PyTorch: Speed up single animal models#3110
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AlexEMG merged 3 commits intoDeepLabCut:mainfrom Oct 18, 2025
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Replace nested loops with vectorized PyTorch operations to extract heatmap scores and locref offsets in parallel.
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maximpavliv
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Thanks a lot for this improvement — great work! 🙌
The vectorized implementation looks clean and efficient, and it passes all integration tests on my side.
Just one small suggestion: the Example section in the docstring should be updated for consistency with the tensor layout assumed by the code. Specifically, the example
>>> heatmap = torch.rand(32, 17, 64, 64)
>>> locref = torch.rand(32, 17, 64, 64, 2)
should be changed to
>>> heatmap = torch.rand(32, 64, 64, 17)
>>> locref = torch.rand(32, 64, 64, 17, 2)
so it matches the (batch_size, height, width, num_joints) format used in the implementation.
AlexEMG
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Oct 14, 2025
AlexEMG
approved these changes
Oct 18, 2025
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deruyter92
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Jan 21, 2026
This commit updates the `HeatmapPredictor` in single_predictor.py to follow the implementation in DeepLabCut 3.0.0rc13. See DeepLabCut/DeepLabCut#3110
MMathisLab
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* DEKRPredictor: add non-maximum suppression (NMS) This commit Updates the DEKR predictor to follow the DeepLabCut implementation in version 3.0.0rc7, see DeepLabCut/DeepLabCut#2907 * DEKRPredictor: speed up with vectorized operations This commit updates the DEKRPredictor to follow the DeepLabCut implementation in version 3.0.0rc13. see DeepLabCut/DeepLabCut#3121 * PartAffinityFieldPredictor (PAF): Speed up cost computation This commit updates the PAF predictor to follow the DeepLabCut implementation in version 3.0.0.rc13. See DeepLabCut/DeepLabCut#3117 * HeatmapPredictor (single animal): speed up with vecorized operations This commit updates the `HeatmapPredictor` in single_predictor.py to follow the implementation in DeepLabCut 3.0.0rc13. See DeepLabCut/DeepLabCut#3110
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This PR improves the prediction performance of various single animal PyTorch models.
The
forloops for extracting values out of theheatmaptensor were replaced with advanced indexing.Details
Profiling results showed
HeatmapPredictor.get_pose_predictionas a major hot spot in single animal inference procedure.After this change, we see a massive speed-up in the major single animal models as shown below (thanks to @maximpavliv for running the benchmark)