Task structure

Before defining a new task in OpenProblems, it’s important to understand the typical structure of an OpenProblems task (Figure 1).

A task typically consists of a dataset processor, methods, control methods and metrics. Each component has a well-defined input-output interface, for which the file formats in the resulting AnnData are also described.

graph LR
  common_dataset[Common<br/>dataset]:::anndata
  subgraph task_specific[Task-specific workflow]
    dataset_processor[/Dataset<br/>processor/]:::component
    solution[Solution]:::anndata
    masked_data[Dataset]:::anndata
    method[/Method/]:::component
    control_method[/Control<br/>method/]:::component
    output[Output]:::anndata
    metric[/Metric/]:::component
    score[Score]:::anndata
  end
  common_dataset --- dataset_processor --> masked_data & solution
  masked_data --- method --> output
  masked_data & solution --- control_method --> output
  solution & output --- metric --> score

Figure 1: Overview of a typical benchmarking workflow in an OpenProblems task. Legend: Grey rectangles are AnnData .h5ad files, purple rhomboids are Viash components.

File and component formats

Path: src/tasks/<task_id>/api

This folder contains YAML specifications for task-specific file formats and component interfaces.

Dataset processor

Path: src/tasks/<task_id>/process_dataset

This components processes a Common dataset into task-specific dataset objects. In supervised tasks, this component will usually output a solution, a training dataset and a test dataset. In unsupervised tasks, this component usually output a solution and a masked dataset.

Methods

Path: src/tasks/<task_id>/methods

This folder contains method components. Each method component outputs a prediction given the training and test datasets (when applicable).

Control methods

Path: src/tasks/<task_id>/control_methods

This folder contains control components for the task. These components have the same interface as the regular methods but also receive the solution object as input. It serves as a starting point to test the relative accuracy of new methods in the task, and also as a quality control for the metrics defined in the task. A control method can either be a positive control or a negative control, which set a maximum and minimum threshold for performance, so any new method should perform better than the negative control methods and worse than the positive control method.

A positive control is a method where the expected results are known, thus resulting in the best possible value for any metric outcome measure.

A negative control is a simple, naive, or random method that does not rely on any sophisticated techniques or domain knowledge.

Metrics

Path: src/tasks/<task_id>/metrics

This folder contains metric components. Each metric component outputs one or more metric results given a solution object and a method output object.

Benchmarking pipeline

Path: src/tasks/<task_id>/workflows

This folder contains a Nextflow pipeline defining the benchmarking workflow for this task.

Resource generation scripts

Path: src/tasks/<task_id>/resources_scripts

This folder contains scripts for generating benchmarking resources required for the task.

Test resource generation scripts

Path: src/tasks/<task_id>/resources_test_scripts

This folder contains scripts for generating test resources for the task.