Towards Gene Expression Convolutions using Gene Interaction Graphs

We study the challenges of applying deep learning to gene expression data. We find experimentally that there exists non-linear signal in the data, however is it not discovered automatically given the noise and low numbers of samples used in most research. We discuss how gene interaction graphs (same pathway, protein-protein, co-expression, or research paper text association) can be used to impose a bias on a deep model similar to the spatial bias imposed by convolutions on an image. We explore the usage of Graph Convolutional Neural Networks coupled with dropout and gene embeddings to utilize the graph information. We find this approach provides an advantage for particular tasks in a low data regime but is very dependent on the quality of the graph used. We conclude that more work should be done in this direction. We design experiments that show why existing methods fail to capture signal that is present in the data when features are added which clearly isolates the problem that needs to be addressed.

Learning to rank for censored survival data

Survival analysis is a type of semi-supervised ranking task where the target output (the survival time) is often right-censored. Utilizing this information is a challenge because it is not obvious how to correctly incorporate these censored examples into a model. We study how three categories of loss functions, namely partial likelihood methods, rank methods, and our classification method based on a Wasserstein metric (WM) and the non-parametric Kaplan Meier estimate of the probability density to impute the labels of censored examples, can take advantage of this information. The proposed method allows us to have a model that predict the probability distribution of an event. If a clinician had access to the detailed probability of an event over time this would help in treatment planning. For example, determining if the risk of kidney graft rejection is constant or peaked after some time. Also, we demonstrate that this approach directly optimizes the expected C-index which is the most common evaluation metric for ranking survival models.

GibbsNet: Iterative Adversarial Inference for Deep Graphical Models

Directed latent variable models that formulate the joint distribution as $p(x,z) = p(z) p(x \mid z)$ have the advantage of fast and exact sampling. However, these models have the weakness of needing to specify $p(z)$, often with a simple fixed prior that limits the expressiveness of the model. Undirected latent variable models discard the requirement that $p(z)$ be specified with a prior, yet sampling from them generally requires an iterative procedure such as blocked Gibbs-sampling that may require many steps to draw samples from the joint distribution $p(x, z)$. We propose a novel approach to learning the joint distribution between the data and a latent code which uses an adversarially learned iterative procedure to gradually refine the joint distribution, $p(x, z)$, to better match with the data distribution on each step. GibbsNet is the best of both worlds both in theory and in practice. Achieving the speed and simplicity of a directed latent variable model, it is guaranteed (assuming the adversarial game reaches the virtual training criteria global minimum) to produce samples from $p(x, z)$ with only a few sampling iterations. Achieving the expressiveness and flexibility of an undirected latent variable model, GibbsNet does away with the need for an explicit $p(z)$ and has the ability to do attribute prediction, class-conditional generation, and joint image-attribute modeling in a single model which is not trained for any of these specific tasks. We show empirically that GibbsNet is able to learn a more complex $p(z)$ and show that this leads to improved inpainting and iterative refinement of $p(x, z)$ for dozens of steps and stable generation without collapse for thousands of steps, despite being trained on only a few steps.

Count-ception: Counting by Fully Convolutional Redundant Counting

Counting objects in digital images is a process that should be replaced by machines. This tedious task is time consuming and prone to errors due to fatigue of human annotators. The goal is to have a system that takes as input an image and returns a count of the objects inside and justification for the prediction in the form of object localization. We repose a problem, originally posed by Lempitsky and Zisserman, to instead predict a count map which contains redundant counts based on the receptive field of a smaller regression network. The regression network predicts a count of the objects that exist inside this frame. By processing the image in a fully convolutional way each pixel is going to be accounted for some number of times, the number of windows which include it, which is the size of each window, (i.e., 32x32 = 1024). To recover the true count we take the average over the redundant predictions. Our contribution is redundant counting instead of predicting a density map in order to average over errors. We also propose a novel deep neural network architecture adapted from the Inception family of networks called the Count-ception network. Together our approach results in a 20% relative improvement (2.9 to 2.3 MAE) over the state of the art method by Xie, Noble, and Zisserman in 2016.

RandomOut: Using a convolutional gradient norm to rescue convolutional filters

Filters in convolutional neural networks are sensitive to their initialization. The random numbers used to initialize filters are a bias and determine if you will "win" and converge to a satisfactory local minimum so we call this The Filter Lottery. We observe that the 28x28 Inception-V3 model without Batch Normalization fails to train 26% of the time when varying the random seed alone. This is a problem that affects the trial and error process of designing a network. Because random seeds have a large impact it makes it hard to evaluate a network design without trying many different random starting weights. This work aims to reduce the bias imposed by the initial weights so a network converges more consistently. We propose to evaluate and replace specific convolutional filters that have little impact on the prediction. We use the gradient norm to evaluate the impact of a filter on error, and re-initialize filters when the gradient norm of its weights falls below a specific threshold. This consistently improves accuracy on the 28x28 Inception-V3 with a median increase of +3.3%. In effect our method RandomOut increases the number of filters explored without increasing the size of the network. We observe that the RandomOut method has more consistent generalization performance, having a standard deviation of 1.3% instead of 2% when varying random seeds, and does so faster and with fewer parameters.

Rapid building detection using machine learning

This work describes algorithms for performing discrete object detection, specifically in the case of buildings, where usually only low quality RGB-only geospatial reflective imagery is available. We utilize new candidate search and feature extraction techniques to reduce the problem to a machine learning (ML) classification task. Here we can harness the complex patterns of contrast features contained in training data to establish a model of buildings. We avoid costly sliding windows to generate candidates; instead we innovatively stitch together well known image processing techniques to produce candidates for building detection that cover 80-85% of buildings. Reducing the number of possible candidates is important due to the scale of the problem. Each candidate is subjected to classification which, although linear, costs time and prohibits large scale evaluation. We propose a candidate alignment algorithm to boost classification performance to 80-90% precision with a linear time algorithm and show it has negligible cost. Also, we propose a new concept called a Permutable Haar Mesh (PHM) which we use to form and traverse a search space to recover candidate buildings which were lost in the initial preprocessing phase.

Crater Detection via Convolutional Neural Networks

Craters are among the most studied geomorphic features in the Solar System because they yield important information about the past and present geological processes and provide information about the relative ages of observed geologic formations. We present a method for automatic crater detection using advanced machine learning to deal with the large amount of satellite imagery collected. The challenge of automatically detecting craters comes from their is complex surface because their shape erodes over time to blend into the surface. Bandeira provided a seminal dataset that embodied this challenge that is still an unsolved pattern recognition problem to this day. There has been work to solve this challenge based on extracting shape and contrast features and then applying classification models on those features. The limiting factor in this existing work is the use of hand crafted filters on the image such as Gabor or Sobel filters or Haar features. These hand crafted methods rely on domain knowledge to construct. We would like to learn the optimal filters and features based on training examples. In order to dynamically learn filters and features we look to Convolutional Neural Networks (CNNs) which have shown their dominance in computer vision. The power of CNNs is that they can learn image filters which generate features for high accuracy classification.