Scoring functions for the dream / sage challenges
Project description
- Online documentation:
Overview
DreamTools aims at sharing code used in the scoring of DREAM challenges.
The main goals are:
provide scoring functions for the Dream challenges for end-users via the dreamtools-scoring standalone application.
provide a place to share-reuse code used before/during/after the challenges for developers and organisers of the challenges
Code related to aggregation, leaderboards, or more complex analysis are not guaranteed to be found in dreamtools even though it may be in some challenges (e.g. D8C1). Some functionalities may be restricted with some access to synapse.
The dreamtools-scoring executable
For users, dreamtools provide one executable called dreamtools-scoring, which should be installed automatically when installing dreamtools. Knowing the name of the challenge (and possibly sub-challenge), it works as follows:
dreamtools-scoring --challenge d8c1 --sub-challenge sc1a --submission alphabeta-Network.zip
It prints some information and the score of the submision for instance for the example above:
Solution for alphabeta-Network.zip in challenge d8c1 (sub-challenge sc1a) is : AUROC: 0.803628919403 Rank LB: 1
Not all DREAM challenges are included but here is the current status.
DREAM10
DREAM9
DREAM8.5
DREAM8
D8C1 (HPN breat cancer) sub challenges named sc1a, sc1b, sc2a, sc2b. See Synapse page D8C1 for details
D8C2 (Toxoxicology) sub challenges named sc1, sc2. See Synapse page D8C2 for details
D8C3 coming soon
DREAM7
D7C1 (Network Parameter Estimation)
DREAM6
D6C1 (Network Parameter Estimation) WONT be included (see D7C1 instead)
DREAM5
D5C2 (transcription factor)
DREAM4
DREAM3
DREAM2
DREAM1
Format for the challenges can be found in the README of each subchallenge. For instance, for Dream8 Challenge1, please see ./dreamtools/dream8/D8C1/README.rst
Installation
pip install dreamtools
Issues
Please fill bug report in https://github.com/dreamtools/dreamtools/issues
For developers
Not all challenges are yet provided. If you wish to contribute, please let us know. See doc/source/developers
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