CNN-RNNs not learning anything

[kren1]

@eadward I've now done the CNN-RNN approach discussed in the meeting.

It is behaving very similarly to the subject independent RNN aproach, meaning it is not learning anything.

For example here is a training trace:

Train on 10721 samples, validate on 10410 samples
Epoch 1/15
10721/10721 [==============================] - 56s - loss: 0.9948 - val_loss: 1.5181
Epoch 2/15
10721/10721 [==============================] - 56s - loss: 0.9000 - val_loss: 1.4525
Epoch 3/15
10721/10721 [==============================] - 55s - loss: 0.8459 - val_loss: 1.4802
Epoch 4/15
10721/10721 [==============================] - 55s - loss: 0.7673 - val_loss: 1.4254
Epoch 5/15
10721/10721 [==============================] - 55s - loss: 0.7109 - val_loss: 1.4720
Epoch 6/15
10721/10721 [==============================] - 55s - loss: 0.7307 - val_loss: 1.4763
Epoch 7/15
10721/10721 [==============================] - 55s - loss: 0.6144 - val_loss: 1.4643
Epoch 8/15
10721/10721 [==============================] - 54s - loss: 0.5660 - val_loss: 1.4857

#Final result on validation set: 
Model r:  (0.044959106007683075, 4.4554423862127374e-06)
Model rmse:  1.2189017562850681

#Final result on test set:
Model r:  (-0.0059427638053850106, 0.48934621677575696)
Model rmse:  1.3999194428042123

The loss (root mean square error in this case) keeps decreasing, but the training has no effect on the validation set performance. This is exactly the same thing as it is happening with the direct RNN approach.

The architecture of the network is (tinkered keras syntax for clarity), shape comments represent the shape of the network at that point:

    # shape (n_images, frequencies, time)
    # shape (1,200,158)

    model.add(Convolution2D(16,in_shape[1],5))  #doing 1d convolutions on the time asix with filter size 5
    model.add(MaxPooling2D((1,2)))

    # shape (16,1,77)
    model.add(Convolution2D(32,1,10))
    model.add(MaxPooling2D((1,2)))

    # shape (32,1,34)
    model.add(Reshape(dims=(...)))
    #shape (32,34)
    model.add(Permute((2,1)))
    #shape (time, features)
    #(34,32)
    model.add(LSTM(200)) 

    model.add(Dense(1))
    model.add(Activation('linear'))

[kren1]

https://docs.google.com/spreadsheets/d/1ZWiciyp-fRBzmOj5dewdBBrCnttDqPFTo8_iuCU8VF0/edit#gid=0&vpid=A1 a google spreadsheet of some of the runs

[kren1]

This is subject depedant case of training. Will update the table with full detials once the run is finnished.

Train on 15819 samples, validate on 5272 samples
Epoch 1/15
15819/15819 [==============================] - 47s - loss: 1.0041 - val_loss: 0.9244
Epoch 2/15
15819/15819 [==============================] - 47s - loss: 0.9064 - val_loss: 0.8358
Epoch 3/15
15819/15819 [==============================] - 47s - loss: 0.8438 - val_loss: 0.8319
Epoch 4/15
15819/15819 [==============================] - 47s - loss: 0.8235 - val_loss: 0.7711
Epoch 5/15
15819/15819 [==============================] - 47s - loss: 0.7947 - val_loss: 0.7190
Epoch 6/15
15819/15819 [==============================] - 47s - loss: 0.7778 - val_loss: 0.8233
Epoch 7/15
15819/15819 [==============================] - 47s - loss: 0.7511 - val_loss: 0.6501
Epoch 8/15
15819/15819 [==============================] - 47s - loss: 0.7112 - val_loss: 0.6251
Epoch 9/15
15819/15819 [==============================] - 47s - loss: 0.6967 - val_loss: 0.6696
Epoch 10/15
15819/15819 [==============================] - 47s - loss: 0.6733 - val_loss: 0.6607
Epoch 11/15
15819/15819 [==============================] - 47s - loss: 0.6539 - val_loss: 0.6705
Epoch 12/15
15819/15819 [==============================] - 47s - loss: 0.6369 - val_loss: 0.5782
Epoch 13/15
15819/15819 [==============================] - 47s - loss: 0.6498 - val_loss: 0.5720
Epoch 14/15
15819/15819 [==============================] - 47s - loss: 0.6290 - val_loss: 0.6046
Epoch 15/15
15819/15819 [==============================] - 47s - loss: 0.6116 - val_loss: 0.5938
Model r:  (0.65146763812233133, 0.0)
Model rmse:  0.77059348390805

It behaves exactly the same as pure RNN aproach, will get solid data for that as well at some point.

[eadward]

Hi Timotej,

Sorry for the slow reply but I’ve been sick.

Without changing more parameters it is a bit hard. Usually this is key to working with NN, nas therefore my recurrent suggestion to be document all the tests and parameters used. The sequences that the LSTM received are quite short, and sometimes LSTM do not work well that way. Also, you are using 200 units, which may be a little to much considering that you only have 34 input features. Try using 20.

Is the RMSE computed on the standardised outputs? If not it actually looks quite low (error of 1.5 BPM is very low). Can you plot the predictions for training, validation and test?

Cheers, E>

From: Timotej Kapus notifications@github.com<mailto:notifications@github.com> Reply-To: group-24/Palpitate reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, 3 December 2015 19:55 To: group-24/Palpitate Palpitate@noreply.github.com<mailto:Palpitate@noreply.github.com> Cc: edebrito e.coutinho@imperial.ac.uk<mailto:e.coutinho@imperial.ac.uk> Subject: [Palpitate] CNN-RNNs not learning anything (#39)

@eadwardhttps://github.com/eadward I've now done the CNN-RNN approach discussed in the meeting.

It is behaving very similarly to the subject independent RNN aproach, meaning it is not learning anything.

For example here is a training trace:

Train on 10721 samples, validate on 10410 samples Epoch 1/15 10721/10721 [==============================] - 56s - loss: 0.9948 - val_loss: 1.5181 Epoch 2/15 10721/10721 [==============================] - 56s - loss: 0.9000 - val_loss: 1.4525 Epoch 3/15 10721/10721 [==============================] - 55s - loss: 0.8459 - val_loss: 1.4802 Epoch 4/15 10721/10721 [==============================] - 55s - loss: 0.7673 - val_loss: 1.4254 Epoch 5/15 10721/10721 [==============================] - 55s - loss: 0.7109 - val_loss: 1.4720 Epoch 6/15 10721/10721 [==============================] - 55s - loss: 0.7307 - val_loss: 1.4763 Epoch 7/15 10721/10721 [==============================] - 55s - loss: 0.6144 - val_loss: 1.4643 Epoch 8/15 10721/10721 [==============================] - 54s - loss: 0.5660 - val_loss: 1.4857

Final result on validation set:

Model r: (0.044959106007683075, 4.4554423862127374e-06) Model rmse: 1.2189017562850681

Final result on test set:

Model r: (-0.0059427638053850106, 0.48934621677575696) Model rmse: 1.3999194428042123

The loss (root mean square error in this case) keeps decreasing, but the training has no effect on the validation set performance. This is exactly the same thing as it is happening with the direct RNN approach.

The architecture of the network is (tinkered keras syntax for clarity), shape comments represent the shape of the network at that point:

# shape (n_images, frequencies, time)
# shape (1,200,158)

model.add(Convolution2D(16,in_shape[1],5))  #doing 1d convolutions on the time asix with filter size 5
model.add(MaxPooling2D((1,2)))

# shape (16,1,77)
model.add(Convolution2D(32,1,10))
model.add(MaxPooling2D((1,2)))

# shape (32,1,34)
model.add(Reshape(dims=(...)))
#shape (32,34)
model.add(Permute((2,1)))
#shape (time, features)
#(34,32)
model.add(LSTM(200))

model.add(Dense(1))
model.add(Activation('linear'))

— Reply to this email directly or view it on GitHubhttps://github.com/group-24/Palpitate/issues/39.

[eadward]

Please send as attachment or add to github. E.

From:

Timotej Kapus notifications@github.com<mailto:notifications@github.com> Reply-To: group-24/Palpitate reply@reply.github.com<mailto:reply@reply.github.com> Date: Thursday, 3 December 2015 22:11 To: group-24/Palpitate Palpitate@noreply.github.com<mailto:Palpitate@noreply.github.com> Cc: edebrito e.coutinho@imperial.ac.uk<mailto:e.coutinho@imperial.ac.uk> Subject: Re: [Palpitate] CNN-RNNs not learning anything (#39)

https://docs.google.com/spreadsheets/d/1ZWiciyp-fRBzmOj5dewdBBrCnttDqPFTo8_iuCU8VF0/edit#gid=0&vpid=A1 a google spreadsheet of some of the runs

— Reply to this email directly or view it on GitHubhttps://github.com/group-24/Palpitate/issues/39#issuecomment-161801107.

[eadward]

So, both RNN and CC+RNN work similarly for subject dependant, right? Make sure that you report this. Make sure that you train a model on a single subject (1 male and 1 female). In the meantime let us try to solve the independent folds issue: are you sure that there is no error in the data preparation? E.

[kren1]

@eadward They also work similarly (bad) for subject independent model.

I'm not sure there is no error in the data preparation, but have no idea how to test it.

[eadward]

I assume that there no errors then, as you are using the same scripts for other tests. Have you checked the if you have a gender balanced folds and also that the HR distributions for the various folds are similar? Male/female unbalance could be a problem, and if the HR disctributions in each fold are very different the event worst.. E.