Faster speed for compare_survival #215
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sebp
requested changes
Jul 10, 2021
sksurv/compare.py
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| @@ -75,6 +75,7 @@ def compare_survival(y, group_indicator, return_stats=False): | |||
| observed = numpy.zeros(n_groups, dtype=numpy.int_) | |||
| expected = numpy.zeros(n_groups, dtype=numpy.float_) | |||
| covar = numpy.zeros((n_groups, n_groups), dtype=numpy.float_) | |||
| group_eye = numpy.eye(n_groups, dtype=bool) | |||
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Since you are only using it for indexing covar, using numpy.diag_indices makes more sense to me.
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I didn't know such thing exist, sure, way less memory consumption
sksurv/compare.py
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| covar[g1, g2] -= temp * at_risk[g2] / total_at_risk | ||
| temp = at_risk * multiplier | ||
| covar[group_eye] += temp | ||
| covar -= (temp[:, None] * at_risk[None, :] / total_at_risk) |
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You don't need the brackets, and temp[:, None] * at_risk[None, :] is the same as numpy.outer(temp, at_risk).
Codecov Report
@@ Coverage Diff @@
## master #215 +/- ##
==========================================
- Coverage 98.33% 98.33% -0.01%
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Files 37 37
Lines 3127 3126 -1
Branches 460 458 -2
==========================================
- Hits 3075 3074 -1
Misses 28 28
Partials 24 24
Continue to review full report at Codecov.
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sebp
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Jul 11, 2021
|
Thanks! Merged in commit ccc6913 |
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Checklist
compare_survivalfunction #214What does this implement/fix? Explain your changes
numpynative syntax/ operation to accelerate the python iteration on a huge cartetian productchisq,pvalue,covarmatrix,table