Proper datasets are key to this project. Because we're analyzing image data, birds in front of different backgrounds, at different scales, or even in different positions could throw off the similarity comparison. I wanted to use illustrations from Sibley's Guides to Birds but couldn't find a large collection of images online. Instead, I used ~2,500 images from Joel Sartore's Photo Ark project, and a 400 images from a database of Audubon's drawings from Bird's of America. I'm not sure about the ethics of my data collection. I needed to programmatically scrape images from both sites, is it ok to use the images here?
I first thought that I would do the clustering in image space. While this approach would be the most straightforward, it would based on the contents of the image rather than the features of the bird. For example, a bird facing to the right may be located far from a bird facing to the left as they differ strongly in image space.
To work around this problem, I needed to cluster based on features of the birds in the images rather than on the image data itself. Once again, neural networks come to the rescue. A typical classification network is composed of convolutional feature extractors followed by fully connected layers. These layers of feature extractors at the top of the network start from simple concepts like curves or edges, and build more complex composite feature detectors out of the simpler components. These features can then be used by the fully-connected half of the network to make a classification of what is in the image. To see more on this topic, read this fascinating series on Distill.pub.
I ran each image through the feature extractor from the VGG16 network to convert a 224x224x3 image into a 512x1 dimensional feature output. I then compressed the dimensionality of these vectors from 512 dimensions down to 2 using an algorithm called tSNE. From there, the scattered points are moved into a regular grid using a Jonker-Volgenant distance minimization algorithm, and the original image is ploted in its gridded location. This whole process was popularized by Andrej Karpathy and is simply implemented here. All code for the scraping and analysis can be accessed and run in this Google Colab notebook.