From e062613c0c34c2860b0364c99b072c5ab50ccbaf Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 28 Nov 2017 14:59:55 -0500
Subject: [PATCH] better progress printing
---
.../class1_affinity_predictor.py | 6 ++++--
.../class1_affinity_prediction/class1_neural_network.py | 3 ---
.../train_allele_specific_models_command.py | 8 +++++++-
3 files changed, 11 insertions(+), 6 deletions(-)
diff --git a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
index d1e0f02c..ada2e9e5 100644
--- a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
@@ -437,7 +437,7 @@ class Class1AffinityPredictor(object):
if models_dir_for_save:
self.save(
models_dir_for_save, model_names_to_write=[model_name])
- return models
+ return models_list
def fit_class1_pan_allele_models(
self,
@@ -498,8 +498,10 @@ class Class1AffinityPredictor(object):
verbose=verbose,
progress_preamble=progress_preamble)
+ models_list = []
for (i, model) in enumerate(models):
model_name = self.model_name("pan-class1", i)
+ models_list.append(model) # models is a generator
self.class1_pan_allele_models.append(model)
row = pandas.Series(collections.OrderedDict([
("model_name", model_name),
@@ -512,7 +514,7 @@ class Class1AffinityPredictor(object):
if models_dir_for_save:
self.save(
models_dir_for_save, model_names_to_write=[model_name])
- return models
+ return models_list
def _fit_predictors(
self,
diff --git a/mhcflurry/class1_affinity_prediction/class1_neural_network.py b/mhcflurry/class1_affinity_prediction/class1_neural_network.py
index c52a07e3..bf385c96 100644
--- a/mhcflurry/class1_affinity_prediction/class1_neural_network.py
+++ b/mhcflurry/class1_affinity_prediction/class1_neural_network.py
@@ -643,7 +643,4 @@ class Class1NeuralNetwork(object):
inputs=inputs,
outputs=[output],
name="predictor")
-
- print("*** ARCHITECTURE ***")
- model.summary()
return model
diff --git a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
index cc9f82a6..c763b92d 100644
--- a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
+++ b/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
@@ -241,7 +241,7 @@ def process_work(
allele))
train_data = sub_df.dropna().sample(frac=1.0)
- predictor.fit_allele_specific_predictors(
+ (model,) = predictor.fit_allele_specific_predictors(
n_models=1,
architecture_hyperparameters=hyperparameters,
allele=allele,
@@ -251,6 +251,12 @@ def process_work(
progress_preamble=progress_preamble,
verbose=verbose)
+ if allele_num == 0 and model_group == 0:
+ # For the first model for the first allele, print the architecture.
+ print("*** ARCHITECTURE FOR HYPERPARAMETER SET %d***" %
+ (hyperparameter_set_num + 1))
+ model.network(borrow=True).summary()
+
return predictor
--
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