From 9e6df3ca4e9b94f96e3ee5a4bebdd7f407f20e27 Mon Sep 17 00:00:00 2001
From: lucas_miranda <lucasmiranda42@gmail.com>
Date: Tue, 13 Apr 2021 19:57:17 +0200
Subject: [PATCH] Added extra branch to main autoencoder for rule_based
prediction
---
deepof/hypermodels.py | 15 +++++++++------
deepof/train_model.py | 4 ++--
deepof/train_utils.py | 24 +++++++++++++++++-------
tests/test_build_hypermodels.py | 2 +-
tests/test_train_utils.py | 4 ++--
5 files changed, 31 insertions(+), 18 deletions(-)
diff --git a/deepof/hypermodels.py b/deepof/hypermodels.py
index 0c2d063b..9c9e983d 100644
--- a/deepof/hypermodels.py
+++ b/deepof/hypermodels.py
@@ -102,8 +102,9 @@ class SEQ_2_SEQ_GMVAE(HyperModel):
mmd_warmup_epochs: int = 0,
number_of_components: int = 10,
overlap_loss: float = False,
- phenotype_predictor: float = 0.0,
- predictor: float = 0.0,
+ next_sequence_prediction: float = 0.0,
+ phenotype_prediction: float = 0.0,
+ rule_based_prediction: float = 0.0,
prior: str = "standard_normal",
):
super().__init__()
@@ -115,8 +116,9 @@ class SEQ_2_SEQ_GMVAE(HyperModel):
self.mmd_warmup_epochs = mmd_warmup_epochs
self.number_of_components = number_of_components
self.overlap_loss = overlap_loss
- self.pheno_class = phenotype_predictor
- self.predictor = predictor
+ self.next_sequence_prediction = next_sequence_prediction
+ self.phenotype_prediction = phenotype_prediction
+ self.rule_based_prediction = rule_based_prediction
self.prior = prior
assert (
@@ -186,8 +188,9 @@ class SEQ_2_SEQ_GMVAE(HyperModel):
mmd_warmup_epochs=self.mmd_warmup_epochs,
number_of_components=k,
overlap_loss=self.overlap_loss,
- phenotype_prediction=self.pheno_class,
- next_sequence_prediction=self.predictor,
+ next_sequence_prediction=self.next_sequence_prediction,
+ phenotype_prediction=self.phenotype_prediction,
+ rule_based_prediction=self.rule_based_prediction,
).build(self.input_shape)[-3]
return gmvaep
diff --git a/deepof/train_model.py b/deepof/train_model.py
index 5b4436cf..b32449b4 100644
--- a/deepof/train_model.py
+++ b/deepof/train_model.py
@@ -415,8 +415,8 @@ else:
loss=loss,
mmd_warmup_epochs=mmd_wu,
overlap_loss=overlap_loss,
- phenotype_class=pheno_class,
- predictor=predictor,
+ phenotype_prediction=pheno_class,
+ next_sequence_prediction=predictor,
project_name="{}-based_{}_{}".format(input_type, hyp, tune.capitalize()),
callbacks=[
tensorboard_callback,
diff --git a/deepof/train_utils.py b/deepof/train_utils.py
index a8cbc1fc..a3c34910 100644
--- a/deepof/train_utils.py
+++ b/deepof/train_utils.py
@@ -472,8 +472,9 @@ def tune_search(
loss: str,
mmd_warmup_epochs: int,
overlap_loss: float,
- phenotype_class: float,
- predictor: float,
+ next_sequence_prediction: float,
+ phenotype_prediction: float,
+ rule_based_prediction: float,
project_name: str,
callbacks: List,
n_epochs: int = 30,
@@ -517,7 +518,7 @@ def tune_search(
if hypermodel == "S2SAE": # pragma: no cover
assert (
- predictor == 0.0 and phenotype_class == 0.0
+ next_sequence_prediction == 0.0 and phenotype_prediction == 0.0
), "Prediction branches are only available for variational models. See documentation for more details"
batch_size = 1
hypermodel = deepof.hypermodels.SEQ_2_SEQ_AE(input_shape=X_train.shape)
@@ -532,8 +533,9 @@ def tune_search(
mmd_warmup_epochs=mmd_warmup_epochs,
number_of_components=k,
overlap_loss=overlap_loss,
- phenotype_predictor=phenotype_class,
- predictor=predictor,
+ next_sequence_prediction=next_sequence_prediction,
+ phenotype_prediction=phenotype_prediction,
+ rule_based_prediction=rule_based_prediction,
)
else:
@@ -574,11 +576,19 @@ def tune_search(
Xs, ys = [X_train], [X_train]
Xvals, yvals = [X_val], [X_val]
- if predictor > 0.0:
+ if next_sequence_prediction > 0.0:
Xs, ys = X_train[:-1], [X_train[:-1], X_train[1:]]
Xvals, yvals = X_val[:-1], [X_val[:-1], X_val[1:]]
- if phenotype_class > 0.0:
+ if phenotype_prediction > 0.0:
+ ys += [y_train[:, 0]]
+ yvals += [y_val[:, 0]]
+
+ # Remove the used column (phenotype) from both y arrays
+ y_train = y_train[:, 1:]
+ y_val = y_val[:, 1:]
+
+ if rule_based_prediction > 0.0:
ys += [y_train]
yvals += [y_val]
diff --git a/tests/test_build_hypermodels.py b/tests/test_build_hypermodels.py
index 47535580..d803789e 100644
--- a/tests/test_build_hypermodels.py
+++ b/tests/test_build_hypermodels.py
@@ -51,5 +51,5 @@ def test_SEQ_2_SEQ_GMVAE_hypermodel_build(
),
loss=loss,
number_of_components=number_of_components,
- predictor=True,
+ next_sequence_prediction=True,
).build(hp=HyperParameters())
diff --git a/tests/test_train_utils.py b/tests/test_train_utils.py
index 53b2d921..e8aa23cf 100644
--- a/tests/test_train_utils.py
+++ b/tests/test_train_utils.py
@@ -193,8 +193,8 @@ def test_tune_search(
loss=loss,
mmd_warmup_epochs=0,
overlap_loss=overlap_loss,
- phenotype_class=pheno_class,
- predictor=predictor,
+ phenotype_prediction=pheno_class,
+ next_sequence_prediction=predictor,
project_name="test_run",
callbacks=callbacks,
n_epochs=1,
--
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