I wrote about this paper before, but I am going to again because it has been so enormously useful to me. I am still working on segmentation of mammograms to highlight abnormalities and I recently decided to scrap the approach I had been taking to upsampling the image and start that part from scratch.

When I started I had been using the earliest approach to upsampling, which basically was take my classifier, remove the last fully-connected layer and upsample that back to full resolution with transpose convolutions. This worked well enough, but the network had to upsample images from 2x2x1024 to 640x640x2 and in order to do this I needed to add skip connections from the downsizing section to the upsampling section. This caused problems because the network would add features of the input image to the output, regardless of whether the features were relevant to the label. I tried to get around this by adding bottleneck layers before the skip connection in order to only select the pertinent features, but this greatly slowed down training and didn't help much and the output ended up with a lot of weird artifacts.

In "Deconvolution and Checkerboard Artifacts", Odena et al. have demonstrated that replacing transpose convolutions with nearest neighbors resizing produces smoother images than using transpose convolutions. I tried replacing a few of my tranpose convolutions with resizes and the results improved.

Then I started reading about dilated convolutions and I started wondering why I was downsizing my input from 640x640 to 5x5 just to have to resize it back up. I removed all the fully-connected layers (which in fact were 1x1 convolutions rather than fully-connected layers) and then replaced the last max pool with a dilated convolution.

I replaced all of the transpose convolutions with resizes, except for the last two layers, as suggested by Odena et al, and the final tranpose convolution has a stride of 1 in order to smooth out artifacts.

In the downsizing section, the current model reduces the input from 640x640x1 to 20x20x512, then it is upsampled by using nearest neighbors resizing followed by plain convolutions to 320x320x32. Finally there is a tranpose convolution with a stride of 2 followed by a transpose convolution with a stride of 1 and then a softmax for the output. As an added bonus, this version of the model trains significantly faster than upsampling with transpose convolutions.

I just started training this model, but I am fairly confident it will perform better than previous upsampling schemes as when I extracted the last downsizing convolutional layer from the model that layer appeared closer to the label (although much smaller) than the final output did. I will update when I have actual results.

Update - After training the model for just one epoch, with the downsizing layer weights initialized from a previous model, the results are already significantly better than under the previous scheme.

Labels: coding, data_science, tensorflow, mammography, convnets, ddsm
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As I continue to work on my mammography project I save a lot of time by re-using weights from models I have already trained rather than training every iteration of every model from scratch, which would be very time consuming. However a drawback to this method is that if I add a new layer or change a layer when I continue training the model the layers which have not changed are prone to overfit as they have been trained for substantially longer than the new layers.

I tried only training certain variables, but when the checkpoint is saved only the trained variables are included in it, which means that the checkpoint can not be restored as it is missing many variables. This could be overcome by restoring certain variables from one checkpoint and others from a different checkpoint, but that is overly complicated and not very convenient.

Earlier today, I had added another deconvolution layer to my model. When I trained just that layer the accuracy of the model went very high very quickly, much more quickly than training all of the layers. But then I couldn't continue training all of the layers because the checkpoint only contained the layer trained. I don't have the time to retrain the entire monstrosity from scratch, so I found an ugly hack that allows me to train mostly the layers I want to train while saving all of the weights in the checkpoint.

I create two training ops - one for all variables (train_op_1) and one for the variables I want to train (train_op_2). I run train_op_2 most of the time. But right before I save the checkpoint I do one iteration of train_op_1 which updates all layers, so all variables are saved in the checkpoint. It's not pretty, but it works and best of all, the code doesn't have to be changed depending on what I want to train. I specify whether I want to train all vars or just the subset as a command line arg and if I want to train all vars, then set train_op_2 = train_op_1.

I just ran a few quick tests with no issues, hopefully this will continue to work.

Labels: python, data_science, machine_learning, tensorflow
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Even though I only have 1/5 of the images uploaded so far, I decided to do some tests to see if this method would work. It does, but it took quite a bit of tweaking to get performance to reasonable levels.

At first I just plugged the new dataset into the old graph, and this worked but was incredibly slow with the GPU sitting idle most of the time. I tried quite a few different methods to speed the pre-processing bottleneck up, but the solution was simpler than I had thought it would be.

The biggest factor was increasing number of threads in the tf.train.batch from the default of 1. This one change made a huge difference, cutting the training time down to about 1/4 of what it had been.

I also experimented with moving some pre-processing operations around, including resizing the images individually when loading them and after being batched. This had negligible effects, but resizing them individually was slightly faster than doing it as a batch. In general I found that the more pre-processing operations I moved to the queue (and the CPU) the better the performance.

This version still trains at about 1/2 the speed the tfrecords version did, which is a big difference, but the size of the training set has increased by orders of magnitude so I guess I can live with it. 

The code is available on my GitHub.

Labels: python, machine_learning, tensorflow, mammography
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My original work with the DDSM and CBIS-DDSM dataset yielded good accuracy and recall on the test and validation data, but the model didn't perform so well when applied to the MIAS images, which came from a completely different dataset. Additional analysis of the images indicated that the negative images (from the DDSM) and the positive images (from the CBIS-DDSM) were different in some subtle but important ways:

1. The negative images had a lower mean, lower maximum and higher minimum. 
2. The negative images also had lower contrast.

We had become concerned about point 2 when we discovered that increasing the contrast of any image made it more likely to be predicted as positive and discovered point 1 while investigating this further. When applying our fully convolutional model trained on the combined data to complete scans, rather than the 299x299 images we had trained on, we noticed that more than 50% of the sections of a positive image were predicted as positive, even if the ROI was, in fact, only present in one section. This indicates that the model was using some feature of the images other than the ROI in its prediction.

When starting this project, we had initially planned to segment the CBIS-DDSM images and use images which did not contain an ROI as negative images, but we were not certain that there were not differences in the tissue of positive and negative scans which might make this approach not generalize to completely negative scans. When we realized that the scans had been pre-processed differently we attempted to adjust the negative images in such a way as to make them more similar to the positive images but were unable to do so without knowledge of how they had been processed.

Our solution to both of these issues was to train the model to do the segmentation of the scans rather than simple classification, using the masks as the labels. This approach had several advantages:

1. Using the mask as the label tells the model where it needs to look, so we can ensure that it actually uses the ROIs rather than other features of the images, such as the contrast or maximum pixel value.
2. This allows us the exclude the DDSM images and only use images from one dataset, as the ROI of most scans only encompasses a small portion of the image.

We recreated the model to do semantic segmentation by removing the last "fully connected" layer (which were implemented as a 1x1 convolution) and the logits layer and upsampling the results with transpose convolutions. In order for the upsampling to work properly we needed to have the size of the images be a multiple of 2 so that the dimension reduction could be properly undone, so we used images of size 320x320.

We were able to get fairly good results training on this data with a pixel level accuracy of about 90% and a pixel recall of 70%. The image level accuracy and recall were 70% and 87%, respectively. While these results were respectable, we noticed certain patterns of incorrect predictions. Images which were mostly dark, with patches that were much brighter, tended to have the bright patches predicted positive regardless of the actual label. This pattern was mostly observed when the bright patch ran off the edge of the image. 

We know that the context of an ROI is important in detecting and diagnosing it, and we suspected that in the absence of context the model was predicting any patch substantially brighter than it's surroundings to be positive. While for cancer detection, it is better to make a false positive than a false negative we thought that this pattern might become problematic when applying the model to images larger than those it was trained on. To address this issue we decided to create a dataset of larger images and continue training our model on those.

We created a dataset of 640x640 images and adjusted our existing model to take those as input. As the model is fully convolutional we can restore the model trained on 320x320 images and continue training it on the larger images with no problems, which we are currently in the process of doing. If the results of this are promising we may create another dataset of even larger images are fine-tune this model on those images until we have a model which takes complete images as input.

Labels: machine_learning, tensorflow, mammography, convnets, ddsm
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I was training a ConvNet and everything was working fine during training. But when I evaluated the model on the validation data I was getting NaN for the cross entropy. I thought it was the cross entropy attempting to take the log of 0 and added a small epsilon value of 1e-10 to the logits to address that. I thought that would fix the problem but it did not.

Further investigation indicated that the NaNs were being introduced somewhere early in the network, in one of the convolutional layers. I checked the validation and training data to make sure there wasn't some fundamental difference between the two, thinking that maybe one was being pre-processed differently than the other, but that was not the case.

In my graph I am using tf.metrics and gathering all of the update ops into one op to be executed during training with:

extra_update_ops = tf.get_collection(tf.GraphKeys.UPDATE_OPS)

Also gathered into this op was the updates to the batch norms. I had done this many times before with no problems at all so never thought this could be a factor. But when I removed the extra update op from the evaluation code the problem went away. Including the ops generated to update my metrics individually caused no problems. 

I am not sure what the issue actually was, but I assume it has something to do with the batch normalization, or maybe there is another op created somewhere in my graph that caused this issue.

Update - I had been restoring the weights from a pre-trained model and I think the restored batch norms caused the problem. NOT restoring the batch norms when loading the weights seems to solve this problem completely. Otherwise the issue still occurred sporadically.

Labels: python, machine_learning, tensorflow
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