Carlos-Francisco Méndez-Cruz / deep-learning-workshop

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Carlos-Francisco Méndez-Cruz
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Deep Learning Workshop

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...@@ -18,13 +18,14 @@ ...@@ -18,13 +18,14 @@
18 18
19 # LAVIS 19 # LAVIS
20 # qlogin 20 # qlogin
21 +# cd /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets
21 # python get-hga-training-test-py27-v1.py 22 # python get-hga-training-test-py27-v1.py
22 # --inputFile hga-sequences-1000.txt 23 # --inputFile hga-sequences-1000.txt
23 # --inputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 24 # --inputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
24 # --outputTraining hga-sequences-training.txt 25 # --outputTraining hga-sequences-training.txt
25 # --outputTest hga-sequences-test.txt 26 # --outputTest hga-sequences-test.txt
26 # --outputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 27 # --outputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
27 -# python get-hga-training-test-py27-v1.py --inputFile hga-sequences-toy.txt --inputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --outputTraining hga-sequences-training.txt --outputTest hga-sequences-test.txt --outputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 28 +# python get-hga-training-test-py27-v1.py --inputFile hga-sequences-1000.txt --inputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --outputTraining hga-sequences-training.txt --outputTest hga-sequences-test.txt --outputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
28 29
29 import argparse 30 import argparse
30 import pandas as pd 31 import pandas as pd
...@@ -148,7 +149,7 @@ if __name__ == "__main__": ...@@ -148,7 +149,7 @@ if __name__ == "__main__":
148 input_shape=(train_features.shape[1], 5))) 149 input_shape=(train_features.shape[1], 5)))
149 # Original: model.add(MaxPooling1D(pool_size=4)) 150 # Original: model.add(MaxPooling1D(pool_size=4))
150 # Do we have to change to 5, because of the 5 nucleotides? 151 # Do we have to change to 5, because of the 5 nucleotides?
151 - model.add(MaxPooling1D(pool_size=4)) 152 + model.add(MaxPooling1D(pool_size=5))
152 model.add(Flatten()) 153 model.add(Flatten())
153 model.add(Dense(16, activation='relu')) 154 model.add(Dense(16, activation='relu'))
154 model.add(Dense(2, activation='softmax')) 155 model.add(Dense(2, activation='softmax'))
......