Obtaining a protein's 3D structure is crucial to the understanding of its functions and interactions with other proteins. It is critical to accelerate the protein crystallization process with improved accuracy for understanding cancer and designing drugs. Systematic high-throughput approaches in protein crystallization have been widely applied, generating a large number of protein crystallization-trial images. Therefore, an efficient and effective automatic analysis for these images is a top priority. In this paper, we present a novel system, CrystalNet, for automatically labeling outcomes of protein crystallization-trial images. CrystalNet is a deep convolutional neural network that automatically extracts features from X-ray protein crystallization images for classification. We show that (1) CrystalNet can provide real-time labels for crystallization images effectively, requiring approximately 2 seconds to provide labels for all 1536 images of crystallization microassay on each plate; (2) compared with the state-of-the-art classification systems in crystallization image analysis, our technique demonstrates an improvement of 8% in accuracy, and achieve 90.8% accuracy in classification. As a part of the high-throughput pipeline which generates millions of images a year, CrystalNet can lead to a substantial reduction of labor-intensive screening.

Recently, fully-connected and convolutional neural networks have been trained to achieve state-of-the-art performance on a wide variety of tasks such as speech recognition, image classification, natural language processing, and bioinformatics. For classification tasks, most of these "deep learning" models employ the softmax activation function for prediction and minimize cross-entropy loss. In this paper, we demonstrate a small but consistent advantage of replacing the softmax layer with a linear support vector machine. Learning minimizes a margin-based loss instead of the cross-entropy loss. While there have been various combinations of neural nets and SVMs in prior art, our results using L2-SVMs show that by simply replacing softmax with linear SVMs gives significant gains on popular deep learning datasets MNIST, CIFAR-10, and the ICML 2013 Representation Learning Workshop's face expression recognition challenge.

Attention has long been proposed by psychologists to be important for efficiently dealing with the massive amounts of sensory stimulus in the neocortex. Inspired by the attention models in visual neuroscience and the need for object-centered data for generative models, we propose a deep-learning based generative framework using attention. The attentional mechanism propagates signals from the region of interest in a scene to an aligned canonical representation for generative modeling. By ignoring scene background clutter, the generative model can concentrate its resources on the object of interest. A convolutional neural net is employed to provide good initializations during posterior inference which uses Hamiltonian Monte Carlo. Upon learning images of faces, our model can robustly attend to the face region of novel test subjects. More importantly, our model can learn generative models of new faces from a novel dataset of large images where the face locations are not known.

Multilayer perceptrons (MLPs) or neural networks are popular models used for nonlinear regression and classification tasks. As regressors, MLPs model the conditional distribution of the predictor variables Y given the input variables X. However, this predictive distribution is assumed to be unimodal (e.g. Gaussian). For tasks such as structured prediction problems, the conditional distribution should be multimodal, forming one-to-many mappings. By using stochastic hidden variables rather than deterministic ones, Sigmoid Belief Nets (SBNs) can induce a rich multimodal distribution in the output space. However, previously proposed learning algorithms for SBNs are very slow and do not work well for real-valued data. In this paper, we propose a stochastic feedforward network with hidden layers having \emph{both deterministic and stochastic} variables. A new Generalized EM training procedure using importance sampling allows us to efficiently learn complicated conditional distributions. We demonstrate the superiority of our model to conditional Restricted Boltzmann Machines and Mixture Density Networks on synthetic datasets and on modeling facial expressions. Moreover, we show that latent features of our model improves classification and provide additional qualitative results on color images.

The ICML 2013 Workshop on Challenges in Representation Learning focused on three challenges: the black box learning challenge, the facial expression recognition challenge, and the multimodal learning challenge. We describe the datasets created for these challenges and summarize the results of the competitions. We provide suggestions for organizers of future challenges and some comments on what kind of knowledge can be gained from machine learning competitions.

Visual perception is a challenging problem in part due to illumination variations. A possible solution is to first estimate an illumination invariant representation before using it for recognition. The object albedo and surface normals are examples of such representations. In this paper, we introduce a multilayer generative model where the latent variables include the albedo, surface normals, and the light source. Combining Deep Belief Nets with the Lambertian reflectance assumption, our model can learn good priors over the albedo from 2D images. Illumination variations can be explained by changing only the lighting latent variable in our model. By transferring learned knowledge from similar objects, albedo and surface normals estimation from a single image is possible in our model. Experiments demonstrate that our model is able to generalize as well as improve over standard baselines in one-shot face recognition.

An efficient way to learn deep density models that have many layers of latent variables is to learn one layer at a time using a model that has only one layer of latent variables. After learning each layer, samples from the posterior distributions for that layer are used as training data for learning the next layer. This approach is commonly used with Restricted Boltzmann Machines, which are undirected graphical models with a single hidden layer, but it can also be used with Mixtures of Factor Analysers (MFAs) which are directed graphical models. In this paper, we present a greedy layer-wise learning algorithm for Deep Mixtures of Factor Analysers (DMFAs). Even though a DMFA can be converted to an equivalent shallow MFA by multiplying together the factor loading matrices at different levels, learning and inference are much more efficient in a DMFA and the sharing of each lower-level factor loading matrix by many different higher level MFAs prevents overfitting. We demonstrate empirically that DMFAs learn better density models than both MFAs and two types of Restricted Boltzmann Machine on a wide variety of datasets.