From 89816bf517f9be22d8ae72559af10dca972963a8 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 15 May 2019 17:36:51 -0400
Subject: [PATCH] fix
---
mhcflurry/train_pan_allele_models_command.py | 21 ++++++++++++++------
1 file changed, 15 insertions(+), 6 deletions(-)
diff --git a/mhcflurry/train_pan_allele_models_command.py b/mhcflurry/train_pan_allele_models_command.py
index 0a202170..994d7c0c 100644
--- a/mhcflurry/train_pan_allele_models_command.py
+++ b/mhcflurry/train_pan_allele_models_command.py
@@ -406,7 +406,7 @@ def train_model(
if pretrain_data_filename:
iterator = pretrain_data_iterator(pretrain_data_filename, allele_encoding)
original_hyperparameters = dict(model.hyperparameters)
- model.hyperparameters['minibatch_size'] = len(next(iterator)[-1])
+ model.hyperparameters['minibatch_size'] = int(len(next(iterator)[-1]) / 100)
model.hyperparameters['max_epochs'] = 1
model.hyperparameters['validation_split'] = 0.0
model.hyperparameters['random_negative_rate'] = 0.0
@@ -443,7 +443,7 @@ def train_model(
print(
progress_preamble,
"PRETRAIN epoch %d [%d values, %0.2f sec]. "
- "Score [%0.2f sec.]: %f" % (
+ "Score [%0.2f sec.]: %10f" % (
epoch, len(affinities), fit_time, score_time, score))
scores.append(score)
@@ -464,8 +464,8 @@ def train_model(
model.fit(
- train_peptides,
- train_data.measurement_value,
+ peptides=train_peptides,
+ affinities=train_data.measurement_value.values,
allele_encoding=train_alleles,
inequalities=(
train_data.measurement_inequality.values
@@ -476,9 +476,18 @@ def train_model(
predictor.class1_pan_allele_models.append(model)
predictor.clear_cache()
- return predictor
+ if save_to:
+ predictor.save(save_to)
+
+ return predictor
if __name__ == '__main__':
- run()
+ try:
+ run()
+ except Exception as e:
+ print(e)
+ import ipdb ; ipdb.set_trace()
+ raise
+
--
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