Improve metrics documentation #204
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MUCDK
reviewed
Apr 9, 2025
src/cellflow/metrics/_metrics.py
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| @@ -54,15 +94,46 @@ def pairwise_squeuclidean(x: ArrayLike, y: ArrayLike) -> ArrayLike: | |||
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| @jax.jit | |||
| def compute_e_distance_fast(x: ArrayLike, y: ArrayLike) -> float: | |||
| """Compute the energy distance as in Peidli et al.""" | |||
| """Compute the energy distance between x and y as in Peidli et al. | |||
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make proper reference with :cite:, you might have to add the reference first.
MUCDK
reviewed
Apr 9, 2025
src/cellflow/metrics/_metrics.py
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| def compute_e_distance(x: ArrayLike, y: ArrayLike) -> float: | ||
| """Compute the energy distance as in Peidli et al.""" | ||
| """Compute the energy distance between x and y as in Peidli et al. |
MUCDK
reviewed
Apr 9, 2025
src/cellflow/metrics/_metrics.py
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| return r2_score(np.mean(x, axis=0), np.mean(y, axis=0)) | ||
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| def compute_sinkhorn_div(x: ArrayLike, y: ArrayLike, epsilon: float = 1e-2) -> float: | ||
| """Compute the Sinkhorn divergence between x and y.""" | ||
| """Compute the Sinkhorn divergence between x and y. |
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cite feydy 2019 (https://proceedings.mlr.press/v89/feydy19a.html) as a ref
MUCDK
reviewed
Apr 9, 2025
src/cellflow/metrics/_metrics.py
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| @@ -21,12 +23,38 @@ | |||
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| def compute_r_squared(x: ArrayLike, y: ArrayLike) -> float: | |||
| """Compute the R squared between true (x) and predicted (y)""" | |||
| """Compute the R squared score between the true (x) and predicted (y) distributions. | |||
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It's actually R squared between the means of x and y, please say so
MUCDK
reviewed
Apr 9, 2025
| Returns | ||
| ------- | ||
| A scalar denoting the average MMD over all gammas. | ||
| """ | ||
| if gammas is None: | ||
| gammas = [2, 1, 0.5, 0.1, 0.01, 0.005] | ||
| mmds = [maximum_mean_discrepancy(x, y, gamma=gamma) for gamma in gammas] # type: ignore[union-attr] | ||
| return np.nanmean(np.array(mmds)) | ||
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| def compute_metrics_fast(x: ArrayLike, y: ArrayLike) -> dict[str, float]: |
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can we expose it, but not add to the docs? to keep it for backward compatibility ,but it's a bit redundant.
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## main #204 +/- ##
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- Coverage 79.88% 77.13% -2.76%
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Files 38 38
Lines 2491 2497 +6
Branches 313 313
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MUCDK
requested changes
Apr 14, 2025
| return r2_score(np.mean(x, axis=0), np.mean(y, axis=0)) | ||
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| def compute_sinkhorn_div(x: ArrayLike, y: ArrayLike, epsilon: float = 1e-2) -> float: | ||
| """Compute the Sinkhorn divergence between x and y.""" | ||
| """Compute the Sinkhorn divergence between x and y as in Feydy et al. :cite:`feydy:19`. |
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Just cite once, i.e. Compute the Sinkhorn divergence between x and y as in :cite:feydy:19`.
Similarly in other places, please.
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