Feat/em composition refactor learning mech #2754
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- all_entries_identical()
first draft of module that implements episodic / external memory Composition
- add error message for specifcation of default_control_allocation or default_gating_allocation
- add error message for specifcation of default_control_allocation or default_gating_allocation
- add error message for specifcation of default_control_allocation or default_gating_allocation
- constructs but wiring still not right
- first draft; needs to be run
- add memory decay and storage
- storage and retrieval working
- exclude value_input_nodes as NodeRole.OUTPUT
- TODO notes
- suppress warning for no efferent projectsions
- add storage_prob and related parameters - docs in progress
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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64): See CI logs for the full diff. |
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
| def _validate_field_types(self, field_types): | ||
| if not len(field_types) or len(field_types) != len(self.fields): | ||
| return f"must be specified with a number of items equal to " \ | ||
| f"the number of fields specified {len(self.fields)}" | ||
| if not all(item in {1,0} for item in field_types): | ||
| return f"must be a list of 1s (for keys) and 0s (for values)." | ||
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| def _validate_field_weights(self, field_weights): |
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| # Get matrix containing memories for the field from the Projection | ||
| field_memory_matrix = field_projection.parameters.matrix.get(context) | ||
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| value.append(super(LearningMechanism, self)._execute(variable=entry_to_store, |
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| field_norms = np.array([np.linalg.norm(field, axis=1) | ||
| for field in [row for row in self.parameters.memory.get(context)]]) | ||
| if purge_by_field_weights: | ||
| field_norms *= self.field_weights |
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| # if concatenate_keys: | ||
| # projections = [self.concatenate_keys_node.input_ports[i].path_afferents[0] for i in range(self.num_keys)] + \ | ||
| # [self.retrieved_nodes[i].input_port.path_afferents[0] for i in range(len(self.input_nodes))] | ||
| # variable = [self.input_nodes[i].value[0] for i in range(self.num_fields)] | ||
| # fields = [self.input_nodes[i] for i in range(self.num_fields)] | ||
| # else: | ||
| # variable = [self.input_nodes[i].value[0] for i in range(self.num_fields)] | ||
| # fields = [self.input_nodes[i] for i in range(self.num_fields)] | ||
| # projections = [self.match_nodes[i].input_port.path_afferents[0] for i in range(self.num_keys)] + \ | ||
| # [self.retrieved_nodes[i].input_port.path_afferents[0] for i in range(len(self.input_nodes))] |
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Commented-out code Note
| pytest.skip('Compilation not yet support for Composition.import.') | ||
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| def temp(context): | ||
| memory = context.composition.parameters.memory.get(context) |
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| if comp_mode != pnl.ExecutionMode.Python: | ||
| pytest.skip('Compilation not yet support for Composition.import.') | ||
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| def temp(context): |
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Unused local variable Note test
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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64): See CI logs for the full diff. |
- _parse_port_specific_specs(): fix bug in which COMBINE was not parsed
- _parse_port_specific_specs(): fix bug in which COMBINE was not parsed when specified in an InputPort specification dict (though still some weirdness)
• port.py
_parse_port_spec():
add passing of Context.string for caller ID
|
This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64): See CI logs for the full diff. |
|
This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64): See CI logs for the full diff. |
- passes tests sequentially but not in parallel.
Error:
> num_fields = len(owning_component.fields)
E TypeError: object of type 'NoneType' has no len()
../../psyneulink/library/components/mechanisms/modulatory/learning/EMstoragemechanism.py:211: TypeError
- refactor memory_matrix to use learning_signals • emcomposition.py - refactor to use memory_matrix of storage_node if that is implemented
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This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64): See CI logs for the full diff. |
|
This PR causes the following changes to the html docs (ubuntu-latest-3.7-x64): See CI logs for the full diff. |
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| # def _memory_matrix_getter(owning_component=None, context=None): | ||
| # if context.composition: | ||
| # return context.composition.parameters.memory._get(context) | ||
| # else: | ||
| # return None |
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Code scanning / CodeQL
Commented-out code Note
kmantel
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* origin/devel: tests/ParameterEstimationComposition: Reduce the number of estimates by 40x tests/ParameterEstimationComposition: Provide expected result instead of relying on tolerance requirements: update dill requirement from <0.3.7 to <0.3.8 (PrincetonUniversity#2743) Feat/em composition refactor learning mech (PrincetonUniversity#2754) Fix/input port combine (PrincetonUniversity#2755) requirements: update beartype requirement from <0.15.0 to <0.16.0 (PrincetonUniversity#2744)
kmantel
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• EMstoragemechanism.py - refactor memory_matrix to use learning_signals • emcomposition.py - refactor to use memory_matrix of storage_node if that is implemented Co-authored-by: jdcpni <pniintel55>
kmantel
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Dec 12, 2023
* origin/master: tests/ParameterEstimationComposition: Reduce the number of estimates by 40x tests/ParameterEstimationComposition: Provide expected result instead of relying on tolerance requirements: update dill requirement from <0.3.7 to <0.3.8 (PrincetonUniversity#2743) Feat/em composition refactor learning mech (PrincetonUniversity#2754) Fix/input port combine (PrincetonUniversity#2755) requirements: update beartype requirement from <0.15.0 to <0.16.0 (PrincetonUniversity#2744)
kmantel
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Dec 12, 2023
Resolve all differences in favor of devel. master changes are stale because they mirror old commits on devel. * master: tests/ParameterEstimationComposition: Reduce the number of estimates by 40x tests/ParameterEstimationComposition: Provide expected result instead of relying on tolerance requirements: update dill requirement from <0.3.7 to <0.3.8 (PrincetonUniversity#2743) Feat/em composition refactor learning mech (PrincetonUniversity#2754) Fix/input port combine (PrincetonUniversity#2755) requirements: update beartype requirement from <0.15.0 to <0.16.0 (PrincetonUniversity#2744)
kmantel
added a commit
to kmantel/PsyNeuLink
that referenced
this pull request
Dec 12, 2023
Resolve all differences in favor of devel. master changes are stale because they mirror old commits on devel. * master: tests/ParameterEstimationComposition: Reduce the number of estimates by 40x tests/ParameterEstimationComposition: Provide expected result instead of relying on tolerance requirements: update dill requirement from <0.3.7 to <0.3.8 (PrincetonUniversity#2743) Feat/em composition refactor learning mech (PrincetonUniversity#2754) Fix/input port combine (PrincetonUniversity#2755) requirements: update beartype requirement from <0.15.0 to <0.16.0 (PrincetonUniversity#2744)
jdcpni
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Dec 13, 2023
* requirements: update beartype requirement from <0.15.0 to <0.16.0 (#2744) * Fix/input port combine (#2755) • inputport.py _parse_port_specific_specs(): fix bug in which COMBINE was not parsed when specified in an InputPort specification dict (though still some weirdness in passing spec through to constructor, requiring function assignment in place) • port.py _parse_port_spec(): add passing of Context.string for local handling based on caller (e.g., warning messages) * Feat/em composition refactor learning mech (#2754) • EMstoragemechanism.py - refactor memory_matrix to use learning_signals • emcomposition.py - refactor to use memory_matrix of storage_node if that is implemented Co-authored-by: jdcpni <pniintel55> * requirements: update dill requirement from <0.3.7 to <0.3.8 (#2743) * tests/ParameterEstimationComposition: Provide expected result instead of relying on tolerance Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> * tests/ParameterEstimationComposition: Reduce the number of estimates by 40x It's still enough to recover the parameters and reduces test time significantly. Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> --------- Signed-off-by: Jan Vesely <jan.vesely@rutgers.edu> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: jdcpni <jdc@princeton.edu> Co-authored-by: Jan Vesely <jan.vesely@rutgers.edu>
kmantel
added a commit
to kmantel/PsyNeuLink
that referenced
this pull request
Dec 13, 2023
Resolve all differences in favor of devel. master changes are stale because they mirror old commits on devel. * master: tests/ParameterEstimationComposition: Reduce the number of estimates by 40x tests/ParameterEstimationComposition: Provide expected result instead of relying on tolerance requirements: update dill requirement from <0.3.7 to <0.3.8 (PrincetonUniversity#2743) Feat/em composition refactor learning mech (PrincetonUniversity#2754) Fix/input port combine (PrincetonUniversity#2755) requirements: update beartype requirement from <0.15.0 to <0.16.0 (PrincetonUniversity#2744)
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• emcomposition.py
• test_emcomposition.py
• composition.py