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[Dimensionality reduction] Add metrics based on NN co-ranking #300

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michalk8 opened this issue Mar 31, 2021 · 1 comment
Closed

[Dimensionality reduction] Add metrics based on NN co-ranking #300

michalk8 opened this issue Mar 31, 2021 · 1 comment
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enhancement New feature or request

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@michalk8
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What is the metric?
Describe it briefly and include a citation if applicable.
There are many metrics described here: https://core.ac.uk/download/pdf/148668147.pdf

How should it be implemented?
Include a link to the publicly available codebase if available.
https://www.sciencedirect.com/science/article/pii/S2405844021003042
contains the code. Scaling will also be an issue (for more than 3k cells [estimate]).
I'd also double-check if the implementation is correct.

Which task(s) could it be used for?
If the method is to be used for a task that is not yet included in the code base, use the issue template propose a new task instead.
Dimensionality reduction (2D), possibly

@bendemeo
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This is a great reference! I think co-k-nearest-neighbor size (Q_NN(k)) is especially useful, although it has a nuisance parameter k. To make it more robust, we might average Q_NN(k) for k up to some threshold, possibly weighting for lower distances. But maybe Q_NN(k) is a good place to start. Not sure if the original authors compute an entire distance matrix, but I could write code to generate a sparse Q_NN matrix using only nearest neighbor data from sklearn.neighbors.

rcannood pushed a commit that referenced this issue Sep 4, 2024
* Add nf-tower cli for dataset loader

* add mising directive labels for dataset loader

* add missing directive labels process datasets

* remove space in file name

* update s3 bucket

* increase yaml limit to 5mb

* Fix dataset schema validation and remove
unnecessary code to fix meta  file size

* Update dataset schema file path in config.vsh.yaml
and main.nf

* Add script for processing datasets on nf-tower
 in bat_int

* Remove dataset_schema input from config.vsh.yaml

* Add output_task_info to workflow configuration

* Update publish directory in process_datasets.sh for bat_int

* Update denoising process_datasets wf
rcannood pushed a commit that referenced this issue Sep 4, 2024
* Add nf-tower cli for dataset loader

* add mising directive labels for dataset loader

* add missing directive labels process datasets

* remove space in file name

* update s3 bucket

* increase yaml limit to 5mb

* Fix dataset schema validation and remove
unnecessary code to fix meta  file size

* Update dataset schema file path in config.vsh.yaml
and main.nf

* Add script for processing datasets on nf-tower
 in bat_int

* Remove dataset_schema input from config.vsh.yaml

* Add output_task_info to workflow configuration

* Update publish directory in process_datasets.sh for bat_int

* Update denoising process_datasets wf

Former-commit-id: 82a6a4d
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