From db90399afdab351d7a54aafbba74bcb3ee153e81 Mon Sep 17 00:00:00 2001
From: lucas_miranda <lucasmiranda42@gmail.com>
Date: Tue, 17 Nov 2020 11:27:29 +0100
Subject: [PATCH] Updated train_model.py to be compatible with phenotype
classification
---
deepof/hypermodels.py | 21 ++++++++++++---------
deepof/train_utils.py | 1 +
tests/test_train_utils.py | 4 ++--
3 files changed, 15 insertions(+), 11 deletions(-)
diff --git a/deepof/hypermodels.py b/deepof/hypermodels.py
index b852bf1b..d20b9184 100644
--- a/deepof/hypermodels.py
+++ b/deepof/hypermodels.py
@@ -71,15 +71,16 @@ class SEQ_2_SEQ_GMVAE(HyperModel):
def __init__(
self,
- input_shape,
- entropy_reg_weight=0.0,
- huber_delta=1.0,
- learn_rate=1e-3,
- loss="ELBO+MMD",
- number_of_components=10,
- overlap_loss=False,
- predictor=0.0,
- prior="standard_normal",
+ input_shape: tuple,
+ entropy_reg_weight: float = 0.0,
+ huber_delta: float = 1.0,
+ learn_rate: float = 1e-3,
+ loss: str = "ELBO+MMD",
+ number_of_components: int = 10,
+ overlap_loss: bool = False,
+ phenotype_predictor: float = 0.0,
+ predictor: float = 0.0,
+ prior: str = "standard_normal",
):
super().__init__()
self.input_shape = input_shape
@@ -89,6 +90,7 @@ class SEQ_2_SEQ_GMVAE(HyperModel):
self.loss = loss
self.number_of_components = number_of_components
self.overlap_loss = overlap_loss
+ self.pheno_class = phenotype_predictor
self.predictor = predictor
self.prior = prior
@@ -161,6 +163,7 @@ class SEQ_2_SEQ_GMVAE(HyperModel):
loss=self.loss,
number_of_components=k,
overlap_loss=self.overlap_loss,
+ phenotype_prediction=self.pheno_class,
predictor=self.predictor,
).build(self.input_shape)[3:]
diff --git a/deepof/train_utils.py b/deepof/train_utils.py
index 5eb99b6e..f4f4f151 100644
--- a/deepof/train_utils.py
+++ b/deepof/train_utils.py
@@ -152,6 +152,7 @@ def tune_search(
loss=loss,
number_of_components=k,
overlap_loss=overlap_loss,
+ phenotype_predictor=pheno_class,
predictor=predictor,
)
diff --git a/tests/test_train_utils.py b/tests/test_train_utils.py
index 74587dbf..0e192a95 100644
--- a/tests/test_train_utils.py
+++ b/tests/test_train_utils.py
@@ -65,7 +65,7 @@ def test_get_callbacks(
assert type(cycle1c) == deepof.model_utils.one_cycle_scheduler
-@settings(max_examples=1, deadline=None)
+@settings(max_examples=5, deadline=None)
@given(
X_train=arrays(
dtype=float,
@@ -93,7 +93,7 @@ def test_tune_search(
)
)[1:]
- y_train = tf.random.uniform(shape=(X_train.shape[0],), maxval=1.0)
+ y_train = tf.random.uniform(shape=(X_train.shape[1],), maxval=1.0)
deepof.train_utils.tune_search(
data=[X_train, y_train, X_train, y_train],
--
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