Add experiments for different minibatch normalizations #264
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anwai98
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Jun 14, 2024
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| ### LIVECell: | ||
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| | Targets | Mini-Batch Norm. | Input Norm. | Dice | mSA | SA50 | | ||
| |----------|------------------|-----------------|--------------------|---------------------|---------------------| | ||
| | Binary | OldDefault | Per Tile | 0.928867041453946 | - | - | | ||
| | Binary | InstanceNorm | Per Tile | 0.9139200411471561 | - | - | | ||
| | Boundary | OldDefault | Per Tile | - | 0.3596574029856674 | 0.5706313962830515 | | ||
| | Boundary | InstanceNorm | Per Tile | - | 0.21136391380220415 | 0.32975049087380925 | | ||
| | Binary | OldDefault | Whole Volume | 0.9288671102955196 | - | - | | ||
| | Binary | InstanceNorm | Whole Volume | 0.9139609056661331 | - | - | | ||
| | Boundary | OldDefault | Whole Volume | - | 0.3596633257789534 | 0.5706479532532667 | | ||
| | Boundary | InstanceNorm | Whole Volume | - | 0.21294970907224356 | 0.33214134838916115 | | ||
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| ### Mouse Embryo (Nuclei): | ||
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| | Targets | Mini-Batch Norm. | Input Norm. | Dice | mSA | SA50 | | ||
| |----------|------------------|-----------------|--------------------|---------------------|---------------------| | ||
| | Binary | OldDefault | Per Tile | 0.773449732035369 | - | - | | ||
| | Binary | InstanceNorm | Per Tile | 0.7413715897174049 | - | - | | ||
| | Boundary | OldDefault | Per Tile | - | 0.2089494345163684 | 0.396692895729518 | | ||
| | Boundary | InstanceNorm | Per Tile | - | 0.15872795687689387 | 0.3200512111903994 | | ||
| | Binary | OldDefault | Whole Volume | 0.7734503020445563 | - | - | | ||
| | Binary | InstanceNorm | Whole Volume | 0.767180298383585 | - | - | | ||
| | Boundary | OldDefault | Whole Volume | - | 0.20882369840046283 | 0.39638644753570157 | | ||
| | Boundary | InstanceNorm | Whole Volume | - | 0.15714229749213487 | 0.3231149929195066 | | ||
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| ## PlantSeg (Root): | ||
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| | Targets | Mini-Batch Norm. | Input Norm. | Dice | mSA | SA50 | | ||
| |----------|------------------|-----------------|--------------------|-----------------------|-----------------------| | ||
| | Binary | OldDefault | Per Tile | 0.9928809913563437 | - | - | | ||
| | Binary | InstanceNorm | Per Tile | 0.981061366019915 | - | - | | ||
| | Boundary | OldDefault | Per Tile | - | 0.014372028994123383 | 0.018482085449422186 | | ||
| | Boundary | InstanceNorm | Per Tile | - | 0.0014261363636363636 | 0.004753787878787879 | | ||
| | Binary | OldDefault | Whole Volume | 0.9928820421405989 | - | - | | ||
| | Binary | InstanceNorm | Whole Volume | 0.9810579911503293 | - | - | | ||
| | Boundary | OldDefault | Whole Volume | - | 0.014372028994123383 | 0.018482085449422186 | | ||
| | Boundary | InstanceNorm | Whole Volume | - | 0.0014396498771498771 | 0.0047988329238329245 | | ||
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| ## MitoEM (Human and Rat): | ||
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| | Targets | Mini-Batch Norm. | Input Norm. | Dice | mSA | SA50 | | ||
| |----------|------------------|-----------------|--------------------|---------------------|---------------------| | ||
| | Binary | OldDefault | Per Tile | 0.9206916296864652 | - | - | | ||
| | Binary | InstanceNorm | Per Tile | 0.9247380570327044 | - | - | | ||
| | Boundary | OldDefault | Per Tile | - | 0.4452180959378787 | 0.5943295393094057 | | ||
| | Boundary | InstanceNorm | Per Tile | - | 0.23307025211315505 | 0.32876735818930347 | | ||
| | Binary | OldDefault | Whole Volume | 0.9206915268071336 | - | - | | ||
| | Binary | InstanceNorm | Whole Volume | 0.9241492985508706 | - | - | | ||
| | Boundary | OldDefault | Whole Volume | - | 0.44530557897744855 | 0.594423580706029 | | ||
| | Boundary | InstanceNorm | Whole Volume | - | 0.24493949819392608 | 0.3480087025599067 | |
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@constantinpape (Just keeping you posted)
Here are the updated results from all experiments. The overall observation here: normalizing the whole volume should be the choice (however it's still not in favor of the new mini-batch norm). I'll go ahead with the plans as discussed.
Re: qualitative results:
Only MitoEM seems to be improved qualitatively (reference: per tile norm vs whole volume norm - does not pick up as many structures besides mitochondria anymore), but LIVECell and Mouse Embryo seem to appear exactly as we observed yesterday.
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