├── .gitignore ├── LICENSE.txt ├── ODEFormer_demo.ipynb ├── README.md ├── evaluate.py ├── odeformer ├── __init__.py ├── baselines │ ├── __init__.py │ ├── baseline_utils.py │ ├── ellyn_wrapper.py │ ├── ffx_wrapper.py │ ├── proged_wrapper.py │ ├── pysr_wrapper.py │ └── sindy_wrapper.py ├── envs │ ├── __init__.py │ ├── encoders.py │ ├── environment.py │ ├── generators.py │ ├── simplifiers.py │ └── utils.py ├── logger.py ├── metrics.py ├── model │ ├── __init__.py │ ├── embedders.py │ ├── mixins.py │ ├── model_wrapper.py │ ├── sklearn_wrapper.py │ ├── transformer.py │ └── utils_wrapper.py ├── odebench │ ├── __init__.py │ ├── solve_and_plot.py │ ├── strogatz_equations.py │ └── strogatz_extended.json ├── optim.py ├── regressors.py ├── slurm.py ├── trainer.py └── utils.py ├── param_optimizer.py ├── parsers.py ├── requirements.txt ├── scripts ├── generate_data.py ├── generate_data_poly.py ├── run.py ├── run_baselines.py ├── run_baselines.sh ├── run_baselines_slurm.sh ├── run_baselines_slurm_job.sh ├── run_distributed.py ├── run_evaluation.py ├── run_line.py ├── run_masked.py ├── run_noise.py ├── run_poly.py ├── test_baselines.py ├── test_baselines.sh └── tests.ipynb ├── setup.cfg ├── setup.py └── train.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/LICENSE.txt -------------------------------------------------------------------------------- /ODEFormer_demo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/ODEFormer_demo.ipynb -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/README.md -------------------------------------------------------------------------------- /evaluate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/evaluate.py -------------------------------------------------------------------------------- /odeformer/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/__init__.py -------------------------------------------------------------------------------- /odeformer/baselines/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/baselines/__init__.py -------------------------------------------------------------------------------- /odeformer/baselines/baseline_utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/baselines/baseline_utils.py -------------------------------------------------------------------------------- /odeformer/baselines/ellyn_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/baselines/ellyn_wrapper.py -------------------------------------------------------------------------------- /odeformer/baselines/ffx_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/baselines/ffx_wrapper.py -------------------------------------------------------------------------------- /odeformer/baselines/proged_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/baselines/proged_wrapper.py -------------------------------------------------------------------------------- /odeformer/baselines/pysr_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/baselines/pysr_wrapper.py -------------------------------------------------------------------------------- /odeformer/baselines/sindy_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/baselines/sindy_wrapper.py -------------------------------------------------------------------------------- /odeformer/envs/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/envs/__init__.py -------------------------------------------------------------------------------- /odeformer/envs/encoders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/envs/encoders.py -------------------------------------------------------------------------------- /odeformer/envs/environment.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/envs/environment.py -------------------------------------------------------------------------------- /odeformer/envs/generators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/envs/generators.py -------------------------------------------------------------------------------- /odeformer/envs/simplifiers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/envs/simplifiers.py -------------------------------------------------------------------------------- /odeformer/envs/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/envs/utils.py -------------------------------------------------------------------------------- /odeformer/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/logger.py -------------------------------------------------------------------------------- /odeformer/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/metrics.py -------------------------------------------------------------------------------- /odeformer/model/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/model/__init__.py -------------------------------------------------------------------------------- /odeformer/model/embedders.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/model/embedders.py -------------------------------------------------------------------------------- /odeformer/model/mixins.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/model/mixins.py -------------------------------------------------------------------------------- /odeformer/model/model_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/model/model_wrapper.py -------------------------------------------------------------------------------- /odeformer/model/sklearn_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/model/sklearn_wrapper.py -------------------------------------------------------------------------------- /odeformer/model/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/model/transformer.py -------------------------------------------------------------------------------- /odeformer/model/utils_wrapper.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/model/utils_wrapper.py -------------------------------------------------------------------------------- /odeformer/odebench/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/odebench/__init__.py -------------------------------------------------------------------------------- /odeformer/odebench/solve_and_plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/odebench/solve_and_plot.py -------------------------------------------------------------------------------- /odeformer/odebench/strogatz_equations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/odebench/strogatz_equations.py -------------------------------------------------------------------------------- /odeformer/odebench/strogatz_extended.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/odebench/strogatz_extended.json -------------------------------------------------------------------------------- /odeformer/optim.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/optim.py -------------------------------------------------------------------------------- /odeformer/regressors.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/regressors.py -------------------------------------------------------------------------------- /odeformer/slurm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/slurm.py -------------------------------------------------------------------------------- /odeformer/trainer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/trainer.py -------------------------------------------------------------------------------- /odeformer/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/odeformer/utils.py -------------------------------------------------------------------------------- /param_optimizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/param_optimizer.py -------------------------------------------------------------------------------- /parsers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/parsers.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/generate_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/generate_data.py -------------------------------------------------------------------------------- /scripts/generate_data_poly.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/generate_data_poly.py -------------------------------------------------------------------------------- /scripts/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run.py -------------------------------------------------------------------------------- /scripts/run_baselines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_baselines.py -------------------------------------------------------------------------------- /scripts/run_baselines.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_baselines.sh -------------------------------------------------------------------------------- /scripts/run_baselines_slurm.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_baselines_slurm.sh -------------------------------------------------------------------------------- /scripts/run_baselines_slurm_job.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_baselines_slurm_job.sh -------------------------------------------------------------------------------- /scripts/run_distributed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_distributed.py -------------------------------------------------------------------------------- /scripts/run_evaluation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_evaluation.py -------------------------------------------------------------------------------- /scripts/run_line.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_line.py -------------------------------------------------------------------------------- /scripts/run_masked.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_masked.py -------------------------------------------------------------------------------- /scripts/run_noise.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_noise.py -------------------------------------------------------------------------------- /scripts/run_poly.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/run_poly.py -------------------------------------------------------------------------------- /scripts/test_baselines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/test_baselines.py -------------------------------------------------------------------------------- /scripts/test_baselines.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/test_baselines.sh -------------------------------------------------------------------------------- /scripts/tests.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/scripts/tests.ipynb -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- 1 | # Inside of setup.cfg 2 | [metadata] 3 | description-file = README.md -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/setup.py -------------------------------------------------------------------------------- /train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sdascoli/odeformer/HEAD/train.py --------------------------------------------------------------------------------