DeepCCI: End-to-end Deep Learning for Chemical-Chemical Interaction Prediction

Chemical-chemical interaction (CCI) plays a key role in predicting candidate drugs, toxicity, therapeutic effects, and biological functions. In various types of chemical analyses, computational approaches are often required due to the amount of data that needs to be handled. The recent remarkable growth and outstanding performance of deep learning have attracted considerable research attention. However,even in state-of-the-art drug analysis methods, deep learning continues to be used only as a classifier, although deep learning is capable of not only simple classification but also automated feature extraction. In this paper, we propose the first end-to-end learning method for CCI, named DeepCCI. Hidden features are derived from a simplified molecular input line entry system (SMILES), which is a string notation representing the chemical structure, instead of learning from crafted features. To discover hidden representations for the SMILES strings, we use convolutional neural networks (CNNs). To guarantee the commutative property for homogeneous interaction, we apply model sharing and hidden representation merging techniques. The performance of DeepCCI was compared with a plain deep classifier and conventional machine learning methods. The proposed DeepCCI showed the best performance in all seven evaluation metrics used. In addition, the commutative property was experimentally validated. The automatically extracted features through end-to-end SMILES learning alleviates the significant efforts required for manual feature engineering. It is expected to improve prediction performance, in drug analyses.Comment: ACM-BCB 201

Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis, and beyond

A wide variety of large-scale data has been produced in bioinformatics. In response, the need for efficient handling of biomedical big data has been partly met by parallel computing. However, the time demand of many bioinformatics programs still remains high for large-scale practical uses due to factors that hinder acceleration by parallelization. Recently, new generations of storage devices have emerged, such as NAND flash-based solid-state drives (SSDs), and with the renewed interest in near-data processing, they are increasingly becoming acceleration methods that can accompany parallel processing. In certain cases, a simple drop-in replacement of hard disk drives (HDDs) by SSDs results in dramatic speedup. Despite the various advantages and continuous cost reduction of SSDs, there has been little review of SSD-based profiling and performance exploration of important but time-consuming bioinformatics programs. For an informative review, we perform in-depth profiling and analysis of 23 key bioinformatics programs using multiple types of devices. Based on the insight we obtain from this research, we further discuss issues related to design and optimize bioinformatics algorithms and pipelines to fully exploit SSDs. The programs we profile cover traditional and emerging areas of importance, such as alignment, assembly, mapping, expression analysis, variant calling, and metagenomics. We explain how acceleration by parallelization can be combined with SSDs for improved performance and also how using SSDs can expedite important bioinformatics pipelines, such as variant calling by the Genome Analysis Toolkit (GATK) and transcriptome analysis using RNA sequencing (RNA-seq). We hope that this review can provide useful directions and tips to accompany future bioinformatics algorithm design procedures that properly consider new generations of powerful storage devices.Comment: Availability: http://best.snu.ac.kr/pub/biossd; to be published in Briefings in Bioinformatic

Manifold Regularized Deep Neural Networks using Adversarial Examples

Learning meaningful representations using deep neural networks involves designing efficient training schemes and well-structured networks. Currently, the method of stochastic gradient descent that has a momentum with dropout is one of the most popular training protocols. Based on that, more advanced methods (i.e., Maxout and Batch Normalization) have been proposed in recent years, but most still suffer from performance degradation caused by small perturbations, also known as adversarial examples. To address this issue, we propose manifold regularized networks (MRnet) that utilize a novel training objective function that minimizes the difference between multi-layer embedding results of samples and those adversarial. Our experimental results demonstrated that MRnet is more resilient to adversarial examples and helps us to generalize representations on manifolds. Furthermore, combining MRnet and dropout allowed us to achieve competitive classification performances for three well-known benchmarks: MNIST, CIFAR-10, and SVHN.Comment: Figure 2, 5, 7, and several descriptions revise

Building a Neural Machine Translation System Using Only Synthetic Parallel Data

Recent works have shown that synthetic parallel data automatically generated by translation models can be effective for various neural machine translation (NMT) issues. In this study, we build NMT systems using only synthetic parallel data. As an efficient alternative to real parallel data, we also present a new type of synthetic parallel corpus. The proposed pseudo parallel data are distinct from previous works in that ground truth and synthetic examples are mixed on both sides of sentence pairs. Experiments on Czech-German and French-German translations demonstrate the efficacy of the proposed pseudo parallel corpus, which shows not only enhanced results for bidirectional translation tasks but also substantial improvement with the aid of a ground truth real parallel corpus

Homomorphic Parameter Compression for Distributed Deep Learning Training

Distributed training of deep neural networks has received significant research interest, and its major approaches include implementations on multiple GPUs and clusters. Parallelization can dramatically improve the efficiency of training deep and complicated models with large-scale data. A fundamental barrier against the speedup of DNN training, however, is the trade-off between computation and communication time. In other words, increasing the number of worker nodes decreases the time consumed in computation while simultaneously increasing communication overhead under constrained network bandwidth, especially in commodity hardware environments. To alleviate this trade-off, we suggest the idea of homomorphic parameter compression, which compresses parameters with the least expense and trains the DNN with the compressed representation. Although the specific method is yet to be discovered, we demonstrate that there is a high probability that the homomorphism can reduce the communication overhead, thanks to little compression and decompression times. We also provide theoretical speedup of homomorphic compression.Comment: 8 pages, 7 figure

HexaGAN: Generative Adversarial Nets for Real World Classification

Most deep learning classification studies assume clean data. However, when dealing with the real world data, we encounter three problems such as 1) missing data, 2) class imbalance, and 3) missing label problems. These problems undermine the performance of a classifier. Various preprocessing techniques have been proposed to mitigate one of these problems, but an algorithm that assumes and resolves all three problems together has not been proposed yet. In this paper, we propose HexaGAN, a generative adversarial network framework that shows promising classification performance for all three problems. We interpret the three problems from a single perspective to solve them jointly. To enable this, the framework consists of six components, which interact with each other. We also devise novel loss functions corresponding to the architecture. The designed loss functions allow us to achieve state-of-the-art imputation performance, with up to a 14% improvement, and to generate high-quality class-conditional data. We evaluate the classification performance (F1-score) of the proposed method with 20% missingness and confirm up to a 5% improvement in comparison with the performance of combinations of state-of-the-art methods.Comment: Accepted to ICML 201

Patch SVDD: Patch-level SVDD for Anomaly Detection and Segmentation

In this paper, we address the problem of image anomaly detection and segmentation. Anomaly detection involves making a binary decision as to whether an input image contains an anomaly, and anomaly segmentation aims to locate the anomaly on the pixel level. Support vector data description (SVDD) is a long-standing algorithm used for an anomaly detection, and we extend its deep learning variant to the patch-based method using self-supervised learning. This extension enables anomaly segmentation and improves detection performance. As a result, anomaly detection and segmentation performances measured in AUROC on MVTec AD dataset increased by 9.8% and 7.0%, respectively, compared to the previous state-of-the-art methods. Our results indicate the efficacy of the proposed method and its potential for industrial application. Detailed analysis of the proposed method offers insights regarding its behavior, and the code is available online

One-Shot Learning for Text-to-SQL Generation

Most deep learning approaches for text-to-SQL generation are limited to the WikiSQL dataset, which only supports very simple queries. Recently, template-based and sequence-to-sequence approaches were proposed to support complex queries, which contain join queries, nested queries, and other types. However, Finegan-Dollak et al. (2018) demonstrated that both the approaches lack the ability to generate SQL of unseen templates. In this paper, we propose a template-based one-shot learning model for the text-to-SQL generation so that the model can generate SQL of an untrained template based on a single example. First, we classify the SQL template using the Matching Network that is augmented by our novel architecture Candidate Search Network. Then, we fill the variable slots in the predicted template using the Pointer Network. We show that our model outperforms state-of-the-art approaches for various text-to-SQL datasets in two aspects: 1) the SQL generation accuracy for the trained templates, and 2) the adaptability to the unseen SQL templates based on a single example without any additional training

Learning Condensed and Aligned Features for Unsupervised Domain Adaptation Using Label Propagation

Unsupervised domain adaptation aiming to learn a specific task for one domain using another domain data has emerged to address the labeling issue in supervised learning, especially because it is difficult to obtain massive amounts of labeled data in practice. The existing methods have succeeded by reducing the difference between the embedded features of both domains, but the performance is still unsatisfactory compared to the supervised learning scheme. This is attributable to the embedded features that lay around each other but do not align perfectly and establish clearly separable clusters. We propose a novel domain adaptation method based on label propagation and cycle consistency to let the clusters of the features from the two domains overlap exactly and become clear for high accuracy. Specifically, we introduce cycle consistency to enforce the relationship between each cluster and exploit label propagation to achieve the association between the data from the perspective of the manifold structure instead of a one-to-one relation. Hence, we successfully formed aligned and discriminative clusters. We present the empirical results of our method for various domain adaptation scenarios and visualize the embedded features to prove that our method is critical for better domain adaptation

How Generative Adversarial Networks and Their Variants Work: An Overview

Generative Adversarial Networks (GAN) have received wide attention in the machine learning field for their potential to learn high-dimensional, complex real data distribution. Specifically, they do not rely on any assumptions about the distribution and can generate real-like samples from latent space in a simple manner. This powerful property leads GAN to be applied to various applications such as image synthesis, image attribute editing, image translation, domain adaptation and other academic fields. In this paper, we aim to discuss the details of GAN for those readers who are familiar with, but do not comprehend GAN deeply or who wish to view GAN from various perspectives. In addition, we explain how GAN operates and the fundamental meaning of various objective functions that have been suggested recently. We then focus on how the GAN can be combined with an autoencoder framework. Finally, we enumerate the GAN variants that are applied to various tasks and other fields for those who are interested in exploiting GAN for their research.Comment: 41 pages, 16 figures, Published in ACM Computing Surveys (CSUR