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feat: add spec2vec_allowed_missing_percentage parameter #34

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feat: add spec2vec_allowed_missing_percentage parameter #34

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1 change: 1 addition & 0 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -203,6 +203,7 @@ Example — multiple selected metrics:
| `--batch-size` | `10` | Replicates per thread-pool batch |
| `--sim-threshold` | `0.7` | Mean similarity threshold for cosine/modcosine/spec2vec graphs |
| `--sim-threshold-ms2dp` | `0.8` | Mean similarity threshold for MS2DeepScore graphs |
| `--spec2vec-allowed-missing-percentage` | `5.0` | Maximum percentage of missing peaks allowed in spec2vec similarity calculation |
| `--support-threshold` | `0.5` | Minimum edge support for threshold graph |
| `--max-component-size` | `100` | Maximum connected-component size |
| `--max-links` | `None` | Maximum edges per node; each node keeps only its top-N neighbours by mean similarity. `None` disables the filter |
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11 changes: 10 additions & 1 deletion specreboot/run_workflow_matchms.py
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Expand Up @@ -149,6 +149,15 @@ def build_parser(p: argparse.ArgumentParser):
"MS2DeepScore often uses a higher cutoff than cosine-based scores."
),
)
p.add_argument(
"--spec2vec-allowed-missing-percentage",
type=float,
default=5.0,
help=(
"Maximum percentage of missing peaks allowed in spec2vec similarity calculation. "
"Prevents failed similarity calculations due to vocabulary gaps, particularly in specific cases involving self-trained models."
),
)
p.add_argument(
"--tolerance",
type=float,
Expand Down Expand Up @@ -358,7 +367,7 @@ def run(args):
similarity_objs["Spec2Vec"] = Spec2Vec(
model=w2v,
intensity_weighting_power=0.5,
allowed_missing_percentage=5.0,
allowed_missing_percentage=args.spec2vec_allowed_missing_percentage,
)

if "ms2deepscore" in sim_keys:
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