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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
272a209
update results
rcannood Jan 7, 2025
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208 changes: 171 additions & 37 deletions results/denoising/data/dataset_info.json
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267 changes: 92 additions & 175 deletions results/denoising/data/method_info.json
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2,858 changes: 2,858 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
}
]
]
796 changes: 363 additions & 433 deletions results/denoising/data/quality_control.json
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