├── Chapter03 ├── mnist.py └── tox21.py ├── Chapter04 └── solubility.py ├── Chapter05 ├── 2D3U_notebook.ipynb ├── 2d3u.pdb ├── pdbbind_nn.py └── pdbbind_rf.py ├── Chapter06 ├── accessibility.txt ├── rnai.py ├── test_dataset │ ├── metadata.csv.gzip │ ├── shard-0-X.joblib │ ├── shard-0-ids.joblib │ ├── shard-0-w.joblib │ ├── shard-0-y.joblib │ └── tasks.json ├── tfbinding.py ├── tfbinding_chromatin.py ├── train_dataset │ ├── metadata.csv.gzip │ ├── shard-0-X.joblib │ ├── shard-0-ids.joblib │ ├── shard-0-w.joblib │ ├── shard-0-y.joblib │ └── tasks.json ├── train_siRNA │ ├── metadata.csv.gzip │ ├── shard-0-X.joblib │ ├── shard-0-ids.joblib │ ├── shard-0-w.joblib │ ├── shard-0-y.joblib │ └── tasks.json ├── valid_dataset │ ├── metadata.csv.gzip │ ├── shard-0-X.joblib │ ├── shard-0-ids.joblib │ ├── shard-0-w.joblib │ ├── shard-0-y.joblib │ └── tasks.json └── valid_siRNA │ ├── metadata.csv.gzip │ ├── shard-0-X.joblib │ ├── shard-0-ids.joblib │ ├── shard-0-w.joblib │ ├── shard-0-y.joblib │ └── tasks.json ├── Chapter07 ├── README.md ├── cell_counting.py ├── cell_segmentation.py ├── get_data.sh └── get_groundtruth.sh ├── Chapter08 ├── README.md ├── data.py ├── get_pretrained_model.sh ├── model.py └── run.py ├── Chapter09 └── vae.py ├── Chapter10 ├── optimize_tf.py └── uncertainty.py ├── Chapter11 ├── README.md ├── chapter_11_01_preparing_to_build_a_predictive_models.ipynb ├── chapter_11_02_erk2_graph_conv.ipynb ├── chapter_11_03_filtering_chemical_libraries.ipynb ├── chapter_11_04_using_the_predictive_model.ipynb ├── dude_erk2_mk01.csv ├── mk01 │ ├── actives_final.ism │ └── decoys_final.ism ├── neutralize.py └── zinc_100k.smi ├── LICENSE └── README.md /Chapter03/mnist.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/deepchem/DeepLearningLifeSciences/HEAD/Chapter03/mnist.py -------------------------------------------------------------------------------- /Chapter03/tox21.py: 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