config.json

{
  "model_name": "Antibody Deep Learning",
  "framework": "TensorFlow",
  "task": "antibody-binder-prediction-and-cdr3-generation",
  "description": "Predict CTLA-4 and PD-1 antibody binders with CNN models and generate synthetic CDR3K/CDR3H antibody sequences with GAN models.",
  "entry_points": {
    "prepare_data": "scripts/01_prepare_data_compat.R",
    "cnn_inference": "scripts/02_cnn_inference.R",
    "gan_inference": "scripts/03_gan_inference.R",
    "export_cnn_npz": "scripts/04_export_cnn_npz.R",
    "train_cnn": "scripts/05_train_cnn.py",
    "export_gan_npz": "scripts/06_export_gan_npz.R",
    "train_gan": "scripts/07_train_gan.py",
    "generate_from_trained_gan": "scripts/08_generate_from_trained_gan.py"
  },
  "source_package": "model",
  "config": "conf/config.json",
  "data": {
    "blosum62": "model/BLOSUM62_with_deletion.Rdata",
    "cnn_raw": "model/CNN/all_ab_pre_post.txt",
    "cnn_preprocessed": [
      "model/CNN/c1.RDS",
      "model/CNN/c1_train.RDS",
      "model/CNN/c1_train_y.RDS",
      "model/CNN/c1_test.RDS",
      "model/CNN/c1_test_y.RDS",
      "model/CNN/p1.RDS",
      "model/CNN/p1_train.RDS",
      "model/CNN/p1_train_y.RDS",
      "model/CNN/p1_test.RDS",
      "model/CNN/p1_test_y.RDS"
    ],
    "gan_preprocessed": [
      "model/GAN/seq_all.RDS",
      "model/GAN/seq_all_encoded.RDS"
    ]
  },
  "weight_dir": {
    "cnn": [
      "weight/CNN/model_c1",
      "weight/CNN/model_p1"
    ],
    "gan": [
      "weight/GAN/GAN_model_1",
      "weight/GAN/GAN_model_2",
      "weight/GAN/GAN_model_3",
      "weight/GAN/GAN_model_4",
      "weight/GAN/GAN_model_5",
      "weight/GAN/GAN_model_6",
      "weight/GAN/GAN_model_7",
      "weight/GAN/GAN_model_8",
      "weight/GAN/GAN_model_9",
      "weight/GAN/GAN_model_10",
      "weight/GAN/GAN_model_11",
      "weight/GAN/GAN_model_12",
      "weight/GAN/GAN_model_13",
      "weight/GAN/GAN_model_14",
      "weight/GAN/GAN_model_15"
    ]
  },
  "runtime": {
    "python": "3.11",
    "tensorflow": "2.13.1 or compatible TensorFlow/DCU build",
    "r": "3.6.3",
    "dcu_module": "compiler/dtk/26.04"
  },
  "license": "CC-BY-NC-SA-4.0"
}