jialinzhang commited on
Commit
3477ac7
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1 Parent(s): 453982c

Add syntheticSuccess c3

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  1. syntheticSuccess/c3/arf/arf-c3-20260321_060642/_arf_generate.py +6 -0
  2. syntheticSuccess/c3/arf/arf-c3-20260321_060642/_arf_train.py +19 -0
  3. syntheticSuccess/c3/arf/arf-c3-20260321_060642/arf-c3-1000-20260321_060705.csv +3 -0
  4. syntheticSuccess/c3/arf/arf-c3-20260321_060642/arf-c3-2551-20260330_065245.csv +3 -0
  5. syntheticSuccess/c3/arf/arf-c3-20260321_060642/arf_model.pkl +3 -0
  6. syntheticSuccess/c3/arf/arf-c3-20260321_060642/gen_20260321_060705.log +3 -0
  7. syntheticSuccess/c3/arf/arf-c3-20260321_060642/gen_20260330_065245.log +3 -0
  8. syntheticSuccess/c3/arf/arf-c3-20260321_060642/input_snapshot.json +36 -0
  9. syntheticSuccess/c3/arf/arf-c3-20260321_060642/public_gate/normalized_schema_snapshot.json +68 -0
  10. syntheticSuccess/c3/arf/arf-c3-20260321_060642/public_gate/public_gate_report.json +37 -0
  11. syntheticSuccess/c3/arf/arf-c3-20260321_060642/public_gate/staged_input_manifest.json +73 -0
  12. syntheticSuccess/c3/arf/arf-c3-20260321_060642/runtime_result.json +14 -0
  13. syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/arf/adapter_report.json +7 -0
  14. syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/arf/adapter_transforms_applied.json +1 -0
  15. syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/arf/model_input_manifest.json +75 -0
  16. syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/public/staged_features.json +17 -0
  17. syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/public/test.csv +3 -0
  18. syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/public/train.csv +3 -0
  19. syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/public/val.csv +3 -0
  20. syntheticSuccess/c3/arf/arf-c3-20260321_060642/train_20260321_060642.log +3 -0
  21. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/_bayesnet_generate.py +43 -0
  22. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/_bayesnet_train.py +62 -0
  23. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/bayesnet-c3-1000-20260321_060813.csv +3 -0
  24. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/bayesnet-c3-2551-20260330_065246.csv +3 -0
  25. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/bayesnet_model.pkl +3 -0
  26. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/const_cols.json +1 -0
  27. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/gen_20260321_060813.log +3 -0
  28. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/gen_20260330_065246.log +3 -0
  29. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/input_snapshot.json +36 -0
  30. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/public_gate/normalized_schema_snapshot.json +68 -0
  31. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/public_gate/public_gate_report.json +37 -0
  32. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/public_gate/staged_input_manifest.json +73 -0
  33. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/runtime_result.json +14 -0
  34. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/staged/bayesnet/adapter_report.json +7 -0
  35. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/staged/bayesnet/adapter_transforms_applied.json +1 -0
  36. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/staged/bayesnet/model_input_manifest.json +75 -0
  37. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/staged/public/staged_features.json +17 -0
  38. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/staged/public/test.csv +3 -0
  39. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/staged/public/train.csv +3 -0
  40. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/staged/public/val.csv +3 -0
  41. syntheticSuccess/c3/bayesnet/bayesnet-c3-20260321_060730/train_20260321_060730.log +3 -0
  42. syntheticSuccess/c3/ctgan/ctgan-c3-20260322_064041/ctgan-c3-1000-20260322_064442.csv +3 -0
  43. syntheticSuccess/c3/ctgan/ctgan-c3-20260322_064041/ctgan-c3-2551-20260330_065244.csv +3 -0
  44. syntheticSuccess/c3/ctgan/ctgan-c3-20260322_064041/ctgan_metadata.json +16 -0
  45. syntheticSuccess/c3/ctgan/ctgan-c3-20260322_064041/gen_20260322_064442.log +0 -0
  46. syntheticSuccess/c3/ctgan/ctgan-c3-20260322_064041/gen_20260330_065244.log +0 -0
  47. syntheticSuccess/c3/ctgan/ctgan-c3-20260322_064041/input_snapshot.json +36 -0
  48. syntheticSuccess/c3/ctgan/ctgan-c3-20260322_064041/models_300epochs/ctgan_300epochs.pt +3 -0
  49. syntheticSuccess/c3/ctgan/ctgan-c3-20260322_064041/models_300epochs/train_20260322_064041.log +3 -0
  50. syntheticSuccess/c3/ctgan/ctgan-c3-20260322_064041/public_gate/normalized_schema_snapshot.json +68 -0
syntheticSuccess/c3/arf/arf-c3-20260321_060642/_arf_generate.py ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ import pickle
2
+ with open("/work/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/arf_model.pkl", "rb") as f:
3
+ model = pickle.load(f)
4
+ syn = model.forge(n=2551)
5
+ syn.to_csv("/work/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/arf-c3-2551-20260330_065245.csv", index=False)
6
+ print(f"[ARF] Generated 2551 rows -> /work/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/arf-c3-2551-20260330_065245.csv")
syntheticSuccess/c3/arf/arf-c3-20260321_060642/_arf_train.py ADDED
@@ -0,0 +1,19 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ import pickle
2
+ import pandas as pd
3
+ from arfpy import arf
4
+
5
+ df = pd.read_csv("/work/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/staged/public/train.csv")
6
+ df = df.dropna(axis=1, how="all")
7
+ print(f"[ARF] Training on {len(df)} rows, {len(df.columns)} cols")
8
+
9
+ model = arf.arf(x=df)
10
+ if hasattr(model, "fit"):
11
+ model.fit()
12
+ elif hasattr(model, "forde"):
13
+ model.forde()
14
+ else:
15
+ raise RuntimeError("arfpy API: no fit() / forde()")
16
+
17
+ with open("/work/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/arf_model.pkl", "wb") as f:
18
+ pickle.dump(model, f)
19
+ print(f"[ARF] Model saved -> /work/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/arf_model.pkl")
syntheticSuccess/c3/arf/arf-c3-20260321_060642/arf-c3-1000-20260321_060705.csv ADDED
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+ oid sha256:cd6feeac5fc8ee5ba53b9fab2fa83e64fb1a51515c93b117742d8717fb3bba38
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+ size 82553
syntheticSuccess/c3/arf/arf-c3-20260321_060642/arf-c3-2551-20260330_065245.csv ADDED
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+ version https://git-lfs.github.com/spec/v1
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+ size 210860
syntheticSuccess/c3/arf/arf-c3-20260321_060642/arf_model.pkl ADDED
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+ version https://git-lfs.github.com/spec/v1
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+ size 11138547
syntheticSuccess/c3/arf/arf-c3-20260321_060642/gen_20260321_060705.log ADDED
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syntheticSuccess/c3/arf/arf-c3-20260321_060642/input_snapshot.json ADDED
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+ {
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+ "dataset_id": "c3",
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+ "model": "arf",
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+ "inputs": {
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+ "train_csv": {
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+ "path": "/data/jialinzhang/SynthesizePipeline-server/DatasetNew/c3/c3-train.csv",
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+ "path": "/data/jialinzhang/SynthesizePipeline-server/DatasetNew/c3/c3-val.csv",
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+ "sha256": "5f384eded9999ef705f6b10ae0d20ce981a1b92339d451e7feb3946e95fdcbd9"
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+ },
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+ "test_csv": {
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+ "path": "/data/jialinzhang/SynthesizePipeline-server/DatasetNew/c3/c3-test.csv",
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+ "exists": true,
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+ "profile_json": {
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+ "sha256": "dfb01e28765bec4ac04cdb273987b23581194b35638d6450dac66f4525614335"
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+ },
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+ "contract_json": {
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+ "path": "/data/jialinzhang/SynthesizePipeline-server/DatasetNew/artifacts/data_core/tabular/c3/c3-dataset_contract_v1.json",
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+ "exists": true,
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+ "size": 2422,
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+ "sha256": "a408b4f800a67fc20e9bc37e847c54de7ed6f608b93d440c3933dead213acfca"
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+ }
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+ }
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+ }
syntheticSuccess/c3/arf/arf-c3-20260321_060642/public_gate/normalized_schema_snapshot.json ADDED
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+ {
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+ "dataset_id": "c3",
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+ "target_column": "EI",
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+ "task_type": "classification",
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+ "columns": [
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+ {
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+ "name": "EI",
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+ "HUMNEBB-NEG-241",
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+ "HUMATP1A2-NEG-2101"
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+ ]
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+ }
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+ },
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+ {
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+ "name": "CCAGCTGCATCACAGGAGGCCAGCGAGCAGGTCTGTTCCAAGGGCCTTCGAGCCAGTCTG",
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+ "role": "id",
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+ "semantic_type": "id",
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+ "nullable": false,
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+ "TCTGGGCTCCCAGAACCCACAACATGAAAGGTGAGGGNCTTCCTGCCACACTTGGGGTGG",
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+ "TTGCTCAGCCTCGCTGCTTGCCTCCTGCAGACGCCGCCAGGCCGAGCCAGTTCCGGGTGT",
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+ "GGGACTCTGACCATCTGTTCCCACATTCAGCAAGTTCATTCCTGAGGGCTCCCAGAGAGT",
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+ "GCCAACTACAGGAACGTGATCCATACCTACAACATGCTTCCTGATGCCATGAGCTTTGAA",
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+ "GGGAGTCCTAGCCTGAGAGGCTGGGGGTCCATTTTGAGGTTAGAGAGGGGCAGTAGAGCA"
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+ ]
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+ }
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+ }
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+ ]
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+ }
syntheticSuccess/c3/arf/arf-c3-20260321_060642/public_gate/public_gate_report.json ADDED
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+ {
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+ "dataset_id": "c3",
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+ "status": "pass",
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+ "check_id": "PG001_csv_parse_ok",
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+ "status": "pass"
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+ "status": "pass"
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+ {
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+ "status": "pass"
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+ },
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+ {
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+ "check_id": "PG005_semantic_type_validated",
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+ "status": "pass"
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+ },
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+ {
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+ "check_id": "PG006_target_defined_and_valid",
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+ "status": "pass"
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+ }
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+ ],
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+ "target_column": "EI",
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+ "task_type": "classification",
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+ "input_splits": {
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+ "train": "/data/jialinzhang/SynthesizePipeline-server/DatasetNew/c3/c3-train.csv",
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+ "val": "/data/jialinzhang/SynthesizePipeline-server/DatasetNew/c3/c3-val.csv",
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+ "test": "/data/jialinzhang/SynthesizePipeline-server/DatasetNew/c3/c3-test.csv"
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+ }
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+ }
syntheticSuccess/c3/arf/arf-c3-20260321_060642/public_gate/staged_input_manifest.json ADDED
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+ {
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+ "dataset_id": "c3",
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+ "target_column": "EI",
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+ "task_type": "classification",
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+ "train_csv": "/data/jialinzhang/SynthesizePipeline-server/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/staged/public/train.csv",
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+ "val_csv": "/data/jialinzhang/SynthesizePipeline-server/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/staged/public/val.csv",
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+ "test_csv": "/data/jialinzhang/SynthesizePipeline-server/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/staged/public/test.csv",
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+ "features_json": "/data/jialinzhang/SynthesizePipeline-server/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/staged/public/staged_features.json",
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+ "public_gate_report": "/data/jialinzhang/SynthesizePipeline-server/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/public_gate/public_gate_report.json",
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+ "column_schema": [
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+ {
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+ "name": "EI",
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+ "role": "target",
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+ "example_values": [
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+ "HUMH19-DONOR-2562",
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+ "HUMMHCD8A-ACCEPTOR-733",
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+ "HUMGCB1-ACCEPTOR-6344",
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+ "HUMNEBB-NEG-241",
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+ "HUMATP1A2-NEG-2101"
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+ ]
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+ }
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+ },
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+ {
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+ "name": "CCAGCTGCATCACAGGAGGCCAGCGAGCAGGTCTGTTCCAAGGGCCTTCGAGCCAGTCTG",
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+ "role": "id",
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+ "semantic_type": "id",
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+ "nullable": false,
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+ "impute_strategy": "keep_raw",
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+ "example_values": [
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+ "TCTGGGCTCCCAGAACCCACAACATGAAAGGTGAGGGNCTTCCTGCCACACTTGGGGTGG",
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+ "GGGACTCTGACCATCTGTTCCCACATTCAGCAAGTTCATTCCTGAGGGCTCCCAGAGAGT",
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+ "GCCAACTACAGGAACGTGATCCATACCTACAACATGCTTCCTGATGCCATGAGCTTTGAA",
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+ "GGGAGTCCTAGCCTGAGAGGCTGGGGGTCCATTTTGAGGTTAGAGAGGGGCAGTAGAGCA"
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+ ]
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+ }
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+ }
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+ ]
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+ }
syntheticSuccess/c3/arf/arf-c3-20260321_060642/runtime_result.json ADDED
@@ -0,0 +1,14 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ {
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+ "dataset_id": "c3",
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+ "model": "arf",
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+ "run_id": "arf-c3-20260321_060642",
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+ "public_gate_status": "pass",
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+ "adapter_ready_status": "pass",
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+ "train_status": "skipped",
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+ "generate_status": "success",
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+ "reason_code": null,
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+ "artifacts": {
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+ "synthetic_csv": "/data/jialinzhang/SynthesizePipeline-server/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/arf-c3-2551-20260330_065245.csv"
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+ }
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+ }
syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/arf/adapter_report.json ADDED
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+ {
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+ "adapter_ready_status": "pass",
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+ "adapter_transforms_applied": [],
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+ "model_input_manifest": "/data/jialinzhang/SynthesizePipeline-server/output-SpecializedModels/c3/arf/arf-c3-20260321_060642/staged/arf/model_input_manifest.json"
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+ }
syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/arf/adapter_transforms_applied.json ADDED
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+ []
syntheticSuccess/c3/arf/arf-c3-20260321_060642/staged/arf/model_input_manifest.json ADDED
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+ {
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+ "dataset_id": "c3",
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+ "model": "arf",
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+ "target_column": "EI",
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+ "task_type": "classification",
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+ "column_schema": [
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+ {
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+ import subprocess, sys, os
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+
3
+ pip_libs = "/pip_libs"
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+ sys.path.insert(0, pip_libs)
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+ os.environ["PYTHONPATH"] = pip_libs + os.pathsep + os.environ.get("PYTHONPATH", "")
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+
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+ def _ensure_deps():
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+ try:
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+ import synthcity
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+ except ModuleNotFoundError:
11
+ print("[BayesNet] synthcity not found - installing to cache...")
12
+ subprocess.run(
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+ [sys.executable, "-m", "pip", "install",
14
+ "--target", pip_libs, "synthcity==0.2.12", "numpy<2", "-q"],
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+ check=True
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+ )
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+ import shutil, glob
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+ for pat in ["torch", "torch-*", "torchvision", "torchvision-*",
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+ "torchvision.libs", "torchgen", "nvidia*", "triton*"]:
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+ for p in glob.glob(os.path.join(pip_libs, pat)):
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+ if os.path.isdir(p): shutil.rmtree(p)
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+ else: os.remove(p)
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+ if pip_libs not in sys.path:
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+ sys.path.insert(0, pip_libs)
25
+
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+ _ensure_deps()
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+
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+ import pickle, json as _json
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+ with open("/work/output-SpecializedModels/c3/bayesnet/bayesnet-c3-20260321_060730/bayesnet_model.pkl", "rb") as f:
30
+ plugin = pickle.load(f)
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+ syn = plugin.generate(count=2551).dataframe()
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+
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+ # Restore zero-variance columns that were dropped during training
34
+ const_path = "/work/output-SpecializedModels/c3/bayesnet/bayesnet-c3-20260321_060730/bayesnet_model.pkl".replace("bayesnet_model.pkl", "const_cols.json")
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+ if os.path.exists(const_path):
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+ const_cols = _json.load(_f)
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+ for col, val in const_cols.items():
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+ syn[col] = val
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+ print(f"[BayesNet] Restored constant column '{col}' = {val}")
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+
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+ print(f"[BayesNet] Generated 2551 rows -> /work/output-SpecializedModels/c3/bayesnet/bayesnet-c3-20260321_060730/bayesnet-c3-2551-20260330_065246.csv")
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1
+ import subprocess, sys, os
2
+
3
+ pip_libs = "/pip_libs"
4
+ sys.path.insert(0, pip_libs)
5
+ os.environ["PYTHONPATH"] = pip_libs + os.pathsep + os.environ.get("PYTHONPATH", "")
6
+
7
+ def _ensure_deps():
8
+ try:
9
+ import synthcity
10
+ except ModuleNotFoundError:
11
+ print("[BayesNet] synthcity not found - installing to cache (first run, may take minutes)...")
12
+ # Install synthcity with numpy<2 to avoid conflicts
13
+ subprocess.run(
14
+ [sys.executable, "-m", "pip", "install",
15
+ "--target", pip_libs, "synthcity==0.2.12", "numpy<2", "-q"],
16
+ check=True
17
+ )
18
+ # Remove torch/torchvision from pip_libs to avoid shadowing system versions
19
+ import shutil, glob
20
+ for pat in ["torch", "torch-*", "torchvision", "torchvision-*",
21
+ "torchvision.libs", "torchgen", "nvidia*", "triton*"]:
22
+ for p in glob.glob(os.path.join(pip_libs, pat)):
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+ if os.path.isdir(p): shutil.rmtree(p)
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+ else: os.remove(p)
25
+ if pip_libs not in sys.path:
26
+ sys.path.insert(0, pip_libs)
27
+
28
+ _ensure_deps()
29
+
30
+ from synthcity.plugins import Plugins
31
+ import pickle
32
+ import pandas as pd
33
+ from synthcity.plugins.core.dataloader import GenericDataLoader
34
+
35
+ df = pd.read_csv("/work/output-SpecializedModels/c3/bayesnet/bayesnet-c3-20260321_060730/staged/public/train.csv")
36
+ df = df.dropna(axis=1, how="all")
37
+
38
+ # Drop zero-variance columns (only 1 unique value) to avoid
39
+ # synthcity encoder KeyError during generation
40
+ import json as _json
41
+ const_cols = {}
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+ for col in list(df.columns):
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+ nuniq = df[col].nunique()
44
+ if nuniq <= 1:
45
+ const_cols[col] = df[col].iloc[0] if len(df) > 0 else None
46
+ df = df.drop(columns=[col])
47
+ print(f"[BayesNet] Dropped zero-variance column '{col}' (value={const_cols[col]})")
48
+
49
+ # Save constant columns info so generate can restore them
50
+ const_path = "/work/output-SpecializedModels/c3/bayesnet/bayesnet-c3-20260321_060730/bayesnet_model.pkl".replace("bayesnet_model.pkl", "const_cols.json")
51
+ with open(const_path, "w") as _f:
52
+ _json.dump({k: str(v) for k, v in const_cols.items()}, _f)
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+
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+ print(f"[BayesNet] Training on {len(df)} rows, {len(df.columns)} cols")
55
+
56
+ loader = GenericDataLoader(df)
57
+ plugin = Plugins().get("bayesian_network")
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+ plugin.fit(loader)
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+
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+ with open("/work/output-SpecializedModels/c3/bayesnet/bayesnet-c3-20260321_060730/bayesnet_model.pkl", "wb") as f:
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+ pickle.dump(plugin, f)
62
+ print(f"[BayesNet] Model saved -> /work/output-SpecializedModels/c3/bayesnet/bayesnet-c3-20260321_060730/bayesnet_model.pkl")
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