Data: Tabular Time Series Specialty: Endocrinology Laboratory: Blood Tests EHR: Demographics Diagnoses Medications Omics: Genomics Multi-omics Transcriptomics Wearable: Activity Clinical Purpose: Treatment Response Assessment Task: Biomarker Discovery
[c23b31]: / src / move / tasks / tune_model.py

Download this file

256 lines (218 with data), 8.7 kB

  1
  2
  3
  4
  5
  6
  7
  8
  9
 10
 11
 12
 13
 14
 15
 16
 17
 18
 19
 20
 21
 22
 23
 24
 25
 26
 27
 28
 29
 30
 31
 32
 33
 34
 35
 36
 37
 38
 39
 40
 41
 42
 43
 44
 45
 46
 47
 48
 49
 50
 51
 52
 53
 54
 55
 56
 57
 58
 59
 60
 61
 62
 63
 64
 65
 66
 67
 68
 69
 70
 71
 72
 73
 74
 75
 76
 77
 78
 79
 80
 81
 82
 83
 84
 85
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
__all__ = ["tune_model"]
from pathlib import Path
from typing import Any, Literal, cast
import hydra
import numpy as np
import pandas as pd
import torch
from hydra.core.hydra_config import HydraConfig
from hydra.types import RunMode
from matplotlib.cbook import boxplot_stats
from numpy.typing import ArrayLike
from omegaconf import OmegaConf
from sklearn.metrics.pairwise import cosine_similarity
from move.analysis.metrics import (
calculate_accuracy,
calculate_cosine_similarity,
)
from move.conf.schema import (
MOVEConfig,
TuneModelConfig,
TuneModelReconstructionConfig,
TuneModelStabilityConfig,
)
from move.core.logging import get_logger
from move.core.typing import BoolArray
from move.data import io
from move.data.dataloaders import MOVEDataset, make_dataloader, split_samples
from move.models.vae import VAE
TaskType = Literal["reconstruction", "stability"]
def _get_task_type(
task_config: TuneModelConfig,
) -> TaskType:
task_type = OmegaConf.get_type(task_config)
if task_type is TuneModelReconstructionConfig:
return "reconstruction"
if task_type is TuneModelStabilityConfig:
return "stability"
raise ValueError("Unsupported type of task!")
def _get_record(values: ArrayLike, **kwargs) -> dict[str, Any]:
record = kwargs
bxp_stats, *_ = boxplot_stats(values)
bxp_stats.pop("fliers")
record.update(bxp_stats)
return record
def tune_model(config: MOVEConfig) -> float:
"""Train multiple models to tune the model hyperparameters."""
hydra_config = HydraConfig.get()
if hydra_config.mode != RunMode.MULTIRUN:
raise ValueError("This task must run in multirun mode.")
# Delete sweep run config
sweep_config_path = Path(hydra_config.sweep.dir).joinpath("multirun.yaml")
if sweep_config_path.exists():
sweep_config_path.unlink()
job_num = hydra_config.job.num + 1
logger = get_logger(__name__)
task_config = cast(TuneModelConfig, config.task)
task_type = _get_task_type(task_config)
logger.info(f"Beginning task: tune model {task_type} {job_num}")
logger.info(f"Job name: {hydra_config.job.override_dirname}")
interim_path = Path(config.data.interim_data_path)
output_path = Path(config.data.results_path) / "tune_model"
output_path.mkdir(exist_ok=True, parents=True)
logger.debug("Reading data")
cat_list, _, con_list, _ = io.load_preprocessed_data(
interim_path,
config.data.categorical_names,
config.data.continuous_names,
)
assert task_config.model is not None
device = torch.device("cuda" if task_config.model.cuda is True else "cpu")
def _tune_stability(
task_config: TuneModelStabilityConfig,
):
label = [hp.split("=") for hp in hydra_config.job.override_dirname.split(",")]
train_dataloader = make_dataloader(
cat_list,
con_list,
shuffle=True,
batch_size=task_config.batch_size,
drop_last=True,
)
test_dataloader = make_dataloader(
cat_list,
con_list,
shuffle=False,
batch_size=task_config.batch_size,
drop_last=False,
)
train_dataset = cast(MOVEDataset, train_dataloader.dataset)
logger.info(f"Training {task_config.num_refits} refits")
cosine_sim0 = None
cosine_sim_diffs = []
for j in range(task_config.num_refits):
logger.debug(f"Refit: {j + 1}/{task_config.num_refits}")
model: VAE = hydra.utils.instantiate(
task_config.model,
continuous_shapes=train_dataset.con_shapes,
categorical_shapes=train_dataset.cat_shapes,
)
model.to(device)
hydra.utils.call(
task_config.training_loop,
model=model,
train_dataloader=train_dataloader,
)
model.eval()
latent, *_ = model.latent(test_dataloader, kld_weight=1)
if cosine_sim0 is None:
cosine_sim0 = cosine_similarity(latent)
else:
cosine_sim = cosine_similarity(latent)
D = np.absolute(cosine_sim - cosine_sim0)
# removing the diagonal element (cos_sim with itself)
diff = D[~np.eye(D.shape[0], dtype=bool)].reshape(D.shape[0], -1)
mean_diff = np.mean(diff)
cosine_sim_diffs.append(mean_diff)
record = _get_record(
cosine_sim_diffs,
job_num=job_num,
**dict(label),
metric="mean_diff_cosine_similarity",
num_refits=task_config.num_refits,
)
logger.info("Writing results")
df_path = output_path / "stability_stats.tsv"
header = not df_path.exists()
df = pd.DataFrame.from_records([record])
df.to_csv(df_path, sep="\t", mode="a", header=header, index=False)
def _tune_reconstruction(
task_config: TuneModelReconstructionConfig,
):
split_path = interim_path / "split_mask.npy"
if split_path.exists():
split_mask: BoolArray = np.load(split_path)
else:
num_samples = cat_list[0].shape[0] if cat_list else con_list[0].shape[0]
split_mask = split_samples(num_samples, 0.9)
np.save(split_path, split_mask)
train_dataloader = make_dataloader(
cat_list,
con_list,
split_mask,
shuffle=True,
batch_size=task_config.batch_size,
drop_last=True,
)
train_dataset = cast(MOVEDataset, train_dataloader.dataset)
model: VAE = hydra.utils.instantiate(
task_config.model,
continuous_shapes=train_dataset.con_shapes,
categorical_shapes=train_dataset.cat_shapes,
)
model.to(device)
logger.debug(f"Model: {model}")
logger.debug("Training model")
hydra.utils.call(
task_config.training_loop,
model=model,
train_dataloader=train_dataloader,
)
model.eval()
logger.info("Reconstructing")
logger.info("Computing reconstruction metrics")
label = [hp.split("=") for hp in hydra_config.job.override_dirname.split(";")]
records = []
splits = zip(["train", "test"], [split_mask, ~split_mask])
for split_name, mask in splits:
dataloader = make_dataloader(
cat_list,
con_list,
mask,
shuffle=False,
batch_size=task_config.batch_size,
)
cat_recons, con_recons = model.reconstruct(dataloader)
con_recons = np.split(
con_recons, np.cumsum(model.continuous_shapes[:-1]), axis=1
)
for cat, cat_recon, dataset_name in zip(
cat_list, cat_recons, config.data.categorical_names
):
logger.debug(f"Computing accuracy: '{dataset_name}'")
accuracy = calculate_accuracy(cat[mask], cat_recon)
record = _get_record(
accuracy,
job_num=job_num,
**dict(label),
metric="accuracy",
dataset=dataset_name,
split=split_name,
)
records.append(record)
for con, con_recon, dataset_name in zip(
con_list, con_recons, config.data.continuous_names
):
logger.debug(f"Computing cosine similarity: '{dataset_name}'")
cosine_sim = calculate_cosine_similarity(con[mask], con_recon)
record = _get_record(
cosine_sim,
job_num=job_num,
**dict(label),
metric="cosine_similarity",
dataset=dataset_name,
split=split_name,
)
records.append(record)
logger.info("Writing results")
df_path = output_path / "reconstruction_stats.tsv"
header = not df_path.exists()
df = pd.DataFrame.from_records(records)
df.to_csv(df_path, sep="\t", mode="a", header=header, index=False)
if task_type == "reconstruction":
task_config = cast(TuneModelReconstructionConfig, task_config)
_tune_reconstruction(task_config)
elif task_type == "stability":
task_config = cast(TuneModelStabilityConfig, task_config)
_tune_stability(task_config)
return 0.0