Add common subexpression elimination (CSE) feature by clinssen · Pull Request #111 · nest/ode-toolbox

clinssen · 2026-09-15T13:25:58Z

This PR primarily contains common sub-expression elimination code under /odetoolbox/expression_optimisation.py which is called in __init__.py to optimise the user's sympy expressions. This PR additionally contains code from #PR107 to enable analytical solving for the AMAT neuronal model.

Replaces #110.

…ed for AMAT neuron model

…t-merge-pr107

Modifying ignore so further pycodestyle errors don't block static checks

allow style check to fail without breaking the testing for odetoolbox

clinssen · 2026-09-15T13:41:31Z

    :param use_alternative_expM: If :python:`False`, use the sympy function ``sympy.exp`` to compute the matrix exponential. If :python:`True`, use an alternative function (see :py:func:`odetoolbox.sympy_helpers.expMt` for details). This can be useful as calls to ``sympy.exp`` can sometimes take a very large amount of time.
    :param preserve_expressions: Set to True, or a list of strings corresponding to individual variable names, to disable internal rewriting of expressions, and return same output as input expression where possible. Only applies to variables specified as first-order differential equations.
    :param log_level: Sets the logging threshold. Logging messages which are less severe than ``log_level`` will be ignored. Log levels can be provided as an integer or string, for example "INFO" (more messages) or "WARN" (fewer messages). For a list of valid logging levels, see https://docs.python.org/3/library/logging.html#logging-levels
+    :param enable_cse: Boolean flag set to False. If enabled it will perform sub-expression elimination on update_expression, propagators and singularity conditions of the generated .cpp nestml file.


TODO: add these to documentation; note that documentation about flags contains a lot of duplication with the docstring here; any way to deduplicate?

clinssen · 2026-09-15T13:43:51Z

    :param preserve_expressions: Set to True, or a list of strings corresponding to individual variable names, to disable internal rewriting of expressions, and return same output as input expression where possible. Only applies to variables specified as first-order differential equations.
    :param log_level: Sets the logging threshold. Logging messages which are less severe than ``log_level`` will be ignored. Log levels can be provided as an integer or string, for example "INFO" (more messages) or "WARN" (fewer messages). For a list of valid logging levels, see https://docs.python.org/3/library/logging.html#logging-levels
+    :param enable_cse: Boolean flag set to False. If enabled it will perform sub-expression elimination on update_expression, propagators and singularity conditions of the generated .cpp nestml file.
+    :param preserves_cse_condition_branches: Boolean flag set to false. Requires enable_cse=True for functionality. If enabled this will perform independent analysis of singularity condition branches.


Flag to be removed.

clinssen · 2026-09-15T13:45:26Z

        :param solve_dict: The results dictionary returned by a call to :python:`odetoolbox.analysis()`.
        :param spike_times: For each variable, used as a key, the list of times at which a spike occurs.
        :param enable_caching: Allow caching of results between requested times.
+        :param enable_cse: Whether to consume CSE metadata containined in the solver dictionary. Disabled by default for backwards compatibility. 


Remove flag, make implicit by searching for "CSE" keys in the dictionary.

clinssen · 2026-09-15T13:54:50Z

+    return False
+
+
+def _contains_internal_control_flow(expressions):


TODO: add test covering piecewise functions.

clinssen · 2026-09-15T14:07:20Z

    # a minimal subset of sympy classes and functions to avoid "from sympy import *"
    _sympy_globals = {"Symbol": sympy.Symbol,
-                      "Integer": sympy.Integer,
+                      "Integer": sympy.Integer, # XXX TO DO: Utilise this in our LOCALS optimisation condition


Suggested change

"Integer": sympy.Integer, # XXX TO DO: Utilise this in our LOCALS optimisation condition

"Integer": sympy.Integer,

clinssen · 2026-09-15T14:15:13Z

+                    connectivity[row, col] = 1 
+
+        # find connected components, grouping state variables into clusters that are coupled 
+        _, component_labels = scipy.sparse.csgraph.connected_components(


Are these changes necessary or just for testing? If necessary, please spin off to a separate function and add docstring.

clinssen · 2026-09-15T14:22:38Z

+from .context import odetoolbox
+
+def test_coupled_inhomogeneous_system_is_analytical():
+


Can you use the AMAT model JSON file here instead?

clinssen · 2026-09-15T14:27:06Z

+            "initial_value": "2"
+        },
+        {
+            "expression": "x' = x**2 + exp(x + y) + sin(x + y)",


Suggested change

"expression": "x' = x**2 + exp(x + y) + sin(x + y)",

"expression": "x' = -x**2 + exp(x + y) + sin(x + y)",

clinssen · 2026-09-15T14:27:38Z

+            spike_times={},
+            random_seed=123,
+            max_step_size=max_step_size,
+            integration_accuracy_abs=1E-4,  # accuaracy leads to number of steps simulation steps taken 


Potentially increase accuracy to 1E-6 and decrease testing tolerances below.

clinssen · 2026-09-15T14:28:00Z

+import json
+import odetoolbox
+
+def test_analysis_cse_is_json_serializable():


Can be removed?

C.A.P. Linssen and others added 30 commits July 30, 2026 11:49

change conditions for analytic solver generation so solver is generat…

4c31adb

…ed for AMAT neuron model

comments learning

7506d31

simple cse and test

c4d801c

preserve cse expression tests

ccdb205

count operations test

a9a0741

implementation debugging

df004d5

test_numeric_solver_cse debugging

66bcbff

finished numerical testing

b59c70b

finished analytical testing

0b926d2

numerical cse testing pipeline

777dd68

analytical test pipeline

5ec2820

test_cse_disabled_preserves_legacy

b6e89b2

value unpacking debugging

8586484

cpython crash upstream changes reverted

425cd4d

test for conditions null

11bb2b9

json serialised and optimised tests

c96954e

inspecting singularity conditions

d572d1e

preserves condition singularity test

4c423f4

logic for cse singularity condition optimisation

86b43be

singularity safety checks before running cse

dbb787e

singularity branches test

0f6bda7

cost calculations and checks

3b4c80b

singularity clean and condition flag

067b1da

test adjustments

5a56f6b

debugging adjustments for amat nestml testing

28ed155

ignore pygsl error for amat test

a9dfbf1

amat testing and sym bug

d602f33

commit before analytical solver merge

b1eaa7c

Merge remote-tracking branch 'clinssen/amat_analytic_solver' into tes…

6fda4c7

…t-merge-pr107

PR107 analytical solver init changes

753348d

awg2024 and others added 6 commits September 14, 2026 10:53

Update ode-toolbox-build.yml

89ebaed

Modifying ignore so further pycodestyle errors don't block static checks

Update ode-toolbox-build.yml

172fab1

allow style check to fail without breaking the testing for odetoolbox

working mixed numerical test for cse

7990365

updated timestep decay

b1a01e8

Merge remote-tracking branch 'origin/main' into HEAD

d3f5919

whitespace fix

307232b

clinssen added the enhancement label Sep 15, 2026

pycodestyle fixes

a32183a

clinssen commented Sep 15, 2026

View reviewed changes

awg2024 added 12 commits September 18, 2026 15:32

updated test scripts based on PR feedback

b046382

working cse singularity test

d455880

adjust cse finder

004fc8a

fixed whitespace warnings for PR

87c3b58

improved doc-strings

7a0c219

generate analytical solver function parsed and updated docstring

ff448a9

solver bug fixed

ad2ea42

updated readthedocs cse section

d3eecf7

add cse to input/output sections

f2d8723

disable_cse flag, default true

d14acf0

commentry and index.rst adjustments

37412e8

adjusted test files matches HEAD

aed5405

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Add common subexpression elimination (CSE) feature - #111

Add common subexpression elimination (CSE) feature#111
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		return False


		def _contains_internal_control_flow(expressions):

	"Integer": sympy.Integer, # XXX TO DO: Utilise this in our LOCALS optimisation condition
	"Integer": sympy.Integer,

		from .context import odetoolbox

		def test_coupled_inhomogeneous_system_is_analytical():

	"expression": "x' = x**2 + exp(x + y) + sin(x + y)",
	"expression": "x' = -x**2 + exp(x + y) + sin(x + y)",

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