From 4cf9fb3f64a29b843cd8b7741d640d080db1256e Mon Sep 17 00:00:00 2001
From: lucas_miranda <lucasmiranda42@gmail.com>
Date: Thu, 27 May 2021 17:44:58 +0200
Subject: [PATCH] Replaced for loop with vectorised mapping on ClusterOverlap
regularization layer
---
deepof/model_utils.py | 31 ++++++++++++++++++-------------
deepof_experiments.smk | 2 +-
2 files changed, 19 insertions(+), 14 deletions(-)
diff --git a/deepof/model_utils.py b/deepof/model_utils.py
index e753bf43..211dc070 100644
--- a/deepof/model_utils.py
+++ b/deepof/model_utils.py
@@ -619,21 +619,23 @@ class ClusterOverlap(Layer):
max_groups, tf.constant(random_idxs)
)
- self.add_metric(
- tf.cast(
- tf.shape(
- tf.unique(
- tf.reshape(
- tf.gather(
- tf.cast(hard_groups, tf.dtypes.float32),
- tf.where(max_groups >= self.min_confidence),
- ),
- [-1],
+ number_of_clusters = tf.cast(
+ tf.shape(
+ tf.unique(
+ tf.reshape(
+ tf.gather(
+ tf.cast(hard_groups, tf.dtypes.float32),
+ tf.where(max_groups >= self.min_confidence),
),
- )[0],
+ [-1],
+ ),
)[0],
- tf.dtypes.float32,
- ),
+ )[0],
+ tf.dtypes.float32,
+ )
+
+ self.add_metric(
+ number_of_clusters,
name="number_of_populated_clusters",
)
@@ -648,6 +650,9 @@ class ClusterOverlap(Layer):
)
if self.loss_weight:
+ # minimize local entropy
self.add_loss(self.loss_weight * tf.reduce_mean(neighbourhood_entropy))
+ # maximize number of clusters
+ self.add_loss(-self.loss_weight * tf.reduce_mean(number_of_clusters))
return encodings
diff --git a/deepof_experiments.smk b/deepof_experiments.smk
index 4a1490fa..cf1e7b4c 100644
--- a/deepof_experiments.smk
+++ b/deepof_experiments.smk
@@ -28,7 +28,7 @@ phenotype_pred_weights = [0.0]
rule_based_pred_weights = [0.0]
window_lengths = [22] # range(11,56,11)
input_types = ["coords"]
-run = list(range(1, 11))
+run = list(range(1, 4))
rule deepof_experiments:
--
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