With the remarkable success achieved by the Convolutional Neural Networks (CNNs) in object recognition recently, deep learning is being widely used in the computer vision community. Deep Metric Learning (DML), integrating deep learning with conventional metric learning, has set new records in many fields, especially in classification task. In this paper, we propose a replicable DML method, called Include and Exclude (IE) loss, to force the distance between a sample and its designated class center away from the mean distance of this sample to other class centers with a large margin in the exponential feature projection space. With the supervision of IE loss, we can train CNNs to enhance the intra-class compactness and inter-class separability, leading to great improvements on several public datasets ranging from object recognition to face verification. We conduct a comparative study of our algorithm with several typical DML methods on three kinds of networks with different capacity. Extensive experiments on three object recognition datasets and two face recognition datasets demonstrate that IE loss is always superior to other mainstream DML methods and approach the state-of-the-art results. Preprint submitted to Neurocomputing March 8, 2018 1. Introduction Recently, Convolutional Neural Networks (CNNs) are continuously setting new records in classification aspect, such as object recognition [1, 2, 3, 4], scene recognition [5, 6], face recognition [7, 8, 9, 10, 11, 12], age estimation [13, 14] and so on. Facing the more and more complex data, the deeper and wider CNNs tend to obtain better accuracies. Meanwhile, many troubles will show up, such as gradient saturating, model overfitting, parameter augmentation, etc. To solve the first problem, some nonlinear activations [15, 16, 17] have been proposed.

We present the ConditionaL Neural Network (CLNN) and the Masked ConditionaL Neural Network (MCLNN) designed for temporal signal recognition. The CLNN takes into consideration the temporal nature of the sound signal and the MCLNN extends upon the CLNN through a binary mask to preserve the spatial locality of the features and allows an automated exploration of the features combination analogous to hand-crafting the most relevant features for the recognition task. MCLNN has achieved competitive recognition accuracies on the GTZAN and the ISMIR2004 music datasets that surpass several state-of-the-art neural network based architectures and hand-crafted methods applied on both datasets.

Protein-ligand scoring is an important step in a structure-based drug design pipeline. Selecting a correct binding pose and predicting the binding affinity of a protein-ligand complex enables effective virtual screening. Machine learning techniques can make use of the increasing amounts of structural data that are becoming publicly available. Convolutional neural network (CNN) scoring functions in particular have shown promise in pose selection and affinity prediction for protein-ligand complexes. Neural networks are known for being difficult to interpret. Understanding the decisions of a particular network can help tune parameters and training data to maximize performance. Visualization of neural networks helps decompose complex scoring functions into pictures that are more easily parsed by humans. Here we present three methods for visualizing how individual protein-ligand complexes are interpreted by 3D convolutional neural networks. We also present a visualization of the convolutional filters and their weights. We describe how the intuition provided by these visualizations aids in network design. Keywords: protein-ligand scoring, molecular visualization, deep learning 1. Introduction Protein-ligand scoring is an important computational method in a drug design pipeline [1-6].

Deep learning has become very popular for tasks such as predictive modeling and pattern recognition in handling big data. Deep learning is a powerful machine learning method that extracts lower level features and feeds them forward for the next layer to identify higher level features that improve performance. However, deep neural networks have drawbacks, which include many hyper-parameters and infinite architectures, opaqueness into results, and relatively slower convergence on smaller datasets. While traditional machine learning algorithms can address these drawbacks, they are not typically capable of the performance levels achieved by deep neural networks. To improve performance, ensemble methods are used to combine multiple base learners. Super learning is an ensemble that finds the optimal combination of diverse learning algorithms. This paper proposes deep super learning as an approach which achieves log loss and accuracy results competitive to deep neural networks while employing traditional machine learning algorithms in a hierarchical structure. The deep super learner is flexible, adaptable, and easy to train with good performance across different tasks using identical hyper-parameter values. Using traditional machine learning requires fewer hyper-parameters, allows transparency into results, and has relatively fast convergence on smaller datasets. Experimental results show that the deep super learner has superior performance compared to the individual base learners, single-layer ensembles, and in some cases deep neural networks. Performance of the deep super learner may further be improved with task-specific tuning.

Superior performance and ease of implementation have fostered the adoption of Convolutional Neural Networks (CNNs) for a wide array of inference and reconstruction tasks. CNNs implement three basic blocks: convolution, pooling and pointwise nonlinearity. Since the two first operations are well-defined only on regular-structured data such as audio or images, application of CNNs to contemporary datasets where the information is defined in irregular domains is challenging. This paper investigates CNNs architectures to operate on signals whose support can be modeled using a graph. Architectures that replace the regular convolution with a so-called linear shift-invariant graph filter have been recently proposed. This paper goes one step further and, under the framework of multiple-input multiple-output (MIMO) graph filters, imposes additional structure on the adopted graph filters, to obtain three new (more parsimonious) architectures. The proposed architectures result in a lower number of model parameters, reducing the computational complexity, facilitating the training, and mitigating the risk of overfitting. Simulations show that the proposed simpler architectures achieve similar performance as more complex models.

We propose a novel online learning algorithm for Restricted Boltzmann Machines (RBM), namely, the Online Generative Discriminative Restricted Boltzmann Machine (OGD-RBM), that provides the ability to build and adapt the network architecture of RBM according to the statistics of streaming data. The OGD-RBM is trained in two phases: (1) an online generative phase for unsupervised feature representation at the hidden layer and (2) a discriminative phase for classification. The online generative training begins with zero neurons in the hidden layer, adds and updates the neurons to adapt to statistics of streaming data in a single pass unsupervised manner, resulting in a feature representation best suited to the data. The discriminative phase is based on stochastic gradient descent and associates the represented features to the class labels. We demonstrate the OGD-RBM on a set of multi-category and binary classification problems for data sets having varying degrees of class-imbalance. We first apply the OGD-RBM algorithm on the multi-class MNIST dataset to characterize the network evolution. We demonstrate that the online generative phase converges to a stable, concise network architecture, wherein individual neurons are inherently discriminative to the class labels despite unsupervised training. We then benchmark OGD-RBM performance to other machine learning, neural network and ClassRBM techniques for credit scoring applications using 3 public non-stationary two-class credit datasets with varying degrees of class-imbalance. We report that OGD-RBM improves accuracy by 2.5-3% over batch learning techniques while requiring at least 24%-70% fewer neurons and fewer training samples. This online generative training approach can be extended greedily to multiple layers for training Deep Belief Networks in non-stationary data mining applications without the need for a priori fixed architectures.

This Perspective provides examples of current and future applications of deep learning in pharmacogenomics, including: (1) identification of novel regulatory variants located in non-coding domains of the genome and their function as applied to pharmacoepigenomics; (2) patient stratification from medical records; and (3) the mechanistic prediction of drug response, targets, and their interactions. Deep learning encapsulates a family of machine learning algorithms that has transformed many important subfields of artificial intelligence (AI) over the last decade, and has demonstrated breakthrough performance improvements on a wide range of tasks in biomedicine. We anticipate that in the future, deep learning will be widely used to predict personalized drug response and optimize medication selection and dosing, using knowledge extracted from large and complex molecular, epidemiological, clinical, and demographic datasets.

Multilayer bootstrap network builds a gradually narrowed multilayer nonlinear network from bottom up for unsupervised nonlinear dimensionality reduction. Each layer of the network is a nonparametric density estimator. It consists of a group of k-centroids clusterings. Each clustering randomly selects data points with randomly selected features as its centroids, and learns a one-hot encoder by one-nearest-neighbor optimization. Geometrically, the nonparametric density estimator at each layer projects the input data space to a uniformly-distributed discrete feature space, where the similarity of two data points in the discrete feature space is measured by the number of the nearest centroids they share in common. The multilayer network gradually reduces the nonlinear variations of data from bottom up by building a vast number of hierarchical trees implicitly on the original data space. Theoretically, the estimation error caused by the nonparametric density estimator is proportional to the correlation between the clusterings, both of which are reduced by the randomization steps.

The explosion in workload complexity and the recent slow-down in Moore's law scaling call for new approaches towards efficient computing. Researchers are now beginning to use recent advances in machine learning in software optimizations, augmenting or replacing traditional heuristics and data structures. However, the space of machine learning for computer hardware architecture is only lightly explored. In this paper, we demonstrate the potential of deep learning to address the von Neumann bottleneck of memory performance. We focus on the critical problem of learning memory access patterns, with the goal of constructing accurate and efficient memory prefetchers. We relate contemporary prefetching strategies to n-gram models in natural language processing, and show how recurrent neural networks can serve as a drop-in replacement. On a suite of challenging benchmark datasets, we find that neural networks consistently demonstrate superior performance in terms of precision and recall. This work represents the first step towards practical neural-network based prefetching, and opens a wide range of exciting directions for machine learning in computer architecture research.

Learn how to use Google's Deep Learning Framework – TensorFlow with Python! Welcome to the Complete Guide to TensorFlow for Deep Learning with Python! This course will guide you through how to use Google's TensorFlow framework to create artificial neural networks for deep learning! This course aims to give you an easy to understand guide to the complexities of Google's TensorFlow framework in a way that is easy to understand. Other courses and tutorials have tended to stay away from pure tensorflow and instead use abstractions that give the user less control.