├── .gitignore ├── LICENSE ├── README.md ├── mol_vae ├── cfg_parser │ ├── cfg_parser.py │ └── parser_demo.py ├── data_processing │ ├── dump_cfg_trees.py │ ├── make_dataset_parallel.py │ ├── make_dataset_sequential.py │ ├── run_cfg_dump.sh │ └── run_data.sh ├── mol_common │ ├── cmd_args.py │ ├── mol_tree.py │ ├── mol_util.py │ └── pytorch_initializer.py ├── mol_decoder │ ├── attribute_tree_decoder.py │ ├── custom_loss.py │ ├── mol_decoder.py │ └── tree_walker.py ├── mol_encoder │ ├── mol_encoder.py │ └── run_test.sh ├── mol_optimization │ ├── bayesian_optimization.py │ ├── fpscores.pkl.gz │ ├── gauss.py │ ├── get_final_results.py │ ├── run_bo.sh │ ├── sascorer.py │ ├── sparse_gp.py │ └── sparse_gp_theano_internal.py ├── mol_vae │ └── mol_vae.py ├── pytorch_eval │ ├── att_model_proxy.py │ ├── dump_encoding.py │ ├── eval_similarity.py │ ├── reconstruct_zinc.py │ ├── run_feature_dump.sh │ ├── run_reconstruct_zinc.sh │ ├── run_sample_prior.sh │ ├── run_valid_prior.sh │ ├── sample_prior.py │ └── valid_prior.py ├── pytorch_train │ ├── run_train.sh │ └── train_zinc.py ├── sparse_gp_regression │ ├── fpscores.pkl.gz │ ├── gauss.py │ ├── regression.py │ ├── run_regression.sh │ ├── sascorer.py │ ├── sparse_gp.py │ └── sparse_gp_theano_internal.py └── visualize │ ├── draw_2dvis.py │ └── run_2dvis.sh └── prog_vae ├── cfg_parser ├── cfg_parser.py └── parser_demo.py ├── data_processing ├── make_dataset_parallel.py └── run_data.sh ├── prog_common ├── cmd_args.py ├── prog_tree.py ├── prog_util.py └── pytorch_initializer.py ├── prog_data ├── bo_target.py ├── evaluate.py ├── generate_data.py ├── gold_prog.txt ├── precompute_bo_target.py ├── run_generate_data.sh └── run_precompute_bo_target.sh ├── prog_decoder ├── custom_loss.py ├── prog_decoder.py ├── prog_tree_decoder.py └── tree_walker.py ├── prog_encoder └── prog_encoder.py ├── prog_eval ├── att_model_proxy.py ├── dump_encoding.py ├── reconstruct_prog.py ├── run_att.sh ├── run_feature_dump.sh ├── run_interpolation.sh ├── run_prior.sh ├── run_reconstruct.sh ├── sdvae_interpolation.py └── valid_prior.py ├── prog_optimization ├── bayesian_optimization.py ├── gauss.py ├── get_results.py ├── pbs_gru.pbs ├── run_bo.sh ├── run_results.sh ├── sparse_gp.py └── sparse_gp_theano_internal.py ├── prog_train ├── run_train.sh └── train_prog.py ├── prog_vae └── prog_vae.py └── sparse_gp_regression ├── gauss.py ├── regression.py ├── run_regression.sh ├── sparse_gp.py └── sparse_gp_theano_internal.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Hanjun-Dai/sdvae/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/Hanjun-Dai/sdvae/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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