# 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