Move methods in cinnabar.stats concerning MLE to the MLEEstimator class#211
Move methods in cinnabar.stats concerning MLE to the MLEEstimator class#211ianmkenney wants to merge 10 commits into
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #211 +/- ##
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Coverage 97.23% 97.24%
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ianmkenney
changed the title
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| @staticmethod | ||
| def mle(graph: nx.DiGraph, factor: str = "f_ij", node_factor: Union[str, None] = None) -> (np.ndarray, np.ndarray): |
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We are free to change this however we want, lets update the factor and node_factor names to be more meaningful or if you think its okay we can leave them.
| # populate the edges of the graph along with their computational binding free energies | ||
| for m in filter(lambda m: m.computational, measurements): | ||
| if isinstance(m.labelA, ReferenceState): | ||
| # TODO this is never hit in the tests and should be supported behavior |
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Good point lets move this to another PR we should be able to support absolute computational values in the solver as well!
| z[i] += -deltaij / varij | ||
| z[j] += deltaij / varij | ||
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| F_matrix[i, i] += 1 / varij | ||
| F_matrix[j, j] += 1 / varij | ||
| F_matrix[i, j] += -1 / varij | ||
| F_matrix[j, i] += -1 / varij |
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Nice this should allow for the forward and backward results do you want to add support for that in this PR? We have some example data in #133 so we can add a test we can punt to another if you want though.
| return f_i, Finv | ||
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| @staticmethod | ||
| def form_edge_matrix(graph: nx.Graph, label: str, step=None, action=None, node_label=None) -> np.ndarray: |
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Lets just remove this if its not needed anymore and all tests associated with it!
jthorton
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Looking great just a couple of things to look at.
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