moving in sider sweet and toxcast

"""

SIDER dataset loader.

"""

from __future__ import print_function

from __future__ import division

from __future__ import unicode_literals

import os

import numpy as np

import shutil

from deepchem.utils.save import load_from_disk

from deepchem.datasets import DiskDataset

from deepchem.featurizers.featurize import DataLoader

from deepchem.featurizers.fingerprints import CircularFingerprint

from deepchem.transformers import BalancingTransformer

def load_sider(base_dir, reload=True, frac_train=.8):

  """Load SIDER datasets. Does not do train/test split"""

  # Set some global variables up top

  reload = True

  verbosity = "high"

  model = "logistic"

  regen = False

  # Create some directories for analysis

  # The base_dir holds the results of all analysis

  if not reload:

    if os.path.exists(base_dir):

      shutil.rmtree(base_dir)

  if not os.path.exists(base_dir):

    os.makedirs(base_dir)

  current_dir = os.path.dirname(os.path.realpath(__file__))

  #Make directories to store the raw and featurized datasets.

  data_dir = os.path.join(base_dir, "dataset")

  train_dir = os.path.join(base_dir, "train_dataset")

  valid_dir = os.path.join(base_dir, "valid_dataset")

  # Load SIDER dataset

  print("About to load SIDER dataset.")

  dataset_file = os.path.join(

      current_dir, "./sider.csv.gz")

  dataset = load_from_disk(dataset_file)

  print("Columns of dataset: %s" % str(dataset.columns.values))

  print("Number of examples in dataset: %s" % str(dataset.shape[0]))

  # Featurize SIDER dataset

  print("About to featurize SIDER dataset.")

  featurizer = CircularFingerprint(size=1024)

  SIDER_tasks = dataset.columns.values[1:].tolist()

  loader = DataLoader(tasks=SIDER_tasks,

                      smiles_field="smiles",

                      featurizer=featurizer,

                      verbosity=verbosity)

  if not reload or not os.path.exists(data_dir):

    dataset = loader.featurize(dataset_file, data_dir)

    regen = True

  else:

    dataset = DiskDataset(data_dir, reload=True)

  # Initialize transformers

  transformers = [

      BalancingTransformer(transform_w=True, dataset=dataset)]

  if regen:

    print("About to transform data")

    for transformer in transformers:

        dataset = transformer.transform(dataset)

  X, y, w, ids = (dataset.X, dataset.y, dataset.w, dataset.ids)

  num_tasks = 17

  num_train = frac_train * len(dataset)

  SIDER_tasks = SIDER_tasks[:num_tasks]

  print("Using following tasks")

  print(SIDER_tasks)

  X_train, X_valid = X[:num_train], X[num_train:]

  y_train, y_valid = y[:num_train, :num_tasks], y[num_train:, :num_tasks]

  w_train, w_valid = w[:num_train, :num_tasks], w[num_train:, :num_tasks]

  ids_train, ids_valid = ids[:num_train], ids[num_train:]

  train_dataset = DiskDataset.from_numpy(train_dir, X_train, y_train,

                                     w_train, ids_train, SIDER_tasks)

  valid_dataset = DiskDataset.from_numpy(valid_dir, X_valid, y_valid,

                                     w_valid, ids_valid, SIDER_tasks)

  return SIDER_tasks, (train_dataset, valid_dataset), transformers

"""

Script that trains Keras multitask models on SIDER dataset.

"""

from __future__ import print_function

from __future__ import division

from __future__ import unicode_literals

import os

import numpy as np

import shutil

from sider_datasets import load_sider

from deepchem.datasets import Dataset

from deepchem import metrics

from deepchem.metrics import Metric

from deepchem.utils.evaluate import Evaluator

from deepchem.models.keras_models.fcnet import MultiTaskDNN

from deepchem.models.keras_models import KerasModel

# Set some global variables up top

np.random.seed(123)

reload = True

verbosity = "high"

model = "logistic"

base_data_dir = "/scratch/users/apappu/sider"

sider_tasks, dataset, transformers = load_sider(

    base_data_dir, reload=reload)

print("len(dataset)")

print(len(dataset))

base_dir = "/scratch/users/apappu/sider_analysis"

model_dir = os.path.join(base_dir, "model")

if os.path.exists(base_dir):

  shutil.rmtree(base_dir)

os.makedirs(base_dir)

# Load SIDER data

sider_tasks, sider_datasets, transformers = load_sider(

    base_dir, reload=reload)

train_dataset, valid_dataset = sider_datasets

n_features = 1024 

# Build model

classification_metric = Metric(metrics.roc_auc_score, np.mean,

                               verbosity=verbosity,

                               mode="classification")

learning_rates = [0.0003, 0.001, 0.003]

hidden_units = [1000, 500]

dropouts = [.5, .25]

num_hidden_layers = [1, 2]

# hyperparameter sweep here

for learning_rate in learning_rates:

  for hidden_unit in hidden_units:

    for dropout in dropouts:

      keras_model = MultiTaskDNN(len(sider_tasks), n_features, "classification",

                                 dropout=.25, learning_rate=.001, decay=1e-4)

      model = KerasModel(keras_model, self.model_dir, verbosity=verbosity)

      # Fit trained model

      model.fit(train_dataset)

      model.save()

      train_evaluator = Evaluator(model, train_dataset, transformers, verbosity=verbosity)

      train_scores = train_evaluator.compute_model_performance([classification_metric])

      print("Train scores")

      print(train_scores)

      valid_evaluator = Evaluator(model, valid_dataset, transformers, verbosity=verbosity)

      valid_scores = valid_evaluator.compute_model_performance([classification_metric])

      print("Validation scores")

      print(valid_scores)

"""

Script that trains Sklearn multitask models on the sider dataset

@Author Bharath Ramsundar, Aneesh Pappu

"""

from __future__ import print_function

from __future__ import division

from __future__ import unicode_literals

import os

import numpy as np

import shutil

from sklearn.ensemble import RandomForestClassifier

from deepchem.datasets import Dataset

from deepchem.models.multitask import SingletaskToMultitask

from deepchem import metrics

from deepchem.metrics import Metric

from deepchem.models.sklearn_models import SklearnModel

from deepchem.utils.evaluate import Evaluator

from sider_datasets import load_sider

from deepchem.splits import StratifiedSplitter, RandomSplitter

# Set some global variables up top

reload = False

verbosity = "high"

base_data_dir = "/home/apappu/deepchem-models/toxcast_models/sider/sider_data"

sider_tasks, sider_dataset, transformers = load_sider(

    base_data_dir, reload=reload)

#removes directory if present -- warning

base_dir = "/home/apappu/deepchem-models/toxcast_models/sider/sider_analysis"

if os.path.exists(base_dir):

  shutil.rmtree(base_dir)

if not os.path.exists(base_dir):

  os.makedirs(base_dir)

train_dir = os.path.join(base_dir, "train_dataset")

valid_dir = os.path.join(base_dir, "valid_dataset")

test_dir = os.path.join(base_dir, "test_dataset")

model_dir = os.path.join(base_dir, "model")

print("About to perform train/valid/test split.")

splitter = RandomSplitter()

train_dataset, valid_dataset, test_dataset = splitter.train_valid_test_split(

  sider_dataset, train_dir, valid_dir, test_dir)

train_dataset.set_verbosity(verbosity)

valid_dataset.set_verbosity(verbosity)

test_dataset.set_verbosity(verbosity)

# Fit Logistic Regression models

sider_task_types = {task: "classification" for task in sider_tasks}

classification_metric = Metric(metrics.roc_auc_score, np.mean,

                               verbosity=verbosity,

                               mode="classification")

params_dict = {

    "batch_size": None,

    "data_shape": train_dataset.get_data_shape(),

}

if os.path.exists(model_dir):

  shutil.rmtree(model_dir)

os.makedirs(model_dir)

def model_builder(tasks, task_types, model_params, model_dir, verbosity=None):

  return SklearnModel(tasks, task_types, model_params, model_dir,

                      model_instance=RandomForestClassifier(

                          class_weight="balanced",

                          n_estimators=500,

                          n_jobs=-1),

                      verbosity=verbosity)

model = SingletaskToMultitask(sider_tasks, sider_task_types, params_dict, model_dir,

                              model_builder, verbosity=verbosity)

# Fit trained model

model.fit(train_dataset)

model.save()

train_evaluator = Evaluator(model, train_dataset, transformers, verbosity=verbosity)

train_scores = train_evaluator.compute_model_performance([classification_metric])

print("Train scores")

#  train_scores_list.append(train_scores)

valid_evaluator = Evaluator(model, valid_dataset, transformers, verbosity=verbosity)

valid_scores = valid_evaluator.compute_model_performance([classification_metric])

print("Validation scores")

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