Publish AlignAIR pretrained registry v1 (IGH, IGK+L, TCRB; pickle-free) + fresh README

.gitattributes

@@ -33,3 +33,6 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+alignair-igh-human/1.0.0.alignair filter=lfs diff=lfs merge=lfs -text
+alignair-igkl-human/1.0.0.alignair filter=lfs diff=lfs merge=lfs -text
+alignair-tcrb-human/1.0.0.alignair filter=lfs diff=lfs merge=lfs -text

HUMAN_IGH_EXTENDED_576/README.md

@@ -1,14 +0,0 @@
-# AlignAIRR Model Bundle
-
-Format Version: 3
-Model Type: single_chain
-Max Sequence Length: 576
-
-## Usage
-```python
-from AlignAIR.Models import SingleChainAlignAIR
-model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
-```
-
-## Integrity
-SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.

HUMAN_IGH_EXTENDED_576/VERSION

@@ -1 +0,0 @@
-FORMAT_VERSION=3

HUMAN_IGH_EXTENDED_576/config.json

@@ -1,434 +0,0 @@
-{
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-  "chain_types": null,
-  "created_utc": "2026-03-03T15:07:27.032391+00:00",
-  "d_allele_count": 38,
-  "d_allele_latent_size": null,
-  "dataconfig_hash": "dfd7f5fe084ba7ded1c0d13c46ff25f8fe1a119c7290ceee819a87148e2f53bc",
-  "dataconfig_metadata": {
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-      "j": 10,
-      "v": 342
-    },
-    "allele_names": {
-      "d": [
-        "IGHD1-5ABL*01",
-        "IGHD1-5ABL*02",
-        "IGHD1-5ABL*03",
-        "IGHD1-5ABL*04",
-        "IGHD1-5ABL*05",
-        "IGHD1-FLTI*01",
-        "IGHD2-7XRZ*02",
-        "IGHD2-7XRZ*03",
-        "IGHD2-7XRZ*04",
-        "IGHD2-AL4M*01",
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-        "IGHD2-IKOP*01",
-        "IGHD2-IKOP*02",
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-        "IGHD3-3HNK*01",
-        "IGHD3-3HNK*02",
-        "IGHD3-FMCQ*01",
-        "IGHD3-FMCQ*02",
-        "IGHD3-I3HM*01",
-        "IGHD3-JHII*01",
-        "IGHD3-LDJE*01",
-        "IGHD3-LDJE*02",
-        "IGHD4-ALRC*01",
-        "IGHD4-ALRC*02",
-        "IGHD4-F473*01",
-        "IGHD4-F473*02",
-        "IGHD5-36AY*01",
-        "IGHD5-36AY*02",
-        "IGHD5-36AY*03",
-        "IGHD5-CGIC*01",
-        "IGHD5-O3PH*01",
-        "IGHD6-5VO4*01",
-        "IGHD6-5VO4*02",
-        "IGHD6-5X42*01",
-        "IGHD6-G3XM*01",
-        "IGHD6-G3XM*02",
-        "IGHD7-3VE7*01"
-      ],
-      "j": [
-        "IGHJ1-VWSM*01",
-        "IGHJ2-AZGQ*01",
-        "IGHJ3-CBX5*01",
-        "IGHJ4-AG67*01",
-        "IGHJ4-AG67*02",
-        "IGHJ5-2TKS*01",
-        "IGHJ6-2SFB*01",
-        "IGHJ6-2SFB*02",
-        "IGHJ6-2SFB*03",
-        "IGHJ6-2SFB*04"
-      ],
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-  "model_type": "single_chain",
-  "notes": null,
-  "number_of_chains": null,
-  "python_version": "3.12.3",
-  "v_allele_count": 342,
-  "v_allele_latent_size": null
-}

HUMAN_IGH_EXTENDED_576/dataconfig.pkl

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:78b38050920cf3cd45cff62b770b9c3495818b2fde50aaa50f6adccf11b70453
-size 16796088

HUMAN_IGH_EXTENDED_576/fingerprint.txt

@@ -1 +0,0 @@
-43d5c77da3d4aefa00a69785c9897837388d2d48cb499046c359d368f36ef5b0

HUMAN_IGH_EXTENDED_576/training_meta.json

@@ -1,109 +0,0 @@
-{
-  "batch_size": 512,
-  "best_epoch": 995,
-  "best_loss": 1.9363010847568511,
-  "created_utc": "2026-03-03T15:07:27.033542+00:00",
-  "epochs_trained": 1000,
-  "extra": {
-    "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"
-  },
-  "final_epoch": 999,
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-    "log_var/log_var_productivity": -3.0,
-    "log_var/log_var_v_classification": -0.9100403302907943,
-    "log_var/log_var_v_end": 0.9727652844786644,
-    "log_var/log_var_v_start": 0.9656437847018242,
-    "loss": 1.9802256536483764,
-    "lr": 1.4999999999999999e-05,
-    "mutation_rate": -1.40669819355011,
-    "mutation_rate_mae": 0.004147736355662346,
-    "orientation": -1.4999999988079071,
-    "orientation_acc": 1.0,
-    "orientation_acc/complement": 0.9999999403953552,
-    "orientation_acc/normal": 1.0,
-    "orientation_acc/revcomp": 1.0,
-    "orientation_acc/reversed": 1.0,
-    "productive": -1.2632013711333274,
-    "productive_acc": 1.0,
-    "raw/d_allele": 0.22103169716894627,
-    "raw/d_end": 1.6159657567739487,
-    "raw/d_start": 1.6268917560577392,
-    "raw/frame_loss": 0.21468963261693716,
-    "raw/hinge_loss": 0.00041688800696647375,
-    "raw/indel_count": 0.30365239836275576,
-    "raw/iou_loss": 0.15741808891296385,
-    "raw/j_allele": 0.2025365286320448,
-    "raw/j_end": 1.1331209546327592,
-    "raw/j_start": 1.1501597076654435,
-    "raw/junction_region": 0.07937577821314334,
-    "raw/len_loss": 1.0310878744721412,
-    "raw/mutation_rate": 0.004645223214756697,
-    "raw/ordering_loss": 0.0011530860774928442,
-    "raw/orientation": 6.311059674857233e-11,
-    "raw/productive": 0.011789509553054814,
-    "raw/regularization": 0.029999999329447746,
-    "raw/v_allele": 0.20122628405690193,
-    "raw/v_end": 1.3210634535551071,
-    "raw/v_start": 1.3098637717962265,
-    "segmentation": 5.678884587287903,
-    "sigma": 0.75,
-    "v_allele_avg_gt_count": 2.401960849761963,
-    "v_allele_setK_precision": 0.9143497134673606,
-    "v_allele_setK_recall": 0.9143497134673606,
-    "v_allele_thresh_precision": 0.8683497309684753,
-    "v_allele_thresh_recall": 0.8631495237350464,
-    "v_allele_top1_acc": 0.9098039865493774,
-    "v_allele_top1_conf": 0.8282101154327393,
-    "v_end_acc": 0.8666667342185974,
-    "v_end_acc_1nt": 0.9313725829124451,
-    "v_end_mae": 0.2764706015586853,
-    "v_start_acc": 0.8941177129745483,
-    "v_start_acc_1nt": 0.9529412388801575,
-    "v_start_mae": 0.24901962280273438
-  },
-  "mixed_precision": true,
-  "optimizer_class": "AdamW",
-  "samples_per_epoch": 102400,
-  "wall_time_seconds": 75114
-}

HUMAN_IGH_OGRDB_576/README.md

@@ -1,14 +0,0 @@
-# AlignAIRR Model Bundle
-
-Format Version: 3
-Model Type: single_chain
-Max Sequence Length: 576
-
-## Usage
-```python
-from AlignAIR.Models import SingleChainAlignAIR
-model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
-```
-
-## Integrity
-SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.

HUMAN_IGH_OGRDB_576/VERSION

@@ -1 +0,0 @@
-FORMAT_VERSION=3

HUMAN_IGH_OGRDB_576/config.json

@@ -1,283 +0,0 @@
-{
-  "alignairr_version": "2.0.2",
-  "chain_types": null,
-  "created_utc": "2026-03-01T15:40:13.636358+00:00",
-  "d_allele_count": 34,
-  "d_allele_latent_size": null,
-  "dataconfig_hash": "f9e3e35bd4a48280b15ec4817d1238a7f495f3452af1201d2ceb7d004e6830e0",
-  "dataconfig_metadata": {
-    "allele_counts": {
-      "d": 33,
-      "j": 7,
-      "v": 198
-    },
-    "allele_names": {
-      "d": [
-        "IGHD1-1*01",
-        "IGHD1-14*01",
-        "IGHD1-20*01",
-        "IGHD1-26*01",
-        "IGHD1-7*01",
-        "IGHD2-15*01",
-        "IGHD2-2*01",
-        "IGHD2-2*02",
-        "IGHD2-21*01",
-        "IGHD2-21*02",
-        "IGHD2-8*01",
-        "IGHD2-8*02",
-        "IGHD3-10*01",
-        "IGHD3-10*03",
-        "IGHD3-16*02",
-        "IGHD3-16*03",
-        "IGHD3-22*01",
-        "IGHD3-3*01",
-        "IGHD3-9*01",
-        "IGHD4-11*01",
-        "IGHD4-17*01",
-        "IGHD4-23*01",
-        "IGHD4-4*01",
-        "IGHD5-12*01",
-        "IGHD5-18*01",
-        "IGHD5-18*02",
-        "IGHD5-24*01",
-        "IGHD5-5*01",
-        "IGHD6-13*01",
-        "IGHD6-19*01",
-        "IGHD6-25*01",
-        "IGHD6-6*01",
-        "IGHD7-27*01"
-      ],
-      "j": [
-        "IGHJ1*01",
-        "IGHJ2*01",
-        "IGHJ3*02",
-        "IGHJ4*02",
-        "IGHJ5*02",
-        "IGHJ6*02",
-        "IGHJ6*03"
-      ],
-      "v": [
-        "IGHVF1-G1*01",
-        "IGHVF1-G1*02",
-        "IGHVF1-G1*03",
-        "IGHVF1-G2*01",
-        "IGHVF1-G2*02",
-        "IGHVF1-G3*01",
-        "IGHVF1-G3*02",
-        "IGHVF1-G3*03",
-        "IGHVF1-G3*04",
-        "IGHVF1-G3*05",
-        "IGHVF1-G3*06",
-        "IGHVF10-G33*01",
-        "IGHVF10-G33*02",
-        "IGHVF10-G33*03",
-        "IGHVF10-G33*04",
-        "IGHVF10-G34*01",
-        "IGHVF10-G34*02",
-        "IGHVF10-G35*01",
-        "IGHVF10-G35*02",
-        "IGHVF10-G35*03",
-        "IGHVF10-G35*04",
-        "IGHVF10-G36*01",
-        "IGHVF10-G37*01",
-        "IGHVF10-G37*02",
-        "IGHVF10-G37*03",
-        "IGHVF10-G37*04",
-        "IGHVF10-G37*05",
-        "IGHVF10-G37*06",
-        "IGHVF10-G37*07",
-        "IGHVF10-G37*08",
-        "IGHVF10-G37*09",
-        "IGHVF10-G37*10",
-        "IGHVF10-G37*11",
-        "IGHVF10-G38*01",
-        "IGHVF10-G38*02",
-        "IGHVF10-G38*03",
-        "IGHVF10-G38*04",
-        "IGHVF10-G38*05",
-        "IGHVF10-G38*06",
-        "IGHVF10-G39*01",
-        "IGHVF10-G40*01",
-        "IGHVF10-G40*02",
-        "IGHVF10-G40*03",
-        "IGHVF10-G40*04",
-        "IGHVF10-G40*05",
-        "IGHVF10-G40*06",
-        "IGHVF10-G40*07",
-        "IGHVF10-G41*01",
-        "IGHVF10-G41*02",
-        "IGHVF10-G41*03",
-        "IGHVF10-G42*01",
-        "IGHVF10-G42*02",
-        "IGHVF10-G42*03",
-        "IGHVF10-G42*04",
-        "IGHVF10-G42*05",
-        "IGHVF10-G43*01",
-        "IGHVF10-G43*02",
-        "IGHVF10-G43*03",
-        "IGHVF10-G44*01",
-        "IGHVF10-G44*02",
-        "IGHVF10-G44*03",
-        "IGHVF10-G44*04",
-        "IGHVF10-G45*01",
-        "IGHVF10-G46*01",
-        "IGHVF10-G46*02",
-        "IGHVF10-G46*03",
-        "IGHVF10-G47*01",
-        "IGHVF10-G48*01",
-        "IGHVF10-G48*02",
-        "IGHVF10-G49*01",
-        "IGHVF10-G49*02",
-        "IGHVF10-G49*03",
-        "IGHVF10-G49*04",
-        "IGHVF10-G50*01",
-        "IGHVF10-G50*02",
-        "IGHVF10-G50*03",
-        "IGHVF10-G50*04",
-        "IGHVF10-G51*01",
-        "IGHVF10-G51*02",
-        "IGHVF10-G51*03",
-        "IGHVF10-G51*04",
-        "IGHVF10-G51*05",
-        "IGHVF10-G52*01",
-        "IGHVF10-G52*02",
-        "IGHVF10-G52*03",
-        "IGHVF10-G52*04",
-        "IGHVF10-G52*05",
-        "IGHVF10-G52*06",
-        "IGHVF2-G4*01",
-        "IGHVF2-G4*02",
-        "IGHVF3-G10*01",
-        "IGHVF3-G10*02",
-        "IGHVF3-G10*03",
-        "IGHVF3-G10*04",
-        "IGHVF3-G10*05",
-        "IGHVF3-G10*06",
-        "IGHVF3-G10*07",
-        "IGHVF3-G11*01",
-        "IGHVF3-G11*02",
-        "IGHVF3-G11*03",
-        "IGHVF3-G11*04",
-        "IGHVF3-G11*05",
-        "IGHVF3-G11*06",
-        "IGHVF3-G12*01",
-        "IGHVF3-G12*02",
-        "IGHVF3-G12*03",
-        "IGHVF3-G12*04",
-        "IGHVF3-G5*01",
-        "IGHVF3-G6*01",
-        "IGHVF3-G6*02",
-        "IGHVF3-G6*03",
-        "IGHVF3-G6*04",
-        "IGHVF3-G6*05",
-        "IGHVF3-G6*06",
-        "IGHVF3-G6*07",
-        "IGHVF3-G6*08",
-        "IGHVF3-G7*01",
-        "IGHVF3-G7*02",
-        "IGHVF3-G7*03",
-        "IGHVF3-G7*04",
-        "IGHVF3-G7*05",
-        "IGHVF3-G8*01",
-        "IGHVF3-G8*02",
-        "IGHVF3-G8*03",
-        "IGHVF3-G8*04",
-        "IGHVF3-G9*01",
-        "IGHVF3-G9*02",
-        "IGHVF3-G9*03",
-        "IGHVF3-G9*04",
-        "IGHVF3-G9*04_A319G",
-        "IGHVF4-G13*01",
-        "IGHVF4-G13*02",
-        "IGHVF4-G14*01",
-        "IGHVF4-G14*02",
-        "IGHVF4-G14*03",
-        "IGHVF4-G14*04",
-        "IGHVF5-G15*01",
-        "IGHVF5-G16*01",
-        "IGHVF5-G16*02",
-        "IGHVF5-G16*03",
-        "IGHVF5-G16*04",
-        "IGHVF6-G17*01",
-        "IGHVF6-G18*01",
-        "IGHVF6-G19*01",
-        "IGHVF6-G19*02",
-        "IGHVF6-G19*03",
-        "IGHVF6-G20*01",
-        "IGHVF6-G20*02",
-        "IGHVF6-G21*01",
-        "IGHVF6-G21*02",
-        "IGHVF6-G21*03",
-        "IGHVF6-G21*04",
-        "IGHVF6-G21*05",
-        "IGHVF6-G21*06",
-        "IGHVF6-G21*07",
-        "IGHVF6-G21*08",
-        "IGHVF6-G21*09",
-        "IGHVF6-G21*10",
-        "IGHVF6-G21*11",
-        "IGHVF6-G21*12",
-        "IGHVF6-G21*13",
-        "IGHVF6-G21*14",
-        "IGHVF6-G21*15",
-        "IGHVF6-G21*16",
-        "IGHVF6-G22*01",
-        "IGHVF6-G22*02",
-        "IGHVF6-G22*03",
-        "IGHVF6-G23*01",
-        "IGHVF6-G23*02",
-        "IGHVF6-G23*03",
-        "IGHVF6-G24*01",
-        "IGHVF6-G24*02",
-        "IGHVF6-G24*03",
-        "IGHVF6-G24*04",
-        "IGHVF6-G24*05",
-        "IGHVF6-G25*01",
-        "IGHVF6-G25*02",
-        "IGHVF6-G25*03",
-        "IGHVF6-G26*01",
-        "IGHVF6-G26*02",
-        "IGHVF6-G26*03",
-        "IGHVF6-G26*04",
-        "IGHVF7-G27*01",
-        "IGHVF7-G27*02",
-        "IGHVF7-G27*03",
-        "IGHVF7-G27*04",
-        "IGHVF8-G28*01",
-        "IGHVF8-G29*01",
-        "IGHVF8-G29*02",
-        "IGHVF8-G30*01",
-        "IGHVF8-G30*02",
-        "IGHVF8-G30*03",
-        "IGHVF8-G31*01",
-        "IGHVF8-G31*02",
-        "IGHVF9-G32*01",
-        "IGHVF9-G32*02",
-        "IGHVF9-G32*03",
-        "IGHVF9-G32*04"
-      ]
-    },
-    "chain_type": "BCR_HEAVY",
-    "has_d": true,
-    "last_updated": "2025-02-01",
-    "reference_set": "OGRDB V8",
-    "species": "Human"
-  },
-  "extra": null,
-  "format_version": 3,
-  "framework": "pytorch",
-  "framework_version": "pytorch-2.10.0+cu128",
-  "genairr_version": "0.6.3",
-  "git_commit": "2f2988e",
-  "has_d_gene": true,
-  "has_orientation_head": true,
-  "j_allele_count": 7,
-  "j_allele_latent_size": null,
-  "max_seq_length": 576,
-  "model_type": "single_chain",
-  "notes": null,
-  "number_of_chains": null,
-  "python_version": "3.12.3",
-  "v_allele_count": 198,
-  "v_allele_latent_size": null
-}

HUMAN_IGH_OGRDB_576/fingerprint.txt

@@ -1 +0,0 @@
-0c8df7b9790a94a7cf0f7ab9c5a69eaa7b2b39891b1f9d10cc2279b873e054d6

HUMAN_IGH_OGRDB_576/training_meta.json

@@ -1,109 +0,0 @@
-{
-  "batch_size": 512,
-  "best_epoch": 995,
-  "best_loss": 1.8584578084945678,
-  "created_utc": "2026-03-01T15:40:13.692179+00:00",
-  "epochs_trained": 1000,
-  "extra": {
-    "notes": "v3: DeepSegHead + ConditionedSegHead + JunctionRegionHead + AlignAIRLoss (hybrid CE+Cramer, inv-freq class weights, reading frame loss, Short-D concordance)"
-  },
-  "final_epoch": 999,
-  "final_loss": 1.885474544763565,
-  "learning_rate": "0.0",
-  "metrics_summary": {
-    "classification": 0.1835135055333376,
-    "d_allele_avg_gt_count": 1.5322896242141724,
-    "d_allele_setK_precision": 0.8797246295778584,
-    "d_allele_setK_recall": 0.8797246295778584,
-    "d_allele_thresh_precision": 0.843770444393158,
-    "d_allele_thresh_recall": 0.8331026434898376,
-    "d_allele_top1_acc": 0.8727984428405762,
-    "d_allele_top1_conf": 0.8446706533432007,
-    "d_end_acc": 0.7514677047729492,
-    "d_end_acc_1nt": 0.8414872884750366,
-    "d_end_mae": 1.039138913154602,
-    "d_start_acc": 0.7573385238647461,
-    "d_start_acc_1nt": 0.8277886509895325,
-    "d_start_mae": 1.189823865890503,
-    "indel_count": 0.1536969581246376,
-    "indel_count_mae": 0.2501048743724823,
-    "j_allele_avg_gt_count": 1.0,
-    "j_allele_setK_precision": 1.0,
-    "j_allele_setK_recall": 1.0,
-    "j_allele_thresh_precision": 1.0,
-    "j_allele_thresh_recall": 1.0,
-    "j_allele_top1_acc": 1.0,
-    "j_allele_top1_conf": 0.9496095776557922,
-    "j_end_acc": 1.0,
-    "j_end_acc_1nt": 1.0,
-    "j_end_mae": 0.0,
-    "j_start_acc": 0.9373776912689209,
-    "j_start_acc_1nt": 0.9784735441207886,
-    "j_start_mae": 0.11741682887077332,
-    "log_var/log_var_d_classification": -0.8107569217681885,
-    "log_var/log_var_d_end": 1.2113195657730103,
-    "log_var/log_var_d_start": 1.1995137929916382,
-    "log_var/log_var_indel": -0.6938347220420837,
-    "log_var/log_var_j_classification": -0.9232622981071472,
-    "log_var/log_var_j_end": 0.82975834608078,
-    "log_var/log_var_j_start": 0.9077933430671692,
-    "log_var/log_var_junction_region": -1.6838476657867432,
-    "log_var/log_var_mutation": -3.0,
-    "log_var/log_var_orientation": -3.0,
-    "log_var/log_var_productivity": -3.0,
-    "log_var/log_var_v_classification": -0.9191080927848816,
-    "log_var/log_var_v_end": 0.9017267227172852,
-    "log_var/log_var_v_start": 0.9413631558418274,
-    "loss": 1.885474544763565,
-    "lr": 0.0,
-    "mutation_rate": -1.3141397738456726,
-    "mutation_rate_mae": 0.009754992090165615,
-    "orientation": -1.5,
-    "orientation_acc": 1.0,
-    "orientation_acc/complement": 1.0,
-    "orientation_acc/normal": 0.9999999403953552,
-    "orientation_acc/revcomp": 1.0,
-    "orientation_acc/reversed": 1.0,
-    "productive": -1.345355775654316,
-    "productive_acc": 1.0,
-    "raw/d_allele": 0.2223323979973793,
-    "raw/d_end": 1.6471605092287063,
-    "raw/d_start": 1.630733658671379,
-    "raw/frame_loss": 0.12696342319250106,
-    "raw/hinge_loss": 0.00035467982070258586,
-    "raw/indel_count": 0.25013513743877414,
-    "raw/iou_loss": 0.21144418716430663,
-    "raw/j_allele": 0.19859787605702878,
-    "raw/j_end": 1.1314865028858185,
-    "raw/j_start": 1.205588527917862,
-    "raw/junction_region": 0.09296022888273,
-    "raw/len_loss": 0.5996542032063007,
-    "raw/mutation_rate": 0.009253435865975917,
-    "raw/ordering_loss": 0.003418139982386492,
-    "raw/orientation": 0.0,
-    "raw/productive": 0.007699282681714976,
-    "raw/regularization": 0.029999999329447746,
-    "raw/v_allele": 0.19943240255117417,
-    "raw/v_end": 1.2012043470144271,
-    "raw/v_start": 1.2461054134368896,
-    "segmentation": 5.677759671211243,
-    "sigma": 0.75,
-    "v_allele_avg_gt_count": 1.281800389289856,
-    "v_allele_setK_precision": 0.9921722113502935,
-    "v_allele_setK_recall": 0.9921722113502935,
-    "v_allele_thresh_precision": 0.9846706390380859,
-    "v_allele_thresh_recall": 0.9868884682655334,
-    "v_allele_top1_acc": 0.9941291809082031,
-    "v_allele_top1_conf": 0.9441247582435608,
-    "v_end_acc": 0.951076328754425,
-    "v_end_acc_1nt": 0.9882583022117615,
-    "v_end_mae": 0.06457925587892532,
-    "v_start_acc": 0.9178082346916199,
-    "v_start_acc_1nt": 0.9823874831199646,
-    "v_start_mae": 0.13111546635627747
-  },
-  "mixed_precision": true,
-  "optimizer_class": "AdamW",
-  "samples_per_epoch": 102400,
-  "wall_time_seconds": 67419
-}

HUMAN_IGK_OGRDB_576/README.md

@@ -1,14 +0,0 @@
-# AlignAIRR Model Bundle
-
-Format Version: 3
-Model Type: single_chain
-Max Sequence Length: 576
-
-## Usage
-```python
-from AlignAIR.Models import SingleChainAlignAIR
-model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
-```
-
-## Integrity
-SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.

HUMAN_IGK_OGRDB_576/VERSION

@@ -1 +0,0 @@
-FORMAT_VERSION=3

HUMAN_IGK_OGRDB_576/config.json

@@ -1,218 +0,0 @@
-{
-  "alignairr_version": "2.0.2",
-  "chain_types": null,
-  "created_utc": "2026-03-04T13:32:53.815450+00:00",
-  "d_allele_count": null,
-  "d_allele_latent_size": null,
-  "dataconfig_hash": "635c92a75e067e8e32caf3d28079afd822793b257404ffbf1185a8649f2e869f",
-  "dataconfig_metadata": {
-    "allele_counts": {
-      "j": 8,
-      "v": 168
-    },
-    "allele_names": {
-      "j": [
-        "IGKJ1-5PHE*01",
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-    "has_d": false,
-    "last_updated": "2025-07-15",
-    "reference_set": "OGRDB V2 & V3 extended",
-    "species": "Human"
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-  "python_version": "3.12.3",
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-  "v_allele_latent_size": null
-}

HUMAN_IGK_OGRDB_576/dataconfig.pkl

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-size 3680760

HUMAN_IGK_OGRDB_576/fingerprint.txt

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-43cff24a37fd1f856d0828ae4820db7192c2e0d2efd9faf58c258a5144803e74

HUMAN_IGK_OGRDB_576/model.pt

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-version https://git-lfs.github.com/spec/v1
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-size 8670647

HUMAN_IGK_OGRDB_576/training_meta.json

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-{
-  "batch_size": 512,
-  "best_epoch": 992,
-  "best_loss": -1.4399833059310914,
-  "created_utc": "2026-03-04T13:32:53.816574+00:00",
-  "epochs_trained": 1000,
-  "extra": {
-    "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"
-  },
-  "final_epoch": 999,
-  "final_loss": -1.4222590343654156,
-  "learning_rate": "1.4999999999999999e-05",
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-}

HUMAN_IGL_OGRDB_576/README.md

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-# AlignAIRR Model Bundle
-
-Format Version: 3
-Model Type: single_chain
-Max Sequence Length: 576
-
-## Usage
-```python
-from AlignAIR.Models import SingleChainAlignAIR
-model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
-```
-
-## Integrity
-SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.

HUMAN_IGL_OGRDB_576/VERSION

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-FORMAT_VERSION=3

HUMAN_IGL_OGRDB_576/config.json

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-{
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-  "d_allele_count": null,
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-  "dataconfig_hash": "4f519381775241d12127b33bcb204af05294e206e444d9b274b09e0e5d973078",
-  "dataconfig_metadata": {
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-        "IGLV4-3HWN*05",
-        "IGLV4-3HWN*06",
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-        "IGLV4-7C4U*02",
-        "IGLV4-7C4U*03",
-        "IGLV5-24IV*01",
-        "IGLV5-24IV*02",
-        "IGLV5-24IV*03",
-        "IGLV5-24IV*04",
-        "IGLV5-24IV*05",
-        "IGLV5-24IV*06",
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-        "IGLV5-6HXL*01",
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-        "IGLV5-7RPJ*02",
-        "IGLV5-7RPJ*03",
-        "IGLV5-7RPJ*04",
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-        "IGLV5-BWX3*01",
-        "IGLV5-FX2U*01",
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HUMAN_IGL_OGRDB_576/training_meta.json

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-{
-  "batch_size": 512,
-  "best_epoch": 456,
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-  "created_utc": "2026-03-05T07:23:10.006254+00:00",
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HUMAN_TCRB_IMGT_576/README.md

@@ -1,14 +0,0 @@
-# AlignAIRR Model Bundle
-
-Format Version: 3
-Model Type: single_chain
-Max Sequence Length: 576
-
-## Usage
-```python
-from AlignAIR.Models import SingleChainAlignAIR
-model = SingleChainAlignAIR.from_pretrained('PATH_TO_BUNDLE')
-```
-
-## Integrity
-SHA256 fingerprint stored in fingerprint.txt. Do not modify bundle contents manually.

HUMAN_TCRB_IMGT_576/VERSION

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-FORMAT_VERSION=3

HUMAN_TCRB_IMGT_576/config.json

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-{
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-  "v_allele_latent_size": null
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-{
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-  "created_utc": "2026-03-06T09:19:44.001784+00:00",
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-    "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"
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-  "wall_time_seconds": 61645
-}

README.md

@@ -1,118 +1,38 @@
 ---
-language: en
 license: gpl-3.0
+library_name: alignair
 tags:
-  - immunoinformatics
-  - antibody
-  - TCR
+  - immunogenomics
   - AIRR
-  - sequence-alignment
-  - bioinformatics
-  - pytorch
-library_name: alignair
-pipeline_tag: token-classification
+  - antibody
+  - tcr
+  - vdj
 ---
 
-# AlignAIR Pretrained Models
-
-**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.
-
-## Available Models
-
-| Model | Chain | Germline DB | V Alleles | D Alleles | J Alleles | Size |
-|-------|-------|-------------|-----------|-----------|-----------|------|
-| `HUMAN_IGH_OGRDB_576` | IGH (Heavy) | OGRDB | 198 | 33 | 7 | 17 MB |
-| `HUMAN_IGH_EXTENDED_576` | IGH (Heavy) | Extended | 342 | 37 | 10 | 28 MB |
-| `HUMAN_IGK_OGRDB_576` | IGK (Kappa) | OGRDB | 168 | — | 8 | 12 MB |
-| `HUMAN_IGL_OGRDB_576` | IGL (Lambda) | OGRDB | 181 | — | 10 | 13 MB |
-| `HUMAN_TCRB_IMGT_576` | TCRB (Beta) | IMGT | 130 | 3 | 14 | 12 MB |
+# AlignAIR pretrained models
 
-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).
+Official pretrained models for [**AlignAIR**](https://github.com/MuteJester/AlignAIR), a neural aligner
+for immunoglobulin (IG) and T-cell-receptor (TCR) repertoires. This repository is the model **registry**
+the AlignAIR CLI reads from: `registry.json` lists every model + version, and each `<id>/<version>.alignair`
+is a self-contained, **pickle-free** artifact (weights + embedded germline reference + model card).
 
-## Quick Start
+## Use from the CLI (no manual download)
 
 ```bash
-pip install alignair[hub]
-```
-
-### Python API
-
-```python
-from AlignAIR.Models import SingleChainAlignAIR
-from AlignAIR.Hub import get_model_path
-
-# Download and load a model (cached automatically)
-model_path = get_model_path("igh")  # or "HUMAN_IGH_OGRDB_576"
-model = SingleChainAlignAIR.from_pretrained(model_path)
-```
-
-### CLI
-
-```bash
-# Run inference with a pretrained model
-alignair --model-dir HUMAN_IGH_OGRDB_576 input_sequences.csv -o results/
-```
-
-## Benchmark Results (100K synthetic sequences)
-
-| Model | AlignAIR V | IgBLAST V | AlignAIR D | IgBLAST D | AlignAIR J | IgBLAST J | AlignAIR Speed |
-|-------|-----------|-----------|-----------|-----------|-----------|-----------|----------------|
-| IGH OGRDB | 94.1% | 95.5% | 81.7% | 69.8% | 99.3% | 99.5% | 4,272 seq/s |
-| IGH Extended | 92.3% | 93.9% | 88.5% | 82.6% | 98.7% | 98.4% | 4,245 seq/s |
-| IGK OGRDB | 94.6% | 95.4% | — | — | 97.2% | 96.0% | 4,807 seq/s |
-| IGL OGRDB | 93.9% | 95.3% | — | — | 98.4% | 96.7% | 5,384 seq/s |
-| TCRB IMGT | 96.5% | 96.2% | 89.6% | 76.3% | 99.6% | 99.1% | 4,317 seq/s |
-
-Speed measured on NVIDIA RTX 3090 Ti (GPU) vs IgBLAST 1.22.0 (8 CPU threads).
-
-## Model Architecture
-
-Each model is a `SingleChainAlignAIR` module combining:
-- **Nucleotide embedding** (5→64 dim) with center-padded tokenization
-- **Spatial segmentation** via 9-layer dilated convolutions (receptive field = 1023 nt)
-- **Conditioned boundary heads** with chain decoding (v_start → v_end → d_start → ...)
-- **Classification heads** for V/D/J allele assignment
-- **Analysis heads** for mutation rate and productivity prediction
-- **In-model orientation correction** (4-class: forward, reverse-complement, complement, reverse)
-
-## Bundle Format
-
-Each model directory contains:
-- `model.pt` — PyTorch state dict
-- `config.json` — Architecture hyperparameters
-- `dataconfig.pkl` — Germline allele database (GenAIRR DataConfig)
-- `training_meta.json` — Training provenance
-- `VERSION` — Bundle format version
-- `fingerprint.txt` — SHA-256 integrity hash
-
-## Citation
-
-If you use AlignAIR in your research, please cite:
-
-> Konstantinovsky, T., Peres, A., Eisenberg, R., Polak, P., Lindenbaum, O., & Yaari, G. (2025). Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning. *Nucleic Acids Research*, 53(13). https://doi.org/10.1093/nar/gkaf651
-
-```bibtex
-@article{Konstantinovsky2025,
-  title = {Enhancing sequence alignment of adaptive immune receptors through multi-task deep learning},
-  volume = {53},
-  ISSN = {1362-4962},
-  url = {http://dx.doi.org/10.1093/nar/gkaf651},
-  DOI = {10.1093/nar/gkaf651},
-  number = {13},
-  journal = {Nucleic Acids Research},
-  publisher = {Oxford University Press (OUP)},
-  author = {Konstantinovsky, Thomas and Peres, Ayelet and Eisenberg, Ran and Polak, Pazit and Lindenbaum, Ofir and Yaari, Gur},
-  year = {2025},
-  month = jul
-}
+pip install "AlignAIR[cli]"
+alignair models list                       # this catalog, fetched live
+alignair predict --input reads.fasta --out out.tsv --model alignair-igh-human
 ```
 
-## License
+`--model <id>` downloads + hash-verifies + caches the artifact automatically. Pin a version with
+`--model <id>@<version>`.
 
-GPL-3.0. See [LICENSE](https://github.com/MuteJester/AlignAIR/blob/main/LICENSE).
+## Models
 
-## Links
+| id | version | locus | species | description |
+| --- | --- | --- | --- | --- |
+| `alignair-igh-human` | 1.0.0 | IGH | Homo sapiens | Human IGH (heavy chain) aligner — calibrated. GenAIRR OGRDB reference (V198/D33/J7). |
+| `alignair-igkl-human` | 1.0.0 | IGK,IGL | Homo sapiens | Human IGK+IGL (light chain) aligner — calibrated. GenAIRR reference (V349/J18). |
+| `alignair-tcrb-human` | 1.0.0 | TRB | Homo sapiens | Human TRB (TCR beta) aligner — calibrated. GenAIRR reference (V98/D3/J16). |
 
-- [GitHub Repository](https://github.com/MuteJester/AlignAIR)
-- [Documentation](https://mutejester.github.io/AlignAIR/)
-- [PyPI Package](https://pypi.org/project/AlignAIR/)
+Each artifact loads without executing any pickle. Reads are anonymous; publishing is maintainer-only.

HUMAN_IGH_EXTENDED_576/model.pt → alignair-igh-human/1.0.0.alignair

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HUMAN_IGH_OGRDB_576/dataconfig.pkl → alignair-igkl-human/1.0.0.alignair

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HUMAN_IGH_OGRDB_576/model.pt → alignair-tcrb-human/1.0.0.alignair

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registry.json

@@ -0,0 +1,68 @@
+{
+  "models": {
+    "alignair-igh-human": {
+      "description": "Human IGH (heavy chain) aligner \u2014 calibrated. GenAIRR OGRDB reference (V198/D33/J7).",
+      "latest": "1.0.0",
+      "locus": "IGH",
+      "receptor": "IG",
+      "species": "Homo sapiens",
+      "versions": {
+        "1.0.0": {
+          "allele_order_sha256": "d615b59babba6902cb876ed415809df8e565682511dc9ab6032d2fc294dd582a",
+          "artifact_sha256": "c418a72cda22e81b0ff5f63eba55c4cb61e7fed7e220f6dc64bd5dfafb801b59",
+          "created_by_alignair": "2.0.0",
+          "file": "alignair-igh-human/1.0.0.alignair",
+          "metrics": null,
+          "min_alignair": "2.0.0",
+          "model_format_version": 1,
+          "reference_fasta_sha256": "b8db09eb86080c888ded27cc430f74b51bad535bfb91c4ba8ab0114c49d5cb8b",
+          "size": 57325936,
+          "trained": "2026-07-13T12:09:45Z"
+        }
+      }
+    },
+    "alignair-igkl-human": {
+      "description": "Human IGK+IGL (light chain) aligner \u2014 calibrated. GenAIRR reference (V349/J18).",
+      "latest": "1.0.0",
+      "locus": "IGK,IGL",
+      "receptor": "IG",
+      "species": "Homo sapiens",
+      "versions": {
+        "1.0.0": {
+          "allele_order_sha256": "d32cd6fe79114117a504def1321ee831d60c95ef585e1127358d6be36a826463",
+          "artifact_sha256": "c6aa29a7ae7eb4f061aead2727d73e2f107db3e249159f959536973dd86451d1",
+          "created_by_alignair": "2.0.0",
+          "file": "alignair-igkl-human/1.0.0.alignair",
+          "metrics": null,
+          "min_alignair": "2.0.0",
+          "model_format_version": 1,
+          "reference_fasta_sha256": "9ac60e7d6b7577b5e383cc3f8b72a1958f0d707cd4a2b9e3c9153fb181a99064",
+          "size": 45704181,
+          "trained": "2026-07-13T12:19:48Z"
+        }
+      }
+    },
+    "alignair-tcrb-human": {
+      "description": "Human TRB (TCR beta) aligner \u2014 calibrated. GenAIRR reference (V98/D3/J16).",
+      "latest": "1.0.0",
+      "locus": "TRB",
+      "receptor": "TR",
+      "species": "Homo sapiens",
+      "versions": {
+        "1.0.0": {
+          "allele_order_sha256": "657d771a8952784d913936d5eef1020ac0395528266790cae23ec928b935c359",
+          "artifact_sha256": "c3824e64cf492faf6647ad3998d3fea21034041f503358fe0f1379987424878c",
+          "created_by_alignair": "2.0.0",
+          "file": "alignair-tcrb-human/1.0.0.alignair",
+          "metrics": null,
+          "min_alignair": "2.0.0",
+          "model_format_version": 1,
+          "reference_fasta_sha256": "3f5e4eee0c096ae2fad547713e7284ff6ab46f7ee148f8479aba077e3545f68d",
+          "size": 56521703,
+          "trained": "2026-07-13T12:19:40Z"
+        }
+      }
+    }
+  },
+  "schema": "alignair.registry.v1"
+}