parameters.json

{
    "exp_param": {
        "experiments_dir": "experiments"
    },
    "experiments": {
        "default_experiment": {
            "input_ds": {
                "filtering": {
                    "min_cells": 3,
                    "min_genes": 400
                },
                "n_cpus_preprocessing": 20,
                "raw_input": [
                    "data/citeseq.h5ad",
                    "data/pbmc8k.h5ad"
                ],
                "scale": {
                    "LSN": 20000,
                    "fixed_scaling": {
                        "mean": "genes",
                        "var": "genes"
                    }
                },
                "split": {
                    "balanced_split": true,
                    "split_seed": 0,
                    "test_cells": 0,
                    "valid_cells": 0.1
                }
            },
            "model": {
                "activation_fn": "tensorflow_addons.activations.mish",
                "conditional_regularization": {
                    "l2": 0.0,
                    "name": "tensorflow.keras.regularizers.L1L2"
                },
                "crossentropy": {
                    "label_smoothing": 0.0,
                    "lower_label_smoothing": 0.1
                },
                "decoder": {
                    "layers": [
                        256,
                        512,
                        1024
                    ],
                    "regularization": 0.0
                },
                "encoder": {
                    "layers": [
                        1024,
                        512,
                        256
                    ],
                    "regularization": 0.4
                },
                "latent_dim": 48,
                "norm_type": [
                    "conditionallayernorm",
                    "conditionallayernorm",
                    "conditionallayernorm"
                ],
                "output_fn": null,
                "reconstruction_loss": {
                    "delta": 9.0,
                    "name": "HuberLoss"
                },
                "wae_lambda": 1500,
                "weighting_decoder_dropout": 10000,
                "weighting_random_encoder": 1e-08
            },
            "training": {
                "GPU": [
                    0
                ],
                "XLA": true,
                "batch_size": 192,
                "early_stopping": {
                    "delay": 5,
                    "min_delta": 0.01,
                    "patience": 30
                },
                "max_steps": 200,
                "optimizer": {
                    "algorithm": "tensorflow_addons.optimizers.RectifiedAdam",
                    "amsgrad": false,
                    "beta_1": 0.85,
                    "beta_2": 0.95,
                    "learning_rate": 0.001
                },
                "parallel_pc": 5
            }
        }
    }
}