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…ts GCS calls - models/joint_model.py: JointProofreader with shared CNN3D backbone, Arborist merge head, and HGAT split head; routes batches by task at forward time - models/new_gnn_models.py: NewVisionHGAT for standalone split correction - split_datasets.py: replace list_gcs_subdirectories(bucket, prefix) calls with list_gcs_subprefixes(full_gcs_path) to match the current util API Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Decouples split head dropout from merge head dropout so each task can be regularized independently. split_dropout defaults to dropout when None for backward compatibility. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
… fixes - models/joint_model.py: add JointProofreader (joint split+merge model with shared CNN3D backbone, Arborist merge head, and 3-layer HGAT split head) - models/new_gnn_models.py: add gat3 (3rd HGAT layer), bump gnn_hidden_dim and img_embed_dim defaults 64→96, add ProposalTreeEncoder - split_proofreading/new_split_feature_extraction.py: add ArboristSplitDataset (prefetched iterator with Arborist tree features alongside image patches) - split_proofreading/split_inference.py: route to ArboristSplitDataset when use_tree_features=True (required by JointProofreader split head) - configs.py: add fov_merge to ImageConfig (load at fov, resize to patch_shape for merge detection); add modality to MergeInferenceConfig; add model_config_path and use_tree_features to SplitInferenceConfig; add keys/__getitem__ to Config base class - machine_learning/image_dataloader.py: DetectionPatchLoader loads at fov_merge when set, then resizes to patch_shape before returning - machine_learning/train.py: add n_mistake_mips reservoir-sampled mistake MIP saving per val epoch - utils/img_util.py: cast img to float32 before np.percentile to fix NaN on float16 arrays (all-white MIP bug) - merge_proofreading/search_datasets.py: fix subgraph_to_tree_sample root arg - proofreading_pipeline.py: pass modality and use_tree_features from configs - proposal_graph.py: accept **kwargs in __init__ for forward-compat - utils/geometry_util.py: guard is_double against empty query_nodes Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…eEncoder Within a batch subgraph, proposals in the same local neighborhood share many of the same surrounding skeleton paths as curves. Previously, arborist.encode() was called once per proposal, causing CurveEncoder to re-encode shared curves redundantly. The fix deduplicates curves across all proposals using (shape, bytes) as the key, runs CurveEncoder once on all unique curves, then does a per-sample GraphTransformer pass (which must remain per-sample since each proposal has a unique tree topology/edge_index). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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…ts GCS calls