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Damiano Piovesan edited this page Jan 22, 2024
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- Ground truth and predictions
- Information accretion
| Argument | Default value | Description |
|---|---|---|
| -out_dir | “results” | Output directory (tsv files + log). Either relative to current path or absolute |
| -ia | Information accretion file | |
| -no_orphans | False (flag) | Exclude orphans nodes (e.g. roots) from the calculation |
| -norm | “cafa” | Normalization strategy CAFA strategy (cafa) Consider predicted targets (pred) Consider ground truth proteins (gt) |
| -prop | “max” | Ancestor propagation strategy Propagate the max score of the traversed subgraph iteratively (max) Propagate with max until a different score is found (fill) |
| -th_step | 0.01 | Threshold step size in the range [0, 1). A smaller step, means more calculation |
| -max_terms | Number of terms for protein and namespace to consider in the evaluation | |
| -threads | 4 | Parallel threads. 0 means use all available CPU threads. Do not use multi thread if you are short in memory |
- Normalization
- Roots
- Score propagation
- Thresholds granularity
- Monotonic curves