deepdrivemd.agents.stream.config

pydantic settings deepdrivemd.agents.stream.config.OutlierDetectionConfig

Outlier detection algorithm configuration.

Show JSON schema

{
   "title": "OutlierDetectionConfig",
   "description": "Outlier detection algorithm configuration.",
   "type": "object",
   "properties": {
      "experiment_directory": {
         "title": "Experiment Directory",
         "default": "set_by_deepdrivemd",
         "env_names": "{'experiment_directory'}",
         "type": "string",
         "format": "path"
      },
      "stage_idx": {
         "title": "Stage Idx",
         "default": 0,
         "env_names": "{'stage_idx'}",
         "type": "integer"
      },
      "task_idx": {
         "title": "Task Idx",
         "default": 0,
         "env_names": "{'task_idx'}",
         "type": "integer"
      },
      "output_path": {
         "title": "Output Path",
         "default": "set_by_deepdrivemd",
         "env_names": "{'output_path'}",
         "type": "string",
         "format": "path"
      },
      "node_local_path": {
         "title": "Node Local Path",
         "default": "set_by_deepdrivemd",
         "env_names": "{'node_local_path'}",
         "type": "string",
         "format": "path"
      },
      "agg_dir": {
         "title": "Agg Dir",
         "default": ".",
         "env_names": "{'agg_dir'}",
         "type": "string",
         "format": "path"
      },
      "num_agg": {
         "title": "Num Agg",
         "default": 2,
         "env_names": "{'num_agg'}",
         "type": "integer"
      },
      "min_step_increment": {
         "title": "Min Step Increment",
         "default": 500,
         "env_names": "{'min_step_increment'}",
         "type": "integer"
      },
      "timeout1": {
         "title": "Timeout1",
         "default": 30,
         "env_names": "{'timeout1'}",
         "type": "integer"
      },
      "timeout2": {
         "title": "Timeout2",
         "default": 10,
         "env_names": "{'timeout2'}",
         "type": "integer"
      },
      "best_model": {
         "title": "Best Model",
         "default": ".",
         "env_names": "{'best_model'}",
         "type": "string",
         "format": "path"
      },
      "lastN": {
         "title": "Lastn",
         "default": 8000,
         "env_names": "{'lastn'}",
         "type": "integer"
      },
      "latent_dim": {
         "title": "Latent Dim",
         "default": 10,
         "env_names": "{'latent_dim'}",
         "type": "integer"
      },
      "conv_layers": {
         "title": "Conv Layers",
         "default": 4,
         "env_names": "{'conv_layers'}",
         "type": "integer"
      },
      "conv_filters": {
         "title": "Conv Filters",
         "default": [
            64,
            64,
            64,
            64
         ],
         "env_names": "{'conv_filters'}",
         "type": "array",
         "items": {
            "type": "integer"
         }
      },
      "conv_filter_shapes": {
         "title": "Conv Filter Shapes",
         "default": [
            [
               3,
               3
            ],
            [
               3,
               3
            ],
            [
               3,
               3
            ],
            [
               3,
               3
            ]
         ],
         "env_names": "{'conv_filter_shapes'}",
         "type": "array",
         "items": {
            "type": "array",
            "minItems": 2,
            "maxItems": 2,
            "items": [
               {
                  "type": "integer"
               },
               {
                  "type": "integer"
               }
            ]
         }
      },
      "conv_strides": {
         "title": "Conv Strides",
         "default": [
            [
               1,
               1
            ],
            [
               2,
               2
            ],
            [
               1,
               1
            ],
            [
               1,
               1
            ]
         ],
         "env_names": "{'conv_strides'}",
         "type": "array",
         "items": {
            "type": "array",
            "minItems": 2,
            "maxItems": 2,
            "items": [
               {
                  "type": "integer"
               },
               {
                  "type": "integer"
               }
            ]
         }
      },
      "dense_layers": {
         "title": "Dense Layers",
         "default": 1,
         "env_names": "{'dense_layers'}",
         "type": "integer"
      },
      "dense_neurons": {
         "title": "Dense Neurons",
         "default": [
            128
         ],
         "env_names": "{'dense_neurons'}",
         "type": "array",
         "items": {
            "type": "integer"
         }
      },
      "dense_dropouts": {
         "title": "Dense Dropouts",
         "default": [
            0.25
         ],
         "env_names": "{'dense_dropouts'}",
         "type": "array",
         "items": {
            "type": "number"
         }
      },
      "outlier_count": {
         "title": "Outlier Count",
         "default": 120,
         "env_names": "{'outlier_count'}",
         "type": "integer"
      },
      "outlier_max": {
         "title": "Outlier Max",
         "default": 4500,
         "env_names": "{'outlier_max'}",
         "type": "integer"
      },
      "outlier_min": {
         "title": "Outlier Min",
         "default": 3000,
         "env_names": "{'outlier_min'}",
         "type": "integer"
      },
      "init_pdb_file": {
         "title": "Init Pdb File",
         "default": ".",
         "env_names": "{'init_pdb_file'}",
         "type": "string",
         "format": "path"
      },
      "ref_pdb_file": {
         "title": "Ref Pdb File",
         "default": ".",
         "env_names": "{'ref_pdb_file'}",
         "type": "string",
         "format": "path"
      },
      "init_eps": {
         "title": "Init Eps",
         "default": 1.3,
         "env_names": "{'init_eps'}",
         "type": "number"
      },
      "init_min_samples": {
         "title": "Init Min Samples",
         "default": 10,
         "env_names": "{'init_min_samples'}",
         "type": "integer"
      },
      "adios_xml_agg": {
         "title": "Adios Xml Agg",
         "default": "",
         "env_names": "{'adios_xml_agg'}",
         "type": "string",
         "format": "path"
      },
      "read_batch": {
         "title": "Read Batch",
         "default": 10000,
         "env_names": "{'read_batch'}",
         "type": "integer"
      },
      "project_gpu": {
         "title": "Project Gpu",
         "default": false,
         "env_names": "{'project_gpu'}",
         "type": "boolean"
      },
      "project_lastN": {
         "title": "Project Lastn",
         "default": 8000,
         "env_names": "{'project_lastn'}",
         "type": "integer"
      },
      "num_sim": {
         "title": "Num Sim",
         "default": 120,
         "env_names": "{'num_sim'}",
         "type": "integer"
      },
      "use_outliers": {
         "title": "Use Outliers",
         "default": true,
         "env_names": "{'use_outliers'}",
         "type": "boolean"
      },
      "use_random_outliers": {
         "title": "Use Random Outliers",
         "default": false,
         "env_names": "{'use_random_outliers'}",
         "type": "boolean"
      },
      "compute_rmsd": {
         "title": "Compute Rmsd",
         "default": true,
         "env_names": "{'compute_rmsd'}",
         "type": "boolean"
      },
      "compute_zcentroid": {
         "title": "Compute Zcentroid",
         "default": false,
         "env_names": "{'compute_zcentroid'}",
         "type": "boolean"
      },
      "final_shape": {
         "title": "Final Shape",
         "default": [
            28,
            28,
            1
         ],
         "env_names": "{'final_shape'}",
         "type": "array",
         "items": {
            "type": "integer"
         }
      },
      "outlier_selection": {
         "title": "Outlier Selection",
         "default": "rmsd",
         "env_names": "{'outlier_selection'}",
         "type": "string"
      },
      "multi_ligand_table": {
         "title": "Multi Ligand Table",
         "default": ".",
         "env_names": "{'multi_ligand_table'}",
         "type": "string",
         "format": "path"
      },
      "model": {
         "title": "Model",
         "default": "cvae",
         "env_names": "{'model'}",
         "type": "string"
      },
      "num_points": {
         "title": "Num Points",
         "default": 539,
         "env_names": "{'num_points'}",
         "type": "integer"
      },
      "num_features": {
         "title": "Num Features",
         "default": 0,
         "env_names": "{'num_features'}",
         "type": "integer"
      }
   }
}

Config

• extra: str = allow

Fields

• adios_xml_agg (pathlib.Path)

• agg_dir (pathlib.Path)

• best_model (pathlib.Path)

• compute_rmsd (bool)

• compute_zcentroid (bool)

• conv_filter_shapes (List[Tuple[int, int]])

• conv_filters (List[int])

• conv_layers (int)

• conv_strides (List[Tuple[int, int]])

• dense_dropouts (List[float])

• dense_layers (int)

• dense_neurons (List[int])

• final_shape (List[int])

• init_eps (float)

• init_min_samples (int)

• init_pdb_file (pathlib.Path)

• lastN (int)

• latent_dim (int)

• min_step_increment (int)

• model (str)

• multi_ligand_table (pathlib.Path)

• num_agg (int)

• num_features (int)

• num_points (int)

• num_sim (int)

• outlier_count (int)

• outlier_max (int)

• outlier_min (int)

• outlier_selection (str)

• project_gpu (bool)

• project_lastN (int)

• read_batch (int)

• ref_pdb_file (pathlib.Path)

• timeout1 (int)

• timeout2 (int)

• use_outliers (bool)

• use_random_outliers (bool)

field adios_xml_agg: pathlib.Path = ''

field agg_dir: pathlib.Path = PosixPath('.')

field best_model: pathlib.Path = PosixPath('.')

field compute_rmsd: bool = True

field compute_zcentroid: bool = False

field conv_filter_shapes: List[Tuple[int, int]] = [(3, 3), (3, 3), (3, 3), (3, 3)]

field conv_filters: List[int] = [64, 64, 64, 64]

field conv_layers: int = 4

field conv_strides: List[Tuple[int, int]] = [(1, 1), (2, 2), (1, 1), (1, 1)]

field dense_dropouts: List[float] = [0.25]

field dense_layers: int = 1

field dense_neurons: List[int] = [128]

field final_shape: List[int] = [28, 28, 1]

field init_eps: float = 1.3

field init_min_samples: int = 10

field init_pdb_file: pathlib.Path = PosixPath('.')

field lastN: int = 8000

field latent_dim: int = 10

field min_step_increment: int = 500

field model: str = 'cvae'

field multi_ligand_table: pathlib.Path = PosixPath('.')

field num_agg: int = 2

field num_features: int = 0

encoder_bias: bool = True encoder_relu_slope: float = 0.0 encoder_filters: List[int] = [64, 128, 256, 256, 512] encoder_kernels: List[int] = [5, 5, 3, 1, 1] decoder_bias: bool = True decoder_relu_slope: float = 0.0 decoder_affine_widths: List[int] = [64, 128, 512, 1024] discriminator_bias: bool = True discriminator_relu_slope: float = 0.0 discriminator_affine_widths: List[int] = [512, 128, 64]

field num_points: int = 539

field num_sim: int = 120

field outlier_count: int = 120

field outlier_max: int = 4500

field outlier_min: int = 3000

field outlier_selection: str = 'rmsd'

field project_gpu: bool = False

field project_lastN: int = 8000

field read_batch: int = 10000

field ref_pdb_file: pathlib.Path = PosixPath('.')

field timeout1: int = 30

field timeout2: int = 10

field use_outliers: bool = True

field use_random_outliers: bool = False