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Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude… (see more) larger than the number of training examples, making it difficult to avoid overfitting, even when using the known regularization techniques. We focus here on tasks in which the input is a description of the genetic variation specific to a patient, the single nucleotide polymorphisms (SNPs), yielding millions of ternary inputs. Improving the ability of deep learning to handle such datasets could have an important impact in medical research, more specifically in precision medicine, where high-dimensional data regarding a particular patient is used to make predictions of interest. Even though the amount of data for such tasks is increasing, this mismatch between the number of examples and the number of inputs remains a concern. Naive implementations of classifier neural networks involve a huge number of free parameters in their first layer (number of input features times number of hidden units): each input feature is associated with as many parameters as there are hidden units. We propose a novel neural network parametrization which considerably reduces the number of free parameters. It is based on the idea that we can first learn or provide a distributed representation for each input feature (e.g. for each position in the genome where variations are observed in data), and then learn (with another neural network called the parameter prediction network) how to map a feature's distributed representation (based on the feature's identity not its value) to the vector of parameters specific to that feature in the classifier neural network (the weights which link the value of the feature to each of the hidden units). This approach views the problem of producing the parameters associated with each feature as a multi-task learning problem. We show experimentally on a population stratification task of interest to medical studies that the proposed approach can significantly reduce both the number of parameters and the error rate of the classifier.
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude… (see more) larger than the number of training examples, making it difficult to avoid overfitting, even when using the known regularization techniques. We focus here on tasks in which the input is a description of the genetic variation specific to a patient, the single nucleotide polymorphisms (SNPs), yielding millions of ternary inputs. Improving the ability of deep learning to handle such datasets could have an important impact in medical research, more specifically in precision medicine, where high-dimensional data regarding a particular patient is used to make predictions of interest. Even though the amount of data for such tasks is increasing, this mismatch between the number of examples and the number of inputs remains a concern. Naive implementations of classifier neural networks involve a huge number of free parameters in their first layer (number of input features times number of hidden units): each input feature is associated with as many parameters as there are hidden units. We propose a novel neural network parametrization which considerably reduces the number of free parameters. It is based on the idea that we can first learn or provide a distributed representation for each input feature (e.g. for each position in the genome where variations are observed in data), and then learn (with another neural network called the parameter prediction network) how to map a feature's distributed representation (based on the feature's identity not its value) to the vector of parameters specific to that feature in the classifier neural network (the weights which link the value of the feature to each of the hidden units). This approach views the problem of producing the parameters associated with each feature as a multi-task learning problem. We show experimentally on a population stratification task of interest to medical studies that the proposed approach can significantly reduce both the number of parameters and the error rate of the classifier.
The true Bayesian posterior of a model such as a neural network may be highly multimodal. In principle, normalizing flows can represent such… (see more) a distribution via compositions of invertible transformations of random noise. In practice, however, existing normalizing flows may fail to capture most of the modes of a distribution. We argue that the conditionally affine structure of the transformations used in [Dinh et al., 2014, 2016, Kingma et al., 2016] is inefficient, and show that flows which instead use (conditional) invertible non-linear transformations naturally enable multimodality in their output distributions. With just two layers of our proposed deep sigmoidal flow, we are able to model complicated 2d energy functions with much higher fidelity than six layers of deep affine flows.
Fetal, Infant and Ophthalmic Medical Image Analysis
Spectral methods of moments provide a powerful tool for learning the parameters of latent variable models. Despite their theoretical appeal,… (see more) the applicability of these methods to real data is still limited due to a lack of robustness to model misspecification. In this paper we present a hierarchical approach to methods of moments to circumvent such limitations. Our method is based on replacing the tensor decomposition step used in previous algorithms with approximate joint diagonalization. Experiments on topic modeling show that our method outperforms previous tensor decomposition methods in terms of speed and model quality.
Generative Adversarial Networks (GANs) are powerful generative models, but suffer from training instability. The recently proposed Wasserste… (see more)in GAN (WGAN) makes progress toward stable training of GANs, but sometimes can still generate only low-quality samples or fail to converge. We find that these problems are often due to the use of weight clipping in WGAN to enforce a Lipschitz constraint on the critic, which can lead to undesired behavior. We propose an alternative to clipping weights: penalize the norm of gradient of the critic with respect to its input. Our proposed method performs better than standard WGAN and enables stable training of a wide variety of GAN architectures with almost no hyperparameter tuning, including 101-layer ResNets and language models over discrete data. We also achieve high quality generations on CIFAR-10 and LSUN bedrooms.
It is commonly assumed that language refers to high-level visual concepts while leaving low-level visual processing unaffected. This view do… (see more)minates the current literature in computational models for language-vision tasks, where visual and linguistic input are mostly processed independently before being fused into a single representation. In this paper, we deviate from this classic pipeline and propose to modulate the \emph{entire visual processing} by linguistic input. Specifically, we condition the batch normalization parameters of a pretrained residual network (ResNet) on a language embedding. This approach, which we call MOdulated RESnet (\MRN), significantly improves strong baselines on two visual question answering tasks. Our ablation study shows that modulating from the early stages of the visual processing is beneficial.
