arXiv subjects

Sungroh Yoon

Publications and source records attributed to Sungroh Yoon.

At least 181 records · Page 10Linked to original sources

arXiv2019

AnomiGAN: Generative adversarial networks for anonymizing private medical data

Typical personal medical data contains sensitive information about individuals. Storing or sharing the personal medical data is thus often risky. For example, a short DNA sequence can provide information that can not only identify an individual, but also his or her relatives. Nonetheless, most countries and researchers agree on the necessity of collecting personal medical data. This stems from the fact that medical data, including genomic data, are an indispensable resource for further research and development regarding disease prevention and treatment. To prevent personal medical data from being misused, techniques to reliably preserve sensitive information should be developed for real world application. In this paper, we propose a framework called anonymized generative adversarial networks (AnomiGAN), to improve the maintenance of privacy of personal medical data, while also maintaining high prediction performance. We compared our method to state-of-the-art techniques and observed that our method preserves the same level of privacy as differential privacy (DP), but had better prediction results. We also observed that there is a trade-off between privacy and performance results depending on the degree of preservation of the original data. Here, we provide a mathematical overview of our proposed model and demonstrate its validation using UCI machine learning repository datasets in order to highlight its utility in practice. Experimentally, our approach delivers a better performance compared to that of the DP approach.

cs.CR↗

arXiv2018

NASCUP: Nucleic Acid Sequence Classification by Universal Probability

Motivated by the need for fast and accurate classification of unlabeled nucleotide sequences on a large scale, we developed NASCUP, a new classification method that captures statistical structures of nucleotide sequences by compact context-tree models and universal probability from information theory. NASCUP achieved BLAST-like classification accuracy consistently for several large-scale databases in orders-of-magnitude reduced runtime, and was applied to other bioinformatics tasks such as outlier detection and synthetic sequence generation.

q-bio.GN↗

arXiv2018

DNA Steganalysis Using Deep Recurrent Neural Networks

Recent advances in next-generation sequencing technologies have facilitated the use of deoxyribonucleic acid (DNA) as a novel covert channels in steganography. There are various methods that exist in other domains to detect hidden messages in conventional covert channels. However, they have not been applied to DNA steganography. The current most common detection approaches, namely frequency analysis-based methods, often overlook important signals when directly applied to DNA steganography because those methods depend on the distribution of the number of sequence characters. To address this limitation, we propose a general sequence learning-based DNA steganalysis framework. The proposed approach learns the intrinsic distribution of coding and non-coding sequences and detects hidden messages by exploiting distribution variations after hiding these messages. Using deep recurrent neural networks (RNNs), our framework identifies the distribution variations by using the classification score to predict whether a sequence is to be a coding or non-coding sequence. We compare our proposed method to various existing methods and biological sequence analysis methods implemented on top of our framework. According to our experimental results, our approach delivers a robust detection performance compared to other tools.

cs.LG↗

arXiv2018

Polyphonic Music Generation with Sequence Generative Adversarial Networks

We propose an application of sequence generative adversarial networks (SeqGAN), which are generative adversarial networks for discrete sequence generation, for creating polyphonic musical sequences. Instead of a monophonic melody generation suggested in the original work, we present an efficient representation of a polyphony MIDI file that simultaneously captures chords and melodies with dynamic timings. The proposed method condenses duration, octaves, and keys of both melodies and chords into a single word vector representation, and recurrent neural networks learn to predict distributions of sequences from the embedded musical word space. We experiment with the original method and the least squares method to the discriminator, which is known to stabilize the training of GANs. The network can create sequences that are musically coherent and shows an improved quantitative and qualitative measures. We also report that careful optimization of reinforcement learning signals of the model is crucial for general application of the model.

cs.SD↗

arXiv2018

Liver Lesion Detection from Weakly-labeled Multi-phase CT Volumes with a Grouped Single Shot MultiBox Detector

We present a focal liver lesion detection model leveraged by custom-designed multi-phase computed tomography (CT) volumes, which reflects real-world clinical lesion detection practice using a Single Shot MultiBox Detector (SSD). We show that grouped convolutions effectively harness richer information of the multi-phase data for the object detection model, while a naive application of SSD suffers from a generalization gap. We trained and evaluated the modified SSD model and recently proposed variants with our CT dataset of 64 subjects by five-fold cross validation. Our model achieved a 53.3% average precision score and ran in under three seconds per volume, outperforming the original model and state-of-the-art variants. Results show that the one-stage object detection model is a practical solution, which runs in near real-time and can learn an unbiased feature representation from a large-volume real-world detection dataset, which requires less tedious and time consuming construction of the weak phase-level bounding box labels.

cs.CV↗

arXiv2018

Robust Tumor Localization with Pyramid Grad-CAM

A meningioma is a type of brain tumor that requires tumor volume size follow ups in order to reach appropriate clinical decisions. A fully automated tool for meningioma detection is necessary for reliable and consistent tumor surveillance. There have been various studies concerning automated lesion detection. Studies on the application of convolutional neural network (CNN)-based methods, which have achieved a state-of-the-art level of performance in various computer vision tasks, have been carried out. However, the applicable diseases are limited, owing to a lack of strongly annotated data being present in medical image analysis. In order to resolve the above issue we propose pyramid gradient-based class activation mapping (PG-CAM) which is a novel method for tumor localization that can be trained in weakly supervised manner. PG-CAM uses a densely connected encoder-decoder-based feature pyramid network (DC-FPN) as a backbone structure, and extracts a multi-scale Grad-CAM that captures hierarchical features of a tumor. We tested our model using meningioma brain magnetic resonance (MR) data collected from the collaborating hospital. In our experiments, PG-CAM outperformed Grad-CAM by delivering a 23 percent higher localization accuracy for the validation set.

cs.CV↗

arXiv2018

Adversarial Training for Disease Prediction from Electronic Health Records with Missing Data

Electronic health records (EHRs) have contributed to the computerization of patient records and can thus be used not only for efficient and systematic medical services, but also for research on biomedical data science. However, there are many missing values in EHRs when provided in matrix form, which is an important issue in many biomedical EHR applications. In this paper, we propose a two-stage framework that includes missing data imputation and disease prediction to address the missing data problem in EHRs. We compared the disease prediction performance of generative adversarial networks (GANs) and conventional learning algorithms in combination with missing data prediction methods. As a result, we obtained a level of accuracy of 0.9777, sensitivity of 0.9521, specificity of 0.9925, area under the receiver operating characteristic curve (AUC-ROC) of 0.9889, and F-score of 0.9688 with a stacked autoencoder as the missing data prediction method and an auxiliary classifier GAN (AC-GAN) as the disease prediction method. The comparison results show that a combination of a stacked autoencoder and an AC-GAN significantly outperforms other existing approaches. Our results suggest that the proposed framework is more robust for disease prediction from EHRs with missing data.

cs.LG↗

arXiv2018

Domain Adaptation Using Adversarial Learning for Autonomous Navigation

Autonomous navigation has become an increasingly popular machine learning application. Recent advances in deep learning have also resulted in great improvements to autonomous navigation. However, prior outdoor autonomous navigation depends on various expensive sensors or large amounts of real labeled data which is difficult to acquire and sometimes erroneous. The objective of this study is to train an autonomous navigation model that uses a simulator (instead of real labeled data) and an inexpensive monocular camera. In order to exploit the simulator satisfactorily, our proposed method is based on domain adaptation with adversarial learning. Specifically, we propose our model with 1) a dilated residual block in the generator, 2) cycle loss, and 3) style loss to improve the adversarial learning performance for satisfactory domain adaptation. In addition, we perform a theoretical analysis that supports the justification of our proposed method. We present empirical results of navigation in outdoor courses with various intersections using a commercial radio controlled car. We observe that our proposed method allows us to learn a favorable navigation model by generating images with realistic textures. To the best of our knowledge, this is the first work to apply domain adaptation with adversarial learning to autonomous navigation in real outdoor environments. Our proposed method can also be applied to precise image generation or other robotic tasks.

cs.CV↗

arXiv2018

Deep Learning on Key Performance Indicators for Predictive Maintenance in SAP HANA

With a new era of cloud and big data, Database Management Systems (DBMSs) have become more crucial in numerous enterprise business applications in all the industries. Accordingly, the importance of their proactive and preventive maintenance has also increased. However, detecting problems by predefined rules or stochastic modeling has limitations, particularly when analyzing the data on high-dimensional Key Performance Indicators (KPIs) from a DBMS. In recent years, Deep Learning (DL) has opened new opportunities for this complex analysis. In this paper, we present two complementary DL approaches to detect anomalies in SAP HANA. A temporal learning approach is used to detect abnormal patterns based on unlabeled historical data, whereas a spatial learning approach is used to classify known anomalies based on labeled data. We implement a system in SAP HANA integrated with Google TensorFlow. The experimental results with real-world data confirm the effectiveness of the system and models.

cs.LG↗

arXiv2018

Extended Abstract: Mimicry Resilient Program Behavior Modeling with LSTM based Branch Models

In the software design, protecting a computer system from a plethora of software attacks or malware in the wild has been increasingly important. One branch of research to detect the existence of attacks or malware, there has been much work focused on modeling the runtime behavior of a program. Stemming from the seminal work of Forrest et al., one of the main tools to model program behavior is system call sequences. Unfortunately, however, since mimicry attacks were proposed, program behavior models based solely on system call sequences could no longer ensure the security of systems and require additional information that comes with its own drawbacks. In this paper, we report our preliminary findings in our research to build a mimicry resilient program behavior model that has lesser drawbacks. We employ branch sequences to harden our program behavior model against mimicry attacks while employing hardware features for efficient extraction of such branch information during program runtime. In order to handle the large scale of branch sequences, we also employ LSTM, the de facto standard in deep learning based sequence modeling and report our preliminary experiments on its interaction with program branch sequences.

cs.CR↗

arXiv2018

Reinforcement Learning based Recommender System using Biclustering Technique

A recommender system aims to recommend items that a user is interested in among many items. The need for the recommender system has been expanded by the information explosion. Various approaches have been suggested for providing meaningful recommendations to users. One of the proposed approaches is to consider a recommender system as a Markov decision process (MDP) problem and try to solve it using reinforcement learning (RL). However, existing RL-based methods have an obvious drawback. To solve an MDP in a recommender system, they encountered a problem with the large number of discrete actions that bring RL to a larger class of problems. In this paper, we propose a novel RL-based recommender system. We formulate a recommender system as a gridworld game by using a biclustering technique that can reduce the state and action space significantly. Using biclustering not only reduces space but also improves the recommendation quality effectively handling the cold-start problem. In addition, our approach can provide users with some explanation why the system recommends certain items. Lastly, we examine the proposed algorithm on a real-world dataset and achieve a better performance than the widely used recommendation algorithm.

cs.IR↗

arXiv2017

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.

cs.LG↗

arXiv2017

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.

cs.DC↗

arXiv2017

Quantized Memory-Augmented Neural Networks

Memory-augmented neural networks (MANNs) refer to a class of neural network models equipped with external memory (such as neural Turing machines and memory networks). These neural networks outperform conventional recurrent neural networks (RNNs) in terms of learning long-term dependency, allowing them to solve intriguing AI tasks that would otherwise be hard to address. This paper concerns the problem of quantizing MANNs. Quantization is known to be effective when we deploy deep models on embedded systems with limited resources. Furthermore, quantization can substantially reduce the energy consumption of the inference procedure. These benefits justify recent developments of quantized multi layer perceptrons, convolutional networks, and RNNs. However, no prior work has reported the successful quantization of MANNs. The in-depth analysis presented here reveals various challenges that do not appear in the quantization of the other networks. Without addressing them properly, quantized MANNs would normally suffer from excessive quantization error which leads to degraded performance. In this paper, we identify memory addressing (specifically, content-based addressing) as the main reason for the performance degradation and propose a robust quantization method for MANNs to address the challenge. In our experiments, we achieved a computation-energy gain of 22x with 8-bit fixed-point and binary quantization compared to the floating-point implementation. Measured on the bAbI dataset, the resulting model, named the quantized MANN (Q-MANN), improved the error rate by 46% and 30% with 8-bit fixed-point and binary quantization, respectively, compared to the MANN quantized using conventional techniques.

cs.LG↗

arXiv2017

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.

cs.CL↗

arXiv2017

DUDE-Seq: Fast, Flexible, and Robust Denoising for Targeted Amplicon Sequencing

We consider the correction of errors from nucleotide sequences produced by next-generation targeted amplicon sequencing. The next-generation sequencing (NGS) platforms can provide a great deal of sequencing data thanks to their high throughput, but the associated error rates often tend to be high. Denoising in high-throughput sequencing has thus become a crucial process for boosting the reliability of downstream analyses. Our methodology, named DUDE-Seq, is derived from a general setting of reconstructing finite-valued source data corrupted by a discrete memoryless channel and effectively corrects substitution and homopolymer indel errors, the two major types of sequencing errors in most high-throughput targeted amplicon sequencing platforms. Our experimental studies with real and simulated datasets suggest that the proposed DUDE-Seq not only outperforms existing alternatives in terms of error-correction capability and time efficiency, but also boosts the reliability of downstream analyses. Further, the flexibility of DUDE-Seq enables its robust application to different sequencing platforms and analysis pipelines by simple updates of the noise model. DUDE-Seq is available at http://data.snu.ac.kr/pub/dude-seq.

q-bio.GN↗

arXiv2017

Energy-Based Sequence GANs for Recommendation and Their Connection to Imitation Learning

Recommender systems aim to find an accurate and efficient mapping from historic data of user-preferred items to a new item that is to be liked by a user. Towards this goal, energy-based sequence generative adversarial nets (EB-SeqGANs) are adopted for recommendation by learning a generative model for the time series of user-preferred items. By recasting the energy function as the feature function, the proposed EB-SeqGANs is interpreted as an instance of maximum-entropy imitation learning.

cs.IR↗

arXiv2017

Near-Data Processing for Differentiable Machine Learning Models

Near-data processing (NDP) refers to augmenting memory or storage with processing power. Despite its potential for acceleration computing and reducing power requirements, only limited progress has been made in popularizing NDP for various reasons. Recently, two major changes have occurred that have ignited renewed interest and caused a resurgence of NDP. The first is the success of machine learning (ML), which often demands a great deal of computation for training, requiring frequent transfers of big data. The second is the popularity of NAND flash-based solid-state drives (SSDs) containing multicore processors that can accommodate extra computation for data processing. In this paper, we evaluate the potential of NDP for ML using a new SSD platform that allows us to simulate instorage processing (ISP) of ML workloads. Our platform (named ISP-ML) is a full-fledged simulator of a realistic multi-channel SSD that can execute various ML algorithms using data stored in the SSD. To conduct a thorough performance analysis and an in-depth comparison with alternative techniques, we focus on a specific algorithm: stochastic gradient descent (SGD), which is the de facto standard for training differentiable models such as logistic regression and neural networks. We implement and compare three SGD variants (synchronous, Downpour, and elastic averaging) using ISP-ML, exploiting the multiple NAND channels to parallelize SGD. In addition, we compare the performance of ISP and that of conventional in-host processing, revealing the advantages of ISP. Based on the advantages and limitations identified through our experiments, we further discuss directions for future research on ISP for accelerating ML.

cs.AR↗