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Sprint 12 Task List #501
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2024-05-21Stats methods topic meeting
We have merged the random matrix theory PR, which will be used and Ilha will be evaluating
Ilha is making progress on this. He is running first simulation now, running different combinations of singular value shrinkage estimators, and the different types of covariance matrix estimators, and he will be evaluating this via mean squared error on the poe effect estimators, that are simulated. |
Covariance Matrix / POEConservativeness:
Publication Plan for Q3
Sprint 13 plan updateAustin will implement some spherical p-value tests that are a direct POIROT competitor Domain AdaptationTest looks really successful at removing batch effects; TAMPOR does not appear to remove them, at least entirely. |
2024-05-31PRS
Pushed back to last week of sprint
Same
Under review
Done
Should be in testing by 6/6
Should be done by 6/6
PR'd, there's a test to fix
@akotlar and @austinTalbot7241993 will talk about this on Monday
Guy at UC Davis has a good implementation, so we're relying on that
We have geodisics in (may use in domain adaptation), we have pyreamann PR'd. We have been working this week on how well the covariance matrix estimation, and conservativeness. Operator norm has the best MSE and worst conservativeness, and nuclear norm had the best conservativeness and ok MSE. The difficulty is estimating the largest singular values, which needs to be done by looking at heterozygotes; we were shafting ourselves by looking at low frequency hets and with small effect sizes. SummaryPRS + ProteomicsWill be done by 6/6 for prototype MLOn track, good progress |
2024-06-07Bystro Sync
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* Updates version of pandas, numpy, ray, torch, tqdm * tqdm update resolve dependabot low severity issue * Finish removing `attrs` from codebase
…json to csv/tsv (#525) * As GIN requested, add ability to convert ancestry json to csv/tsv from command line CLI: ```sh bystro-api ancestry convert --input-json /home/ubuntu/bystro/python/python/bystro/api/tests/ancestry_input.json --output foobar/ancestry_test_output.tsv --format csv ``` API: ```python from bystro.api.ancestry import ancestry_json_to_format ancestry_json_to_format(input_json_path='../api/tests/ancestry_input.json', output_path='foo/bar.tsv', output_format='tsv') ```
Due date: June 6 2024
Documentation
Proteomics
PRS
Covariance Matrix Estimation/ML library
Goal: Make more accurate predictions, more tailored test, better control false positive rate
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