcription profiling",
+    "token_index": 43
+  },
+  {
+    "cond_value": "lung parenchyma",
+    "token_index": 44
+  },
+  {
+    "cond_value": "lower lobe of left lung",
+    "token_index": 45
+  },
+  {
+    "cond_value": "upper lobe of left lung",
+    "token_index": 46
+  },
+  {
+    "cond_value": "brodmann (1909) area 4",
+    "token_index": 47
+  },
+  {
+    "cond_value": "prefrontal cortex",
+    "token_index": 48
+  },
+  {
+    "cond_value": "orbitofrontal cortex",
+    "token_index": 49
+  },
+  {
+    "cond_value": "anterior cingulate cortex",
+    "token_index": 50
+  },
+  {
+    "cond_value": "primary visual cortex",
+    "token_index": 51
+  },
+  {
+    "cond_value": "microwell-seq",
+    "token_index": 52
+  },
+  {
+    "cond_value": "smart-seq v4",
+    "token_index": 53
+  },
+  {
+    "cond_value": "mouse",
+    "token_index": 54
+  },
+  {
+    "cond_value": "brain meninx",
+    "token_index": 55
+  },
+  {
+    "cond_value": "sci-rna-seq",
+    "token_index": 56
+  },
+  {
+    "cond_value": "telencephalon",
+    "token_index": 57
+  },
+  {
+    "cond_value": "parietal cortex",
+    "token_index": 58
+  },
+  {
+    "cond_value": "visual cortex",
+    "token_index": 59
+  },
+  {
+    "cond_value": "entorhinal cortex",
+    "token_index": 60
+  },
+  {
+    "cond_value": "primary somatosensory cortex",
+    "token_index": 61
+  },
+  {
+    "cond_value": "agranular insular cortex",
+    "token_index": 62
+  },
+  {
+    "cond_value": "subicular complex",
+    "token_index": 63
+  },
+  {
+    "cond_value": "retrosplenial granular cortex",
+    "token_index": 64
+  },
+  {
+    "cond_value": "posterior parietal association areas",
+    "token_index": 65
+  },
+  {
+    "cond_value": "auditory cortex",
+    "token_index": 66
+  },
+  {
+    "cond_value": "temporal cortex",
+    "token_index": 67
+  },
+  {
+    "cond_value": "medial orbital frontal cortex",
+    "token_index": 68
+  },
+  {
+    "cond_value": "lateral visual area",
+    "token_index": 69
+  },
+  {
+    "cond_value": "caudate nucleus",
+    "token_index": 70
+  },
+  {
+    "cond_value": "putamen",
+    "token_index": 71
+  },
+  {
+    "cond_value": "primary auditory cortex",
+    "token_index": 72
+  },
+  {
+    "cond_value": "angular gyrus",
+    "token_index": 73
+  },
+  {
+    "cond_value": "right cardiac atrium",
+    "token_index": 74
+  },
+  {
+    "cond_value": "interventricular septum",
+    "token_index": 75
+  },
+  {
+    "cond_value": "apex of heart",
+    "token_index": 76
+  },
+  {
+    "cond_value": "heart left ventricle",
+    "token_index": 77
+  },
+  {
+    "cond_value": "heart right ventricle",
+    "token_index": 78
+  },
+  {
+    "cond_value": "left cardiac atrium",
+    "token_index": 79
+  },
+  {
+    "cond_value": "smart-seq",
+    "token_index": 80
+  },
+  {
+    "cond_value": "smart-seq2",
+    "token_index": 81
+  },
+  {
+    "cond_value": "diencephalon",
+    "token_index": 82
+  },
+  {
+    "cond_value": "brain gray matter",
+    "token_index": 83
+  },
+  {
+    "cond_value": "brain white matter",
+    "token_index": 84
+  },
+  {
+    "cond_value": "barrel cortex",
+    "token_index": 85
+  },
+  {
+    "cond_value": "cerebellar hemisphere",
+    "token_index": 86
+  },
+  {
+    "cond_value": "frontal cortex",
+    "token_index": 87
+  },
+  {
+    "cond_value": "trudrop",
+    "token_index": 88
+  },
+  {
+    "cond_value": "liver",
+    "token_index": 89
+  },
+  {
+    "cond_value": "lower lobe of right lung",
+    "token_index": 90
+  },
+  {
+    "cond_value": "upper lobe of right lung",
+    "token_index": 91
+  },
+  {
+    "cond_value": "right lung",
+    "token_index": 92
+  },
+  {
+    "cond_value": "left lung",
+    "token_index": 93
+  },
+  {
+    "cond_value": "middle lobe of right lung",
+    "token_index": 94
+  },
+  {
+    "cond_value": "transverse colon",
+    "token_index": 95
+  },
+  {
+    "cond_value": "sigmoid colon",
+    "token_index": 96
+  },
+  {
+    "cond_value": "descending colon",
+    "token_index": 97
+  },
+  {
+    "cond_value": "ascending colon",
+    "token_index": 98
+  },
+  {
+    "cond_value": "hepatic flexure of colon",
+    "token_index": 99
+  },
+  {
+    "cond_value": "hepatic cecum",
+    "token_index": 100
+  },
+  {
+    "cond_value": "rectum",
+    "token_index": 101
+  },
+  {
+    "cond_value": "kidney",
+    "token_index": 102
+  },
+  {
+    "cond_value": "lymph node",
+    "token_index": 103
+  },
+  {
+    "cond_value": "blastoma",
+    "token_index": 104
+  },
+  {
+    "cond_value": "colorectal cancer",
+    "token_index": 105
+  },
+  {
+    "cond_value": "tubular adenoma",
+    "token_index": 106
+  },
+  {
+    "cond_value": "tubulovillous adenoma",
+    "token_index": 107
+  },
+  {
+    "cond_value": "clear cell renal carcinoma",
+    "token_index": 108
+  },
+  {
+    "cond_value": "renal papilla",
+    "token_index": 109
+  },
+  {
+    "cond_value": "cortex of kidney",
+    "token_index": 110
+  },
+  {
+    "cond_value": "renal medulla",
+    "token_index": 111
+  },
+  {
+    "cond_value": "cingulate cortex",
+    "token_index": 112
+  },
+  {
+    "cond_value": "split-seq",
+    "token_index": 113
+  },
+  {
+    "cond_value": "10x 3' transcription profiling",
+    "token_index": 114
+  },
+  {
+    "cond_value": "strt-seq",
+    "token_index": 115
+  },
+  {
+    "cond_value": "pleural effusion",
+    "token_index": 116
+  },
+  {
+    "cond_value": "adrenal gland",
+    "token_index": 117
+  },
+  {
+    "cond_value": "axilla",
+    "token_index": 118
+  },
+  {
+    "cond_value": "bone spine",
+    "token_index": 119
+  },
+  {
+    "cond_value": "right parietal lobe",
+    "token_index": 120
+  },
+  {
+    "cond_value": "temporoparietal junction",
+    "token_index": 121
+  },
+  {
+    "cond_value": "left parietal lobe",
+    "token_index": 122
+  },
+  {
+    "cond_value": "small cell lung carcinoma",
+    "token_index": 123
+  },
+  {
+    "cond_value": "body of stomach",
+    "token_index": 124
+  },
+  {
+    "cond_value": "gastric cancer",
+    "token_index": 125
+  },
+  {
+    "cond_value": "lateral entorhinal cortex",
+    "token_index": 126
+  },
+  {
+    "cond_value": "retrosplenial region",
+    "token_index": 127
+  },
+  {
+    "cond_value": "anterolateral visual area",
+    "token_index": 128
+  },
+  {
+    "cond_value": "secondary somatosensory cortex",
+    "token_index": 129
+  },
+  {
+    "cond_value": "medial entorhinal cortex",
+    "token_index": 130
+  },
+  {
+    "cond_value": "gustatory cortex",
+    "token_index": 131
+  },
+  {
+    "cond_value": "claustrum of brain",
+    "token_index": 132
+  },
+  {
+    "cond_value": "caudate lobe of liver",
+    "token_index": 133
+  },
+  {
+    "cond_value": "occipital cortex",
+    "token_index": 134
+  },
+  {
+    "cond_value": "renal pelvis",
+    "token_index": 135
+  },
+  {
+    "cond_value": "kidney blood vessel",
+    "token_index": 136
+  },
+  {
+    "cond_value": "heart",
+    "token_index": 137
+  },
+  {
+    "cond_value": "scalebio single cell rna sequencing",
+    "token_index": 138
+  },
+  {
+    "cond_value": "10x 3' v1",
+    "token_index": 139
+  },
+  {
+    "cond_value": "adrenal tissue",
+    "token_index": 140
+  },
+  {
+    "cond_value": "bone marrow",
+    "token_index": 141
+  },
+  {
+    "cond_value": "b-cell non-hodgkin lymphoma",
+    "token_index": 142
+  },
+  {
+    "cond_value": "follicular lymphoma",
+    "token_index": 143
+  },
+  {
+    "cond_value": "anterior wall of left ventricle",
+    "token_index": 144
+  },
+  {
+    "cond_value": "cardiac atrium",
+    "token_index": 145
+  },
+  {
+    "cond_value": "cardiac ventricle",
+    "token_index": 146
+  },
+  {
+    "cond_value": "coronary artery",
+    "token_index": 147
+  },
+  {
+    "cond_value": "alveolus of lung",
+    "token_index": 148
+  },
+  {
+    "cond_value": "superior frontal gyrus",
+    "token_index": 149
+  },
+  {
+    "cond_value": "basal ganglion",
+    "token_index": 150
+  },
+  {
+    "cond_value": "insular cortex",
+    "token_index": 151
+  },
+  {
+    "cond_value": "dronc-seq",
+    "token_index": 152
+  },
+  {
+    "cond_value": "mesonephros",
+    "token_index": 153
+  },
+  {
+    "cond_value": "renal glomerulus",
+    "token_index": 154
+  },
+  {
+    "cond_value": "outer medulla of kidney",
+    "token_index": 155
+  },
+  {
+    "cond_value": "inner medulla of kidney",
+    "token_index": 156
+  },
+  {
+    "cond_value": "anterior cingulate gyrus",
+    "token_index": 157
+  },
+  {
+    "cond_value": "cel-seq2",
+    "token_index": 158
+  },
+  {
+    "cond_value": "bd rhapsody targeted mrna",
+    "token_index": 159
+  },
+  {
+    "cond_value": "venous blood",
+    "token_index": 160
+  },
+  {
+    "cond_value": "cerebellar cortex",
+    "token_index": 161
+  },
+  {
+    "cond_value": "hemisphere part of cerebellar posterior lobe",
+    "token_index": 162
+  },
+  {
+    "cond_value": "dentate nucleus",
+    "token_index": 163
+  },
+  {
+    "cond_value": "basal zone of heart",
+    "token_index": 164
+  },
+  {
+    "cond_value": "intestine",
+    "token_index": 165
+  },
+  {
+    "cond_value": "ileum",
+    "token_index": 166
+  },
+  {
+    "cond_value": "acute myeloid leukemia",
+    "token_index": 167
+  },
+  {
+    "cond_value": "acute promyelocytic leukemia",
+    "token_index": 168
+  },
+  {
+    "cond_value": "chromophobe renal cell carcinoma",
+    "token_index": 169
+  },
+  {
+    "cond_value": "adenocarcinoma",
+    "token_index": 170
+  },
+  {
+    "cond_value": "neuroendocrine carcinoma",
+    "token_index": 171
+  },
+  {
+    "cond_value": "wilms tumor",
+    "token_index": 172
+  },
+  {
+    "cond_value": "pilocytic astrocytoma",
+    "token_index": 173
+  },
+  {
+    "cond_value": "upper outer quadrant of breast",
+    "token_index": 174
+  },
+  {
+    "cond_value": "right occipital lobe",
+    "token_index": 175
+  },
+  {
+    "cond_value": "lingula of left lung",
+    "token_index": 176
+  }
+]