website/src/data/generated/model_leaderboard.json

{
 "metrics": [
  "auroc",
  "auprc",
  "accuracy",
  "mcc",
  "f1",
  "precision",
  "recall",
  "specificity",
  "brier",
  "ece"
 ],
 "metricLabels": {
  "auroc": "AUROC",
  "auprc": "AUC-PR",
  "accuracy": "Accuracy",
  "mcc": "MCC",
  "f1": "F1",
  "precision": "Precision",
  "recall": "Sensitivity / recall",
  "specificity": "Specificity",
  "brier": "Brier",
  "ece": "ECE"
 },
 "nSpecies": 7,
 "nDatasets": 28,
 "note": "Aggregated across species from 5-fold protein-grouped CV on the 28 usable datasets. Each value is the mean over folds, then over a species' datasets, then across species. Brier and ECE are calibration metrics where lower is better.",
 "models": [
  {
   "id": "xgb__esm2_phys",
   "classifier": "xgb",
   "featureSet": "esm2_phys",
   "label": "XGBoost \u00b7 ESM2 + physicochemical",
   "description": "Gradient-boosted decision trees. The most consistent winner across datasets. ESM2 embeddings plus the 14 physicochemical descriptors. Best overall.",
   "nSpecies": 7,
   "nDatasets": 28,
   "agg": {
    "auroc": {
     "mean": 0.8129,
     "min": 0.7219,
     "max": 0.8914,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "auprc": {
     "mean": 0.7979,
     "min": 0.7374,
     "max": 0.8811,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "accuracy": {
     "mean": 0.7452,
     "min": 0.658,
     "max": 0.8096,
     "minSpecies": "Tetradesmus obliquus (microalga)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "mcc": {
     "mean": 0.4486,
     "min": 0.2749,
     "max": 0.6194,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "f1": {
     "mean": 0.7588,
     "min": 0.6798,
     "max": 0.8395,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "precision": {
     "mean": 0.7423,
     "min": 0.6692,
     "max": 0.8194,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "recall": {
     "mean": 0.801,
     "min": 0.705,
     "max": 0.8961,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "specificity": {
     "mean": 0.6536,
     "min": 0.3823,
     "max": 0.7867,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "brier": {
     "mean": 0.2058,
     "min": 0.1454,
     "max": 0.3123,
     "minSpecies": "Spirulina (Arthrospira platensis)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "ece": {
     "mean": 0.1639,
     "min": 0.0684,
     "max": 0.2343,
     "minSpecies": "Potato (Solanum tuberosum)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    }
   },
   "bySpecies": [
    {
     "species": "Spirulina (Arthrospira platensis)",
     "n": 3,
     "auroc": 0.8914,
     "auprc": 0.8811,
     "accuracy": 0.8096,
     "mcc": 0.6194,
     "f1": 0.8161,
     "precision": 0.8009,
     "recall": 0.8394,
     "specificity": 0.7867,
     "brier": 0.1454,
     "ece": 0.1218
    },
    {
     "species": "Potato (Solanum tuberosum)",
     "n": 16,
     "auroc": 0.8721,
     "auprc": 0.8556,
     "accuracy": 0.7891,
     "mcc": 0.5761,
     "f1": 0.7895,
     "precision": 0.7781,
     "recall": 0.804,
     "specificity": 0.7759,
     "brier": 0.1492,
     "ece": 0.0684
    },
    {
     "species": "Soybean (Glycine max)",
     "n": 1,
     "auroc": 0.8553,
     "auprc": 0.7809,
     "accuracy": 0.7588,
     "mcc": 0.533,
     "f1": 0.7253,
     "precision": 0.7045,
     "recall": 0.7994,
     "specificity": 0.7512,
     "brier": 0.1795,
     "ece": 0.1552
    },
    {
     "species": "wheat",
     "n": 5,
     "auroc": 0.8247,
     "auprc": 0.8122,
     "accuracy": 0.7462,
     "mcc": 0.4944,
     "f1": 0.7691,
     "precision": 0.7208,
     "recall": 0.8322,
     "specificity": 0.6561,
     "brier": 0.1854,
     "ece": 0.1304
    },
    {
     "species": "Tetradesmus obliquus (microalga)",
     "n": 1,
     "auroc": 0.7745,
     "auprc": 0.7597,
     "accuracy": 0.658,
     "mcc": 0.3489,
     "f1": 0.6923,
     "precision": 0.703,
     "recall": 0.7307,
     "specificity": 0.6084,
     "brier": 0.2279,
     "ece": 0.2338
    },
    {
     "species": "Faba bean (Vicia faba)",
     "n": 1,
     "auroc": 0.7505,
     "auprc": 0.7374,
     "accuracy": 0.7929,
     "mcc": 0.2749,
     "f1": 0.8395,
     "precision": 0.8194,
     "recall": 0.8961,
     "specificity": 0.3823,
     "brier": 0.3123,
     "ece": 0.2343
    },
    {
     "species": "Red rice bran (Oryza sativa)",
     "n": 1,
     "auroc": 0.7219,
     "auprc": 0.7581,
     "accuracy": 0.6619,
     "mcc": 0.2934,
     "f1": 0.6798,
     "precision": 0.6692,
     "recall": 0.705,
     "specificity": 0.6143,
     "brier": 0.2408,
     "ece": 0.2031
    }
   ],
   "partial": false
  },
  {
   "id": "xgb__pep_phys",
   "classifier": "xgb",
   "featureSet": "pep_phys",
   "label": "XGBoost \u00b7 PepBERT + physicochemical",
   "description": "Gradient-boosted decision trees. The most consistent winner across datasets. PepBERT embeddings concatenated with the 14 physicochemical descriptors.",
   "nSpecies": 7,
   "nDatasets": 28,
   "agg": {
    "auroc": {
     "mean": 0.8121,
     "min": 0.7295,
     "max": 0.8926,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "auprc": {
     "mean": 0.7847,
     "min": 0.7179,
     "max": 0.8788,
     "minSpecies": "Tetradesmus obliquus (microalga)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "accuracy": {
     "mean": 0.7569,
     "min": 0.6844,
     "max": 0.8157,
     "minSpecies": "Tetradesmus obliquus (microalga)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "mcc": {
     "mean": 0.4602,
     "min": 0.2287,
     "max": 0.6286,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "f1": {
     "mean": 0.7682,
     "min": 0.7062,
     "max": 0.8394,
     "minSpecies": "Tetradesmus obliquus (microalga)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "precision": {
     "mean": 0.7503,
     "min": 0.7047,
     "max": 0.8158,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "recall": {
     "mean": 0.8083,
     "min": 0.7249,
     "max": 0.8932,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "specificity": {
     "mean": 0.6689,
     "min": 0.3798,
     "max": 0.779,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Potato (Solanum tuberosum)",
     "nSpecies": 7
    },
    "brier": {
     "mean": 0.2008,
     "min": 0.1394,
     "max": 0.3059,
     "minSpecies": "Spirulina (Arthrospira platensis)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "ece": {
     "mean": 0.1562,
     "min": 0.0626,
     "max": 0.2361,
     "minSpecies": "Potato (Solanum tuberosum)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    }
   },
   "bySpecies": [
    {
     "species": "Spirulina (Arthrospira platensis)",
     "n": 3,
     "auroc": 0.8926,
     "auprc": 0.8788,
     "accuracy": 0.8157,
     "mcc": 0.6286,
     "f1": 0.8249,
     "precision": 0.8005,
     "recall": 0.8569,
     "specificity": 0.7778,
     "brier": 0.1394,
     "ece": 0.1071
    },
    {
     "species": "Potato (Solanum tuberosum)",
     "n": 16,
     "auroc": 0.8735,
     "auprc": 0.8571,
     "accuracy": 0.7929,
     "mcc": 0.5842,
     "f1": 0.7936,
     "precision": 0.7814,
     "recall": 0.8093,
     "specificity": 0.779,
     "brier": 0.1469,
     "ece": 0.0626
    },
    {
     "species": "Soybean (Glycine max)",
     "n": 1,
     "auroc": 0.8457,
     "auprc": 0.7482,
     "accuracy": 0.7626,
     "mcc": 0.5449,
     "f1": 0.7349,
     "precision": 0.7065,
     "recall": 0.8187,
     "specificity": 0.7451,
     "brier": 0.1834,
     "ece": 0.1672
    },
    {
     "species": "wheat",
     "n": 5,
     "auroc": 0.8261,
     "auprc": 0.8125,
     "accuracy": 0.7499,
     "mcc": 0.4996,
     "f1": 0.7695,
     "precision": 0.7272,
     "recall": 0.8239,
     "specificity": 0.6711,
     "brier": 0.1809,
     "ece": 0.1174
    },
    {
     "species": "Tetradesmus obliquus (microalga)",
     "n": 1,
     "auroc": 0.7645,
     "auprc": 0.7179,
     "accuracy": 0.6844,
     "mcc": 0.3668,
     "f1": 0.7062,
     "precision": 0.716,
     "recall": 0.7314,
     "specificity": 0.6509,
     "brier": 0.2272,
     "ece": 0.2209
    },
    {
     "species": "Red rice bran (Oryza sativa)",
     "n": 1,
     "auroc": 0.7525,
     "auprc": 0.7521,
     "accuracy": 0.6961,
     "mcc": 0.3688,
     "f1": 0.709,
     "precision": 0.7047,
     "recall": 0.7249,
     "specificity": 0.6785,
     "brier": 0.222,
     "ece": 0.1823
    },
    {
     "species": "Faba bean (Vicia faba)",
     "n": 1,
     "auroc": 0.7295,
     "auprc": 0.726,
     "accuracy": 0.7967,
     "mcc": 0.2287,
     "f1": 0.8394,
     "precision": 0.8158,
     "recall": 0.8932,
     "specificity": 0.3798,
     "brier": 0.3059,
     "ece": 0.2361
    }
   ],
   "partial": false
  },
  {
   "id": "pfly_ft",
   "classifier": "pfly",
   "featureSet": null,
   "label": "Pfly (fine-tuned)",
   "description": "External dlomix Prosit-style detectability model, fine-tuned per dataset on peptide sequence only. Statistically indistinguishable from our XGB/RF/MLP on matched CV. Full metric panel computed on the matched protein-grouped folds.",
   "nSpecies": 7,
   "nDatasets": 28,
   "agg": {
    "auroc": {
     "mean": 0.8077,
     "min": 0.6917,
     "max": 0.9036,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "auprc": {
     "mean": 0.7756,
     "min": 0.6796,
     "max": 0.8928,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "accuracy": {
     "mean": 0.706,
     "min": 0.5696,
     "max": 0.8196,
     "minSpecies": "Potato (Solanum tuberosum)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "mcc": {
     "mean": 0.4361,
     "min": 0.2159,
     "max": 0.6397,
     "minSpecies": "Potato (Solanum tuberosum)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "f1": {
     "mean": 0.6705,
     "min": 0.2331,
     "max": 0.8285,
     "minSpecies": "Potato (Solanum tuberosum)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "precision": {
     "mean": 0.715,
     "min": 0.5737,
     "max": 0.8142,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Potato (Solanum tuberosum)",
     "nSpecies": 7
    },
    "recall": {
     "mean": 0.7299,
     "min": 0.1549,
     "max": 0.9287,
     "minSpecies": "Potato (Solanum tuberosum)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "specificity": {
     "mean": 0.6968,
     "min": 0.4033,
     "max": 0.9855,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Potato (Solanum tuberosum)",
     "nSpecies": 7
    },
    "brier": {
     "mean": 0.2185,
     "min": 0.1262,
     "max": 0.3654,
     "minSpecies": "Spirulina (Arthrospira platensis)",
     "maxSpecies": "Potato (Solanum tuberosum)",
     "nSpecies": 7
    },
    "ece": {
     "mean": 0.1895,
     "min": 0.0851,
     "max": 0.3843,
     "minSpecies": "wheat",
     "maxSpecies": "Potato (Solanum tuberosum)",
     "nSpecies": 7
    }
   },
   "bySpecies": [
    {
     "species": "Spirulina (Arthrospira platensis)",
     "n": 3,
     "auroc": 0.9036,
     "auprc": 0.8928,
     "accuracy": 0.8196,
     "mcc": 0.6397,
     "f1": 0.8285,
     "precision": 0.8074,
     "recall": 0.8588,
     "specificity": 0.7869,
     "brier": 0.1262,
     "ece": 0.0958
    },
    {
     "species": "wheat",
     "n": 5,
     "auroc": 0.8588,
     "auprc": 0.8392,
     "accuracy": 0.788,
     "mcc": 0.5773,
     "f1": 0.7946,
     "precision": 0.7859,
     "recall": 0.8124,
     "specificity": 0.7658,
     "brier": 0.1489,
     "ece": 0.0851
    },
    {
     "species": "Soybean (Glycine max)",
     "n": 1,
     "auroc": 0.8575,
     "auprc": 0.7578,
     "accuracy": 0.7675,
     "mcc": 0.538,
     "f1": 0.7376,
     "precision": 0.7075,
     "recall": 0.822,
     "specificity": 0.7483,
     "brier": 0.1644,
     "ece": 0.1497
    },
    {
     "species": "Tetradesmus obliquus (microalga)",
     "n": 1,
     "auroc": 0.7956,
     "auprc": 0.7828,
     "accuracy": 0.7039,
     "mcc": 0.4307,
     "f1": 0.7015,
     "precision": 0.6704,
     "recall": 0.7678,
     "specificity": 0.6815,
     "brier": 0.2058,
     "ece": 0.167
    },
    {
     "species": "Potato (Solanum tuberosum)",
     "n": 16,
     "auroc": 0.7951,
     "auprc": 0.7746,
     "accuracy": 0.5696,
     "mcc": 0.2159,
     "f1": 0.2331,
     "precision": 0.8142,
     "recall": 0.1549,
     "specificity": 0.9855,
     "brier": 0.3654,
     "ece": 0.3843
    },
    {
     "species": "Faba bean (Vicia faba)",
     "n": 1,
     "auroc": 0.7517,
     "auprc": 0.6796,
     "accuracy": 0.6508,
     "mcc": 0.387,
     "f1": 0.7088,
     "precision": 0.5737,
     "recall": 0.9287,
     "specificity": 0.4033,
     "brier": 0.2828,
     "ece": 0.2687
    },
    {
     "species": "Red rice bran (Oryza sativa)",
     "n": 1,
     "auroc": 0.6917,
     "auprc": 0.7025,
     "accuracy": 0.6428,
     "mcc": 0.264,
     "f1": 0.6891,
     "precision": 0.6458,
     "recall": 0.7646,
     "specificity": 0.5066,
     "brier": 0.236,
     "ece": 0.1757
    }
   ],
   "partial": false
  },
  {
   "id": "xgb__esm2",
   "classifier": "xgb",
   "featureSet": "esm2",
   "label": "XGBoost \u00b7 ESM2",
   "description": "Gradient-boosted decision trees. The most consistent winner across datasets. ESM2-t12-35M protein-language-model embeddings of the peptide sequence.",
   "nSpecies": 7,
   "nDatasets": 28,
   "agg": {
    "auroc": {
     "mean": 0.8065,
     "min": 0.6785,
     "max": 0.8876,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "auprc": {
     "mean": 0.7945,
     "min": 0.7249,
     "max": 0.8779,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "accuracy": {
     "mean": 0.743,
     "min": 0.6431,
     "max": 0.8022,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "mcc": {
     "mean": 0.4453,
     "min": 0.2452,
     "max": 0.5992,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Spirulina (Arthrospira platensis)",
     "nSpecies": 7
    },
    "f1": {
     "mean": 0.7578,
     "min": 0.6698,
     "max": 0.8476,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "precision": {
     "mean": 0.7404,
     "min": 0.6519,
     "max": 0.8217,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "recall": {
     "mean": 0.8016,
     "min": 0.7036,
     "max": 0.9112,
     "minSpecies": "Red rice bran (Oryza sativa)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "specificity": {
     "mean": 0.6467,
     "min": 0.3785,
     "max": 0.779,
     "minSpecies": "Faba bean (Vicia faba)",
     "maxSpecies": "Potato (Solanum tuberosum)",
     "nSpecies": 7
    },
    "brier": {
     "mean": 0.2086,
     "min": 0.1477,
     "max": 0.2995,
     "minSpecies": "Spirulina (Arthrospira platensis)",
     "maxSpecies": "Faba bean (Vicia faba)",
     "nSpecies": 7
    },
    "ece": {
     "mean": 0.1649,
     "min": 0.0685,
     "max": 0.2382,
     "minSpecies": "Potato (Solanum tuberosum)",
     "maxSpecies": "Tetradesmus obliquus (microalga)",
     "nSpecies": 7
    }
   },
   "bySpecies": [
    {
     "species": "Spirulina (Arthrospira platensis)",
     "n": 3,
     "auroc": 0.8876,
     "auprc": 0.8779,
     "accuracy": 0.7982,
     "mcc": 0.5992,
     "f1": 0.8062,
     "precision": 0.7921,
     "recall": 0.8305,
     "specificity": 0.7758,
     "brier": 0.1477,
     "ece": 0.1146
    },
    {
     "species": "Potato (Solanum tuberosum)",
     "n": 16,
     "auroc": 0.87,
     "auprc": 0.8535,
     "accuracy": 0.7881,
     "mcc": 0.5743,
     "f1": 0.7876,
     "precision": 0.7791,
     "recall": 0.7993,
     "specificity": 0.779,
     "brier": 0.1504,
     "ece": 0.0685
    },
    {
     "species": "Soybean (Glycine max)",
     "n": 1,
     "auroc": 0.8559,
     "auprc": 0.7848,
     "accuracy": 0.7595,
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 ]
}