Toward Scalable Machine Learning and Data Mining: the Bioinformatics Case

In an effort to overcome the data deluge in computational biology and bioinformatics and to facilitate bioinformatics research in the era of big data, we identify some of the most influential algorithms that have been widely used in the bioinformatics community. These top data mining and machine learning algorithms cover classification, clustering, regression, graphical model-based learning, and dimensionality reduction. The goal of this study is to guide the focus of scalable computing experts in the endeavor of applying new storage and scalable computation designs to bioinformatics algorithms that merit their attention most, following the engineering maxim of "optimize the common case".

Fast Generation for Convolutional Autoregressive Models

Convolutional autoregressive models have recently demonstrated state-of-the-art performance on a number of generation tasks. While fast, parallel training methods have been crucial for their success, generation is typically implemented in a na\"{i}ve fashion where redundant computations are unnecessarily repeated. This results in slow generation, making such models infeasible for production environments. In this work, we describe a method to speed up generation in convolutional autoregressive models. The key idea is to cache hidden states to avoid redundant computation. We apply our fast generation method to the Wavenet and PixelCNN++ models and achieve up to $21\times$ and $183\times$ speedups respectively.

Reinforcement Learning through Asynchronous Advantage Actor-Critic on a GPU

We introduce a hybrid CPU/GPU version of the Asynchronous Advantage Actor-Critic (A3C) algorithm, currently the state-of-the-art method in reinforcement learning for various gaming tasks. We analyze its computational traits and concentrate on aspects critical to leveraging the GPU's computational power. We introduce a system of queues and a dynamic scheduling strategy, potentially helpful for other asynchronous algorithms as well. Our hybrid CPU/GPU version of A3C, based on TensorFlow, achieves a significant speed up compared to a CPU implementation; we make it publicly available to other researchers at https://github.com/NVlabs/GA3C .

NoiseOut: A Simple Way to Prune Neural Networks

Neural networks are usually over-parameterized with significant redundancy in the number of required neurons which results in unnecessary computation and memory usage at inference time. One common approach to address this issue is to prune these big networks by removing extra neurons and parameters while maintaining the accuracy. In this paper, we propose NoiseOut, a fully automated pruning algorithm based on the correlation between activations of neurons in the hidden layers. We prove that adding additional output neurons with entirely random targets results into a higher correlation between neurons which makes pruning by NoiseOut even more efficient. Finally, we test our method on various networks and datasets. These experiments exhibit high pruning rates while maintaining the accuracy of the original network.

Seq-NMS for Video Object Detection

Video object detection is challenging because objects that are easily detected in one frame may be difficult to detect in another frame within the same clip. Recently, there have been major advances for doing object detection in a single image. These methods typically contain three phases: (i) object proposal generation (ii) object classification and (iii) post-processing. We propose a modification of the post-processing phase that uses high-scoring object detections from nearby frames to boost scores of weaker detections within the same clip. We show that our method obtains superior results to state-of-the-art single image object detection techniques. Our method placed 3rd in the video object detection (VID) task of the ImageNet Large Scale Visual Recognition Challenge 2015 (ILSVRC2015).