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change allowed_missing_percentage default #72

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merged 4 commits into from
Feb 2, 2022
Merged

change allowed_missing_percentage default #72

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146ff9d
change allowed_missing_percentage default
florian-huber Feb 2, 2022
35a6abc
update code example
florian-huber Feb 2, 2022
9ec43de
Update CHANGELOG.md
florian-huber Feb 2, 2022
9d36ff7
Update vector_operations.py
florian-huber Feb 2, 2022
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4 changes: 4 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -11,6 +11,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- Now supports Python 3.9 (including CI test runs) [#40](https://github.com/iomega/spec2vec/issues/40)

## Changed

- changed default setting for `allowed_missing_percentage` to 50.0 to be less strict on model coverage [#72](https://github.com/iomega/spec2vec/pull/72)

## [0.5.0] - 2021-06-18

## Changed
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8 changes: 3 additions & 5 deletions spec2vec/Spec2Vec.py
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Expand Up @@ -78,13 +78,11 @@ def spectrum_processing(s):

.. testoutput::

Removed adduct M-H from compound name.
...
['CCMSLIB00001058300', 'CCMSLIB00001058289', 'CCMSLIB00001058303', ...

"""
def __init__(self, model: Word2Vec, intensity_weighting_power: Union[float, int] = 0,
allowed_missing_percentage: Union[float, int] = 0, progress_bar: bool = False):
allowed_missing_percentage: Union[float, int] = 50, progress_bar: bool = False):
"""

Parameters
Expand All @@ -99,8 +97,8 @@ def __init__(self, model: Word2Vec, intensity_weighting_power: Union[float, int]
allowed_missing_percentage:
Set the maximum allowed percentage of the document that may be missing
from the input model. This is measured as percentage of the weighted, missing
words compared to all word vectors of the document. Default is 0, which
means no missing words are allowed.
words compared to all word vectors of the document. Default is 100, which
means up to 50% missing words are allowed (not a very strict setting!).
progress_bar:
Set to True to monitor the embedding creating with a progress bar.
Default is False.
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2 changes: 1 addition & 1 deletion spec2vec/vector_operations.py
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Expand Up @@ -45,7 +45,7 @@ def _check_model_coverage():
f"Weighted missing percentage not covered by the given model is {missing_percentage:.2f}%.")

message = ("Missing percentage is larger than set maximum.",
"Consider retraining the used model or increasing the allowed percentage.")
"Consider retraining the used model or change the `allowed_missing_percentage`.")
assert missing_percentage <= allowed_missing_percentage, message

idx_not_in_model = [i for i, x in enumerate(document.words) if x not in model.wv.key_to_index]
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