Initial siRBench model artifacts

.gitignore

@@ -0,0 +1,3 @@
+__pycache__/
+*.pyc
+*.pyo

README.md

@@ -0,0 +1,38 @@
+# siRBench Model
+
+Runtime artifacts for the siRBench predictor Space.
+
+This repo is intended to store the files required for inference:
+
+- `xgb_model.json`
+- `lgbm_model.txt`
+- `calibrator.joblib`
+- `feature_artifacts.json`
+
+Optional diagnostics included for inspection:
+
+- `metrics.json`
+- `training_summary.json`
+- `validation_predictions.csv`
+- `quintile_bias.csv`
+- `source_bias.csv`
+- `cell_line_bias.csv`
+
+## Intended consumer
+
+The main consumer is the Docker Space:
+
+- `dimostzim/siRBench-predictor`
+
+That app expects two input sequences:
+
+- `siRNA`
+- `mRNA` target window
+
+The app then computes the engineered feature set and loads these model artifacts
+from the Hub.
+
+## Notes
+
+- This repo stores inference artifacts, not training code.
+- The final prediction is a calibrated ensemble of XGBoost and LightGBM models.

cell_line_bias.csv

@@ -0,0 +1,7 @@
+cell_line,true_mean,pred_mean,bias,count
+h1299,0.5130985379219055,0.5078434794030154,-0.005255058518890077,213
+halacat,0.550000011920929,0.5331791661679744,-0.016820845752954505,4
+hek293,0.722631573677063,0.7566094329615726,0.03397785928450958,19
+hek293t,0.5916666388511658,0.6565767838916264,0.06491014504046067,6
+hep3b,0.7516667246818542,0.7609096513707019,0.00924292668884763,30
+t24,0.5862499475479126,0.5705365809016832,-0.015713366646229354,8

feature_artifacts.json

@@ -0,0 +1,507 @@
+{
+  "categories": [
+    [
+      "Huesken",
+      "Simone",
+      "amarz",
+      "hsieh",
+      "khvorova",
+      "reynolds",
+      "vickers"
+    ],
+    [
+      "h1299",
+      "halacat",
+      "hek293",
+      "hek293t",
+      "hep3b",
+      "t24"
+    ]
+  ],
+  "category_feature_names": [
+    "source_Huesken",
+    "source_Simone",
+    "source_amarz",
+    "source_hsieh",
+    "source_khvorova",
+    "source_reynolds",
+    "source_vickers",
+    "cell_line_h1299",
+    "cell_line_halacat",
+    "cell_line_hek293",
+    "cell_line_hek293t",
+    "cell_line_hep3b",
+    "cell_line_t24"
+  ],
+  "numeric_cols": [
+    "ends",
+    "DG_total",
+    "DH_total",
+    "DG_pos1",
+    "DG_pos2",
+    "DG_pos3",
+    "DG_pos4",
+    "DG_pos5",
+    "DG_pos6",
+    "DG_pos7",
+    "DG_pos8",
+    "DG_pos9",
+    "DG_pos10",
+    "DG_pos11",
+    "DG_pos12",
+    "DG_pos13",
+    "DG_pos14",
+    "DG_pos15",
+    "DG_pos16",
+    "DG_pos17",
+    "DG_pos18",
+    "DH_pos1",
+    "DH_pos2",
+    "DH_pos3",
+    "DH_pos4",
+    "DH_pos5",
+    "DH_pos6",
+    "DH_pos7",
+    "DH_pos8",
+    "DH_pos9",
+    "DH_pos10",
+    "DH_pos11",
+    "DH_pos12",
+    "DH_pos13",
+    "DH_pos14",
+    "DH_pos15",
+    "DH_pos16",
+    "DH_pos17",
+    "DH_pos18",
+    "single_energy_total",
+    "single_energy_pos1",
+    "single_energy_pos2",
+    "single_energy_pos3",
+    "single_energy_pos4",
+    "single_energy_pos5",
+    "single_energy_pos6",
+    "single_energy_pos7",
+    "single_energy_pos8",
+    "single_energy_pos9",
+    "single_energy_pos10",
+    "single_energy_pos11",
+    "single_energy_pos12",
+    "single_energy_pos13",
+    "single_energy_pos14",
+    "single_energy_pos15",
+    "single_energy_pos16",
+    "single_energy_pos17",
+    "single_energy_pos18",
+    "single_energy_pos19",
+    "duplex_energy_total",
+    "duplex_energy_sirna_pos1",
+    "duplex_energy_sirna_pos2",
+    "duplex_energy_sirna_pos3",
+    "duplex_energy_sirna_pos4",
+    "duplex_energy_sirna_pos5",
+    "duplex_energy_sirna_pos6",
+    "duplex_energy_sirna_pos7",
+    "duplex_energy_sirna_pos8",
+    "duplex_energy_sirna_pos9",
+    "duplex_energy_sirna_pos10",
+    "duplex_energy_sirna_pos11",
+    "duplex_energy_sirna_pos12",
+    "duplex_energy_sirna_pos13",
+    "duplex_energy_sirna_pos14",
+    "duplex_energy_sirna_pos15",
+    "duplex_energy_sirna_pos16",
+    "duplex_energy_sirna_pos17",
+    "duplex_energy_sirna_pos18",
+    "duplex_energy_sirna_pos19",
+    "duplex_energy_target_pos1",
+    "duplex_energy_target_pos2",
+    "duplex_energy_target_pos3",
+    "duplex_energy_target_pos4",
+    "duplex_energy_target_pos5",
+    "duplex_energy_target_pos6",
+    "duplex_energy_target_pos7",
+    "duplex_energy_target_pos8",
+    "duplex_energy_target_pos9",
+    "duplex_energy_target_pos10",
+    "duplex_energy_target_pos11",
+    "duplex_energy_target_pos12",
+    "duplex_energy_target_pos13",
+    "duplex_energy_target_pos14",
+    "duplex_energy_target_pos15",
+    "duplex_energy_target_pos16",
+    "duplex_energy_target_pos17",
+    "duplex_energy_target_pos18",
+    "duplex_energy_target_pos19",
+    "RNAup_open_dG",
+    "RNAup_interaction_dG"
+  ],
+  "feature_names": [
+    "siRNA_pos1_A",
+    "siRNA_pos1_C",
+    "siRNA_pos1_G",
+    "siRNA_pos1_U",
+    "siRNA_pos2_A",
+    "siRNA_pos2_C",
+    "siRNA_pos2_G",
+    "siRNA_pos2_U",
+    "siRNA_pos3_A",
+    "siRNA_pos3_C",
+    "siRNA_pos3_G",
+    "siRNA_pos3_U",
+    "siRNA_pos4_A",
+    "siRNA_pos4_C",
+    "siRNA_pos4_G",
+    "siRNA_pos4_U",
+    "siRNA_pos5_A",
+    "siRNA_pos5_C",
+    "siRNA_pos5_G",
+    "siRNA_pos5_U",
+    "siRNA_pos6_A",
+    "siRNA_pos6_C",
+    "siRNA_pos6_G",
+    "siRNA_pos6_U",
+    "siRNA_pos7_A",
+    "siRNA_pos7_C",
+    "siRNA_pos7_G",
+    "siRNA_pos7_U",
+    "siRNA_pos8_A",
+    "siRNA_pos8_C",
+    "siRNA_pos8_G",
+    "siRNA_pos8_U",
+    "siRNA_pos9_A",
+    "siRNA_pos9_C",
+    "siRNA_pos9_G",
+    "siRNA_pos9_U",
+    "siRNA_pos10_A",
+    "siRNA_pos10_C",
+    "siRNA_pos10_G",
+    "siRNA_pos10_U",
+    "siRNA_pos11_A",
+    "siRNA_pos11_C",
+    "siRNA_pos11_G",
+    "siRNA_pos11_U",
+    "siRNA_pos12_A",
+    "siRNA_pos12_C",
+    "siRNA_pos12_G",
+    "siRNA_pos12_U",
+    "siRNA_pos13_A",
+    "siRNA_pos13_C",
+    "siRNA_pos13_G",
+    "siRNA_pos13_U",
+    "siRNA_pos14_A",
+    "siRNA_pos14_C",
+    "siRNA_pos14_G",
+    "siRNA_pos14_U",
+    "siRNA_pos15_A",
+    "siRNA_pos15_C",
+    "siRNA_pos15_G",
+    "siRNA_pos15_U",
+    "siRNA_pos16_A",
+    "siRNA_pos16_C",
+    "siRNA_pos16_G",
+    "siRNA_pos16_U",
+    "siRNA_pos17_A",
+    "siRNA_pos17_C",
+    "siRNA_pos17_G",
+    "siRNA_pos17_U",
+    "siRNA_pos18_A",
+    "siRNA_pos18_C",
+    "siRNA_pos18_G",
+    "siRNA_pos18_U",
+    "siRNA_pos19_A",
+    "siRNA_pos19_C",
+    "siRNA_pos19_G",
+    "siRNA_pos19_U",
+    "mRNA_pos1_A",
+    "mRNA_pos1_C",
+    "mRNA_pos1_G",
+    "mRNA_pos1_U",
+    "mRNA_pos2_A",
+    "mRNA_pos2_C",
+    "mRNA_pos2_G",
+    "mRNA_pos2_U",
+    "mRNA_pos3_A",
+    "mRNA_pos3_C",
+    "mRNA_pos3_G",
+    "mRNA_pos3_U",
+    "mRNA_pos4_A",
+    "mRNA_pos4_C",
+    "mRNA_pos4_G",
+    "mRNA_pos4_U",
+    "mRNA_pos5_A",
+    "mRNA_pos5_C",
+    "mRNA_pos5_G",
+    "mRNA_pos5_U",
+    "mRNA_pos6_A",
+    "mRNA_pos6_C",
+    "mRNA_pos6_G",
+    "mRNA_pos6_U",
+    "mRNA_pos7_A",
+    "mRNA_pos7_C",
+    "mRNA_pos7_G",
+    "mRNA_pos7_U",
+    "mRNA_pos8_A",
+    "mRNA_pos8_C",
+    "mRNA_pos8_G",
+    "mRNA_pos8_U",
+    "mRNA_pos9_A",
+    "mRNA_pos9_C",
+    "mRNA_pos9_G",
+    "mRNA_pos9_U",
+    "mRNA_pos10_A",
+    "mRNA_pos10_C",
+    "mRNA_pos10_G",
+    "mRNA_pos10_U",
+    "mRNA_pos11_A",
+    "mRNA_pos11_C",
+    "mRNA_pos11_G",
+    "mRNA_pos11_U",
+    "mRNA_pos12_A",
+    "mRNA_pos12_C",
+    "mRNA_pos12_G",
+    "mRNA_pos12_U",
+    "mRNA_pos13_A",
+    "mRNA_pos13_C",
+    "mRNA_pos13_G",
+    "mRNA_pos13_U",
+    "mRNA_pos14_A",
+    "mRNA_pos14_C",
+    "mRNA_pos14_G",
+    "mRNA_pos14_U",
+    "mRNA_pos15_A",
+    "mRNA_pos15_C",
+    "mRNA_pos15_G",
+    "mRNA_pos15_U",
+    "mRNA_pos16_A",
+    "mRNA_pos16_C",
+    "mRNA_pos16_G",
+    "mRNA_pos16_U",
+    "mRNA_pos17_A",
+    "mRNA_pos17_C",
+    "mRNA_pos17_G",
+    "mRNA_pos17_U",
+    "mRNA_pos18_A",
+    "mRNA_pos18_C",
+    "mRNA_pos18_G",
+    "mRNA_pos18_U",
+    "mRNA_pos19_A",
+    "mRNA_pos19_C",
+    "mRNA_pos19_G",
+    "mRNA_pos19_U",
+    "inter_wc_pos1",
+    "inter_wc_pos2",
+    "inter_wc_pos3",
+    "inter_wc_pos4",
+    "inter_wc_pos5",
+    "inter_wc_pos6",
+    "inter_wc_pos7",
+    "inter_wc_pos8",
+    "inter_wc_pos9",
+    "inter_wc_pos10",
+    "inter_wc_pos11",
+    "inter_wc_pos12",
+    "inter_wc_pos13",
+    "inter_wc_pos14",
+    "inter_wc_pos15",
+    "inter_wc_pos16",
+    "inter_wc_pos17",
+    "inter_wc_pos18",
+    "inter_wc_pos19",
+    "inter_wobble_pos1",
+    "inter_wobble_pos2",
+    "inter_wobble_pos3",
+    "inter_wobble_pos4",
+    "inter_wobble_pos5",
+    "inter_wobble_pos6",
+    "inter_wobble_pos7",
+    "inter_wobble_pos8",
+    "inter_wobble_pos9",
+    "inter_wobble_pos10",
+    "inter_wobble_pos11",
+    "inter_wobble_pos12",
+    "inter_wobble_pos13",
+    "inter_wobble_pos14",
+    "inter_wobble_pos15",
+    "inter_wobble_pos16",
+    "inter_wobble_pos17",
+    "inter_wobble_pos18",
+    "inter_wobble_pos19",
+    "inter_mismatch_pos1",
+    "inter_mismatch_pos2",
+    "inter_mismatch_pos3",
+    "inter_mismatch_pos4",
+    "inter_mismatch_pos5",
+    "inter_mismatch_pos6",
+    "inter_mismatch_pos7",
+    "inter_mismatch_pos8",
+    "inter_mismatch_pos9",
+    "inter_mismatch_pos10",
+    "inter_mismatch_pos11",
+    "inter_mismatch_pos12",
+    "inter_mismatch_pos13",
+    "inter_mismatch_pos14",
+    "inter_mismatch_pos15",
+    "inter_mismatch_pos16",
+    "inter_mismatch_pos17",
+    "inter_mismatch_pos18",
+    "inter_mismatch_pos19",
+    "total_wc",
+    "total_wobble",
+    "total_mismatch",
+    "seed_wc",
+    "seed_wobble",
+    "si_mono_A",
+    "si_mono_C",
+    "si_mono_G",
+    "si_mono_U",
+    "si_di_0",
+    "si_di_1",
+    "si_di_2",
+    "si_di_3",
+    "si_di_4",
+    "si_di_5",
+    "si_di_6",
+    "si_di_7",
+    "si_di_8",
+    "si_di_9",
+    "si_di_10",
+    "si_di_11",
+    "si_di_12",
+    "si_di_13",
+    "si_di_14",
+    "si_di_15",
+    "mr_mono_A",
+    "mr_mono_C",
+    "mr_mono_G",
+    "mr_mono_U",
+    "mr_di_0",
+    "mr_di_1",
+    "mr_di_2",
+    "mr_di_3",
+    "mr_di_4",
+    "mr_di_5",
+    "mr_di_6",
+    "mr_di_7",
+    "mr_di_8",
+    "mr_di_9",
+    "mr_di_10",
+    "mr_di_11",
+    "mr_di_12",
+    "mr_di_13",
+    "mr_di_14",
+    "mr_di_15",
+    "ends",
+    "DG_total",
+    "DH_total",
+    "DG_pos1",
+    "DG_pos2",
+    "DG_pos3",
+    "DG_pos4",
+    "DG_pos5",
+    "DG_pos6",
+    "DG_pos7",
+    "DG_pos8",
+    "DG_pos9",
+    "DG_pos10",
+    "DG_pos11",
+    "DG_pos12",
+    "DG_pos13",
+    "DG_pos14",
+    "DG_pos15",
+    "DG_pos16",
+    "DG_pos17",
+    "DG_pos18",
+    "DH_pos1",
+    "DH_pos2",
+    "DH_pos3",
+    "DH_pos4",
+    "DH_pos5",
+    "DH_pos6",
+    "DH_pos7",
+    "DH_pos8",
+    "DH_pos9",
+    "DH_pos10",
+    "DH_pos11",
+    "DH_pos12",
+    "DH_pos13",
+    "DH_pos14",
+    "DH_pos15",
+    "DH_pos16",
+    "DH_pos17",
+    "DH_pos18",
+    "single_energy_total",
+    "single_energy_pos1",
+    "single_energy_pos2",
+    "single_energy_pos3",
+    "single_energy_pos4",
+    "single_energy_pos5",
+    "single_energy_pos6",
+    "single_energy_pos7",
+    "single_energy_pos8",
+    "single_energy_pos9",
+    "single_energy_pos10",
+    "single_energy_pos11",
+    "single_energy_pos12",
+    "single_energy_pos13",
+    "single_energy_pos14",
+    "single_energy_pos15",
+    "single_energy_pos16",
+    "single_energy_pos17",
+    "single_energy_pos18",
+    "single_energy_pos19",
+    "duplex_energy_total",
+    "duplex_energy_sirna_pos1",
+    "duplex_energy_sirna_pos2",
+    "duplex_energy_sirna_pos3",
+    "duplex_energy_sirna_pos4",
+    "duplex_energy_sirna_pos5",
+    "duplex_energy_sirna_pos6",
+    "duplex_energy_sirna_pos7",
+    "duplex_energy_sirna_pos8",
+    "duplex_energy_sirna_pos9",
+    "duplex_energy_sirna_pos10",
+    "duplex_energy_sirna_pos11",
+    "duplex_energy_sirna_pos12",
+    "duplex_energy_sirna_pos13",
+    "duplex_energy_sirna_pos14",
+    "duplex_energy_sirna_pos15",
+    "duplex_energy_sirna_pos16",
+    "duplex_energy_sirna_pos17",
+    "duplex_energy_sirna_pos18",
+    "duplex_energy_sirna_pos19",
+    "duplex_energy_target_pos1",
+    "duplex_energy_target_pos2",
+    "duplex_energy_target_pos3",
+    "duplex_energy_target_pos4",
+    "duplex_energy_target_pos5",
+    "duplex_energy_target_pos6",
+    "duplex_energy_target_pos7",
+    "duplex_energy_target_pos8",
+    "duplex_energy_target_pos9",
+    "duplex_energy_target_pos10",
+    "duplex_energy_target_pos11",
+    "duplex_energy_target_pos12",
+    "duplex_energy_target_pos13",
+    "duplex_energy_target_pos14",
+    "duplex_energy_target_pos15",
+    "duplex_energy_target_pos16",
+    "duplex_energy_target_pos17",
+    "duplex_energy_target_pos18",
+    "duplex_energy_target_pos19",
+    "RNAup_open_dG",
+    "RNAup_interaction_dG",
+    "source_Huesken",
+    "source_Simone",
+    "source_amarz",
+    "source_hsieh",
+    "source_khvorova",
+    "source_reynolds",
+    "source_vickers",
+    "cell_line_h1299",
+    "cell_line_halacat",
+    "cell_line_hek293",
+    "cell_line_hek293t",
+    "cell_line_hep3b",
+    "cell_line_t24"
+  ]
+}

metrics.json

@@ -0,0 +1,7 @@
+{
+  "rmse": 0.12202202042059986,
+  "mae": 0.0935055242999176,
+  "r2": 0.6058431979617869,
+  "pearson": 0.7783592987571915,
+  "spearman": 0.7635321903434975
+}

quintile_bias.csv

@@ -0,0 +1,6 @@
+quintile,true_mean,pred_mean,bias,rmse,count
+0,0.29245615005493164,0.41739668654671713,0.12494053649178549,0.17287117900472243,57
+1,0.4485454559326172,0.47935770199935684,0.030812246066739657,0.09201099268807923,55
+2,0.5552542209625244,0.531404687175394,-0.023849533787130395,0.09012039136712612,59
+3,0.6632142663002014,0.6074591139015421,-0.05575515239865936,0.11992789171308253,56
+4,0.8447169065475464,0.7638326081227593,-0.08088429842478706,0.11617889692021227,53

source_bias.csv

@@ -0,0 +1,8 @@
+source,true_mean,pred_mean,bias,count
+Huesken,0.5130985379219055,0.5078434794030154,-0.005255058518890077,213
+Simone,0.7516667246818542,0.7609096513707019,0.00924292668884763,30
+amarz,0.550000011920929,0.5331791661679744,-0.016820845752954505,4
+hsieh,0.5916666388511658,0.6565767838916264,0.06491014504046067,6
+khvorova,0.05000000074505806,0.4215789437784176,0.37157894303335953,1
+reynolds,0.7600000500679016,0.7752222379161924,0.015222187848290769,18
+vickers,0.5862499475479126,0.5705365809016832,-0.015713366646229354,8

training_summary.json

@@ -0,0 +1,149 @@
+{
+  "metrics": {
+    "rmse": 0.12202202042059986,
+    "mae": 0.0935055242999176,
+    "r2": 0.6058431979617869,
+    "pearson": 0.7783592987571915,
+    "spearman": 0.7635321903434975
+  },
+  "quintile_bias": [
+    {
+      "quintile": 0,
+      "true_mean": 0.29245615005493164,
+      "pred_mean": 0.41739668654671713,
+      "bias": 0.12494053649178549,
+      "rmse": 0.17287117900472243,
+      "count": 57
+    },
+    {
+      "quintile": 1,
+      "true_mean": 0.4485454559326172,
+      "pred_mean": 0.47935770199935684,
+      "bias": 0.030812246066739657,
+      "rmse": 0.09201099268807923,
+      "count": 55
+    },
+    {
+      "quintile": 2,
+      "true_mean": 0.5552542209625244,
+      "pred_mean": 0.531404687175394,
+      "bias": -0.023849533787130395,
+      "rmse": 0.09012039136712612,
+      "count": 59
+    },
+    {
+      "quintile": 3,
+      "true_mean": 0.6632142663002014,
+      "pred_mean": 0.6074591139015421,
+      "bias": -0.05575515239865936,
+      "rmse": 0.11992789171308253,
+      "count": 56
+    },
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