I was training a model on a Google Cloud instance with a Tesla K80 GPU. This particular model had more data pre-processing required than normal. The model was training very slowly, the GPU usage was oscillating between 0% and 75-100%. I thought the CPU was the bottleneck and was trying to put as much pre-processing on the GPU as possible.

I read TensorFlow's optimization guide, which suggested forcing the pre-processing to be on the CPU by enclosing it with:

with tf.device('/cpu:0'):

Since I thought the CPU was the bottleneck I didn't think that would help, but I tried it anyway because I had no other good ideas and was surprised that it worked like magic! The GPU usage now stays constant around 95-100% while the CPU usage stays at about the same levels as before.

Labels: machine_learning, tensorflow, google_cloud
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I have been working on a project to detect abnormalities in mammograms. I have been training it on Google Cloud instances with Nvidia Tesla K80 GPUs, which allow a model to be trained in days rather than weeks or months. However when I tried to do online data augmentation it became a huge bottleneck because it did the data augmentation on the CPU.

I had been using tf.image.random_flip_left_right and tf.image.random_flip_up_down but since those operations were run on the CPU the training slowed down to a crawl as the GPU sat idle waiting for the queue to be filled.

I found this post on Medium, Data Augmentation on GPU in Tensorflow, which uses tf.contrib.image instead of tf.image. tf.contrib.image is written to run on the GPU, so using this code allows the data augmentation to be performed on the GPU instead of the CPU and thus eliminates the bottleneck.

This has been a life saver for me. Adding it to my graph allows me to train for longer without overfitting and this get better results.

Labels: python, machine_learning, tensorflow
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Tainted Love from Eric Scuccimarra on Vimeo.

Tainted Love from Eric Scuccimarra on Vimeo.

My new song, an abstract impressionist jazz cover of Gloria Jone's "Tainted Love."

Labels: music, jazz
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While we tend to think of ourselves as being at the pinnacle of evolution, in reality humans are barely a step up from monkeys. Our only real differentiation from them is that we have language, which allows us to communicate knowledge to others and to preserve that knowledge through time. Language gives us a huge advantage, allowing us to progressively accumulate new knowledge by building up on previous discoveries, but in the end we are just animals who have evolved to survive, like all other animals. We are not adapted to having civilizations and technology, we evolved to find food and procreate and the results of this can be seen all over - from how tech companies use simple tricks like noises and bright colors and intermittent rewards to keep us hooked, to how food companies load their food with salt, fat and sugar to keep us eating unhealthy food, to the cognitive biases and heuristics we use to make decisions under uncertainty. The point of all of this is that humans evolved to find food and avoid predators, and our brains are incredibly ill-suited to processing the large amounts of data that are required to make evaluations about the types of issues that we face everyday in today's complex world.

Computers on the other hand are designed for processing large amounts of data - they can do this very efficiently if programmed correctly. However they lack our creativity - the ability to combine seemingly unrelated ideas into new ideas, and to come up with novel solutions to problems. Machine learning combines our creativity with the ability of computers to handle large amounts of data, specifically the ability to find patterns in data. In 2015 a journalist ran a study on chocolate, the results of which were that chocolate helps you lose weight. The study was commissioned as an example of "junk science" and only had 15 participants with 18 measurements for each participant. The author said “here’s a dirty little science secret: If you measure a large number of things about a small number of people, you are almost guaranteed to get a ‘statistically significant’ result.” Unfortunately much of science is conducted like this - the authors start a study to proof a hypothesis and maybe they'll ignore some results which contradict the hypothesis if other results confirm it. No one likes to be wrong and if the results are a bit ambiguous you can maybe just cherry pick the numbers you like. In Darrell Huff's 1954 book "How to Lie with Statistics" he says "if you torture the data long enough it will confess to anything" and this is in fact the case. 

Machine learning is about letting the data speak for itself. With machine learning you set up a system of symbolic equations for transforming data into predictions and then feed the data into that system and see what happens. If you don't like the results you can change the system or the data, but the process is far too complex to be able to cherry pick the data you like and discard the rest. This combines the strengths of humans with the strengths of computers - the humans use their creativity and domain knowledge to create the system which they hope will find patterns in the data and the computers run the data through the system. While technically possible to do so, the process of analyzing the data is far more complex than could ever be done without a computer, and the computers can only do what they are told to do - they can not create novel ideas from nothing.

In my opinion, machine learning is the most important scientific technology in recent history. Just like electricity allowed energy to become uncoupled from the previous sources - fire and animal energy - machine learning uncouples the ability to process data from the constraints of the human brain. Properly used, I think machine learning will be as revolutionary as electricity was.

Labels: machine_learning
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I am working on classifying mammography scans with a TensorFlow ConvNet. The scans are classified into five classes:

• Normal
• Benign Calcification
• Malignant Calcification
• Benign Mass
• Malignant Mass

I was unsure of how I wanted to classify the scans so I created the model in such a way that it would work for any combination of classes. I initially started training with binary classification - normal or abnormal, with the goal of then expanding the number of classes once I had a model that made decent predictions on the binary case.

For the binary prediction I used precision, recall and a pr curve as metrics. When I expanded to multiple classes obviously those metrics no longer worked. As far as precision and recall I don't really care what type of abnormal the scan is - I just care that it is abnormal at all. And I wanted to have the same metrics to compare for all my models so I had to figure out a way to do precision and recall for all versions of the model.

The solution I came to was to "squash" my multi-class labels and predictions down into binary labels and predictions and feed those into the p/r metrics. I set up the classes so that 0 was always normal, so I can do the squashing as follows:

zero = tf.constant(0, dtype=tf.int64)
collapsed_predictions = tf.greater(predictions, zero)
collapsed_labels = tf.greater(y, zero)

Collapsed_predictions and collapsed_labels will then contain True if the prediction or label is NOT 0 and False if it is. Then I can feed these into my precision and recall metrics:

recall, rec_op = tf.metrics.recall(labels=collapsed_labels, predictions=collapsed_predictions)
precision, prec_op = tf.metrics.precision(labels=collapsed_labels, predictions=collapsed_predictions)

I also created a pr curve metric to see how the thresholds would affect the predictions. First I convert the logits to probabilities via a softmax and then feed that into a pr_curve_streaming_op as the predictions. In order to make this work with multi-class classification I squash the probabilities down to the probability that the item is NOT normal. Since my labels are created such that normal is always 0, the probability that it is not normal is just 1 - the probability that it is:

probabilities = tf.nn.softmax(logits, name="probabilities")

_, update_op = summary_lib.pr_curve_streaming_op(name='pr_curve',
                                                predictions=(1 - probabilities[:, 0]),
                                                labels=collapsed_labels,
                                                updates_collections=tf.GraphKeys.UPDATE_OPS,
                                                num_thresholds=20)

Labels: python, machine_learning, tensorflow
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