Mercurial > repos > goeckslab > ludwig_render_config
diff test-data/temp_description.json @ 0:ed8a9ea5bc73 draft default tip
planemo upload for repository https://github.com/goeckslab/Galaxy-Ludwig.git commit bdea9430787658783a51cc6c2ae951a01e455bb4
| author | goeckslab |
|---|---|
| date | Tue, 07 Jan 2025 22:45:58 +0000 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/temp_description.json Tue Jan 07 22:45:58 2025 +0000 @@ -0,0 +1,868 @@ +{ + "command": "/home/ubuntu24/Galaxy-Ludwig/tools/ludwig_experiment.py --config /tmp/tmp0u6yc1yw/job_working_directory/000/3/working/config.yml --dataset /tmp/tmp0u6yc1yw/job_working_directory/000/3/working/temperature_la.csv --output_directory /tmp/tmp0u6yc1yw/job_working_directory/000/3/working --data_format csv --backend local --eval_split test --random_seed 42 --skip_save_unprocessed_output --skip_save_k_fold_split_indices", + "compute": { + "num_nodes": 1 + }, + "config": { + "backend": null, + "combiner": { + "activation": "relu", + "bias_initializer": "zeros", + "dropout": 0.0, + "fc_layers": null, + "flatten_inputs": false, + "norm": null, + "norm_params": null, + "num_fc_layers": 0, + "output_size": 256, + "residual": false, + "type": "concat", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "defaults": { + "audio": { + "encoder": { + "activation": "relu", + "bias_initializer": "zeros", + "conv_layers": null, + "dropout": 0.0, + "embedding_size": 256, + "embeddings_on_cpu": false, + "embeddings_trainable": true, + "fc_layers": null, + "filter_size": 3, + "max_sequence_length": null, + "norm": null, + "norm_params": null, + "num_conv_layers": null, + "num_fc_layers": null, + "num_filters": 256, + "output_size": 256, + "pool_function": "max", + "pool_size": null, + "pretrained_embeddings": null, + "reduce_output": "sum", + "representation": "dense", + "should_embed": true, + "skip": false, + "type": "parallel_cnn", + "use_bias": true, + "vocab": null, + "weights_initializer": "xavier_uniform" + }, + "preprocessing": { + "audio_file_length_limit_in_s": 7.5, + "computed_fill_value": null, + "fill_value": null, + "in_memory": true, + "missing_value_strategy": "bfill", + "norm": null, + "num_fft_points": null, + "num_filter_bands": 80, + "padding_value": 0.0, + "type": "fbank", + "window_length_in_s": 0.04, + "window_shift_in_s": 0.02, + "window_type": "hamming" + } + }, + "bag": { + "encoder": { + "activation": "relu", + "bias_initializer": "zeros", + "dropout": 0.0, + "embedding_size": 50, + "embeddings_on_cpu": false, + "embeddings_trainable": true, + "fc_layers": null, + "force_embedding_size": false, + "norm": null, + "norm_params": null, + "num_fc_layers": 0, + "output_size": 10, + "pretrained_embeddings": null, + "representation": "dense", + "skip": false, + "type": "embed", + "use_bias": true, + "vocab": null, + "weights_initializer": "xavier_uniform" + }, + "preprocessing": { + "computed_fill_value": "<UNK>", + "fill_value": "<UNK>", + "lowercase": false, + "missing_value_strategy": "fill_with_const", + "most_common": 10000, + "tokenizer": "space" + } + }, + "binary": { + "decoder": { + "bias_initializer": "zeros", + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "input_size": null, + "num_fc_layers": 0, + "type": "regressor", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "encoder": { + "skip": false, + "type": "passthrough" + }, + "loss": { + "confidence_penalty": 0, + "positive_class_weight": null, + "robust_lambda": 0, + "type": "binary_weighted_cross_entropy", + "weight": 1.0 + }, + "preprocessing": { + "computed_fill_value": null, + "fallback_true_label": null, + "fill_value": null, + "missing_value_strategy": "fill_with_false" + } + }, + "category": { + "decoder": { + "bias_initializer": "zeros", + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "input_size": null, + "num_classes": null, + "num_fc_layers": 0, + "type": "classifier", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "encoder": { + "dropout": 0.0, + "embedding_initializer": null, + "embedding_size": 50, + "embeddings_on_cpu": false, + "embeddings_trainable": true, + "pretrained_embeddings": null, + "skip": false, + "type": "dense", + "vocab": null + }, + "loss": { + "class_similarities": null, + "class_similarities_temperature": 0, + "class_weights": null, + "confidence_penalty": 0, + "robust_lambda": 0, + "type": "softmax_cross_entropy", + "weight": 1.0 + }, + "preprocessing": { + "cache_encoder_embeddings": false, + "computed_fill_value": "<UNK>", + "fill_value": "<UNK>", + "lowercase": false, + "missing_value_strategy": "fill_with_const", + "most_common": 10000 + } + }, + "date": { + "encoder": { + "activation": "relu", + "bias_initializer": "zeros", + "dropout": 0.0, + "embedding_size": 10, + "embeddings_on_cpu": false, + "fc_layers": null, + "norm": null, + "norm_params": null, + "num_fc_layers": 0, + "output_size": 10, + "skip": false, + "type": "embed", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "preprocessing": { + "computed_fill_value": "", + "datetime_format": null, + "fill_value": "", + "missing_value_strategy": "fill_with_const" + } + }, + "h3": { + "encoder": { + "activation": "relu", + "bias_initializer": "zeros", + "dropout": 0.0, + "embedding_size": 10, + "embeddings_on_cpu": false, + "fc_layers": null, + "norm": null, + "norm_params": null, + "num_fc_layers": 0, + "output_size": 10, + "reduce_output": "sum", + "skip": false, + "type": "embed", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "preprocessing": { + "computed_fill_value": 576495936675512319, + "fill_value": 576495936675512319, + "missing_value_strategy": "fill_with_const" + } + }, + "image": { + "augmentation": [], + "decoder": { + "conv_norm": "batch", + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "height": null, + "input_size": 1024, + "num_channels": null, + "num_classes": null, + "num_fc_layers": 0, + "type": "unet", + "width": null + }, + "encoder": { + "conv_activation": "relu", + "conv_dropout": 0.0, + "conv_layers": null, + "conv_norm": null, + "conv_norm_params": null, + "conv_use_bias": true, + "dilation": 1, + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "groups": 1, + "height": null, + "kernel_size": 3, + "num_channels": null, + "num_conv_layers": null, + "num_fc_layers": 1, + "out_channels": 32, + "output_size": 128, + "padding": "valid", + "padding_mode": "zeros", + "pool_dilation": 1, + "pool_function": "max", + "pool_kernel_size": 2, + "pool_padding": 0, + "pool_stride": null, + "skip": false, + "stride": 1, + "type": "stacked_cnn", + "width": null + }, + "loss": { + "class_similarities": null, + "class_similarities_temperature": 0, + "class_weights": null, + "confidence_penalty": 0, + "robust_lambda": 0, + "type": "softmax_cross_entropy", + "weight": 1.0 + }, + "preprocessing": { + "computed_fill_value": null, + "fill_value": null, + "height": null, + "in_memory": true, + "infer_image_dimensions": true, + "infer_image_max_height": 256, + "infer_image_max_width": 256, + "infer_image_num_channels": true, + "infer_image_num_classes": false, + "infer_image_sample_size": 100, + "missing_value_strategy": "bfill", + "num_channels": null, + "num_classes": null, + "num_processes": 1, + "requires_equal_dimensions": false, + "resize_method": "interpolate", + "standardize_image": null, + "width": null + } + }, + "number": { + "decoder": { + "bias_initializer": "zeros", + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "input_size": null, + "num_fc_layers": 0, + "type": "regressor", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "encoder": { + "skip": false, + "type": "passthrough" + }, + "loss": { + "type": "mean_squared_error", + "weight": 1.0 + }, + "preprocessing": { + "computed_fill_value": 0.0, + "computed_outlier_fill_value": 0.0, + "fill_value": 0.0, + "missing_value_strategy": "fill_with_const", + "normalization": "zscore", + "outlier_strategy": null, + "outlier_threshold": 3.0 + } + }, + "sequence": { + "decoder": { + "cell_type": "gru", + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "input_size": 256, + "max_sequence_length": null, + "num_fc_layers": 0, + "num_layers": 1, + "reduce_input": "sum", + "type": "generator", + "vocab_size": null + }, + "encoder": { + "dropout": 0.0, + "embedding_size": 256, + "embeddings_on_cpu": false, + "embeddings_trainable": true, + "max_sequence_length": null, + "pretrained_embeddings": null, + "reduce_output": "sum", + "representation": "dense", + "skip": false, + "type": "embed", + "vocab": null, + "weights_initializer": "uniform" + }, + "loss": { + "class_similarities": null, + "class_similarities_temperature": 0, + "class_weights": null, + "confidence_penalty": 0, + "robust_lambda": 0, + "type": "sequence_softmax_cross_entropy", + "unique": false, + "weight": 1.0 + }, + "preprocessing": { + "cache_encoder_embeddings": false, + "computed_fill_value": "<UNK>", + "fill_value": "<UNK>", + "lowercase": false, + "max_sequence_length": 256, + "missing_value_strategy": "fill_with_const", + "most_common": 20000, + "ngram_size": 2, + "padding": "right", + "padding_symbol": "<PAD>", + "sequence_length": null, + "tokenizer": "space", + "unknown_symbol": "<UNK>", + "vocab_file": null + } + }, + "set": { + "decoder": { + "bias_initializer": "zeros", + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "input_size": null, + "num_classes": null, + "num_fc_layers": 0, + "type": "classifier", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "encoder": { + "activation": "relu", + "bias_initializer": "zeros", + "dropout": 0.0, + "embedding_size": 50, + "embeddings_on_cpu": false, + "embeddings_trainable": true, + "fc_layers": null, + "norm": null, + "norm_params": null, + "num_fc_layers": 0, + "output_size": 10, + "pretrained_embeddings": null, + "representation": "dense", + "skip": false, + "type": "embed", + "use_bias": true, + "vocab": null, + "weights_initializer": "xavier_uniform" + }, + "loss": { + "class_weights": null, + "type": "sigmoid_cross_entropy", + "weight": 1.0 + }, + "preprocessing": { + "computed_fill_value": "<UNK>", + "fill_value": "<UNK>", + "lowercase": false, + "missing_value_strategy": "fill_with_const", + "most_common": 10000, + "tokenizer": "space" + } + }, + "text": { + "decoder": { + "cell_type": "gru", + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "input_size": 256, + "max_sequence_length": null, + "num_fc_layers": 0, + "num_layers": 1, + "reduce_input": "sum", + "type": "generator", + "vocab_size": null + }, + "encoder": { + "activation": "relu", + "bias_initializer": "zeros", + "conv_layers": null, + "dropout": 0.0, + "embedding_size": 256, + "embeddings_on_cpu": false, + "embeddings_trainable": true, + "fc_layers": null, + "filter_size": 3, + "max_sequence_length": null, + "norm": null, + "norm_params": null, + "num_conv_layers": null, + "num_fc_layers": null, + "num_filters": 256, + "output_size": 256, + "pool_function": "max", + "pool_size": null, + "pretrained_embeddings": null, + "reduce_output": "sum", + "representation": "dense", + "should_embed": true, + "skip": false, + "type": "parallel_cnn", + "use_bias": true, + "vocab": null, + "weights_initializer": "xavier_uniform" + }, + "loss": { + "class_similarities": null, + "class_similarities_temperature": 0, + "class_weights": null, + "confidence_penalty": 0, + "robust_lambda": 0, + "type": "sequence_softmax_cross_entropy", + "unique": false, + "weight": 1.0 + }, + "preprocessing": { + "cache_encoder_embeddings": false, + "compute_idf": false, + "computed_fill_value": "<UNK>", + "fill_value": "<UNK>", + "lowercase": false, + "max_sequence_length": 256, + "missing_value_strategy": "fill_with_const", + "most_common": 20000, + "ngram_size": 2, + "padding": "right", + "padding_symbol": "<PAD>", + "pretrained_model_name_or_path": null, + "prompt": { + "retrieval": { + "index_name": null, + "k": 0, + "model_name": null, + "type": null + }, + "task": null, + "template": null + }, + "sequence_length": null, + "tokenizer": "space_punct", + "unknown_symbol": "<UNK>", + "vocab_file": null + } + }, + "timeseries": { + "decoder": { + "activation": null, + "bias_initializer": "zeros", + "clip": null, + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "input_size": null, + "multiplier": 1.0, + "num_fc_layers": 0, + "output_size": null, + "type": "projector", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "encoder": { + "activation": "relu", + "bias_initializer": "zeros", + "conv_layers": null, + "dropout": 0.0, + "embedding_size": 256, + "embeddings_on_cpu": false, + "embeddings_trainable": true, + "fc_layers": null, + "filter_size": 3, + "max_sequence_length": null, + "norm": null, + "norm_params": null, + "num_conv_layers": null, + "num_fc_layers": null, + "num_filters": 256, + "output_size": 256, + "pool_function": "max", + "pool_size": null, + "pretrained_embeddings": null, + "reduce_output": "sum", + "representation": "dense", + "should_embed": true, + "skip": false, + "type": "parallel_cnn", + "use_bias": true, + "vocab": null, + "weights_initializer": "xavier_uniform" + }, + "loss": { + "delta": 1.0, + "type": "huber", + "weight": 1.0 + }, + "preprocessing": { + "computed_fill_value": "", + "fill_value": "", + "missing_value_strategy": "fill_with_const", + "padding": "right", + "padding_value": 0.0, + "timeseries_length_limit": 256, + "tokenizer": "space", + "window_size": 0 + } + }, + "vector": { + "decoder": { + "activation": null, + "bias_initializer": "zeros", + "clip": null, + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "input_size": null, + "multiplier": 1.0, + "num_fc_layers": 0, + "output_size": null, + "type": "projector", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "encoder": { + "activation": "relu", + "bias_initializer": "zeros", + "dropout": 0.0, + "fc_layers": null, + "input_size": null, + "norm": null, + "norm_params": null, + "num_layers": 1, + "output_size": 256, + "skip": false, + "type": "dense", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "loss": { + "type": "mean_squared_error", + "weight": 1.0 + }, + "preprocessing": { + "computed_fill_value": "", + "fill_value": "", + "missing_value_strategy": "fill_with_const", + "vector_size": null + } + } + }, + "hyperopt": null, + "input_features": [ + { + "active": true, + "column": "temperature_feature", + "encoder": { + "activation": "tanh", + "bias_initializer": "zeros", + "bidirectional": false, + "cell_type": "rnn", + "dropout": 0.0, + "embedding_size": 32, + "embeddings_on_cpu": false, + "embeddings_trainable": true, + "fc_activation": "relu", + "fc_dropout": 0.0, + "fc_layers": null, + "max_sequence_length": null, + "norm": null, + "norm_params": null, + "num_fc_layers": 0, + "num_layers": 1, + "output_size": 256, + "pretrained_embeddings": null, + "recurrent_activation": "sigmoid", + "recurrent_dropout": 0.0, + "recurrent_initializer": "orthogonal", + "reduce_output": "last", + "representation": "dense", + "should_embed": true, + "skip": false, + "state_size": 32, + "type": "rnn", + "unit_forget_bias": true, + "use_bias": true, + "vocab": null, + "weights_initializer": "xavier_uniform" + }, + "name": "temperature_feature", + "preprocessing": { + "cache_encoder_embeddings": false, + "computed_fill_value": "", + "fill_value": "", + "missing_value_strategy": "fill_with_const", + "padding": "right", + "padding_value": 0.0, + "timeseries_length_limit": 256, + "tokenizer": "space", + "window_size": 0 + }, + "proc_column": "temperature_feature_XJMv7q", + "tied": null, + "type": "timeseries" + } + ], + "ludwig_version": "0.10.1", + "model_type": "ecd", + "output_features": [ + { + "active": true, + "clip": null, + "column": "temperature", + "decoder": { + "bias_initializer": "zeros", + "fc_activation": "relu", + "fc_bias_initializer": "zeros", + "fc_dropout": 0.0, + "fc_layers": null, + "fc_norm": null, + "fc_norm_params": null, + "fc_output_size": 256, + "fc_use_bias": true, + "fc_weights_initializer": "xavier_uniform", + "input_size": null, + "num_fc_layers": 0, + "type": "regressor", + "use_bias": true, + "weights_initializer": "xavier_uniform" + }, + "default_validation_metric": "mean_squared_error", + "dependencies": [], + "input_size": null, + "loss": { + "type": "mean_squared_error", + "weight": 1.0 + }, + "name": "temperature", + "num_classes": null, + "preprocessing": { + "computed_fill_value": 0.0, + "computed_outlier_fill_value": 0.0, + "fill_value": 0.0, + "missing_value_strategy": "drop_row", + "normalization": null, + "outlier_strategy": null, + "outlier_threshold": 3.0 + }, + "proc_column": "temperature_VO1XAD", + "reduce_dependencies": "sum", + "reduce_input": "sum", + "type": "number" + } + ], + "preprocessing": { + "global_max_sequence_length": null, + "oversample_minority": null, + "sample_ratio": 1.0, + "sample_size": null, + "split": { + "probabilities": [ + 0.7, + 0.1, + 0.2 + ], + "type": "random" + }, + "undersample_majority": null + }, + "trainer": { + "batch_size": "auto", + "bucketing_field": null, + "checkpoints_per_epoch": 0, + "compile": false, + "early_stop": 5, + "effective_batch_size": "auto", + "enable_gradient_checkpointing": false, + "enable_profiling": false, + "epochs": 2, + "eval_batch_size": null, + "eval_steps": null, + "evaluate_training_set": false, + "gradient_accumulation_steps": "auto", + "gradient_clipping": { + "clipglobalnorm": 0.5, + "clipnorm": null, + "clipvalue": null + }, + "increase_batch_size_eval_metric": "loss", + "increase_batch_size_eval_split": "training", + "increase_batch_size_on_plateau": 0, + "increase_batch_size_on_plateau_patience": 5, + "increase_batch_size_on_plateau_rate": 2.0, + "learning_rate": 0.001, + "learning_rate_scaling": "linear", + "learning_rate_scheduler": { + "decay": null, + "decay_rate": 0.96, + "decay_steps": 10000, + "eta_min": 0, + "reduce_eval_metric": "loss", + "reduce_eval_split": "training", + "reduce_on_plateau": 0, + "reduce_on_plateau_patience": 10, + "reduce_on_plateau_rate": 0.1, + "staircase": false, + "t_0": null, + "t_mult": 1, + "warmup_evaluations": 0, + "warmup_fraction": 0.0 + }, + "max_batch_size": 1099511627776, + "optimizer": { + "amsgrad": false, + "betas": [ + 0.9, + 0.999 + ], + "eps": 1e-08, + "type": "adam", + "weight_decay": 0.0 + }, + "profiler": { + "active": 3, + "repeat": 5, + "skip_first": 0, + "wait": 1, + "warmup": 1 + }, + "regularization_lambda": 0.0, + "regularization_type": "l2", + "should_shuffle": true, + "skip_all_evaluation": false, + "steps_per_checkpoint": 0, + "train_steps": null, + "use_mixed_precision": false, + "validation_field": "temperature", + "validation_metric": "mean_squared_error" + } + }, + "data_format": "csv", + "dataset": "/tmp/tmp0u6yc1yw/job_working_directory/000/3/working/temperature_la.csv", + "ludwig_version": "0.10.1", + "random_seed": 42, + "torch_version": "2.1.0+cu118" +} \ No newline at end of file