Add benchmark data (16/37): tasks/track_c/C3.json

tasks/track_c/C3.json

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+{
+  "task_id": "C3",
+  "task_name": "PPI-Guided GNN Gene Classification",
+  "task_type": "binary_classification",
+  "difficulty_tier": "advanced",
+  "track": "C",
+  "description": "Node classification on STRING PPI graph for spaceflight DEG prediction. Transductive setting: full graph structure visible during training and testing, only labels are split. Tests whether protein-protein interaction network topology improves gene-level predictions beyond flat tabular classifiers.",
+  "data_files": [
+    "cfrna_3group_de_noleak.csv"
+  ],
+  "ground_truth_files": [
+    "cfrna_466drr.csv"
+  ],
+  "graph_data": {
+    "source": "STRING v12.0 (Homo sapiens, score > 700)",
+    "nodes": 26845,
+    "connected_nodes": 14900,
+    "isolated_nodes": 11945,
+    "edges": 213753,
+    "node_features": "29 effect-size statistics (same as B1)"
+  },
+  "input_spec": {
+    "node_features": "29 effect-size statistics per gene",
+    "feature_count": 29,
+    "edge_source": "STRING PPI v12.0 (combined_score > 700)",
+    "gene_mapping": "Gene symbol -> ENSP via STRING aliases (67% coverage)",
+    "isolated_node_behavior": "GNN degenerates to MLP for isolated nodes (no message passing)"
+  },
+  "output_spec": {
+    "type": "binary",
+    "positive_class": "DRR gene",
+    "positive_count": 466,
+    "negative_count": 26379,
+    "positive_rate": "1.7%"
+  },
+  "evaluation": {
+    "primary_metric": "auprc",
+    "secondary_metrics": [
+      "auroc",
+      "f1"
+    ],
+    "additional_analysis": [
+      "isolated_vs_connected_node_performance",
+      "architecture_comparison"
+    ]
+  },
+  "models": [
+    {
+      "name": "GCN",
+      "layers": 2,
+      "hidden_dim": 64,
+      "dropout": 0.3
+    },
+    {
+      "name": "GAT",
+      "layers": 2,
+      "hidden_dim": 64,
+      "heads": 2,
+      "dropout": 0.3
+    },
+    {
+      "name": "GraphSAGE",
+      "layers": 2,
+      "hidden_dim": 64,
+      "aggregator": "mean",
+      "dropout": 0.3
+    }
+  ],
+  "training": {
+    "epochs": 200,
+    "optimizer": "Adam",
+    "learning_rate": 0.01,
+    "loss": "BCEWithLogitsLoss",
+    "pos_weight": "balanced (~56.5)",
+    "seed": 42
+  },
+  "split": "feature_split_B1",
+  "setting": "transductive",
+  "n_samples": 26845,
+  "caveats": [
+    "Transductive: full graph structure (all edges) visible during both training and testing",
+    "~44% of nodes are isolated (no PPI edges) — GNN degenerates to MLP for these",
+    "Stage 2 showed PPI topology features provide zero value (net_only AUPRC=0.019, combined < base_only)",
+    "Expected negative result: GNN unlikely to outperform flat XGBoost (AUPRC=0.922)",
+    "Gene symbol to ENSP mapping coverage 67% (non-protein-coding genes unmapped)"
+  ],
+  "status": "design_complete"
+}