SingleCellOpenProblems

Formalizing and benchmarking open problems in single-cell genomics.

Visit the Open Problems Website

API

Each task consists of datasets, methods, and metrics.

Datasets should take no arguments and return an AnnData object. If test is True, then the method should load the full dataset, but only return a small version of the same data (preferably <200 cells and <500 genes) for faster downstream analysis.

function dataset(bool test=False) -> AnnData adata

Methods should take an AnnData object and store the output in-place in adata.obs according to the specification of the task.

function method(AnnData adata) -> None

Metrics should take an AnnData object and return a float.

function metric(AnnData adata) -> float

Task-specific APIs are described in the README for each task.

Adding a new dataset

Datasets are loaded under openproblems/data. Each data loading function should download the appropriate dataset from a stable location (e.g. from Figshare) be decorated with openproblems.data.utils.loader in order to cache the result.

Adding a dataset / method / metric to a task

To add a dataset, method, or metric to a task, simply create a new .py file corresponding to your proposed new functionality and import the main function in the corresponding __init__.py. E.g., to add a "F2" metric to the label projection task, we would create openproblems/tasks/label_projection/metrics/f2.py and add a line

from .f2 import f2

to openproblems/tasks/label_projection/metrics/__init__.py.

For datasets in particular, these should be loaded using a loader function from openproblems.data, with only task-specific annotations added in the task-specific data file.

For methods and metrics, they should be decorated with the appropriate function in openproblems.tools.decorators to include metadata required for the evaluation and presentation of results.

Note that data is not normalized in the data loader; normalization should be performed as part of each method. For ease of use, we provide a collection of common normalization functions in openproblems.tools.normalize.

Adding a new task

The task directory structure is as follows

opensproblems/
  - tasks/
    - task_name/
      - README.md
      - __init__.py
      - checks.py
      - datasets/
        - __init__.py
        - dataset1.py
        - ...
      - methods/
        - __init__.py
        - method1.py
        - ...
      - metrics/
        - __init__.py
        - metric1.py
        - ...

task_name/__init__.py can be copied from an existing task.

checks.py should implement the following functions:

check_dataset(AnnData adata) -> bool # checks that a dataset fits the task-specific schema
check_method(AnnData adata) -> bool # checks that the output from a method fits the task-specific schema

For adding datasets, methods and metrics, see above.

License

dynverse/SingleCellOpenProblems

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