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update denoising results #372

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update denoising results #372

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a93a917
update denoising results
rcannood Dec 19, 2024
1eb2c4d
Merge remote-tracking branch 'origin/main' into update-denoising
rcannood Dec 19, 2024
b18e161
update
rcannood Dec 19, 2024
83ec88d
remove datasets and methods which don't pass qc
rcannood Dec 19, 2024
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188 changes: 151 additions & 37 deletions results/denoising/data/dataset_info.json
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257 changes: 79 additions & 178 deletions results/denoising/data/method_info.json
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2,522 changes: 2,522 additions & 0 deletions results/denoising/data/metric_execution_info.json
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44 changes: 25 additions & 19 deletions results/denoising/data/metric_info.json
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Original file line number Diff line number Diff line change
@@ -1,26 +1,32 @@
[
{
"metric_name": "Mean-squared error",
"metric_summary": "The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighting by the train/test ratio.",
"paper_reference": "batson2019molecular",
"maximize": false,
"image": "https://github.com/openproblems-bio/openproblems/pkgs/container/openproblems",
"task_id": "denoising",
"commit_sha": "b3456fd73c04c28516f6df34c57e6e3e8b0dab32",
"task_id": "metrics",
"component_name": "mse",
"metric_id": "mse",
"implementation_url": "https://github.com/openproblems-bio/openproblems/blob/v1.0.0/openproblems/tasks/denoising/metrics/mse.py",
"code_version": "v1.0.0"
"metric_name": "Mean-squared error",
"metric_summary": "The mean squared error between the denoised counts and the true counts.",
"metric_description": "The mean squared error between the denoised counts of the training dataset and the true counts of the test dataset after reweighing by the train/test ratio",
"references_doi": "10.1101/786269",
"references_bibtex": null,
"implementation_url": "https://github.com/openproblems-bio/task_denoising/blob/252731bc7276eb8a6a3398dc4bea026ae70eca80/src/metrics/mse",
"image": "https://ghcr.io/openproblems-bio/task_denoising/metrics/mse:1.0.0",
"code_version": "1.0.0",
"commit_sha": "252731bc7276eb8a6a3398dc4bea026ae70eca80",
"maximize": false
},
{
"metric_name": "Poisson loss",
"metric_summary": "The Poisson log likelihood of observing the true counts of the test dataset given the distribution given in the denoised dataset.",
"paper_reference": "batson2019molecular",
"maximize": false,
"image": "https://github.com/openproblems-bio/openproblems/pkgs/container/openproblems-python-pytorch",
"task_id": "denoising",
"commit_sha": "b3456fd73c04c28516f6df34c57e6e3e8b0dab32",
"task_id": "metrics",
"component_name": "poisson",
"metric_id": "poisson",
"implementation_url": "https://github.com/openproblems-bio/openproblems/blob/v1.0.0/openproblems/tasks/denoising/metrics/poisson.py",
"code_version": "v1.0.0"
"metric_name": "Poisson Loss",
"metric_summary": "The Poisson log likelihood of the true counts observed in the distribution of denoised counts",
"metric_description": "The Poisson log likelihood of observing the true counts of the test dataset given the distribution given in the denoised dataset.",
"references_doi": "10.1101/786269",
"references_bibtex": null,
"implementation_url": "https://github.com/openproblems-bio/task_denoising/blob/252731bc7276eb8a6a3398dc4bea026ae70eca80/src/metrics/poisson",
"image": "https://ghcr.io/openproblems-bio/task_denoising/metrics/poisson:1.0.0",
"code_version": "1.0.0",
"commit_sha": "252731bc7276eb8a6a3398dc4bea026ae70eca80",
"maximize": false
}
]
]
768 changes: 314 additions & 454 deletions results/denoising/data/quality_control.json
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