darpa-askem / experiments

small experiments and prototypes

Experiments

Research prototypes and small experiments, organized as a series of notebooks.

experiments's Issues

Test SKEMA equation-to-model API with new AMR format

Validation on ASKENET models

@bgyori we were scanning through some of the ASKE-net models and it seems like there could have been some parsing issues. E.g. https://github.com/DARPA-ASKEM/experiments/blob/main/thin-thread-examples/mira_v2/biomodels/BIOMD0000000970/model_askenet.json#LL137C12-L137C12

Could you take a look? Let me know if it would help for us to run a validator over these.

Add a more general "add_reflexives" function in Catlab

From our earlier discussion on our model-stratification workflow sketch (based around this notebook), we'd need:

• a more general add_reflexives function that adds a transition with any dependent state node (not really a reflexive anymore), e.g. adding a Vaccinate transition node to a Pop state node should also add a required Vaccine state node (since Vaccinate(Pop, Vaccine; Pop))
• the parent-child relationship between nodes of the base & strata models and those of the stratified model (currently we'd reverse engineer those relationships using the labels of the stratified model).

Infer model rules from model framework schema

Reference: AlgebraicJulia/ACSets.jl#27

The task is about how to get the AlgebraicJulia schemas of different model frameworks and how to infer the rules of model editing from them.

Use case: how does the Terarium HMI know to enforce bipartite-ness of a model's Petri net representation while the user is adding/removing nodes and edges.

Strange stratification behaviour with multiple node types

The issue is that state nodes of different types are combined during stratification (via typed_product).

An example that produces this mis-behaviour is here:
https://github.com/DARPA-ASKEM/experiments/blob/main/notebooks/Nelson/multi-stratify-experiment/SIRV-Age-Travel-example.ipynb

• The base model is SIRV: SIR with vaccine production and vaccination of S.
• There are two types of state nodes - Pop and Vac - representing humans and vaccine doses.
• I stratified this model with a 2-age-group contact model; it has the vaccine production and vaccination interactions (necessary for correct stratification).
• The resulting stratified model is mostly correct: the connected part is correct but there are many unconnected state nodes (e.g. (vaccine, A1) and (S, vaccine)) which shouldn't be there.
• The "bad" state nodes are combination of state nodes of different types ((Pop, Vac) and (Vac, Pop)).
• As I understand, stratification has the correct behaviour with respect to transition nodes since it only combines transition nodes of the same type.

I think this is a bug with typed_product but I could be misusing the API while trying to create an example with different state node types.

TA1 FUNMAN integration

• Setup FUNMAN service (https://github.com/ml4ai/funman)
• Experiment with FUNMAN tools using the unit tests as templates (https://github.com/ml4ai/funman/tree/develop/test)
• Design model debugging workflows using these tools