Simulated RNA circuits

Datasets used to train CVAE models.

Sequence-sampled dataset:
- Dataset: 2024_12_05_210221__ensemble_config
- Configuration file: 2024_12_05_210221__tabulated_mutation_info

Parameter-sampled dataset:
- Dataset: 2025_02_11__13_56_51__tabulated_mutation_info
- Configuration file: 2025_02_11__13_56_51__config

Pair of circuits from UMAP:
- Concentrations: ruggedness_umap_pair_ys.npy
- Time-steps: ruggedness_umap_pair_ts.npy

Model trained on 'adaptation':
- Dynamics metric: model1_adaptation_analytics.json
- Generated circuit interactions: model1_adaptation_generated_circuits.npy 
- Prompts:
   - model1_adaptation_sampled_cond_14.npy
   - model1_adaptation_sampled_cond_56.npy
   - model1_adaptation_sampled_cond_112.npy

Model trained on ['adaptation', 'ruggedness']:
- Dynamics metrics: model2_adaptation_ruggedness_analytics.json
- Generated circuit interactions: model2_adaptation_ruggedness_generated_circuits.npy
- Prompts: model2_adaptation_ruggedness_sampled_cond.npy

--> Simulated using IntaRNA 2.0 and JAX solvers for dynamics