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Fix edge cases of csr_array #39

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Merged
aarmey merged 2 commits into from
Jul 2, 2025
Merged

Fix edge cases of csr_array #39

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8a3de9c
Fix edge cases of csr_array
aarmey Jul 2, 2025
d429fd2
Update parafac2/normalize.py
aarmey Jul 2, 2025
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5 changes: 4 additions & 1 deletion parafac2/normalize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -79,6 +79,9 @@ def get_deviance(data: csr_array) -> np.ndarray:
where y=0 or n-y=0, and ensures the final deviance values are non-negative
before taking the square root.
"""
# merge duplicate entries in the sparse matrix by summing their values
data.sum_duplicates()
data.eliminate_zeros()

# counts per gene
pi_j = data.sum(axis=0)
Expand All @@ -104,7 +107,7 @@ def get_deviance(data: csr_array) -> np.ndarray:
# Term 1: y * log(y / mu) = xlogy(y, y) - xlogy(y, mu)
# xlogy handles y=0 case correctly returning 0.
row, col = data.nonzero()
mu_ij_nn = n_i_col[row, 0] * pi_j[0, col]
mu_ij_nn = n_i[row] * pi_j[col]
term1 = data.data * np.log(data.data / mu_ij_nn)

# Term 2: (n-y) * log((n-y) / (n-mu)) = xlogy(n-y, n-y) - xlogy(n-y, n-mu)
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