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Switched to Geometric Mean for Peptide Level Scores #392

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merged 2 commits into from
Oct 15, 2024
Merged

Switched to Geometric Mean for Peptide Level Scores #392

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103c763
switched to geometric mean for peptide level score
Lilferrit Oct 14, 2024
83a40c7
non zero aa score test case, changelog item
Lilferrit Oct 15, 2024
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2 changes: 1 addition & 1 deletion casanovo/denovo/model.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1076,7 +1076,7 @@ def _aa_pep_score(
peptide_score : float
The peptide score.
"""
peptide_score = np.mean(aa_scores)
peptide_score = np.exp(np.mean(np.log(aa_scores)))
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aa_scores = (aa_scores + peptide_score) / 2
if not fits_precursor_mz:
peptide_score -= 1
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8 changes: 4 additions & 4 deletions tests/unit_tests/test_unit.py
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Expand Up @@ -439,12 +439,12 @@ def test_aa_pep_score():
aa_scores_raw = np.asarray([0.0, 0.5, 1.0])

aa_scores, peptide_score = _aa_pep_score(aa_scores_raw, True)
np.testing.assert_array_equal(aa_scores, np.asarray([0.25, 0.5, 0.75]))
assert peptide_score == pytest.approx(0.5)
np.testing.assert_array_equal(aa_scores, np.asarray([0.0, 0.25, 0.5]))
assert peptide_score == pytest.approx(0.0)

aa_scores, peptide_score = _aa_pep_score(aa_scores_raw, False)
np.testing.assert_array_equal(aa_scores, np.asarray([0.25, 0.5, 0.75]))
assert peptide_score == pytest.approx(-0.5)
np.testing.assert_array_equal(aa_scores, np.asarray([0.0, 0.25, 0.5]))
assert peptide_score == pytest.approx(-1.0)


def test_beam_search_decode():
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