Comments (3)
Results on local environment are very promising.
Before:
Loaded model in 12.3 s
Ran prediction in 1.25 s; success: True
After:
Loaded model in 0.84 s
Ran prediction in 1.19 s; success: True
This is the time to load the model from disk, not to fetch it from storage.
Once the PR is merged we can test on cloud.
from deepcell-imaging.
The new model is uploaded:
gs://genomics-data-public-central1/cellular-segmentation/vanvalenlab/deep-cell/vanvalenlab-tf-model-multiplex-downloaded-20230706/MultiplexSegmentation-resaved-20240710.h5
Its md5 hash is: 56b0f246081fe6b730ca74eab8a37d60
gs://genomics-data-public-central1/cellular-segmentation/vanvalenlab/deep-cell/vanvalenlab-tf-model-multiplex-downloaded-20230706/MultiplexSegmentation-resaved-20240710-md5.txt
It was generated like so:
model = tf.keras.models.load_model("/Users/davidhaley/.keras/models/MultiplexSegmentation")
model.save("MultiplexSegmentation-resaved-20240710.h5")
It seems to be really that simple⦠but, see upcoming PR for caveats on loading the .h5
model.
from deepcell-imaging.
Cloud results π
Before:
Reading model from /root/.keras/models/MultiplexSegmentation.
Loaded model in 8.99 s
Ran prediction in 2.82 s; success: True
After:
Loading model from: /root/.keras/models/MultiplexSegmentation-resaved-20240710.h5
Loaded model in 2.68 s
Ran prediction in 2.79 s; success: True
Summary of results:
Environment | Before | After | Diff |
---|---|---|---|
Macbook M3 Max Pro | 12.3 s | 0.84 s | -11.46 s (-93%) |
n1-standard-8 w/ 1 T4 GPU | 8.99 s | 2.68 s | -6.31 s (-70%) |
n1-standard-32 w/ 1 T4 GPU | 8.21s | 2.72 s | -5.49 s (-67%) |
Of note, loading the model into memory used to take ~3x the time of predicting the 512x512 image. Now it's roughly the same.
from deepcell-imaging.
Related Issues (20)
- Fix broken optional arguments
- VULNs: Can we update TF?
- Update README to share batch benchmark results HOT 2
- Create runnable for submitting downstream job on completion
- Don't create segment job gather-benchmark tasks if the BigQuery table is blank
- Container & other settings have to come from config or params HOT 1
- Scale preprocessing
- Scale prediction
- Scale postprocessing
- Quiet error messages for getting GCP info on local
- Create segmentation-only job launcher
- Benchmarking input file names are wrong
- Add BQ benchmarking table to segment-and-measure.py script
- Add instructions for benchmarking schema
- Fix required parameters for segment-only script HOT 1
- Add networking & service account to environment config
- Rename benchmarking pixels_m to pixels
- Update container tag from "batch" to "latest"
- Update readme with Batch process
- Update benchmarking to include total time
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from deepcell-imaging.