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experiments/gnn_decoder_topology.yaml

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+# Fleet Spec: Decoder Topology Fix (Track 4)
+#
+# Tests tree-aware decoding vs chain baseline across architectures and loss functions.
+# The critical insight: decoder uses chain edges (0→1→2→...) instead of tree edges.
+#
+# Launch:
+#   ratiocinator fleet run experiments/gnn_decoder_topology.yaml
+
+name: gnn-decoder-topology
+description: "Tree-aware decoder topology vs chain baseline"
+
+hardware:
+  gpu: "RTX 4090"
+  num_gpus: 1
+  min_cpu_ram_gb: 32
+  min_inet_down: 1000.0
+  min_cuda_version: 12.0
+  max_dph: 0.40
+  disk_gb: 50.0
+  image: pytorch/pytorch:2.7.0-cuda12.8-cudnn9-runtime
+
+repo:
+  url: https://github.com/timlawrenz/jubilant-palm-tree.git
+  branch: experiment/ratiocinator-gnn-study
+  clone_depth: 1
+
+data:
+  source: none
+
+deps:
+  pre_install:
+    - "apt-get update -qq && apt-get install -y -qq git-lfs > /dev/null 2>&1 || true"
+    - "cd /workspace/experiment && git lfs install && git lfs pull"
+    - "pip install torch-geometric torch-scatter torch-sparse -f https://data.pyg.org/whl/torch-2.7.0+cu128.html"
+    - "pip install pandas tqdm sentence-transformers nltk scikit-learn numpy"
+  requirements: requirements.txt
+  exclude_from_requirements:
+    - torch
+    - torchvision
+    - torch_geometric
+  verify: "python -c \"import torch_geometric; print(f'PyG {torch_geometric.__version__}')\""
+
+arms:
+  # ── Edge mode comparison (GAT decoder, improved loss) ──
+  - name: chain-gat
+    description: "Chain edges (legacy baseline), GAT decoder"
+    command: "bash scripts/run_topology_arm.sh"
+    env:
+      DECODER_EDGE_MODE: "chain"
+      DECODER_CONV_TYPE: "GAT"
+      LOSS_FN: "improved"
+      HIDDEN_DIM: "256"
+      NUM_LAYERS: "5"
+      EPOCHS: "30"
+
+  - name: teacher-forced-gat
+    description: "Teacher-forced tree edges, GAT decoder"
+    command: "bash scripts/run_topology_arm.sh"
+    env:
+      DECODER_EDGE_MODE: "teacher_forced"
+      DECODER_CONV_TYPE: "GAT"
+      LOSS_FN: "improved"
+      HIDDEN_DIM: "256"
+      NUM_LAYERS: "5"
+      EPOCHS: "30"
+
+  - name: iterative-gat
+    description: "Iterative predict→refine, GAT decoder"
+    command: "bash scripts/run_topology_arm.sh"
+    env:
+      DECODER_EDGE_MODE: "iterative"
+      DECODER_CONV_TYPE: "GAT"
+      LOSS_FN: "improved"
+      HIDDEN_DIM: "256"
+      NUM_LAYERS: "5"
+      EPOCHS: "30"
+
+  # ── Best edge mode × different architectures ──
+  - name: teacher-forced-sage
+    description: "Teacher-forced tree edges, SAGE decoder"
+    command: "bash scripts/run_topology_arm.sh"
+    env:
+      DECODER_EDGE_MODE: "teacher_forced"
+      DECODER_CONV_TYPE: "SAGE"
+      LOSS_FN: "improved"
+      HIDDEN_DIM: "256"
+      NUM_LAYERS: "5"
+      EPOCHS: "30"
+
+  - name: teacher-forced-gin
+    description: "Teacher-forced tree edges, GIN decoder"
+    command: "bash scripts/run_topology_arm.sh"
+    env:
+      DECODER_EDGE_MODE: "teacher_forced"
+      DECODER_CONV_TYPE: "GIN"
+      LOSS_FN: "improved"
+      HIDDEN_DIM: "256"
+      NUM_LAYERS: "5"
+      EPOCHS: "30"
+
+  # ── Loss function × topology interaction ──
+  - name: teacher-forced-gat-comprehensive
+    description: "Teacher-forced, GAT, comprehensive loss"
+    command: "bash scripts/run_topology_arm.sh"
+    env:
+      DECODER_EDGE_MODE: "teacher_forced"
+      DECODER_CONV_TYPE: "GAT"
+      LOSS_FN: "comprehensive"
+      HIDDEN_DIM: "256"
+      NUM_LAYERS: "5"
+      EPOCHS: "30"
+
+metrics:
+  protocol: json_line
+  json_prefix: "METRICS:"
+
+budget:
+  max_dollars: 10.00
+  train_timeout_s: 3600
+  download_timeout_s: 600