Upload AlignAIR 3.0 pretrained models (5 models)
Browse files- HUMAN_IGH_EXTENDED_576/README.md +14 -0
- HUMAN_IGH_EXTENDED_576/VERSION +1 -0
- HUMAN_IGH_EXTENDED_576/config.json +434 -0
- HUMAN_IGH_EXTENDED_576/dataconfig.pkl +3 -0
- HUMAN_IGH_EXTENDED_576/fingerprint.txt +1 -0
- HUMAN_IGH_EXTENDED_576/model.pt +3 -0
- HUMAN_IGH_EXTENDED_576/training_meta.json +109 -0
- HUMAN_IGH_OGRDB_576/README.md +14 -0
- HUMAN_IGH_OGRDB_576/VERSION +1 -0
- HUMAN_IGH_OGRDB_576/config.json +283 -0
- HUMAN_IGH_OGRDB_576/dataconfig.pkl +3 -0
- HUMAN_IGH_OGRDB_576/fingerprint.txt +1 -0
- HUMAN_IGH_OGRDB_576/model.pt +3 -0
- HUMAN_IGH_OGRDB_576/training_meta.json +109 -0
- HUMAN_IGK_OGRDB_576/README.md +14 -0
- HUMAN_IGK_OGRDB_576/VERSION +1 -0
- HUMAN_IGK_OGRDB_576/config.json +218 -0
- HUMAN_IGK_OGRDB_576/dataconfig.pkl +3 -0
- HUMAN_IGK_OGRDB_576/fingerprint.txt +1 -0
- HUMAN_IGK_OGRDB_576/model.pt +3 -0
- HUMAN_IGK_OGRDB_576/training_meta.json +90 -0
- HUMAN_IGL_OGRDB_576/README.md +14 -0
- HUMAN_IGL_OGRDB_576/VERSION +1 -0
- HUMAN_IGL_OGRDB_576/config.json +233 -0
- HUMAN_IGL_OGRDB_576/dataconfig.pkl +3 -0
- HUMAN_IGL_OGRDB_576/fingerprint.txt +1 -0
- HUMAN_IGL_OGRDB_576/model.pt +3 -0
- HUMAN_IGL_OGRDB_576/training_meta.json +90 -0
- HUMAN_TCRB_IMGT_576/README.md +14 -0
- HUMAN_TCRB_IMGT_576/VERSION +1 -0
- HUMAN_TCRB_IMGT_576/config.json +192 -0
- HUMAN_TCRB_IMGT_576/dataconfig.pkl +3 -0
- HUMAN_TCRB_IMGT_576/fingerprint.txt +1 -0
- HUMAN_TCRB_IMGT_576/model.pt +3 -0
- HUMAN_TCRB_IMGT_576/training_meta.json +109 -0
- README.md +108 -3
HUMAN_IGH_EXTENDED_576/README.md
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# AlignAIRR Model Bundle
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Format Version: 3
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Model Type: single_chain
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Max Sequence Length: 576
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## Usage
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```python
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from AlignAIR.Models import SingleChainAlignAIR
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model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
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```
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## Integrity
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SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.
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HUMAN_IGH_EXTENDED_576/VERSION
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FORMAT_VERSION=3
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HUMAN_IGH_EXTENDED_576/config.json
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| 1 |
+
{
|
| 2 |
+
"alignairr_version": "2.0.2",
|
| 3 |
+
"chain_types": null,
|
| 4 |
+
"created_utc": "2026-03-03T15:07:27.032391+00:00",
|
| 5 |
+
"d_allele_count": 38,
|
| 6 |
+
"d_allele_latent_size": null,
|
| 7 |
+
"dataconfig_hash": "dfd7f5fe084ba7ded1c0d13c46ff25f8fe1a119c7290ceee819a87148e2f53bc",
|
| 8 |
+
"dataconfig_metadata": {
|
| 9 |
+
"allele_counts": {
|
| 10 |
+
"d": 37,
|
| 11 |
+
"j": 10,
|
| 12 |
+
"v": 342
|
| 13 |
+
},
|
| 14 |
+
"allele_names": {
|
| 15 |
+
"d": [
|
| 16 |
+
"IGHD1-5ABL*01",
|
| 17 |
+
"IGHD1-5ABL*02",
|
| 18 |
+
"IGHD1-5ABL*03",
|
| 19 |
+
"IGHD1-5ABL*04",
|
| 20 |
+
"IGHD1-5ABL*05",
|
| 21 |
+
"IGHD1-FLTI*01",
|
| 22 |
+
"IGHD2-7XRZ*02",
|
| 23 |
+
"IGHD2-7XRZ*03",
|
| 24 |
+
"IGHD2-7XRZ*04",
|
| 25 |
+
"IGHD2-AL4M*01",
|
| 26 |
+
"IGHD2-AL4M*02",
|
| 27 |
+
"IGHD2-IKOP*01",
|
| 28 |
+
"IGHD2-IKOP*02",
|
| 29 |
+
"IGHD2-XRP6*01",
|
| 30 |
+
"IGHD3-3HNK*01",
|
| 31 |
+
"IGHD3-3HNK*02",
|
| 32 |
+
"IGHD3-FMCQ*01",
|
| 33 |
+
"IGHD3-FMCQ*02",
|
| 34 |
+
"IGHD3-I3HM*01",
|
| 35 |
+
"IGHD3-JHII*01",
|
| 36 |
+
"IGHD3-LDJE*01",
|
| 37 |
+
"IGHD3-LDJE*02",
|
| 38 |
+
"IGHD4-ALRC*01",
|
| 39 |
+
"IGHD4-ALRC*02",
|
| 40 |
+
"IGHD4-F473*01",
|
| 41 |
+
"IGHD4-F473*02",
|
| 42 |
+
"IGHD5-36AY*01",
|
| 43 |
+
"IGHD5-36AY*02",
|
| 44 |
+
"IGHD5-36AY*03",
|
| 45 |
+
"IGHD5-CGIC*01",
|
| 46 |
+
"IGHD5-O3PH*01",
|
| 47 |
+
"IGHD6-5VO4*01",
|
| 48 |
+
"IGHD6-5VO4*02",
|
| 49 |
+
"IGHD6-5X42*01",
|
| 50 |
+
"IGHD6-G3XM*01",
|
| 51 |
+
"IGHD6-G3XM*02",
|
| 52 |
+
"IGHD7-3VE7*01"
|
| 53 |
+
],
|
| 54 |
+
"j": [
|
| 55 |
+
"IGHJ1-VWSM*01",
|
| 56 |
+
"IGHJ2-AZGQ*01",
|
| 57 |
+
"IGHJ3-CBX5*01",
|
| 58 |
+
"IGHJ4-AG67*01",
|
| 59 |
+
"IGHJ4-AG67*02",
|
| 60 |
+
"IGHJ5-2TKS*01",
|
| 61 |
+
"IGHJ6-2SFB*01",
|
| 62 |
+
"IGHJ6-2SFB*02",
|
| 63 |
+
"IGHJ6-2SFB*03",
|
| 64 |
+
"IGHJ6-2SFB*04"
|
| 65 |
+
],
|
| 66 |
+
"v": [
|
| 67 |
+
"IGHV1-27JB*01",
|
| 68 |
+
"IGHV1-27JB*02",
|
| 69 |
+
"IGHV1-27JB*03",
|
| 70 |
+
"IGHV1-27JB*04",
|
| 71 |
+
"IGHV1-27JB*05",
|
| 72 |
+
"IGHV1-27JB*06",
|
| 73 |
+
"IGHV1-27JB*07",
|
| 74 |
+
"IGHV1-27JB*08",
|
| 75 |
+
"IGHV1-27JB*09",
|
| 76 |
+
"IGHV1-2DHF*01",
|
| 77 |
+
"IGHV1-2DHF*02",
|
| 78 |
+
"IGHV1-2DHF*03",
|
| 79 |
+
"IGHV1-2DHF*04",
|
| 80 |
+
"IGHV1-2DHF*05",
|
| 81 |
+
"IGHV1-2DHF*06",
|
| 82 |
+
"IGHV1-2DHF*07",
|
| 83 |
+
"IGHV1-2DHF*08",
|
| 84 |
+
"IGHV1-2DHF*09",
|
| 85 |
+
"IGHV1-2DHF*10",
|
| 86 |
+
"IGHV1-2DHF*11",
|
| 87 |
+
"IGHV1-2DHF*12",
|
| 88 |
+
"IGHV1-2DHF*13",
|
| 89 |
+
"IGHV1-2DHF*14",
|
| 90 |
+
"IGHV1-2DHF*15",
|
| 91 |
+
"IGHV1-2DHF*16",
|
| 92 |
+
"IGHV1-2DHF*17",
|
| 93 |
+
"IGHV1-2DHF*18",
|
| 94 |
+
"IGHV1-2DHF*19",
|
| 95 |
+
"IGHV1-2DHF*20",
|
| 96 |
+
"IGHV1-2DHF*21",
|
| 97 |
+
"IGHV1-2DHF*22",
|
| 98 |
+
"IGHV1-2DHF*23",
|
| 99 |
+
"IGHV1-2DHF*24",
|
| 100 |
+
"IGHV1-2DHF*25",
|
| 101 |
+
"IGHV1-2DHF*26",
|
| 102 |
+
"IGHV1-2DHF*27",
|
| 103 |
+
"IGHV1-2DHF*28",
|
| 104 |
+
"IGHV1-2DHF*29",
|
| 105 |
+
"IGHV1-2DHF*30",
|
| 106 |
+
"IGHV1-2DHF*31",
|
| 107 |
+
"IGHV1-2DHF*32",
|
| 108 |
+
"IGHV1-5JOY*01",
|
| 109 |
+
"IGHV1-5JOY*02",
|
| 110 |
+
"IGHV1-5JOY*03",
|
| 111 |
+
"IGHV1-5JOY*04",
|
| 112 |
+
"IGHV1-5JOY*05",
|
| 113 |
+
"IGHV1-5LBE*01",
|
| 114 |
+
"IGHV1-5LBE*02",
|
| 115 |
+
"IGHV1-5LBE*03",
|
| 116 |
+
"IGHV1-5LBE*04",
|
| 117 |
+
"IGHV1-5LBE*05",
|
| 118 |
+
"IGHV1-ARUH*01",
|
| 119 |
+
"IGHV1-ARUH*02",
|
| 120 |
+
"IGHV1-ARUH*03",
|
| 121 |
+
"IGHV1-ARUH*04",
|
| 122 |
+
"IGHV1-ARUH*05",
|
| 123 |
+
"IGHV1-ARUH*06",
|
| 124 |
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|
| 125 |
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|
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|
| 127 |
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|
| 128 |
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| 130 |
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| 131 |
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| 133 |
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| 138 |
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|
| 144 |
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| 145 |
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| 146 |
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|
| 147 |
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|
| 148 |
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|
| 149 |
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|
| 150 |
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| 151 |
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| 152 |
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| 154 |
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| 155 |
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| 156 |
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| 157 |
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| 158 |
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|
| 159 |
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| 160 |
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|
| 161 |
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|
| 162 |
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| 163 |
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| 164 |
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| 192 |
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|
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|
| 194 |
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|
| 195 |
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| 197 |
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|
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|
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|
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|
| 209 |
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|
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|
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|
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|
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|
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|
| 216 |
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|
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| 219 |
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|
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|
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|
| 223 |
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|
| 224 |
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|
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|
| 226 |
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|
| 227 |
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|
| 228 |
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|
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|
| 230 |
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|
| 231 |
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|
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|
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|
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|
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|
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|
| 244 |
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|
| 245 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 304 |
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|
| 305 |
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|
| 306 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 330 |
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|
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|
| 332 |
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|
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|
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|
| 335 |
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|
| 336 |
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|
| 337 |
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|
| 338 |
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|
| 339 |
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|
| 340 |
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|
| 341 |
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|
| 342 |
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|
| 343 |
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|
| 344 |
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|
| 345 |
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|
| 346 |
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|
| 347 |
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|
| 348 |
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|
| 349 |
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|
| 350 |
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|
| 351 |
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|
| 352 |
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|
| 353 |
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|
| 354 |
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|
| 355 |
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|
| 356 |
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|
| 357 |
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|
| 358 |
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|
| 359 |
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|
| 360 |
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|
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|
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|
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|
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|
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|
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|
| 368 |
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|
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|
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|
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|
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|
| 373 |
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|
| 374 |
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|
| 375 |
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|
| 376 |
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|
| 377 |
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|
| 378 |
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|
| 379 |
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|
| 380 |
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|
| 381 |
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|
| 382 |
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|
| 383 |
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|
| 384 |
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|
| 385 |
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|
| 386 |
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|
| 387 |
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|
| 388 |
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|
| 389 |
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|
| 390 |
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|
| 391 |
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|
| 392 |
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|
| 393 |
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|
| 394 |
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|
| 395 |
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|
| 396 |
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|
| 397 |
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|
| 398 |
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|
| 399 |
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|
| 400 |
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|
| 401 |
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|
| 402 |
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|
| 403 |
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|
| 404 |
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|
| 405 |
+
"IGHV8-DOWS*02",
|
| 406 |
+
"IGHV8-DOWS*04",
|
| 407 |
+
"IGHV8-DOWS*06",
|
| 408 |
+
"IGHV8-DOWS*07"
|
| 409 |
+
]
|
| 410 |
+
},
|
| 411 |
+
"chain_type": "BCR_HEAVY",
|
| 412 |
+
"has_d": true,
|
| 413 |
+
"last_updated": "2025-08-02",
|
| 414 |
+
"reference_set": "OGRDB V8 extended",
|
| 415 |
+
"species": "Human"
|
| 416 |
+
},
|
| 417 |
+
"extra": null,
|
| 418 |
+
"format_version": 3,
|
| 419 |
+
"framework": "pytorch",
|
| 420 |
+
"framework_version": "pytorch-2.10.0+cu128",
|
| 421 |
+
"genairr_version": "0.6.3",
|
| 422 |
+
"git_commit": "2f2988e",
|
| 423 |
+
"has_d_gene": true,
|
| 424 |
+
"has_orientation_head": true,
|
| 425 |
+
"j_allele_count": 10,
|
| 426 |
+
"j_allele_latent_size": null,
|
| 427 |
+
"max_seq_length": 576,
|
| 428 |
+
"model_type": "single_chain",
|
| 429 |
+
"notes": null,
|
| 430 |
+
"number_of_chains": null,
|
| 431 |
+
"python_version": "3.12.3",
|
| 432 |
+
"v_allele_count": 342,
|
| 433 |
+
"v_allele_latent_size": null
|
| 434 |
+
}
|
HUMAN_IGH_EXTENDED_576/dataconfig.pkl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:78b38050920cf3cd45cff62b770b9c3495818b2fde50aaa50f6adccf11b70453
|
| 3 |
+
size 16796088
|
HUMAN_IGH_EXTENDED_576/fingerprint.txt
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
43d5c77da3d4aefa00a69785c9897837388d2d48cb499046c359d368f36ef5b0
|
HUMAN_IGH_EXTENDED_576/model.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:31430081031b9e3da952325dfa47be89aa38975005981191375642eb7196c9d5
|
| 3 |
+
size 11996687
|
HUMAN_IGH_EXTENDED_576/training_meta.json
ADDED
|
@@ -0,0 +1,109 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
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|
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|
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|
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|
|
|
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|
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|
|
|
|
| 1 |
+
{
|
| 2 |
+
"batch_size": 512,
|
| 3 |
+
"best_epoch": 995,
|
| 4 |
+
"best_loss": 1.9363010847568511,
|
| 5 |
+
"created_utc": "2026-03-03T15:07:27.033542+00:00",
|
| 6 |
+
"epochs_trained": 1000,
|
| 7 |
+
"extra": {
|
| 8 |
+
"notes": "IGH HUMAN_IGH_EXTENDED (V=342, D=37, J=10), CrossAttentionPooling, Uniform mutation (0.01-0.05), Kendall uncertainty weighting, orientation head, sigma schedule cosine 3.0\u21920.75, 6 workers"
|
| 9 |
+
},
|
| 10 |
+
"final_epoch": 999,
|
| 11 |
+
"final_loss": 1.9802256536483764,
|
| 12 |
+
"learning_rate": "1.4999999999999999e-05",
|
| 13 |
+
"metrics_summary": {
|
| 14 |
+
"classification": 0.19060173973441125,
|
| 15 |
+
"d_allele_avg_gt_count": 1.4607844352722168,
|
| 16 |
+
"d_allele_setK_precision": 0.8681917211328976,
|
| 17 |
+
"d_allele_setK_recall": 0.8681917211328976,
|
| 18 |
+
"d_allele_thresh_precision": 0.8330066204071045,
|
| 19 |
+
"d_allele_thresh_recall": 0.8193464279174805,
|
| 20 |
+
"d_allele_top1_acc": 0.8607843518257141,
|
| 21 |
+
"d_allele_top1_conf": 0.8420405983924866,
|
| 22 |
+
"d_end_acc": 0.7196078896522522,
|
| 23 |
+
"d_end_acc_1nt": 0.8294118046760559,
|
| 24 |
+
"d_end_mae": 0.8843137621879578,
|
| 25 |
+
"d_start_acc": 0.7098039388656616,
|
| 26 |
+
"d_start_acc_1nt": 0.8352941870689392,
|
| 27 |
+
"d_start_mae": 0.8235294818878174,
|
| 28 |
+
"indel_count": 0.25063891351222994,
|
| 29 |
+
"indel_count_mae": 0.310779333114624,
|
| 30 |
+
"j_allele_avg_gt_count": 1.0,
|
| 31 |
+
"j_allele_setK_precision": 0.984313725490196,
|
| 32 |
+
"j_allele_setK_recall": 0.984313725490196,
|
| 33 |
+
"j_allele_thresh_precision": 0.9843137860298157,
|
| 34 |
+
"j_allele_thresh_recall": 0.9843137860298157,
|
| 35 |
+
"j_allele_top1_acc": 0.9843137860298157,
|
| 36 |
+
"j_allele_top1_conf": 0.9409783482551575,
|
| 37 |
+
"j_end_acc": 1.0,
|
| 38 |
+
"j_end_acc_1nt": 1.0,
|
| 39 |
+
"j_end_mae": 0.0,
|
| 40 |
+
"j_start_acc": 0.9745098352432251,
|
| 41 |
+
"j_start_acc_1nt": 0.9980392456054688,
|
| 42 |
+
"j_start_mae": 0.027450982481241226,
|
| 43 |
+
"log_var/log_var_d_classification": -0.8180696344375611,
|
| 44 |
+
"log_var/log_var_d_end": 1.1709008902311324,
|
| 45 |
+
"log_var/log_var_d_start": 1.1773365020751954,
|
| 46 |
+
"log_var/log_var_indel": -0.5003187489509583,
|
| 47 |
+
"log_var/log_var_j_classification": -0.9034614259004593,
|
| 48 |
+
"log_var/log_var_j_end": 0.8181240218877792,
|
| 49 |
+
"log_var/log_var_j_start": 0.8338462087512016,
|
| 50 |
+
"log_var/log_var_junction_region": -1.8439301317930221,
|
| 51 |
+
"log_var/log_var_mutation": -3.0,
|
| 52 |
+
"log_var/log_var_orientation": -3.0,
|
| 53 |
+
"log_var/log_var_productivity": -3.0,
|
| 54 |
+
"log_var/log_var_v_classification": -0.9100403302907943,
|
| 55 |
+
"log_var/log_var_v_end": 0.9727652844786644,
|
| 56 |
+
"log_var/log_var_v_start": 0.9656437847018242,
|
| 57 |
+
"loss": 1.9802256536483764,
|
| 58 |
+
"lr": 1.4999999999999999e-05,
|
| 59 |
+
"mutation_rate": -1.40669819355011,
|
| 60 |
+
"mutation_rate_mae": 0.004147736355662346,
|
| 61 |
+
"orientation": -1.4999999988079071,
|
| 62 |
+
"orientation_acc": 1.0,
|
| 63 |
+
"orientation_acc/complement": 0.9999999403953552,
|
| 64 |
+
"orientation_acc/normal": 1.0,
|
| 65 |
+
"orientation_acc/revcomp": 1.0,
|
| 66 |
+
"orientation_acc/reversed": 1.0,
|
| 67 |
+
"productive": -1.2632013711333274,
|
| 68 |
+
"productive_acc": 1.0,
|
| 69 |
+
"raw/d_allele": 0.22103169716894627,
|
| 70 |
+
"raw/d_end": 1.6159657567739487,
|
| 71 |
+
"raw/d_start": 1.6268917560577392,
|
| 72 |
+
"raw/frame_loss": 0.21468963261693716,
|
| 73 |
+
"raw/hinge_loss": 0.00041688800696647375,
|
| 74 |
+
"raw/indel_count": 0.30365239836275576,
|
| 75 |
+
"raw/iou_loss": 0.15741808891296385,
|
| 76 |
+
"raw/j_allele": 0.2025365286320448,
|
| 77 |
+
"raw/j_end": 1.1331209546327592,
|
| 78 |
+
"raw/j_start": 1.1501597076654435,
|
| 79 |
+
"raw/junction_region": 0.07937577821314334,
|
| 80 |
+
"raw/len_loss": 1.0310878744721412,
|
| 81 |
+
"raw/mutation_rate": 0.004645223214756697,
|
| 82 |
+
"raw/ordering_loss": 0.0011530860774928442,
|
| 83 |
+
"raw/orientation": 6.311059674857233e-11,
|
| 84 |
+
"raw/productive": 0.011789509553054814,
|
| 85 |
+
"raw/regularization": 0.029999999329447746,
|
| 86 |
+
"raw/v_allele": 0.20122628405690193,
|
| 87 |
+
"raw/v_end": 1.3210634535551071,
|
| 88 |
+
"raw/v_start": 1.3098637717962265,
|
| 89 |
+
"segmentation": 5.678884587287903,
|
| 90 |
+
"sigma": 0.75,
|
| 91 |
+
"v_allele_avg_gt_count": 2.401960849761963,
|
| 92 |
+
"v_allele_setK_precision": 0.9143497134673606,
|
| 93 |
+
"v_allele_setK_recall": 0.9143497134673606,
|
| 94 |
+
"v_allele_thresh_precision": 0.8683497309684753,
|
| 95 |
+
"v_allele_thresh_recall": 0.8631495237350464,
|
| 96 |
+
"v_allele_top1_acc": 0.9098039865493774,
|
| 97 |
+
"v_allele_top1_conf": 0.8282101154327393,
|
| 98 |
+
"v_end_acc": 0.8666667342185974,
|
| 99 |
+
"v_end_acc_1nt": 0.9313725829124451,
|
| 100 |
+
"v_end_mae": 0.2764706015586853,
|
| 101 |
+
"v_start_acc": 0.8941177129745483,
|
| 102 |
+
"v_start_acc_1nt": 0.9529412388801575,
|
| 103 |
+
"v_start_mae": 0.24901962280273438
|
| 104 |
+
},
|
| 105 |
+
"mixed_precision": true,
|
| 106 |
+
"optimizer_class": "AdamW",
|
| 107 |
+
"samples_per_epoch": 102400,
|
| 108 |
+
"wall_time_seconds": 75114
|
| 109 |
+
}
|
HUMAN_IGH_OGRDB_576/README.md
ADDED
|
@@ -0,0 +1,14 @@
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
| 1 |
+
# AlignAIRR Model Bundle
|
| 2 |
+
|
| 3 |
+
Format Version: 3
|
| 4 |
+
Model Type: single_chain
|
| 5 |
+
Max Sequence Length: 576
|
| 6 |
+
|
| 7 |
+
## Usage
|
| 8 |
+
```python
|
| 9 |
+
from AlignAIR.Models import SingleChainAlignAIR
|
| 10 |
+
model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
|
| 11 |
+
```
|
| 12 |
+
|
| 13 |
+
## Integrity
|
| 14 |
+
SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.
|
HUMAN_IGH_OGRDB_576/VERSION
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
FORMAT_VERSION=3
|
HUMAN_IGH_OGRDB_576/config.json
ADDED
|
@@ -0,0 +1,283 @@
|
|
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|
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|
|
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|
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|
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|
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|
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|
|
|
|
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|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"alignairr_version": "2.0.2",
|
| 3 |
+
"chain_types": null,
|
| 4 |
+
"created_utc": "2026-03-01T15:40:13.636358+00:00",
|
| 5 |
+
"d_allele_count": 34,
|
| 6 |
+
"d_allele_latent_size": null,
|
| 7 |
+
"dataconfig_hash": "f9e3e35bd4a48280b15ec4817d1238a7f495f3452af1201d2ceb7d004e6830e0",
|
| 8 |
+
"dataconfig_metadata": {
|
| 9 |
+
"allele_counts": {
|
| 10 |
+
"d": 33,
|
| 11 |
+
"j": 7,
|
| 12 |
+
"v": 198
|
| 13 |
+
},
|
| 14 |
+
"allele_names": {
|
| 15 |
+
"d": [
|
| 16 |
+
"IGHD1-1*01",
|
| 17 |
+
"IGHD1-14*01",
|
| 18 |
+
"IGHD1-20*01",
|
| 19 |
+
"IGHD1-26*01",
|
| 20 |
+
"IGHD1-7*01",
|
| 21 |
+
"IGHD2-15*01",
|
| 22 |
+
"IGHD2-2*01",
|
| 23 |
+
"IGHD2-2*02",
|
| 24 |
+
"IGHD2-21*01",
|
| 25 |
+
"IGHD2-21*02",
|
| 26 |
+
"IGHD2-8*01",
|
| 27 |
+
"IGHD2-8*02",
|
| 28 |
+
"IGHD3-10*01",
|
| 29 |
+
"IGHD3-10*03",
|
| 30 |
+
"IGHD3-16*02",
|
| 31 |
+
"IGHD3-16*03",
|
| 32 |
+
"IGHD3-22*01",
|
| 33 |
+
"IGHD3-3*01",
|
| 34 |
+
"IGHD3-9*01",
|
| 35 |
+
"IGHD4-11*01",
|
| 36 |
+
"IGHD4-17*01",
|
| 37 |
+
"IGHD4-23*01",
|
| 38 |
+
"IGHD4-4*01",
|
| 39 |
+
"IGHD5-12*01",
|
| 40 |
+
"IGHD5-18*01",
|
| 41 |
+
"IGHD5-18*02",
|
| 42 |
+
"IGHD5-24*01",
|
| 43 |
+
"IGHD5-5*01",
|
| 44 |
+
"IGHD6-13*01",
|
| 45 |
+
"IGHD6-19*01",
|
| 46 |
+
"IGHD6-25*01",
|
| 47 |
+
"IGHD6-6*01",
|
| 48 |
+
"IGHD7-27*01"
|
| 49 |
+
],
|
| 50 |
+
"j": [
|
| 51 |
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}
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|
| 42 |
+
"j_start_mae": 0.11741682887077332,
|
| 43 |
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"log_var/log_var_d_classification": -0.8107569217681885,
|
| 44 |
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"log_var/log_var_d_end": 1.2113195657730103,
|
| 45 |
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"log_var/log_var_d_start": 1.1995137929916382,
|
| 46 |
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"log_var/log_var_indel": -0.6938347220420837,
|
| 47 |
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"log_var/log_var_j_classification": -0.9232622981071472,
|
| 48 |
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"log_var/log_var_j_end": 0.82975834608078,
|
| 49 |
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"log_var/log_var_j_start": 0.9077933430671692,
|
| 50 |
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"log_var/log_var_junction_region": -1.6838476657867432,
|
| 51 |
+
"log_var/log_var_mutation": -3.0,
|
| 52 |
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"log_var/log_var_orientation": -3.0,
|
| 53 |
+
"log_var/log_var_productivity": -3.0,
|
| 54 |
+
"log_var/log_var_v_classification": -0.9191080927848816,
|
| 55 |
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"log_var/log_var_v_end": 0.9017267227172852,
|
| 56 |
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"log_var/log_var_v_start": 0.9413631558418274,
|
| 57 |
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"loss": 1.885474544763565,
|
| 58 |
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"lr": 0.0,
|
| 59 |
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"mutation_rate": -1.3141397738456726,
|
| 60 |
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"mutation_rate_mae": 0.009754992090165615,
|
| 61 |
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"orientation": -1.5,
|
| 62 |
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"orientation_acc": 1.0,
|
| 63 |
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"orientation_acc/complement": 1.0,
|
| 64 |
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"orientation_acc/normal": 0.9999999403953552,
|
| 65 |
+
"orientation_acc/revcomp": 1.0,
|
| 66 |
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"orientation_acc/reversed": 1.0,
|
| 67 |
+
"productive": -1.345355775654316,
|
| 68 |
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"productive_acc": 1.0,
|
| 69 |
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"raw/d_allele": 0.2223323979973793,
|
| 70 |
+
"raw/d_end": 1.6471605092287063,
|
| 71 |
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"raw/d_start": 1.630733658671379,
|
| 72 |
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"raw/frame_loss": 0.12696342319250106,
|
| 73 |
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"raw/hinge_loss": 0.00035467982070258586,
|
| 74 |
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"raw/indel_count": 0.25013513743877414,
|
| 75 |
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"raw/iou_loss": 0.21144418716430663,
|
| 76 |
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"raw/j_allele": 0.19859787605702878,
|
| 77 |
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"raw/j_end": 1.1314865028858185,
|
| 78 |
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"raw/j_start": 1.205588527917862,
|
| 79 |
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"raw/junction_region": 0.09296022888273,
|
| 80 |
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"raw/len_loss": 0.5996542032063007,
|
| 81 |
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"raw/mutation_rate": 0.009253435865975917,
|
| 82 |
+
"raw/ordering_loss": 0.003418139982386492,
|
| 83 |
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"raw/orientation": 0.0,
|
| 84 |
+
"raw/productive": 0.007699282681714976,
|
| 85 |
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"raw/regularization": 0.029999999329447746,
|
| 86 |
+
"raw/v_allele": 0.19943240255117417,
|
| 87 |
+
"raw/v_end": 1.2012043470144271,
|
| 88 |
+
"raw/v_start": 1.2461054134368896,
|
| 89 |
+
"segmentation": 5.677759671211243,
|
| 90 |
+
"sigma": 0.75,
|
| 91 |
+
"v_allele_avg_gt_count": 1.281800389289856,
|
| 92 |
+
"v_allele_setK_precision": 0.9921722113502935,
|
| 93 |
+
"v_allele_setK_recall": 0.9921722113502935,
|
| 94 |
+
"v_allele_thresh_precision": 0.9846706390380859,
|
| 95 |
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"v_allele_thresh_recall": 0.9868884682655334,
|
| 96 |
+
"v_allele_top1_acc": 0.9941291809082031,
|
| 97 |
+
"v_allele_top1_conf": 0.9441247582435608,
|
| 98 |
+
"v_end_acc": 0.951076328754425,
|
| 99 |
+
"v_end_acc_1nt": 0.9882583022117615,
|
| 100 |
+
"v_end_mae": 0.06457925587892532,
|
| 101 |
+
"v_start_acc": 0.9178082346916199,
|
| 102 |
+
"v_start_acc_1nt": 0.9823874831199646,
|
| 103 |
+
"v_start_mae": 0.13111546635627747
|
| 104 |
+
},
|
| 105 |
+
"mixed_precision": true,
|
| 106 |
+
"optimizer_class": "AdamW",
|
| 107 |
+
"samples_per_epoch": 102400,
|
| 108 |
+
"wall_time_seconds": 67419
|
| 109 |
+
}
|
HUMAN_IGK_OGRDB_576/README.md
ADDED
|
@@ -0,0 +1,14 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# AlignAIRR Model Bundle
|
| 2 |
+
|
| 3 |
+
Format Version: 3
|
| 4 |
+
Model Type: single_chain
|
| 5 |
+
Max Sequence Length: 576
|
| 6 |
+
|
| 7 |
+
## Usage
|
| 8 |
+
```python
|
| 9 |
+
from AlignAIR.Models import SingleChainAlignAIR
|
| 10 |
+
model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
|
| 11 |
+
```
|
| 12 |
+
|
| 13 |
+
## Integrity
|
| 14 |
+
SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.
|
HUMAN_IGK_OGRDB_576/VERSION
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
FORMAT_VERSION=3
|
HUMAN_IGK_OGRDB_576/config.json
ADDED
|
@@ -0,0 +1,218 @@
|
|
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|
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|
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|
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|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"alignairr_version": "2.0.2",
|
| 3 |
+
"chain_types": null,
|
| 4 |
+
"created_utc": "2026-03-04T13:32:53.815450+00:00",
|
| 5 |
+
"d_allele_count": null,
|
| 6 |
+
"d_allele_latent_size": null,
|
| 7 |
+
"dataconfig_hash": "635c92a75e067e8e32caf3d28079afd822793b257404ffbf1185a8649f2e869f",
|
| 8 |
+
"dataconfig_metadata": {
|
| 9 |
+
"allele_counts": {
|
| 10 |
+
"j": 8,
|
| 11 |
+
"v": 168
|
| 12 |
+
},
|
| 13 |
+
"allele_names": {
|
| 14 |
+
"j": [
|
| 15 |
+
"IGKJ1-5PHE*01",
|
| 16 |
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"IGKJ2-27FL*01",
|
| 17 |
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"IGKJ2-27FL*02",
|
| 18 |
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"IGKJ2-27FL*03",
|
| 19 |
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"IGKJ2-27FL*04",
|
| 20 |
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"IGKJ3-DD27*01",
|
| 21 |
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"IGKJ4-ZOFQ*01",
|
| 22 |
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"IGKJ5-CLVV*01"
|
| 23 |
+
],
|
| 24 |
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"v": [
|
| 25 |
+
"IGKV1-2YQT*01",
|
| 26 |
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"IGKV1-2YQT*02",
|
| 27 |
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"IGKV1-2YQT*03",
|
| 28 |
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"IGKV1-2YQT*04",
|
| 29 |
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"IGKV1-2YQT*05",
|
| 30 |
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"IGKV1-2YQT*06",
|
| 31 |
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"IGKV1-2YQT*07",
|
| 32 |
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"IGKV1-2YQT*08",
|
| 33 |
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"IGKV1-2YQT*09",
|
| 34 |
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"IGKV1-3EZB*01",
|
| 35 |
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"IGKV1-3EZB*02",
|
| 36 |
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"IGKV1-3EZB*03",
|
| 37 |
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"IGKV1-3EZB*04",
|
| 38 |
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"IGKV1-3EZB*05",
|
| 39 |
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"IGKV1-5TCS*03",
|
| 40 |
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"IGKV1-5TCS*04",
|
| 41 |
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"IGKV1-5TCS*05",
|
| 42 |
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"IGKV1-5TCS*07",
|
| 43 |
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"IGKV1-6FMK*01",
|
| 44 |
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"IGKV1-6FMK*02",
|
| 45 |
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|
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|
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|
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|
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|
| 53 |
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| 54 |
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|
| 55 |
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|
| 56 |
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|
| 57 |
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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|
| 65 |
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|
| 66 |
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|
| 67 |
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|
| 68 |
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|
| 69 |
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|
| 70 |
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|
| 71 |
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|
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| 74 |
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|
| 75 |
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|
| 76 |
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| 77 |
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|
| 78 |
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|
| 79 |
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| 80 |
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|
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|
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|
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|
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|
| 93 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 149 |
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|
| 150 |
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|
| 151 |
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|
| 152 |
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|
| 153 |
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|
| 154 |
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|
| 155 |
+
"IGKV3-3IAK*15",
|
| 156 |
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"IGKV3-3P4Y*01",
|
| 157 |
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|
| 158 |
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|
| 159 |
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|
| 160 |
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|
| 161 |
+
"IGKV3-5PXT*01",
|
| 162 |
+
"IGKV3-5PXT*02",
|
| 163 |
+
"IGKV3-5PXT*03",
|
| 164 |
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"IGKV3-5PXT*04",
|
| 165 |
+
"IGKV3-5PXT*05",
|
| 166 |
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|
| 167 |
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|
| 168 |
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"IGKV3-5PXT*09",
|
| 169 |
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|
| 170 |
+
"IGKV3-CJIB*02",
|
| 171 |
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"IGKV3-CJIB*03",
|
| 172 |
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"IGKV3-CJIB*04",
|
| 173 |
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"IGKV3-CJIB*05",
|
| 174 |
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"IGKV3-CJIB*06",
|
| 175 |
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"IGKV4-7TN7*01",
|
| 176 |
+
"IGKV4-7TN7*02",
|
| 177 |
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|
| 178 |
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"IGKV4-7TN7*04",
|
| 179 |
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"IGKV5-D65I*01",
|
| 180 |
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"IGKV5-D65I*02",
|
| 181 |
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"IGKV5-D65I*03",
|
| 182 |
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"IGKV5-D65I*04",
|
| 183 |
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"IGKV6-227Y*01",
|
| 184 |
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"IGKV6-227Y*02",
|
| 185 |
+
"IGKV6-227Y*03",
|
| 186 |
+
"IGKV6-227Y*04",
|
| 187 |
+
"IGKV6-227Y*05",
|
| 188 |
+
"IGKV6-227Y*06",
|
| 189 |
+
"IGKV6-227Y*07",
|
| 190 |
+
"IGKV6-5WQW*01",
|
| 191 |
+
"IGKV6-5WQW*02",
|
| 192 |
+
"IGKV6-5WQW*03"
|
| 193 |
+
]
|
| 194 |
+
},
|
| 195 |
+
"chain_type": "BCR_LIGHT_KAPPA",
|
| 196 |
+
"has_d": false,
|
| 197 |
+
"last_updated": "2025-07-15",
|
| 198 |
+
"reference_set": "OGRDB V2 & V3 extended",
|
| 199 |
+
"species": "Human"
|
| 200 |
+
},
|
| 201 |
+
"extra": null,
|
| 202 |
+
"format_version": 3,
|
| 203 |
+
"framework": "pytorch",
|
| 204 |
+
"framework_version": "pytorch-2.10.0+cu128",
|
| 205 |
+
"genairr_version": "0.6.3",
|
| 206 |
+
"git_commit": "2f2988e",
|
| 207 |
+
"has_d_gene": false,
|
| 208 |
+
"has_orientation_head": true,
|
| 209 |
+
"j_allele_count": 8,
|
| 210 |
+
"j_allele_latent_size": null,
|
| 211 |
+
"max_seq_length": 576,
|
| 212 |
+
"model_type": "single_chain",
|
| 213 |
+
"notes": null,
|
| 214 |
+
"number_of_chains": null,
|
| 215 |
+
"python_version": "3.12.3",
|
| 216 |
+
"v_allele_count": 168,
|
| 217 |
+
"v_allele_latent_size": null
|
| 218 |
+
}
|
HUMAN_IGK_OGRDB_576/dataconfig.pkl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:d72aec84874d99e547164306543f22cf6e033b7b2a0eb351b2b85c5d5796361c
|
| 3 |
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size 3680760
|
HUMAN_IGK_OGRDB_576/fingerprint.txt
ADDED
|
@@ -0,0 +1 @@
|
|
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|
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|
|
| 1 |
+
43cff24a37fd1f856d0828ae4820db7192c2e0d2efd9faf58c258a5144803e74
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HUMAN_IGK_OGRDB_576/model.pt
ADDED
|
@@ -0,0 +1,3 @@
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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oid sha256:431f33b0bb8175f393bb50f69b7c18c26a2a3b4ffff50b0fa814ffbc05d60e5f
|
| 3 |
+
size 8670647
|
HUMAN_IGK_OGRDB_576/training_meta.json
ADDED
|
@@ -0,0 +1,90 @@
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|
|
|
|
|
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|
|
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| 1 |
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{
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"batch_size": 512,
|
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"best_loss": -1.4399833059310914,
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"created_utc": "2026-03-04T13:32:53.816574+00:00",
|
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"epochs_trained": 1000,
|
| 7 |
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"extra": {
|
| 8 |
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"notes": "IGK HUMAN_IGK_OGRDB (V=168, D=0, J=8), light chain (no D segment), CrossAttentionPooling, Uniform mutation (0.01-0.05), Kendall uncertainty weighting, orientation head, sigma schedule cosine 3.0\u21920.75, 6 workers"
|
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},
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"final_epoch": 999,
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"learning_rate": "1.4999999999999999e-05",
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"metrics_summary": {
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"classification": 0.10841067031025886,
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"indel_count": 0.16907258480787277,
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"j_allele_setK_precision": 0.978515625,
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|
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"j_allele_top1_acc": 0.978515625,
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|
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"j_end_acc": 1.0,
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"j_end_acc_1nt": 1.0,
|
| 26 |
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"j_end_mae": 0.0,
|
| 27 |
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"j_start_acc": 0.9453125,
|
| 28 |
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"j_start_acc_1nt": 0.982421875,
|
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"j_start_mae": 0.080078125,
|
| 30 |
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"log_var/log_var_indel": -0.6573320901393891,
|
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|
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|
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|
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|
| 35 |
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|
| 36 |
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|
| 37 |
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|
| 38 |
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|
| 39 |
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|
| 40 |
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|
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"loss": -1.4222590343654156,
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"lr": 1.4999999999999999e-05,
|
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|
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|
| 48 |
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|
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|
| 50 |
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"orientation_acc/reversed": 1.0,
|
| 51 |
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"productive": -1.3008609154820443,
|
| 52 |
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"productive_acc": 1.0,
|
| 53 |
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"raw/frame_loss": 0.1685053576156497,
|
| 54 |
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|
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|
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|
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|
| 58 |
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|
| 59 |
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|
| 60 |
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|
| 61 |
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|
| 62 |
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"raw/mutation_rate": 0.0030324714817106723,
|
| 63 |
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"raw/ordering_loss": 0.001164478063583374,
|
| 64 |
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"raw/orientation": 0.0,
|
| 65 |
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"raw/productive": 0.009914551141846459,
|
| 66 |
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"raw/regularization": 0.03999999910593033,
|
| 67 |
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"raw/v_allele": 0.2014396557956934,
|
| 68 |
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"raw/v_end": 1.2592456096410751,
|
| 69 |
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"raw/v_start": 1.281528382897377,
|
| 70 |
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"segmentation": 2.5002098369598387,
|
| 71 |
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"sigma": 0.75,
|
| 72 |
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"v_allele_avg_gt_count": 1.73828125,
|
| 73 |
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"v_allele_setK_precision": 0.9382440476190477,
|
| 74 |
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"v_allele_setK_recall": 0.9382440476190477,
|
| 75 |
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"v_allele_thresh_precision": 0.9306513667106628,
|
| 76 |
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"v_allele_thresh_recall": 0.9378255605697632,
|
| 77 |
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"v_allele_top1_acc": 0.939453125,
|
| 78 |
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"v_allele_top1_conf": 0.8940415382385254,
|
| 79 |
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"v_end_acc": 0.91015625,
|
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|
| 81 |
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"v_end_mae": 0.15625,
|
| 82 |
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"v_start_acc": 0.908203125,
|
| 83 |
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"v_start_acc_1nt": 0.953125,
|
| 84 |
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"v_start_mae": 0.2578125
|
| 85 |
+
},
|
| 86 |
+
"mixed_precision": true,
|
| 87 |
+
"optimizer_class": "AdamW",
|
| 88 |
+
"samples_per_epoch": 102400,
|
| 89 |
+
"wall_time_seconds": 54802
|
| 90 |
+
}
|
HUMAN_IGL_OGRDB_576/README.md
ADDED
|
@@ -0,0 +1,14 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# AlignAIRR Model Bundle
|
| 2 |
+
|
| 3 |
+
Format Version: 3
|
| 4 |
+
Model Type: single_chain
|
| 5 |
+
Max Sequence Length: 576
|
| 6 |
+
|
| 7 |
+
## Usage
|
| 8 |
+
```python
|
| 9 |
+
from AlignAIR.Models import SingleChainAlignAIR
|
| 10 |
+
model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
|
| 11 |
+
```
|
| 12 |
+
|
| 13 |
+
## Integrity
|
| 14 |
+
SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.
|
HUMAN_IGL_OGRDB_576/VERSION
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
FORMAT_VERSION=3
|
HUMAN_IGL_OGRDB_576/config.json
ADDED
|
@@ -0,0 +1,233 @@
|
|
|
|
|
|
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|
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| 213 |
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},
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| 216 |
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}
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HUMAN_IGL_OGRDB_576/dataconfig.pkl
ADDED
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version https://git-lfs.github.com/spec/v1
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| 3 |
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HUMAN_IGL_OGRDB_576/fingerprint.txt
ADDED
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| 1 |
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ADDED
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ADDED
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| 1 |
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{
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| 8 |
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"notes": "IGL HUMAN_IGL_OGRDB (V=181, D=0, J=10), light chain (no D segment), CrossAttentionPooling, Uniform mutation (0.01-0.05), Kendall uncertainty weighting, orientation head, sigma schedule cosine 3.0\u21920.75, 6 workers"
|
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},
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|
| 21 |
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|
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|
| 43 |
+
"mutation_rate": -1.4223034703731536,
|
| 44 |
+
"mutation_rate_mae": 0.003901875577867031,
|
| 45 |
+
"orientation": -1.4999748712778092,
|
| 46 |
+
"orientation_acc": 1.0,
|
| 47 |
+
"orientation_acc/complement": 1.0,
|
| 48 |
+
"orientation_acc/normal": 1.0,
|
| 49 |
+
"orientation_acc/revcomp": 0.9999999403953552,
|
| 50 |
+
"orientation_acc/reversed": 1.0,
|
| 51 |
+
"productive": -1.26833356320858,
|
| 52 |
+
"productive_acc": 0.994140625,
|
| 53 |
+
"raw/frame_loss": 0.1913288650661707,
|
| 54 |
+
"raw/hinge_loss": 0.00015748143196105956,
|
| 55 |
+
"raw/indel_count": 0.28712632328271864,
|
| 56 |
+
"raw/iou_loss": 0.009658987820148467,
|
| 57 |
+
"raw/j_allele": 0.20400346301496028,
|
| 58 |
+
"raw/j_end": 2.124738314151764,
|
| 59 |
+
"raw/j_start": 2.144471411705017,
|
| 60 |
+
"raw/junction_region": 0.010529722792562098,
|
| 61 |
+
"raw/len_loss": 0.46119194373488426,
|
| 62 |
+
"raw/mutation_rate": 0.0038682823721319435,
|
| 63 |
+
"raw/ordering_loss": 0.0009547075629234313,
|
| 64 |
+
"raw/orientation": 1.2510997341794173e-06,
|
| 65 |
+
"raw/productive": 0.011533992557087914,
|
| 66 |
+
"raw/regularization": 0.03999999910593033,
|
| 67 |
+
"raw/v_allele": 0.20139127671718599,
|
| 68 |
+
"raw/v_end": 2.1715712904930116,
|
| 69 |
+
"raw/v_start": 2.225696895122528,
|
| 70 |
+
"segmentation": 3.700576022863388,
|
| 71 |
+
"sigma": 2.0249105240388445,
|
| 72 |
+
"v_allele_avg_gt_count": 1.54296875,
|
| 73 |
+
"v_allele_setK_precision": 0.9485677083333333,
|
| 74 |
+
"v_allele_setK_recall": 0.9485677083333333,
|
| 75 |
+
"v_allele_thresh_precision": 0.92431640625,
|
| 76 |
+
"v_allele_thresh_recall": 0.9188213348388672,
|
| 77 |
+
"v_allele_top1_acc": 0.947265625,
|
| 78 |
+
"v_allele_top1_conf": 0.8756070137023926,
|
| 79 |
+
"v_end_acc": 0.791015625,
|
| 80 |
+
"v_end_acc_1nt": 0.93359375,
|
| 81 |
+
"v_end_mae": 0.322265625,
|
| 82 |
+
"v_start_acc": 0.7890625,
|
| 83 |
+
"v_start_acc_1nt": 0.9375,
|
| 84 |
+
"v_start_mae": 0.470703125
|
| 85 |
+
},
|
| 86 |
+
"mixed_precision": true,
|
| 87 |
+
"optimizer_class": "AdamW",
|
| 88 |
+
"samples_per_epoch": 102400,
|
| 89 |
+
"wall_time_seconds": 28409
|
| 90 |
+
}
|
HUMAN_TCRB_IMGT_576/README.md
ADDED
|
@@ -0,0 +1,14 @@
|
|
|
|
|
|
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|
|
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|
|
| 1 |
+
# AlignAIRR Model Bundle
|
| 2 |
+
|
| 3 |
+
Format Version: 3
|
| 4 |
+
Model Type: single_chain
|
| 5 |
+
Max Sequence Length: 576
|
| 6 |
+
|
| 7 |
+
## Usage
|
| 8 |
+
```python
|
| 9 |
+
from AlignAIR.Models import SingleChainAlignAIR
|
| 10 |
+
model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
|
| 11 |
+
```
|
| 12 |
+
|
| 13 |
+
## Integrity
|
| 14 |
+
SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.
|
HUMAN_TCRB_IMGT_576/VERSION
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
FORMAT_VERSION=3
|
HUMAN_TCRB_IMGT_576/config.json
ADDED
|
@@ -0,0 +1,192 @@
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|
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|
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|
|
|
|
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|
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|
|
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|
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|
|
|
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|
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|
|
|
|
|
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|
|
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|
|
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|
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|
|
|
|
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|
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|
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|
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|
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|
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|
|
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|
|
|
|
|
|
|
|
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|
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|
|
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|
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|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"alignairr_version": "2.0.2",
|
| 3 |
+
"chain_types": null,
|
| 4 |
+
"created_utc": "2026-03-06T09:19:44.000587+00:00",
|
| 5 |
+
"d_allele_count": 4,
|
| 6 |
+
"d_allele_latent_size": null,
|
| 7 |
+
"dataconfig_hash": "adabac1ea19b736dc1f7e01cee18ba3581ed7d5549d3aafb4824337b018c1b2a",
|
| 8 |
+
"dataconfig_metadata": {
|
| 9 |
+
"allele_counts": {
|
| 10 |
+
"d": 3,
|
| 11 |
+
"j": 14,
|
| 12 |
+
"v": 130
|
| 13 |
+
},
|
| 14 |
+
"allele_names": {
|
| 15 |
+
"d": [
|
| 16 |
+
"TRBD1*01",
|
| 17 |
+
"TRBD2*01",
|
| 18 |
+
"TRBD2*02"
|
| 19 |
+
],
|
| 20 |
+
"j": [
|
| 21 |
+
"TRBJ1-1*01",
|
| 22 |
+
"TRBJ1-2*01",
|
| 23 |
+
"TRBJ1-3*01",
|
| 24 |
+
"TRBJ1-4*01",
|
| 25 |
+
"TRBJ1-5*01",
|
| 26 |
+
"TRBJ1-6*01",
|
| 27 |
+
"TRBJ1-6*02",
|
| 28 |
+
"TRBJ2-1*01",
|
| 29 |
+
"TRBJ2-2*01",
|
| 30 |
+
"TRBJ2-3*01",
|
| 31 |
+
"TRBJ2-4*01",
|
| 32 |
+
"TRBJ2-5*01",
|
| 33 |
+
"TRBJ2-6*01",
|
| 34 |
+
"TRBJ2-7*01"
|
| 35 |
+
],
|
| 36 |
+
"v": [
|
| 37 |
+
"TRBV1*01",
|
| 38 |
+
"TRBV10-1*01",
|
| 39 |
+
"TRBV10-1*02",
|
| 40 |
+
"TRBV10-2*01",
|
| 41 |
+
"TRBV10-2*02",
|
| 42 |
+
"TRBV10-3*01",
|
| 43 |
+
"TRBV10-3*02",
|
| 44 |
+
"TRBV10-3*03",
|
| 45 |
+
"TRBV10-3*04",
|
| 46 |
+
"TRBV11-1*01",
|
| 47 |
+
"TRBV11-2*01",
|
| 48 |
+
"TRBV11-2*02",
|
| 49 |
+
"TRBV11-2*03",
|
| 50 |
+
"TRBV11-3*01",
|
| 51 |
+
"TRBV11-3*02",
|
| 52 |
+
"TRBV11-3*03",
|
| 53 |
+
"TRBV11-3*04",
|
| 54 |
+
"TRBV12-1*01",
|
| 55 |
+
"TRBV12-2*01",
|
| 56 |
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"TRBV12-3*01",
|
| 57 |
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"TRBV12-4*01",
|
| 58 |
+
"TRBV12-4*02",
|
| 59 |
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"TRBV12-5*01",
|
| 60 |
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"TRBV13*01",
|
| 61 |
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"TRBV13*02",
|
| 62 |
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"TRBV14*01",
|
| 63 |
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"TRBV14*02",
|
| 64 |
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"TRBV15*01",
|
| 65 |
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"TRBV15*02",
|
| 66 |
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"TRBV15*03",
|
| 67 |
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"TRBV16*01",
|
| 68 |
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"TRBV16*02",
|
| 69 |
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"TRBV16*03",
|
| 70 |
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"TRBV18*01",
|
| 71 |
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"TRBV19*01",
|
| 72 |
+
"TRBV19*02",
|
| 73 |
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"TRBV19*03",
|
| 74 |
+
"TRBV2*01",
|
| 75 |
+
"TRBV2*02",
|
| 76 |
+
"TRBV2*03",
|
| 77 |
+
"TRBV20-1*01",
|
| 78 |
+
"TRBV20-1*02",
|
| 79 |
+
"TRBV20-1*03",
|
| 80 |
+
"TRBV20-1*04",
|
| 81 |
+
"TRBV20-1*05",
|
| 82 |
+
"TRBV20-1*06",
|
| 83 |
+
"TRBV20-1*07",
|
| 84 |
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"TRBV21-1*01",
|
| 85 |
+
"TRBV21-1*02",
|
| 86 |
+
"TRBV23-1*01",
|
| 87 |
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"TRBV24-1*01",
|
| 88 |
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"TRBV24-1*02",
|
| 89 |
+
"TRBV25-1*01",
|
| 90 |
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"TRBV27*01",
|
| 91 |
+
"TRBV28*01",
|
| 92 |
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"TRBV29-1*01",
|
| 93 |
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"TRBV29-1*02",
|
| 94 |
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"TRBV29-1*03",
|
| 95 |
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"TRBV3-1*01",
|
| 96 |
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"TRBV3-1*02",
|
| 97 |
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"TRBV3-2*01",
|
| 98 |
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"TRBV3-2*02",
|
| 99 |
+
"TRBV3-2*03",
|
| 100 |
+
"TRBV30*01",
|
| 101 |
+
"TRBV30*02",
|
| 102 |
+
"TRBV30*03",
|
| 103 |
+
"TRBV30*04",
|
| 104 |
+
"TRBV30*05",
|
| 105 |
+
"TRBV4-1*01",
|
| 106 |
+
"TRBV4-1*02",
|
| 107 |
+
"TRBV4-2*01",
|
| 108 |
+
"TRBV4-2*02",
|
| 109 |
+
"TRBV4-3*01",
|
| 110 |
+
"TRBV4-3*02",
|
| 111 |
+
"TRBV4-3*03",
|
| 112 |
+
"TRBV4-3*04",
|
| 113 |
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"TRBV5-1*01",
|
| 114 |
+
"TRBV5-1*02",
|
| 115 |
+
"TRBV5-3*01",
|
| 116 |
+
"TRBV5-3*02",
|
| 117 |
+
"TRBV5-4*01",
|
| 118 |
+
"TRBV5-4*02",
|
| 119 |
+
"TRBV5-4*03",
|
| 120 |
+
"TRBV5-4*04",
|
| 121 |
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"TRBV5-5*01",
|
| 122 |
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"TRBV5-5*02",
|
| 123 |
+
"TRBV5-5*03",
|
| 124 |
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"TRBV5-6*01",
|
| 125 |
+
"TRBV5-7*01",
|
| 126 |
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"TRBV5-8*01",
|
| 127 |
+
"TRBV5-8*02",
|
| 128 |
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"TRBV6-1*01",
|
| 129 |
+
"TRBV6-23*01",
|
| 130 |
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"TRBV6-4*01",
|
| 131 |
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"TRBV6-4*02",
|
| 132 |
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"TRBV6-5*01",
|
| 133 |
+
"TRBV6-6*01",
|
| 134 |
+
"TRBV6-6*02",
|
| 135 |
+
"TRBV6-6*03",
|
| 136 |
+
"TRBV6-6*04",
|
| 137 |
+
"TRBV6-6*05",
|
| 138 |
+
"TRBV6-7*01",
|
| 139 |
+
"TRBV6-8*01",
|
| 140 |
+
"TRBV6-9*01",
|
| 141 |
+
"TRBV7-1*01",
|
| 142 |
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"TRBV7-2*01",
|
| 143 |
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"TRBV7-2*02",
|
| 144 |
+
"TRBV7-2*03",
|
| 145 |
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"TRBV7-2*04",
|
| 146 |
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"TRBV7-3*01",
|
| 147 |
+
"TRBV7-3*04",
|
| 148 |
+
"TRBV7-3*05",
|
| 149 |
+
"TRBV7-4*01",
|
| 150 |
+
"TRBV7-6*01",
|
| 151 |
+
"TRBV7-6*02",
|
| 152 |
+
"TRBV7-7*01",
|
| 153 |
+
"TRBV7-7*02",
|
| 154 |
+
"TRBV7-8*01",
|
| 155 |
+
"TRBV7-8*02",
|
| 156 |
+
"TRBV7-8*03",
|
| 157 |
+
"TRBV7-9*01",
|
| 158 |
+
"TRBV7-9*02",
|
| 159 |
+
"TRBV7-9*03",
|
| 160 |
+
"TRBV7-9*04",
|
| 161 |
+
"TRBV7-9*05",
|
| 162 |
+
"TRBV7-9*06",
|
| 163 |
+
"TRBV7-9*07",
|
| 164 |
+
"TRBV9*01",
|
| 165 |
+
"TRBV9*02",
|
| 166 |
+
"TRBV9*03"
|
| 167 |
+
]
|
| 168 |
+
},
|
| 169 |
+
"chain_type": "TCR_BETA",
|
| 170 |
+
"has_d": true,
|
| 171 |
+
"last_updated": "2025-03-01",
|
| 172 |
+
"reference_set": "IMGT 2022",
|
| 173 |
+
"species": "Human"
|
| 174 |
+
},
|
| 175 |
+
"extra": null,
|
| 176 |
+
"format_version": 3,
|
| 177 |
+
"framework": "pytorch",
|
| 178 |
+
"framework_version": "pytorch-2.10.0+cu128",
|
| 179 |
+
"genairr_version": "0.6.3",
|
| 180 |
+
"git_commit": "2f2988e",
|
| 181 |
+
"has_d_gene": true,
|
| 182 |
+
"has_orientation_head": true,
|
| 183 |
+
"j_allele_count": 14,
|
| 184 |
+
"j_allele_latent_size": null,
|
| 185 |
+
"max_seq_length": 576,
|
| 186 |
+
"model_type": "single_chain",
|
| 187 |
+
"notes": null,
|
| 188 |
+
"number_of_chains": null,
|
| 189 |
+
"python_version": "3.12.3",
|
| 190 |
+
"v_allele_count": 130,
|
| 191 |
+
"v_allele_latent_size": null
|
| 192 |
+
}
|
HUMAN_TCRB_IMGT_576/dataconfig.pkl
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:b515060219674840319fae5562c9ec7cd3098102d63b0d1bf4ab73146f405da5
|
| 3 |
+
size 2161540
|
HUMAN_TCRB_IMGT_576/fingerprint.txt
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
2f1e07d3515b6475a122654e1738402f8527f7d513098f506b666f3a0aeff7c7
|
HUMAN_TCRB_IMGT_576/model.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
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| 2 |
+
oid sha256:3391ffe358452e925a0ed2fc52b20bea86a81f6c41266b4c143f02dc650f83a2
|
| 3 |
+
size 9705679
|
HUMAN_TCRB_IMGT_576/training_meta.json
ADDED
|
@@ -0,0 +1,109 @@
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|
| 1 |
+
{
|
| 2 |
+
"batch_size": 512,
|
| 3 |
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"best_epoch": 989,
|
| 4 |
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"best_loss": 2.4513723576068878,
|
| 5 |
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"created_utc": "2026-03-06T09:19:44.001784+00:00",
|
| 6 |
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"epochs_trained": 1000,
|
| 7 |
+
"extra": {
|
| 8 |
+
"notes": "TCRB HUMAN_TCRB_IMGT (V=130, D=3, J=14), TCR beta chain, CrossAttentionPooling, Uniform mutation (0.01-0.05), Kendall uncertainty weighting, orientation head, sigma schedule cosine 3.0\u21920.75, 6 workers"
|
| 9 |
+
},
|
| 10 |
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"final_epoch": 999,
|
| 11 |
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"final_loss": 2.4653986859321595,
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| 12 |
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"learning_rate": "1.4999999999999999e-05",
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| 13 |
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"metrics_summary": {
|
| 14 |
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"classification": 0.45702348902821543,
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| 15 |
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| 16 |
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|
| 17 |
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|
| 18 |
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|
| 19 |
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|
| 20 |
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|
| 21 |
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"d_allele_top1_conf": 0.8624882698059082,
|
| 22 |
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"d_end_acc": 0.796875,
|
| 23 |
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"d_end_acc_1nt": 0.87890625,
|
| 24 |
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|
| 25 |
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"d_start_acc": 0.78125,
|
| 26 |
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|
| 27 |
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"indel_count": 0.2868698977679014,
|
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| 30 |
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"j_allele_avg_gt_count": 1.0,
|
| 31 |
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"j_allele_setK_precision": 0.99609375,
|
| 32 |
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|
| 33 |
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"j_allele_thresh_precision": 0.99609375,
|
| 34 |
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|
| 35 |
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|
| 36 |
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|
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|
| 38 |
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|
| 39 |
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"j_end_mae": 0.0,
|
| 40 |
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"j_start_acc": 0.888671875,
|
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| 42 |
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|
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"log_var/log_var_d_classification": -0.48912922754883764,
|
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|
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"log_var/log_var_indel": -0.42073034107685087,
|
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"log_var/log_var_j_classification": -0.9194741976261139,
|
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"log_var/log_var_j_end": 0.8163983130455017,
|
| 49 |
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"log_var/log_var_j_start": 0.9725048473477363,
|
| 50 |
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"log_var/log_var_junction_region": -1.5473183602094651,
|
| 51 |
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"log_var/log_var_mutation": -3.0,
|
| 52 |
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"log_var/log_var_orientation": -3.0,
|
| 53 |
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"log_var/log_var_productivity": -3.0,
|
| 54 |
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"log_var/log_var_v_classification": -0.9029719170928001,
|
| 55 |
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"log_var/log_var_v_end": 1.012418593764305,
|
| 56 |
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"log_var/log_var_v_start": 1.00545921087265,
|
| 57 |
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"loss": 2.4653986859321595,
|
| 58 |
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"lr": 1.4999999999999999e-05,
|
| 59 |
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"mutation_rate": -1.4241796892881393,
|
| 60 |
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"mutation_rate_mae": 0.0037339571863412857,
|
| 61 |
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"orientation": -1.4999981981515884,
|
| 62 |
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"orientation_acc": 1.0,
|
| 63 |
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"orientation_acc/complement": 1.0,
|
| 64 |
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"orientation_acc/normal": 1.0,
|
| 65 |
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"orientation_acc/revcomp": 0.9999999403953552,
|
| 66 |
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"orientation_acc/reversed": 1.0,
|
| 67 |
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"productive": -1.258803428709507,
|
| 68 |
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"productive_acc": 0.998046875,
|
| 69 |
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"raw/d_allele": 0.3075159652531147,
|
| 70 |
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"raw/d_end": 1.4717569786310196,
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| 71 |
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"raw/d_start": 1.5389642435312272,
|
| 72 |
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"raw/frame_loss": 0.3637680508941412,
|
| 73 |
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"raw/hinge_loss": 0.0016483981907367707,
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| 74 |
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"raw/indel_count": 0.3264681005477905,
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| 75 |
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"raw/iou_loss": 0.17637170106172562,
|
| 76 |
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"raw/j_allele": 0.19935014188289643,
|
| 77 |
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"raw/j_end": 1.1311669862270355,
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"raw/j_start": 1.3211141312122345,
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"raw/junction_region": 0.10658789347857237,
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"raw/len_loss": 1.078130791783333,
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"raw/mutation_rate": 0.0037748710624873638,
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"raw/ordering_loss": 0.0017432171106338502,
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"raw/orientation": 8.977160144474361e-08,
|
| 84 |
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"raw/productive": 0.012008470067521558,
|
| 85 |
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"raw/regularization": 0.029999999329447746,
|
| 86 |
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"raw/v_allele": 0.2026680625230074,
|
| 87 |
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"raw/v_end": 1.3741984504461289,
|
| 88 |
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"raw/v_start": 1.3644738376140595,
|
| 89 |
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"segmentation": 5.874486618041992,
|
| 90 |
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"sigma": 0.75,
|
| 91 |
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"v_allele_avg_gt_count": 1.453125,
|
| 92 |
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"v_allele_setK_precision": 0.970703125,
|
| 93 |
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"v_allele_setK_recall": 0.970703125,
|
| 94 |
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"v_allele_thresh_precision": 0.9624255895614624,
|
| 95 |
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"v_allele_thresh_recall": 0.9584728479385376,
|
| 96 |
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"v_allele_top1_acc": 0.97265625,
|
| 97 |
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"v_allele_top1_conf": 0.9090657234191895,
|
| 98 |
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"v_end_acc": 0.837890625,
|
| 99 |
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"v_end_acc_1nt": 0.908203125,
|
| 100 |
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"v_end_mae": 0.306640625,
|
| 101 |
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"v_start_acc": 0.8828125,
|
| 102 |
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"v_start_acc_1nt": 0.939453125,
|
| 103 |
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"v_start_mae": 0.33203125
|
| 104 |
+
},
|
| 105 |
+
"mixed_precision": true,
|
| 106 |
+
"optimizer_class": "AdamW",
|
| 107 |
+
"samples_per_epoch": 102400,
|
| 108 |
+
"wall_time_seconds": 61645
|
| 109 |
+
}
|
README.md
CHANGED
|
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|
| 1 |
-
---
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|
| 1 |
+
---
|
| 2 |
+
language: en
|
| 3 |
+
license: gpl-3.0
|
| 4 |
+
tags:
|
| 5 |
+
- immunoinformatics
|
| 6 |
+
- antibody
|
| 7 |
+
- TCR
|
| 8 |
+
- AIRR
|
| 9 |
+
- sequence-alignment
|
| 10 |
+
- bioinformatics
|
| 11 |
+
- pytorch
|
| 12 |
+
library_name: alignair
|
| 13 |
+
pipeline_tag: token-classification
|
| 14 |
+
---
|
| 15 |
+
|
| 16 |
+
# AlignAIR Pretrained Models
|
| 17 |
+
|
| 18 |
+
**AlignAIR** is a deep learning tool for aligning immunoglobulin (IG) and T-cell receptor (TCR) sequences to germline gene databases. It simultaneously predicts V/D/J gene assignments, segment boundaries, mutation rates, and productivity — all in a single forward pass.
|
| 19 |
+
|
| 20 |
+
## Available Models
|
| 21 |
+
|
| 22 |
+
| Model | Chain | Germline DB | V Alleles | D Alleles | J Alleles | Size |
|
| 23 |
+
|-------|-------|-------------|-----------|-----------|-----------|------|
|
| 24 |
+
| `HUMAN_IGH_OGRDB_576` | IGH (Heavy) | OGRDB | 198 | 33 | 7 | 17 MB |
|
| 25 |
+
| `HUMAN_IGH_EXTENDED_576` | IGH (Heavy) | Extended | 342 | 37 | 10 | 28 MB |
|
| 26 |
+
| `HUMAN_IGK_OGRDB_576` | IGK (Kappa) | OGRDB | 168 | — | 8 | 12 MB |
|
| 27 |
+
| `HUMAN_IGL_OGRDB_576` | IGL (Lambda) | OGRDB | 181 | — | 10 | 13 MB |
|
| 28 |
+
| `HUMAN_TCRB_IMGT_576` | TCRB (Beta) | IMGT | 130 | 3 | 14 | 12 MB |
|
| 29 |
+
|
| 30 |
+
All models use a maximum sequence length of 576 nucleotides and were trained on 1000 epochs of synthetic data generated by [GenAIRR](https://github.com/MuteJester/GenAIRR).
|
| 31 |
+
|
| 32 |
+
## Quick Start
|
| 33 |
+
|
| 34 |
+
```bash
|
| 35 |
+
pip install alignair[hub]
|
| 36 |
+
```
|
| 37 |
+
|
| 38 |
+
### Python API
|
| 39 |
+
|
| 40 |
+
```python
|
| 41 |
+
from AlignAIR.Models import SingleChainAlignAIR
|
| 42 |
+
from AlignAIR.Hub import get_model_path
|
| 43 |
+
|
| 44 |
+
# Download and load a model (cached automatically)
|
| 45 |
+
model_path = get_model_path("igh") # or "HUMAN_IGH_OGRDB_576"
|
| 46 |
+
model = SingleChainAlignAIR.from_pretrained(model_path)
|
| 47 |
+
```
|
| 48 |
+
|
| 49 |
+
### CLI
|
| 50 |
+
|
| 51 |
+
```bash
|
| 52 |
+
# Run inference with a pretrained model
|
| 53 |
+
alignair --model-dir HUMAN_IGH_OGRDB_576 input_sequences.csv -o results/
|
| 54 |
+
```
|
| 55 |
+
|
| 56 |
+
## Benchmark Results (100K synthetic sequences)
|
| 57 |
+
|
| 58 |
+
| Model | AlignAIR V | IgBLAST V | AlignAIR D | IgBLAST D | AlignAIR J | IgBLAST J | AlignAIR Speed |
|
| 59 |
+
|-------|-----------|-----------|-----------|-----------|-----------|-----------|----------------|
|
| 60 |
+
| IGH OGRDB | 94.1% | 95.5% | 81.7% | 69.8% | 99.3% | 99.5% | 4,272 seq/s |
|
| 61 |
+
| IGH Extended | 92.3% | 93.9% | 88.5% | 82.6% | 98.7% | 98.4% | 4,245 seq/s |
|
| 62 |
+
| IGK OGRDB | 94.6% | 95.4% | — | — | 97.2% | 96.0% | 4,807 seq/s |
|
| 63 |
+
| IGL OGRDB | 93.9% | 95.3% | — | — | 98.4% | 96.7% | 5,384 seq/s |
|
| 64 |
+
| TCRB IMGT | 96.5% | 96.2% | 89.6% | 76.3% | 99.6% | 99.1% | 4,317 seq/s |
|
| 65 |
+
|
| 66 |
+
Speed measured on NVIDIA RTX 3090 Ti (GPU) vs IgBLAST 1.22.0 (8 CPU threads).
|
| 67 |
+
|
| 68 |
+
## Model Architecture
|
| 69 |
+
|
| 70 |
+
Each model is a `SingleChainAlignAIR` module combining:
|
| 71 |
+
- **Nucleotide embedding** (5→64 dim) with center-padded tokenization
|
| 72 |
+
- **Spatial segmentation** via 9-layer dilated convolutions (receptive field = 1023 nt)
|
| 73 |
+
- **Conditioned boundary heads** with chain decoding (v_start → v_end → d_start → ...)
|
| 74 |
+
- **Classification heads** for V/D/J allele assignment
|
| 75 |
+
- **Analysis heads** for mutation rate and productivity prediction
|
| 76 |
+
- **In-model orientation correction** (4-class: forward, reverse-complement, complement, reverse)
|
| 77 |
+
|
| 78 |
+
## Bundle Format
|
| 79 |
+
|
| 80 |
+
Each model directory contains:
|
| 81 |
+
- `model.pt` — PyTorch state dict
|
| 82 |
+
- `config.json` — Architecture hyperparameters
|
| 83 |
+
- `dataconfig.pkl` — Germline allele database (GenAIRR DataConfig)
|
| 84 |
+
- `training_meta.json` — Training provenance
|
| 85 |
+
- `VERSION` — Bundle format version
|
| 86 |
+
- `fingerprint.txt` — SHA-256 integrity hash
|
| 87 |
+
|
| 88 |
+
## Citation
|
| 89 |
+
|
| 90 |
+
If you use AlignAIR in your research, please cite:
|
| 91 |
+
|
| 92 |
+
```bibtex
|
| 93 |
+
@article{alignair2024,
|
| 94 |
+
title={AlignAIR: Deep Learning for Multi-Task Immunoglobulin Sequence Alignment},
|
| 95 |
+
author={Konstantinovsky, Thomas and Peres, Ayelet},
|
| 96 |
+
year={2024}
|
| 97 |
+
}
|
| 98 |
+
```
|
| 99 |
+
|
| 100 |
+
## License
|
| 101 |
+
|
| 102 |
+
GPL-3.0. See [LICENSE](https://github.com/MuteJester/AlignAIR/blob/main/LICENSE).
|
| 103 |
+
|
| 104 |
+
## Links
|
| 105 |
+
|
| 106 |
+
- [GitHub Repository](https://github.com/MuteJester/AlignAIR)
|
| 107 |
+
- [Documentation](https://mutejester.github.io/AlignAIR/)
|
| 108 |
+
- [PyPI Package](https://pypi.org/project/AlignAIR/)
|