From dd62bd2e44fc3c34fc3ded04bef4cc414426305d Mon Sep 17 00:00:00 2001
From: lucas_miranda <lucasmiranda42@gmail.com>
Date: Fri, 12 Mar 2021 04:08:04 +0100
Subject: [PATCH] Implemented KNN_purity callback
---
deepof/model_utils.py | 7 +++++--
deepof/models.py | 4 ++--
deepof/train_utils.py | 1 +
tests/test_train_utils.py | 4 ++++
4 files changed, 12 insertions(+), 4 deletions(-)
diff --git a/deepof/model_utils.py b/deepof/model_utils.py
index ad94d9db..209eb2d4 100644
--- a/deepof/model_utils.py
+++ b/deepof/model_utils.py
@@ -209,8 +209,11 @@ class knn_cluster_purity(tf.keras.callbacks.Callback):
"""
- def __init__(self, validation_data=None, k=100, samples=10000, log_dir="."):
+ def __init__(
+ self, variational=True, validation_data=None, k=100, samples=10000, log_dir="."
+ ):
super().__init__()
+ self.variational = variational
self.validation_data = validation_data
self.k = k
self.samples = samples
@@ -220,7 +223,7 @@ class knn_cluster_purity(tf.keras.callbacks.Callback):
def on_epoch_end(self, epoch, logs=None):
""" Passes samples through the encoder and computes cluster purity on the latent embedding """
- if self.validation_data is not None:
+ if self.validation_data is not None and self.variational:
# Get encoer and grouper from full model
cluster_means = [
diff --git a/deepof/models.py b/deepof/models.py
index cd4b2b42..d34f909d 100644
--- a/deepof/models.py
+++ b/deepof/models.py
@@ -253,7 +253,7 @@ class SEQ_2_SEQ_GMVAE:
montecarlo_kl: int = 1,
neuron_control: bool = False,
number_of_components: int = 1,
- overlap_loss: float = -1.,
+ overlap_loss: float = -1.0,
phenotype_prediction: float = 0.0,
predictor: float = 0.0,
reg_cat_clusters: bool = False,
@@ -606,7 +606,7 @@ class SEQ_2_SEQ_GMVAE:
z_gauss = deepof.model_utils.Cluster_overlap(
self.ENCODING,
self.number_of_components,
- loss=tf.maximum(0., self.overlap_loss).numpy(),
+ loss=tf.maximum(0.0, self.overlap_loss).numpy(),
)(z_gauss)
z = tfpl.DistributionLambda(
diff --git a/deepof/train_utils.py b/deepof/train_utils.py
index f9e09bdf..77da7c98 100644
--- a/deepof/train_utils.py
+++ b/deepof/train_utils.py
@@ -117,6 +117,7 @@ def get_callbacks(
samples=knn_samples,
validation_data=X_val,
log_dir=os.path.join(outpath, "metrics"),
+ variational=variational,
)
onecycle = deepof.model_utils.one_cycle_scheduler(
diff --git a/tests/test_train_utils.py b/tests/test_train_utils.py
index b35a1978..f4899f71 100644
--- a/tests/test_train_utils.py
+++ b/tests/test_train_utils.py
@@ -117,6 +117,8 @@ def test_autoencoder_fitting(
phenotype_class=pheno_class,
predictor=predictor,
variational=variational,
+ knn_neighbors=10,
+ knn_samples=10,
)
@@ -168,6 +170,8 @@ def test_tune_search(
True,
True,
None,
+ knn_neighbors=10,
+ knn_samples=10,
)
)[1:]
--
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