feat: Add random state feature. #150
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john-halloran
commented
Jun 6, 2025
john-halloran
commented
- feat: Added random_state feature for reproducibility.
| components=None, | ||
| random_state=None, | ||
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| self.MM = MM |
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Changed to n_components, which is what sklearn.decomposition.NMF uses.
| MM, | ||
| Y0=None, | ||
| X0=None, | ||
| A=None, |
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There are many different standards for what to name these matrices. Zero agreement between sources that use NMF. I'm inclined to eventually use what sklearn.decomposition.non_negative_factorization uses, which would mean MM->X, X->W, Y->H. But I'd like to leave this as is for the moment until there's a consensus about what would be the most clear or standard. If people will be finding this tool from the sNMF paper, there's also an argument for using the X, Y, and A names because that was used there.
| @@ -4,8 +4,20 @@ | |||
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| class SNMFOptimizer: | |||
| def __init__(self, MM, Y0=None, X0=None, A=None, rho=1e12, eta=610, max_iter=500, tol=5e-7, components=None): | |||
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we need a docstring here and in the init. Please see scikit-package FAQ about how to write these. Also, look at Yucong's code or diffpy.utils?
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Added one here. The package init dates back to the old codebase, but as soon as that is updated it will get a docstring as well.
| @@ -15,23 +27,22 @@ def __init__(self, MM, Y0=None, X0=None, A=None, rho=1e12, eta=610, max_iter=500 | |||
| # Capture matrix dimensions | |||
| self.N, self.M = MM.shape | |||
| self.num_updates = 0 | |||
| self.rng = np.random.default_rng(random_state) | |||
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can we have a more descriptive variable name? Is this a range? What is the range?
| if self.A is None: | ||
| self.A = np.ones((self.K, self.M)) + np.random.randn(self.K, self.M) * 1e-3 # Small perturbation | ||
| self.A = np.ones((self.K, self.M)) + self.rng.normal(0, 1e-3, size=(self.K, self.M)) |
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K and M are probably good names if the matrix decomposition equation is in hte docstring, so they get defined there.
Thanks, will work on resolving these. To be clear, for things like the docstrings would you prefer I make new PRs, get those merged, then rebase this one, or just add to this existing PR? |
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For now, I will assume anything given as feedback in this PR could be in scope to include. |
