From 8d39e5e0e073797ccc85f7b9e61c729d843e5d1d Mon Sep 17 00:00:00 2001
From: lucas_miranda <lucasmiranda42@gmail.com>
Date: Wed, 17 Mar 2021 11:48:39 +0100
Subject: [PATCH] Fixed a bug in model_utils.py that yielded nan entropy values
when there were no neighbors in the radius and the selected cluster was 0
---
deepof_experiments.smk | 43 ++++++++++++++++++++++--------------------
1 file changed, 23 insertions(+), 20 deletions(-)
diff --git a/deepof_experiments.smk b/deepof_experiments.smk
index 8d901f2c..ee337bd7 100644
--- a/deepof_experiments.smk
+++ b/deepof_experiments.smk
@@ -18,7 +18,7 @@ losses = ["ELBO"] # , "MMD", "ELBO+MMD"]
encodings = [6] # [2, 4, 6, 8, 10, 12, 14, 16]
cluster_numbers = [25] # [1, 5, 10, 15, 20, 25]
latent_reg = ["none", "categorical", "variance", "categorical+variance"]
-entropy_min_n = [2,5,8,12]
+entropy_min_n = [2, 5, 8, 12]
pheno_weights = [0.01, 0.1, 0.25, 0.5, 1.0, 2.0, 4.0, 10.0, 100.0]
@@ -34,22 +34,22 @@ rule deepof_experiments:
# enc=encodings,
# ),
expand(
- "/psycl/g/mpsstatgen/lucas/DLC/DLC_autoencoders/DeepOF/deepof/logs/latent_regularization_experiments/trained_weights/"
- "GMVAE_loss={loss}_encoding={encs}_k={k}_latreg={latreg}_entropymink={entmin}_final_weights.h5",
- loss=losses,
- encs=encodings,
- k=cluster_numbers,
- latreg=latent_reg,
- entmin=entropy_min_n,
- )
- # expand(
- # "/psycl/g/mpsstatgen/lucas/DLC/DLC_autoencoders/DeepOF/deepof/logs/pheno_classification_experiments/trained_weights/"
- # "GMVAE_loss={loss}_encoding={encs}_k={k}_pheno={phenos}_run_1_final_weights.h5",
- # loss=losses,
- # encs=encodings,
- # k=cluster_numbers,
- # phenos=pheno_weights,
- # ),
+ "/psycl/g/mpsstatgen/lucas/DLC/DLC_autoencoders/DeepOF/deepof/logs/latent_regularization_experiments/trained_weights/"
+ "GMVAE_loss={loss}_encoding={encs}_k={k}_latreg={latreg}_entropymink={entmin}_final_weights.h5",
+ loss=losses,
+ encs=encodings,
+ k=cluster_numbers,
+ latreg=latent_reg,
+ entmin=entropy_min_n,
+ ),
+ # expand(
+ # "/psycl/g/mpsstatgen/lucas/DLC/DLC_autoencoders/DeepOF/deepof/logs/pheno_classification_experiments/trained_weights/"
+ # "GMVAE_loss={loss}_encoding={encs}_k={k}_pheno={phenos}_run_1_final_weights.h5",
+ # loss=losses,
+ # encs=encodings,
+ # k=cluster_numbers,
+ # phenos=pheno_weights,
+ # ),
rule coarse_hyperparameter_tuning:
@@ -83,11 +83,13 @@ rule coarse_hyperparameter_tuning:
rule latent_regularization_experiments:
input:
- data_path=ancient("/psycl/g/mpsstatgen/lucas/DLC/DLC_models/deepof_single_topview/"),
+ data_path=ancient(
+ "/psycl/g/mpsstatgen/lucas/DLC/DLC_models/deepof_single_topview/"
+ ),
output:
trained_models=os.path.join(
outpath,
- "latent_regularization_experiments/trained_weights/GMVAE_loss={loss}_encoding={encs}_k={k}_latreg={latreg}_final_weights.h5",
+ "latent_regularization_experiments/trained_weights/GMVAE_loss={loss}_encoding={encs}_k={k}_latreg={latreg}_entropymink={entmin}_final_weights.h5",
),
shell:
"pipenv run python -m deepof.train_model "
@@ -104,10 +106,11 @@ rule latent_regularization_experiments:
"--mmd-warmup 20 "
"--montecarlo-kl 10 "
"--encoding-size {wildcards.encs} "
+ "--entropy-min-n {wildcards.entmin} "
"--batch-size 256 "
"--window-size 24 "
"--window-step 12 "
- "--exclude-bodyparts Tail_base,Tail_1,Tail_2,Tail_tip "
+ # "--exclude-bodyparts Tail_base,Tail_1,Tail_2,Tail_tip "
"--output-path {outpath}latent_regularization_experiments"
--
GitLab