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fix: improve the numerical stability of lfc_shrink #370

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fix: improve the numerical stability of lfc_shrink #370

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10 changes: 6 additions & 4 deletions pydeseq2/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -56,9 +56,10 @@ def load_example_data(
pandas.DataFrame
Requested data modality.
"""
assert modality in ["raw_counts", "metadata"], (
"The modality argument must be one of the following: " "raw_counts, metadata"
)
assert modality in [
"raw_counts",
"metadata",
], "The modality argument must be one of the following: raw_counts, metadata"

assert dataset in [
"synthetic"
Expand Down Expand Up @@ -1078,13 +1079,14 @@ def f(beta: np.ndarray, cnst: float = scale_cnst) -> float:
def df(beta: np.ndarray, cnst: float = scale_cnst) -> np.ndarray:
# Gradient of the function to optimize
xbeta = design_matrix @ beta
exp_xbeta_off = np.exp(xbeta + offset)
d_neg_prior = (
beta * no_shrink_mask / prior_no_shrink_scale**2
+ 2 * beta * shrink_mask / (prior_scale**2 + beta[shrink_index] ** 2)
)

d_nll = (
counts - (counts + size) / (1 + size * np.exp(-xbeta - offset))
size * (counts - exp_xbeta_off) / (size + exp_xbeta_off)
) @ design_matrix

return (d_neg_prior - d_nll) / cnst
Expand Down