├── .gitignore ├── .project-root ├── Makefile ├── README.md ├── configs ├── __init__.py ├── callbacks │ ├── default.yaml │ ├── early_stopping.yaml │ ├── model_checkpoint.yaml │ ├── model_summary.yaml │ ├── none.yaml │ ├── retrobridge.yaml │ └── rich_progress_bar.yaml ├── data │ ├── enhancer.yaml │ ├── promoter_design.yaml │ ├── qm9.yaml │ └── toy_dfm.yaml ├── debug │ ├── default.yaml │ ├── fdr.yaml │ ├── limit.yaml │ ├── overfit.yaml │ └── profiler.yaml ├── eval.yaml ├── experiment │ ├── enhancer_fly_sfm_cnn.yaml │ ├── enhancer_mel_sfm_cnn.yaml │ ├── enhancer_sfm_bmlp.yaml │ ├── promoter_dfm.yaml │ ├── promoter_rfm_tmlp.yaml │ ├── promoter_sfm_cnn.yaml │ ├── promoter_sfm_promdfm.yaml │ ├── promoter_sfm_tmlp.yaml │ ├── promoter_sfm_unet1d.yaml │ ├── qm_clean_sfm.yaml │ ├── qm_euclid.yaml │ ├── qm_simplex.yaml │ ├── qm_simplex_boost.yaml │ ├── qm_simplex_pushing.yaml │ ├── qm_sphere.yaml │ ├── qm_sphere_pushing.yaml │ ├── qm_vecfield_sfm.yaml │ ├── toy_dfm_bmlp.yaml │ ├── toy_dfm_cnn.yaml │ ├── toy_dfm_sfm_cnn.yaml │ ├── toy_dfm_sfm_tmlp.yaml │ ├── toy_dfm_sfm_unet1d.yaml │ ├── toy_dfm_temb.yaml │ ├── toy_rfm_cnn.yaml │ └── toy_rfm_tmlp.yaml ├── extras │ └── default.yaml ├── hparams_search │ └── mnist_optuna.yaml ├── hydra │ └── default.yaml ├── local │ └── .gitkeep ├── logger │ ├── aim.yaml │ ├── comet.yaml │ ├── csv.yaml │ ├── many_loggers.yaml │ ├── mlflow.yaml │ ├── neptune.yaml │ ├── tensorboard.yaml │ └── wandb.yaml ├── misc │ └── qm9_sfm.yaml ├── model │ ├── benhancer_mlp.yaml │ ├── bsignal_mlp.yaml │ ├── mel_cnn.yaml │ ├── molecule_module.yaml │ ├── promoter_dfm.yaml │ ├── promoter_model.yaml │ ├── promoter_sfm_unet1d.yaml │ ├── qm_vecfield_sfm.yaml │ ├── sfm_tmlp.yaml │ ├── sfm_tmlp_signal.yaml │ ├── toy_bmlp.yaml │ ├── toy_cnn_model.yaml │ ├── toy_cnn_sfm.yaml │ ├── toy_temb.yaml │ └── toy_unet1d.yaml ├── paths │ └── default.yaml ├── train.yaml └── trainer │ ├── cpu.yaml │ ├── ddp.yaml │ ├── ddp_sim.yaml │ ├── default.yaml │ └── gpu.yaml ├── environment.yaml ├── process_qm9.py ├── pyproject.toml ├── requirements.txt ├── script ├── submit.sh ├── submit_bmlp_sfm.sh ├── submit_bmlp_sfm_lin.sh ├── submit_bmlp_sfm_noot.sh ├── submit_bmlp_sfm_simplex_noot.sh ├── submit_bmlp_sfm_simplex_ot.sh ├── submit_cnn_dfm_toy.sh ├── submit_cnn_sfm_toy.sh ├── submit_cnn_sfm_toy_lsmooth.sh ├── submit_enhancer_bmlp.sh ├── submit_enhancer_cnn_sfm.sh ├── submit_enhancer_cnn_sfm_dna.sh ├── submit_eval_fly.sh ├── submit_eval_mel.sh ├── submit_eval_promoter.sh ├── submit_promoter_sfm_bmlp.sh ├── submit_promoter_sfm_promdfm.sh ├── submit_qm_clean.sh ├── submit_qm_sfm.sh ├── submit_qm_sfm_single.sh ├── submit_rfm_cnn_toy.sh ├── submit_tmlp_sfm_promoter.sh ├── submit_unet1d_toy.sh ├── submit_unet_sfm_promoter.sh ├── toy_all_bmlp_sfm.sh ├── toy_all_bmlp_sfm_noot.sh ├── toy_all_bmlp_sfm_simplex_noot.sh ├── toy_all_bmlp_sfm_simplex_ot.sh ├── toy_all_cnn_dfm.sh ├── toy_all_cnn_sfm.sh ├── toy_bmlp_lin.sh └── toy_cnn_sfm_lsmooth.sh ├── setup.py ├── src ├── __init__.py ├── data │ ├── __init__.py │ ├── components │ │ ├── __init__.py │ │ ├── fbd.py │ │ ├── ff_energy.py │ │ ├── molecule.py │ │ ├── molecule_builder.py │ │ ├── molecule_prior.py │ │ ├── promoter_back.py │ │ ├── promoter_eval.py │ │ ├── qm_utils.py │ │ ├── sample_analyzer.py │ │ └── sei.py │ ├── dna_enhancer_datamodule.py │ ├── promoter_datamodule.py │ ├── qm9_datamodule.py │ └── toy_dfm_datamodule.py ├── dfm │ ├── __init__.py │ └── flow_utils.py ├── eval.py ├── models │ ├── __init__.py │ ├── dfm_module.py │ ├── molecule_module.py │ ├── net │ │ ├── __init__.py │ │ ├── gvp.py │ │ ├── interpolant_scheduler.py │ │ ├── model.py │ │ ├── promoter_model.py │ │ └── vector_field.py │ └── sfm_module.py ├── sfm │ ├── __init__.py │ ├── distribution.py │ ├── manifold.py │ ├── maths.py │ ├── plot.py │ ├── sampler.py │ └── train.py ├── train.py └── utils │ ├── __init__.py │ ├── instantiators.py │ ├── logging_utils.py │ ├── pylogger.py │ ├── rich_utils.py │ └── utils.py └── tests ├── 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