Mismatch between rate law symbols and state variable names #189
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Yes, this can indeed happen if both an id and a name are specified and they are different. We will look into the best option to fix this. |
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The main issue is that I need a reliable way to associate a symbol with a concept. One possibility is to include the symbol as an additional attribute of the Concept |
djinnome
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Jul 6, 2023
…w_p False by default
SamWitty
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Jul 10, 2023
* I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law
anirban-chaudhuri
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Jul 10, 2023
* Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test * Symbolic Rate law to Pytorch Rate law (#201) * I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com>
anirban-chaudhuri
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Jul 10, 2023
* Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test * Symbolic Rate law to Pytorch Rate law (#201) * I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law * 12-Month Hackathon Notebooks (#207) * started hackathon prep scenario notebooks * more on hackathon scenarios * more work on hackathon notebooks * created AMR for scenario1 with constant beta * Vs hackathon prep (#203) * beginning of ensemble challenge ipynb * Update ensemble_challenge.ipynb * added to scenario2 notebook, ready for scenario3 * added to scenario2 notebook, ready for scenario3 * Update scenario1.ipynb * Update scenario1 * changes to scenario3, and new AMR * pre-hackathon prep update - scenario1 task 1 almost done (pending AMR changes) - ensemble challenge layout started * more on scenario notebooks, added AMR to scenario2 * Fixed the nan inside the intervened parameters column output * updates to scenario3 notebook * merged from main --------- Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov>
anirban-chaudhuri
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Jul 12, 2023
* Optimize TA4 interface * Update interfaces.py * Change setup to fix MIRA name error (#205) (#206) * changed mira version before bug * fix error Co-authored-by: Sam Witty <samawitty@gmail.com> * Update demo notebook * Update demo.ipynb * Update MIRA loading (#209) * Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test --------- Co-authored-by: Sam Witty <samawitty@gmail.com> * Updated interface with string inputs for QOI * Interface to optimize after calibrating * Update demo.ipynb * Update sample csv file to avoid merge conflicts * Updating file to avoid merge conflict with main * Updating from main to fix model loading errors (#211) * Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test * Symbolic Rate law to Pytorch Rate law (#201) * I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> * Update notebooks to avoid merge conflicts * Update NB to resolve conflicts * Update from main to avoid conflicts (#212) * Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test * Symbolic Rate law to Pytorch Rate law (#201) * I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law * 12-Month Hackathon Notebooks (#207) * started hackathon prep scenario notebooks * more on hackathon scenarios * more work on hackathon notebooks * created AMR for scenario1 with constant beta * Vs hackathon prep (#203) * beginning of ensemble challenge ipynb * Update ensemble_challenge.ipynb * added to scenario2 notebook, ready for scenario3 * added to scenario2 notebook, ready for scenario3 * Update scenario1.ipynb * Update scenario1 * changes to scenario3, and new AMR * pre-hackathon prep update - scenario1 task 1 almost done (pending AMR changes) - ensemble challenge layout started * more on scenario notebooks, added AMR to scenario2 * Fixed the nan inside the intervened parameters column output * updates to scenario3 notebook * merged from main --------- Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> * Update demo.ipynb * Update demo.ipynb * updated demo with new MIRA model * Fixed setup.cfg * Update demo.ipynb * Updated solution key in demo * finished demo notebook run * Added test for samples obtained after OUU * Update output format and description * Fixed mira on setup to help pass tests * Added `self.intervened_samples` to `test_ode_interfaces' --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov>
anirban-chaudhuri
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Jul 13, 2023
* Added get_name on the mira parameter keys for safety (#218) * Added get_name on the mira parameter keys for safety * Removed test for SIDARTHE which fails due to gyorilab/mira#195 * checked out scenario1 from main so that it doesn't clobber Vignesh's changes * Added test that confirms gyorilab/mira#196 solves gyorilab/mira#195 * Added pin to latest mira commit * bump mira (#227) * bump mira * bumped AMR file * Provisional support for time_unit in TA4 interface dataframe (#221) * Provisional support for time_unit in TA4 interface dataframe * Missed format identifier * Default time-unit * Testing time_unit behaviors * Updating tests for new TA4 itnerface behavior * To preserve context in failure messages, changed to * Decorator logging function (#232) * Logging function name where error occurs * updated text * Optimize interface for TA4 integration (#204) * Optimize TA4 interface * Update interfaces.py * Change setup to fix MIRA name error (#205) (#206) * changed mira version before bug * fix error Co-authored-by: Sam Witty <samawitty@gmail.com> * Update demo notebook * Update demo.ipynb * Update MIRA loading (#209) * Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test --------- Co-authored-by: Sam Witty <samawitty@gmail.com> * Updated interface with string inputs for QOI * Interface to optimize after calibrating * Update demo.ipynb * Update sample csv file to avoid merge conflicts * Updating file to avoid merge conflict with main * Updating from main to fix model loading errors (#211) * Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test * Symbolic Rate law to Pytorch Rate law (#201) * I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> * Update notebooks to avoid merge conflicts * Update NB to resolve conflicts * Update from main to avoid conflicts (#212) * Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test * Symbolic Rate law to Pytorch Rate law (#201) * I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law * 12-Month Hackathon Notebooks (#207) * started hackathon prep scenario notebooks * more on hackathon scenarios * more work on hackathon notebooks * created AMR for scenario1 with constant beta * Vs hackathon prep (#203) * beginning of ensemble challenge ipynb * Update ensemble_challenge.ipynb * added to scenario2 notebook, ready for scenario3 * added to scenario2 notebook, ready for scenario3 * Update scenario1.ipynb * Update scenario1 * changes to scenario3, and new AMR * pre-hackathon prep update - scenario1 task 1 almost done (pending AMR changes) - ensemble challenge layout started * more on scenario notebooks, added AMR to scenario2 * Fixed the nan inside the intervened parameters column output * updates to scenario3 notebook * merged from main --------- Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> * Update demo.ipynb * Update demo.ipynb * updated demo with new MIRA model * Fixed setup.cfg * Update demo.ipynb * Updated solution key in demo * finished demo notebook run * Added test for samples obtained after OUU * Update output format and description * Fixed mira on setup to help pass tests * Added `self.intervened_samples` to `test_ode_interfaces' --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> * 234 visualization support for trajectory distributions (#235) * Trajectory distribution schema * Sample trajectory data and notebook * Interactive legend * Removing extraneous encoding * replace-by-name utility added Removes index-based replacements (a source of brittleness in the substitutions being done.) * Types improvements and linting fixes * Relabeling * Example trajectories working * calibration viz notebook * clean up * heatmap vega * triangle plot in triangle_vega_demo * Points and tracks on trajectory visualization. * Ignoring typechecking temporaries * Adjusting z-order * EXPERIEMENT: dataframe based input to trajectory visualizations * REVERTING to prep for a TA4-defined dataframe. * Ignoring temporaries that start with an underscore. * Joining line for provided datapoints. * Color control. * TA4 dataframe: Distributions and points working * Distributions, traces and points all work from TA4 interface dataframe. * Improved Color handling * triangle notebook * vega with n-dimensional heatmap * vega with n-dimensional heatmap * Basic timepoint markers added * Permanantly labeled timepoint markers. * Support to NOT join points This is useful when the sample points are relatively dense. * More flexible timepoint for traces. * LotkaVolterra examples NOTE: Its possible the `convert_to_output_format` has a bug. It is returning step-ids, not time-values. As-such, intervention markers were set to 250 instead of 25. * Trajectory and barycenter/proababilty-density plots Extended integration interface to preserve timepoint (not just timepoint_id) Renamed 'vega' to 'plots' Updated examples (Some) Utility tests Cleanup of various files * Basic support for calibrate chart * Calibration supports name-discovery from the dataset. * Provisional support for time_unit in TA4 interface dataframe * Missed format identifier * Updated TA4 dataframe interface. * Using 'Optional' for types instead of Union with None * Visualzation of non-ensembles supported. * Demo of visulaizations through the interface. * Default time-unit * Testing time_unit behaviors * Updating tests for new TA4 itnerface behavior * To preserve context in failure messages, changed to * Tests for visualizations; Visuals avaialble through the TA4 interface. --------- Co-authored-by: Oostrom, Marjolein T <marjolein.oostrom@pnnl.gov> * add json files to package (#240) * Updated setup.cfg to work with pyciemss install (#242) * add json files to package * For some reason the last pr worked locally but not with the simulation service install. hoping this solves it --------- Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Joseph Cottam <jacottam@gmail.com> Co-authored-by: marshHawk4 <kyle@jataware.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> Co-authored-by: Oostrom, Marjolein T <marjolein.oostrom@pnnl.gov>
SamWitty
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Jul 13, 2023
* Ensemble quantiles - Updated `convert_to_output_format` to return quantiles for ensemble models * Updated utilities to produce quantiles as extra output for ensembles * Update sample_results.csv resolving conflicts with main branch * Updating from main (#230) * Added get_name on the mira parameter keys for safety (#218) * Added get_name on the mira parameter keys for safety * Removed test for SIDARTHE which fails due to gyorilab/mira#195 * checked out scenario1 from main so that it doesn't clobber Vignesh's changes * Added test that confirms gyorilab/mira#196 solves gyorilab/mira#195 * Added pin to latest mira commit * bump mira (#227) * bump mira * bumped AMR file --------- Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: Sam Witty <samawitty@gmail.com> * Update interface_utils.py * Data formatting update * Added options for data formatting * Finalized notebook * resolving conflicts with main for notebook * resolving conflicts in csv files * resolving conflicts with main * resolving conflict on rate law test * resolving conflicts on interfaces * Update from main branch (#249) * Added get_name on the mira parameter keys for safety (#218) * Added get_name on the mira parameter keys for safety * Removed test for SIDARTHE which fails due to gyorilab/mira#195 * checked out scenario1 from main so that it doesn't clobber Vignesh's changes * Added test that confirms gyorilab/mira#196 solves gyorilab/mira#195 * Added pin to latest mira commit * bump mira (#227) * bump mira * bumped AMR file * Provisional support for time_unit in TA4 interface dataframe (#221) * Provisional support for time_unit in TA4 interface dataframe * Missed format identifier * Default time-unit * Testing time_unit behaviors * Updating tests for new TA4 itnerface behavior * To preserve context in failure messages, changed to * Decorator logging function (#232) * Logging function name where error occurs * updated text * Optimize interface for TA4 integration (#204) * Optimize TA4 interface * Update interfaces.py * Change setup to fix MIRA name error (#205) (#206) * changed mira version before bug * fix error Co-authored-by: Sam Witty <samawitty@gmail.com> * Update demo notebook * Update demo.ipynb * Update MIRA loading (#209) * Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test --------- Co-authored-by: Sam Witty <samawitty@gmail.com> * Updated interface with string inputs for QOI * Interface to optimize after calibrating * Update demo.ipynb * Update sample csv file to avoid merge conflicts * Updating file to avoid merge conflict with main * Updating from main to fix model loading errors (#211) * Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test * Symbolic Rate law to Pytorch Rate law (#201) * I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> * Update notebooks to avoid merge conflicts * Update NB to resolve conflicts * Update from main to avoid conflicts (#212) * Change setup to fix MIRA name error (#205) * changed mira version before bug * fix error * Add utilities for loading distributions from AMR (#200) * added mira distribution loading * added normal distribution * fixed Normal2 and Normal3 * nit * added minimal mira_distribution_to_pyro test * Symbolic Rate law to Pytorch Rate law (#201) * I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law * 12-Month Hackathon Notebooks (#207) * started hackathon prep scenario notebooks * more on hackathon scenarios * more work on hackathon notebooks * created AMR for scenario1 with constant beta * Vs hackathon prep (#203) * beginning of ensemble challenge ipynb * Update ensemble_challenge.ipynb * added to scenario2 notebook, ready for scenario3 * added to scenario2 notebook, ready for scenario3 * Update scenario1.ipynb * Update scenario1 * changes to scenario3, and new AMR * pre-hackathon prep update - scenario1 task 1 almost done (pending AMR changes) - ensemble challenge layout started * more on scenario notebooks, added AMR to scenario2 * Fixed the nan inside the intervened parameters column output * updates to scenario3 notebook * merged from main --------- Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> * Update demo.ipynb * Update demo.ipynb * updated demo with new MIRA model * Fixed setup.cfg * Update demo.ipynb * Updated solution key in demo * finished demo notebook run * Added test for samples obtained after OUU * Update output format and description * Fixed mira on setup to help pass tests * Added `self.intervened_samples` to `test_ode_interfaces' --------- Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> * 234 visualization support for trajectory distributions (#235) * Trajectory distribution schema * Sample trajectory data and notebook * Interactive legend * Removing extraneous encoding * replace-by-name utility added Removes index-based replacements (a source of brittleness in the substitutions being done.) * Types improvements and linting fixes * Relabeling * Example trajectories working * calibration viz notebook * clean up * heatmap vega * triangle plot in triangle_vega_demo * Points and tracks on trajectory visualization. * Ignoring typechecking temporaries * Adjusting z-order * EXPERIEMENT: dataframe based input to trajectory visualizations * REVERTING to prep for a TA4-defined dataframe. * Ignoring temporaries that start with an underscore. * Joining line for provided datapoints. * Color control. * TA4 dataframe: Distributions and points working * Distributions, traces and points all work from TA4 interface dataframe. * Improved Color handling * triangle notebook * vega with n-dimensional heatmap * vega with n-dimensional heatmap * Basic timepoint markers added * Permanantly labeled timepoint markers. * Support to NOT join points This is useful when the sample points are relatively dense. * More flexible timepoint for traces. * LotkaVolterra examples NOTE: Its possible the `convert_to_output_format` has a bug. It is returning step-ids, not time-values. As-such, intervention markers were set to 250 instead of 25. * Trajectory and barycenter/proababilty-density plots Extended integration interface to preserve timepoint (not just timepoint_id) Renamed 'vega' to 'plots' Updated examples (Some) Utility tests Cleanup of various files * Basic support for calibrate chart * Calibration supports name-discovery from the dataset. * Provisional support for time_unit in TA4 interface dataframe * Missed format identifier * Updated TA4 dataframe interface. * Using 'Optional' for types instead of Union with None * Visualzation of non-ensembles supported. * Demo of visulaizations through the interface. * Default time-unit * Testing time_unit behaviors * Updating tests for new TA4 itnerface behavior * To preserve context in failure messages, changed to * Tests for visualizations; Visuals avaialble through the TA4 interface. --------- Co-authored-by: Oostrom, Marjolein T <marjolein.oostrom@pnnl.gov> * add json files to package (#240) * Updated setup.cfg to work with pyciemss install (#242) * add json files to package * For some reason the last pr worked locally but not with the simulation service install. hoping this solves it --------- Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Joseph Cottam <jacottam@gmail.com> Co-authored-by: marshHawk4 <kyle@jataware.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> Co-authored-by: Oostrom, Marjolein T <marjolein.oostrom@pnnl.gov> * Added back changes for quantile estimations * Added time units * Update test_ensemble_interfaces.py --------- Co-authored-by: Jeremy Zucker <djinnome@gmail.com> Co-authored-by: Sam Witty <samawitty@gmail.com> Co-authored-by: Joseph Cottam <jacottam@gmail.com> Co-authored-by: marshHawk4 <kyle@jataware.com> Co-authored-by: sabinala <130604122+sabinala@users.noreply.github.com> Co-authored-by: vsella <vsella@utexas.edu> Co-authored-by: Jeremy Zucker <Jeremy.Zucker@pnnl.gov> Co-authored-by: Oostrom, Marjolein T <marjolein.oostrom@pnnl.gov>
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* I believe I wrote the correct code, based on experiments in the notebook. Will test next. * FAILED test/test_mira/test_rate_law.py::TestRateLaw::test_rate_law_compilation - AttributeError: 'ScaledBetaNoisePetriNetODESystem' object has no attribute 'beta' * Added Symbolic_Deriv_Experiments notebook * Something weird is happening. I can confirm that 'beta' is an attribute of ScaledBetaNoisePetriNetODESystem after setting up the model, but then it can't be found at sample time * Clarified the bug in the Symbolic derivatives notebook * Expected and actual derivative match * Time varying parameter rate law correctly read * Thought we added this already * Added kwargs to from_askenet and from_mira and compile_rate_law_p to load_petri_net * Blocked on gyorilab/mira#189 but tests pass by making compile_rate_law_p False by default * Removed unnecessary pygraphviz dependency * Unit test to fail when concept name does not equal rate law symbols * All tests pass with default compile_rate_law_p = False * Merged from main. removed dependency on older version of mira * point mira to the github repo main branch * point mira to the github repo main branch * load_and_calibrate_and_sample(..., compile_rate_law_p=True) works with the caveat that the ScaledBetaNoisePetriNetODESystem solution was returning very slightly negative values, so I set mean = torch.abs(solution[var_name]) to address the issue * merged changes to MiraPetriNetODESystem and ScaledBetaNoisePetriNetODESystem from main. ScaledBetaNoisePetriNetODESystem has default compiled_rate_law_p=True * observation_function for ScaledBetaNoisePetriNetODESystem now uses torch.maximum(solution[var_name], torch.tensor(1e-9)) to deal with overshooting derivatives * aggregate parameters is now by default opt-out, and AMR models with multiple parameters per transition can be interpreted using compile_rate_law
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Hi folks,
In the AMR format, rate laws are expressed as symbols using ASKENET State
idnot ASKENET Statename,https://github.com/indralab/mira/blob/82421e4465edfb6eb27f811726d9745afb3d28e4/mira/sources/askenet/petrinet.py#L101
but MIRA only preserves the
namefield (unless the name is not present), and not theidwhen reading the AMR into a Mira model.https://github.com/indralab/mira/blob/82421e4465edfb6eb27f811726d9745afb3d28e4/mira/sources/askenet/petrinet.py#L229
This makes it difficult to automatically associate each sympy symbol with its corresponding state variable.
Is there a way to associate AMR ids with state variables in the MIRA model? Maybe just add
idas another key in thevariable.datadictionary or perhaps as anaskenet:<id>in theidentifiersorcontextattribute?The text was updated successfully, but these errors were encountered: