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JWR15-Synapse-BCE.yaml

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+MODEL:
+  LOSS_OPTION: [["WeightedBCEWithLogitsLoss"]]
+  LOSS_WEIGHT: [[1.0]]
+  WEIGHT_OPT: [["1"]]
+  OUTPUT_ACT: [["none"]]
+DATASET:
+  OUTPUT_PATH: outputs/JWR15_Syn_BCE/syn 

JWR15-Synapse-Base.yaml

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+SYSTEM:
+  NUM_GPUS: 1
+  NUM_CPUS: 1
+MODEL:
+  ARCHITECTURE: unet_plus_3d
+  BLOCK_TYPE: residual_se
+  INPUT_SIZE: [17, 257, 257]
+  OUTPUT_SIZE: [17, 257, 257]
+  IN_PLANES: 1
+  OUT_PLANES: 3
+  TARGET_OPT: ["1"] # non-exclusive synaptic masks
+  NORM_MODE: gn
+  FILTERS: [32, 64, 96, 128, 192]
+DATASET:
+  IMAGE_NAME:
+    - w08_tr5_tc4.h5
+  LABEL_NAME:
+    - w08_tr5_tc4_label_v3.1_polarity.h5
+  INPUT_PATH: /data/projects/weilab/dataset/h01/syn/
+  OUTPUT_PATH: outputs/JWR15_Synapse/syn
+  PAD_SIZE: [4, 48, 48]
+  DISTRIBUTED: True
+  REJECT_SAMPLING:
+    SIZE_THRES: 2000
+    P: 0.95
+  DATA_CHUNK_NUM: [20, 7, 8] # only for inference
+SOLVER:
+  LR_SCHEDULER_NAME: WarmupCosineLR
+  BASE_LR: 0.04
+  ITERATION_STEP: 1
+  ITERATION_SAVE: 5000
+  ITERATION_TOTAL: 200000
+  SAMPLES_PER_BATCH: 2
+INFERENCE:
+  INPUT_SIZE: [33, 257, 257]
+  OUTPUT_SIZE: [33, 257, 257]
+  OUTPUT_ACT: ["sigmoid"]
+  IS_ABSOLUTE_PATH: False
+  DO_CHUNK_TITLE: 1
+  INPUT_PATH: /n/boslfs02/LABS/lichtman_lab/donglai/xiaomeng/alzheimer/test/
+  OUTPUT_PATH: /n/boslfs02/LABS/lichtman_lab/donglai/xiaomeng/alzheimer/result/
+  PAD_SIZE: [8, 128, 128]
+  AUG_MODE: mean
+  AUG_NUM: None
+  STRIDE: [16, 128, 128]
+  SAMPLES_PER_BATCH: 16