Publications

Selected Papers (2014~)

2018

arXiv

Security and Privacy Issues in Deep Learning

Ho Bae, Jaehee Jang, Dahuin Jung, Hyemi Jang, Heonseok Ha, Sungroh Yoon, arXiv:1807.11655 [cs.CR], July 2018.
paper  link

Robust Tumor Localization with Pyramid Grad-CAM

Sungmin Lee, Jangho Lee, Jungbeom Lee, Chul-Kee Park, Sungroh Yoon, arXiv:1805.11393 [cs.CV], May 2018.
paper  link

Intelligent Knowledge Tracing: More Like a Real Learning Process of a Student

Heonseok Ha, Yongjun Hong, Uiwon Hwang, Sungroh Yoon, arXiv:1805.10768 [cs.AI], May 2018.
paper  link

Streaming MANN: A Streaming-Based Inference for Energy-Efficient Memory-Augmented Neural Networks

Seongsik Park, Jaehee Jang, Seijoon Kim, Sungroh Yoon, arXiv:1805.07978 [cs.LG], May 2018.
paper  link

MSnet: Mutual Suppression Network for Disentangled Video Representations

Jungbeom Lee, Jangho Lee, Sungmin Lee, Sungroh Yoon, arXiv:1804.04810 [cs.CV], April 2018.
paper  link

Conference

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

Sang-gil Lee, Jae Seok Bae, Hyunjae Kim, Jung Hoon Kim, Sungroh Yoon, in Proceedings of the 21st International Conference on Medical Image Computing & Computer Assisted Intervention (MICCAI) , Granada, Spain, September 2018.
preprint  link  arXiv

XGBoost-Based Instantaneous Drowsiness Detection Framework Using Multitaper Spectral Information of Electroencephalography

Hyun-Soo Choi, Siwon Kim, Jung Eun Oh, Jee Eun Yoon, Jung Ah Park, Chang-Ho Yun, Sungroh Yoon, in Proceedings of the 9th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), Washington DC, USA, August 2018.
paper  link

Mimicry Resilient Program Behavior Modeling with LSTM based Branch Models

Hayoon Yi, Gyuwan Kim, Jangho Lee, Sunwoo Ahn, Younghan Lee, Sungroh Yoon, Yunheung Paek, Deep Learning and Security (DLS) Workshop, IEEE Symposium on Security and Privacy (S&P), San Francisco, USA, May 2018.
preprint  link

Quantized Memory-Augmented Neural Networks

Seongsik Park, Seijoon Kim, Seil Lee, Ho Bae, and Sungroh Yoon, in Proceedings of the Thirty-Second AAAI Conference on Artificial Intelligence (AAAI), New Orleans, USA, February 2018.
paper  suppl  link  arxiv

Reinforcement Learning based Recommender System using Biclustering Technique

Sungwoon Choi, Heonseok Ha, Uiwon Hwang, Chanju Kim, Jung-Woo Ha, Sungroh Yoon, in Proceedings of WSDM Workshop on Multi-dimensional Information Fusion for User Modeling and Personalization (IFUP), Los Angeles, USA, February 2018.
preprint  link arxiv

Customization of IBM Intu’s Voice by Connecting Text-to-Speech Services and a Voice Conversion Network

Jongyoon Song, Hyunjae Kim, Jaekoo Lee, Euishin Choi, Minseok, Kim, Sungroh Yoon, in Proceedings of the Hawaii International Conference on System Sciences (HICSS), pp. 830-839, Waikoloa Village, USA, January 2018.
paper  link

Journal

Deep Learning Based Low-cost High-accuracy Diagnostic Framework for Dementia Using Comprehensive Neuropsychological Assessment Profiles

Hyun-Soo Choi, Jin Yeong Choe, Hanjoo Kim, Ji Won Han, Yeon Kyung Chi, Kayoung Kim, Jongwoo Hong, Taehyun Kim, Tae Hui Kim, Sungroh Yoon, Ki Woong Kim, BMC Geriatrics, in press.
preprint  link

CloudSocket: Fine-Grained Power Sensing System for Datacenters

Seil Lee, Hanjoo Kim, Seongsik Park, Seijoon Kim, Hyeokjun Choe, Sungroh Yoon, IEEE Access, in press.
preprint  link

End-to-end Representation Learning for Chemical-Chemical Interaction Prediction

Sunyoung Kwon and Sungroh Yoon, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
preprint  link

Deep learning improves prediction of CRISPR–Cpf1 guide RNA activity

Hui Kwon Kim, Seonwoo Min, Myungjae Song, Soobin Jung, Jae Woo Choi, Younggwang Kim, Sangeun Lee, Sungroh Yoon, Hyongbum Kim, Nature Biotechnology, vol. 36, no. 3, pp. 239-241, March 2018.
paper  link  code  suppl

hc-OTU: A Fast and Accurate Method for Clustering Operational Taxonomic Units based on Homopolymer Compaction

Seunghyun Park, Hyun-Soo Choi, Byunghan Lee, Jongsik Chun, Joong-Ho Won, and Sungroh Yoon, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 15, no. 2, pp. 441-451, March/April 2018.
paper  link

TensorLightning: A Traffic-efficient Distributed Deep Learning on Commodity Spark Clusters

Seil Lee, Hanjoo Kim, Jaehong Park, Jaehee Jang, Chang-Sung Jeong, Sungroh Yoon, IEEE Access, vol. 6, no. 1, pp. 27671-27680, May 2018.
paper  link

LncRNAnet: Long Noncoding RNA Identification using Deep Learning

Junghwan Baek, Byunghan Lee, Sunyoung Kwon, Sungroh Yoon, Bioinformatics, in press.
preprint   link

MUGAN: Multi-GPU Accelerated AmpliconNoise Server for Rapid Microbial Diversity Assessment

Byunghan Lee, Hyeyoung Min, and Sungroh Yoon, Bioinformatics, in press.
preprint   link

HiComet: A High-Throughput Comet Analysis Tool for Large-Scale DNA Damage Assessment

Taehoon Lee, Sungmin Lee, Woo Young Sim, Yu Mi Jung, Sunmi Han, Joong-Ho Won, Hyeyoung Min, and Sungroh Yoon, BMC Bioinformatics, vol. 19(Suppl 1), no. 44, pp. 49-61, February 2018.
paper  link

2017

arXiv

Autonomous UAV Navigation with Domain Adaptation

Jaeyoon Yoo, Yongjun Hong, Sungroh Yoon, arXiv:1712.03742 [cs.CV], December 2017.
paper  link

Homomorphic Parameter Compression for Distributed Deep Learning Training

Jaehee Jang, Byungook Na, Sungroh Yoon, arXiv:1711.10123 [cs.DC], November 2017.
paper  link

How Generative Adversarial Nets and its variants Work: An Overview of GAN

Yongjun Hong, Uiwon Hwang, Jaeyoon Yoo, Sungroh Yoon, arXiv:1711.05914 [cs.LG], November 2017.
paper  link

Disease Prediction from Electronic Health Records Using Generative Adversarial Networks

Uiwon Hwang, Sungwoon Choi, Sungroh Yoon, arXiv:1711.04126 [cs.LG], November 2017.
paper  link

Polyphonic Music Generation with Sequence Generative Adversarial Networks

Sang-gil Lee, Uiwon Hwang, Seonwoo Min, Sungroh Yoon, arXiv:1710.11418 [cs.SD], October 2017.
paper  link

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

Jaeyoon Yoo, Heonseok Ha, Jihun Yi, Jongha Ryu, Chanju Kim, Jung-Woo Ha, Young-Han Kim, Sungroh Yoon, arXiv:1706.09200 [cs.IR], June 2017.
paper  link

Building a Neural Machine Translation System Using Only Synthetic Parallel Data

Jaehong Park, Byunggook Na, and Sungroh Yoon, arXiv:1704.00253 [cs.CL], April 2017.
paper  link

DNA Steganalysis Using Deep Recurrent Neural Networks

Ho Bae, Byunghan Lee, Sunyoung Kwon and Sungroh Yoon, arXiv:1704.08443 [cs.LG], April 2017.
paper  link

Conference

Deep Recurrent Neural Network-Based Identification of Precursor microRNAs

Seunghyun Park, Seonwoo Min, Hyun-Soo Choi, and Sungroh Yoon, in Proceedings of the Annual Conference on Neural Information Processing Systems (NIPS), Long Beach, USA, December 2017.
paper  suppl  link

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

Sunyoung Kwon and Sungroh Yoon, in Proceedings of the 8th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), Boston, USA, August 2017.
preprint  link  arXiv

Near-Data Processing for Differentiable Machine Learning Models

Hyeokjun Choe, Seil Lee, Hyunha Nam, Seongsik Park, Seijoon Kim, Eui-Young Chung, and Sungroh Yoon, in Proceedings of the 33rd International Conference on Massive Storage Systems and Technology (MSST), Santa Clara, USA, May 2017.
paper  link

Transfer Learning for Deep Learning on Graph-Structured Data

Jaekoo Lee, Hyunjae Kim, Jongsun Lee, and Sungroh Yoon, in Proceedings of the Thirty-First AAAI Conference on Artificial Intelligence (AAAI), San Francisco, USA, February 2017.
paper  link

Training IBM Watson using Automatically Generated Question-Answer Pairs

Jangho Lee, Gyuwan Kim, Jaeyoon Yoo, Changwoo Jung, Minseok Kim, and Sungroh Yoon, in Proceedings of the Hawaii International Conference on System Sciences (HICSS), pp. 1683-1691, Waikoloa Village, USA, January 2017.
paper  link  arXiv

Journal

A genetic variant in SLC28A3, rs56350726, is associated with progression to castration-resistant prostate cancer in a Korean population with metastatic prostate cancer

Jung Ku Jo, Jong Jin Oh, Yong Tae Kim, Hong Sang Moon, Hong Yong Choi, Seunghyun Park, Jin-Nyoung Ho, Sungroh Yoon, Hae Young Park, and Seok-Soo Byun, Oncotarget, vol. 8, no. 57, pp. 96893-96902, November 2017.
paper  link

Large-Scale Structured Sparsity via Parallel Fused Lasso on Multiple GPUs

Taehoon Lee, Joong-Ho Won, Johan Lim, and Sungroh Yoon, Journal of Computational and Graphical Statistics, vol. 26, no. 4, pp. 851-864, October 2017.
paper  link

Large-Scale Machine Learning of Media Outlets for Understanding Public Reactions to Nation-Wide Viral Infection Outbreaks

Sungwoon Choi, Jangho Lee, Min-Gyu Kang, Hyeyoung Min, Yoon-Seok Chang, and Sungroh Yoon, Methods, vol. 129, pp. 50-59, October 2017.
paper  link

Machine Learning-Based Identification of Endogenous Cellular microRNA Sponges against Viral microRNAs

Soowon Kang, Seunghyun Park, Sungroh Yoon, and Hyeyoung Min, Methods, vol. 129, pp. 33-40, October 2017.
paper  link

Deep Learning in Bioinformatics

Seonwoo Min, Byunghan Lee, and Sungroh Yoon, Briefings in Bioinformatics, vol. 18, no. 5, pp. 851-869, September 2017.
paper  link  arXiv

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

Byunghan Lee, Taesup Moon, Sungroh Yoon, and Tsachy Weissman, PLOS ONE, 12(7):e0181463, July 2017.
paper  link  arXiv  suppl

Prediction of pathologic femoral fractures in patients with lung cancer using machine learning algorithms: Comparison of computed tomography-based radiological features with clinical features versus without clinical features

Eunsun Oh, Sung Wook Seo, Young Cheol Yoon, Dong Wook Kim, Sunyoung Kwon, Sungroh Yoon, Journal of Orthopaedic Surgery, vol. 25, no. 2, pp. 1-7, June 2017.
paper  link

Genetic risk score to predict biochemical recurrence after radical prostatectomy in prostate cancer: prospective cohort study

Jong Jin Oh, Seunghyun Park, Sang Eun Lee, Sung Kyu Hong, Sangchul Lee, Tae Jin Kim, In Jae Lee, Jin-Nyoung Ho, Sungroh Yoon, and Seok-Soo Byun, Oncotarget, vol. 8, no. 44, pp. 75979-75988, May 2017.
paper  link

An Effective Pre-Store/Pre-Load Method Exploiting Intra-Request Idle Time of NAND Flash-Based Storage Devices

Jin-Young Kim, Tae-Hee You, Hyeokjun Seo, Sungroh Yoon, Jean-Luc Gaudiot, Eui-Young Chung, Microprocessors and Microsystems, vol. 50, pp. 222-236, May 2017.
paper  link

NC-link: A New Linkage Method for Efficient Hierarchical Clustering of Large-Scale Data

Yongkweon Jeon, Jaeyoon Yoo, Jongsun Lee, and Sungroh Yoon, IEEE Access, vol. 5, no. 1, pp. 5594-5608, April 2017
paper  link

Exome-Based Genome-Wide Association Study and Risk Assessment using Genetic Risk Score to Prostate Cancer in the Korean Population

Jong Jin Oh, Soo Ji Lee, Joo-Yeon Hwang, Dokyoon Kim, Sang Eun Lee, Sung Kyu Hong, Jin-Nyoung Ho, Sungroh Yoon, Joohon Sung, Wun-Jae Kim, and Seok-Soo Byun, Oncotarget, vol. 8, no. 27, pp. 43934-43943, March 2017.
paper  link

Development and External Validation of the Korean Prostate Cancer Risk Calculator for High-grade Prostate Cancer: Comparison with Two Western Risk Calculators in an Asian Cohort

Jae Young Park, Sungroh Yoon, Man Sik Park, Hoon Choi, Jae Hyun Bae, Du Geon Moon, Sung Kyu Hong, Sang Eun Lee, Chanwang Park, and Seok-Soo Byun, PLOS ONE, 12(1): e0168917, January 2017.
paper  link

2016

arXiv

LSTM-Based System-Call Language Modeling and Robust Ensemble Method for Designing Host-Based Intrusion Detection Systems

Gyuwan Kim, Hayoon Yi, Jangho Lee, Yunheung Paek, and Sungroh Yoon, arXiv:1611.01726 [cs.CR], November 2016.
paper  link

deepMiRGene: Deep Neural Network based Precursor microRNA Prediction

Seunghyun Park, Seonwoo Min, Hyun-Soo Choi, and Sungroh Yoon, arXiv:1605.00017 [cs.LG], May 2016.
paper  link

DeepSpark: Spark-Based Deep Learning Supporting Asynchronous Updates and Caffe Compatibility

Hanjoo Kim, Jaehong Park, Jaehee Jang, and Sungroh Yoon, arXiv:1602.08191v2 [cs.LG], Februaray 2016.
paper  link  code

Conference

Neural Universal Discrete Denoiser

Taesup Moon, Seonwoo Min, Byunghan Lee, and Sungroh Yoon,  in Proceedings of the Thirtieth Annual Conference on Neural Information Processing Systems (NIPS), Barcelona, Spain, December 2016.
preprint  suppl  link

An Efficient Method to Boosting Performance of Spiking Neural Network Training

Seongsik Park, Sang-gil Lee, Hyunha Nam, and Sungroh Yoon,  in the Thirtieth Annual Conference on Neural Information Processing Systems (NIPS) Workshop on Computing with Spikes, Barcelona, Spain, December 2016.
paper  link  arXiv

CloudSocket: Smart Grid Platform for Datacenters

Seil Lee, Hanjoo Kim, Seongsik Park, Seijoon Kim, Hyeokjun Choe, Chang-Sung Jeong, and Sungroh Yoon,  in Proceedings of the 34th IEEE International Conference on Computer Design (ICCD), pp. 436-439, Phoenix, USA, October 2016.
paper  link

Deep Learning for Bioinformatics and Health Informatics

Sungroh Yoon, tutorial given at the 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), Seattle, USA, October 2016.
slides  slides (domestic server)  link

deepTarget: End-to-end Learning Framework for microRNA Target Prediction using Deep Recurrent Neural Networks

Byunghan Lee, Junghwan Baek, Seunghyun Park, and Sungroh Yoon,  in Proceedings of the 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), pp. 434-442, Seattle, USA, October 2016.
paper  code

Collaborative Analytics for Data Silos

Jinkyu Kim, Heonseok Ha, Byung-Gon Chun, Sungroh Yoon, and Sang K Cha, in Proceedings of IEEE International Conference on Data Engineering (ICDE), pp. 743-754, Helsinki, Finland, May 2016.
paper  link

Mining Internet Media for Monitoring Changes of Public Emotions about Infectious Diseases

Sungwoon Choi, Jangho Lee, Sangheon Pack, Yoon-Seok Chang, and Sungroh Yoon, in Proceedings of  ICDE Workshop on Health Data Management and Mining, Helsinki, Finland, May 2016.
link

NASCUP: Nucleic Acid Sequence Classification by Universal Probability

Sunyoung Kwon, Gyuwan Kim, Byunghan Lee, Sungroh Yoon, and Young-Han Kim, in 2016 RECOMB-Seq (Massively Parallel Sequencing), Los Angeles, USA, April 2016.
paper  suppl  arXiv

Journal

Exploiting Compression-Induced Internal Fragmentation for Power-Off Recovery in SSD

Dongwook Kim, Youjip Won, Jaehyuk Cha, Sungroh Yoon, Jongmoo Choi, and Sooyong Kang, IEEE Transactions on Computers, vol. 65, no. 6, pp. 1720-1733, July 2016.
paper  link

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

Sungmin Lee, Hyeyoung Min, and Sungroh Yoon, Briefings in Bioinformatics, vol. 17, no. 4, pp. 713-727, July 2016.
paper  link  suppl

Regularization and Kernelization of the Maximin Correlation Approach

Taehoon Lee, Taesup Moon, Seung Jean Kim, and Sungroh Yoon, IEEE Access, vol. 4, pp. 1385-1392, April 2016.
paper  link  code  arXiv

Biometric Authentication Using Noisy Electrocardiograms Acquired by Mobile Sensors

Hyun-Soo Choi, Byunghan Lee, and Sungroh Yoon, IEEE Access, vol. 4, pp. 1266-1273, March 2016.
paper  link

NAND Flash Memory with Multiple Page Sizes for High Performance Storage Devices

Jin-Young Kim, Sang-Hoon Park, Hyeokjun Seo, Ki-Whan Song, Sungroh Yoon, and Eui-Young Chung, IEEE Transactions on Very Large Scale Integration (VLSI) Systems, vol. 24, no.2, pp. 764-768, February 2016.
paper  link

2015

arXiv

Manifold Regularized Deep Neural Networks using Adversarial Examples

Taehoon Lee, Minsuk Choi, and Sungroh Yoon, arXiv:1511.06381 [cs.LG], November 2015.
paper  link

Conference

DNA-Level Splice Junction Prediction using Deep Recurrent Neural Networks

Byunghan Lee, Taehoon Lee, Byunggook Na, and Sungroh Yoon, in NIPS Workshop on Machine Learning in Computational Biology/Systems Biology, Montreal, Canada, December 2015.
paper  link

Distributed Ensemble Learning for Analyzing Nationwide Health-Insurance Databases

Heonseok Ha, Jinkyu Kim, Jaehong Park and Sungroh Yoon, in NIPS Workshop on Machine Learning in Machine Learning for Healthcare, Montreal, Canada, December 2015.
link

Measuring Large-Scale Dynamic Graph Similarity by RICom: RWR with Intergraph Compression

Jaekoo Lee, Gunn Kim, and Sungroh Yoon, in Proceedings of IEEE International Conference on Data Mining (ICDM), pp. 829-834, Atlantic City, New Jersey, USA, November 2015.
paper  link

Big/Little Deep Neural Network for Ultra Low-Power Inference

Eunhyeok Park, Dongyoung Kim, Soobeom Kim, Sungroh Yoon, Gunhee Kim, and Sungjoo Yoo, in Proceedings of International Conference on Hardware/Software Codesign and System Synthesis (CODES+ISSS), pp. 124-132, Amsterdam, The Netherlands, October 2015.
paper  link

FingerNet: Deep Learning-Based Robust Finger Joint Detection from Radiographs

Sungmin Lee, Minsuk Choi, Hyun-Soo Choi, and Sungroh Yoon, in Proceedings of IEEE Biomedical Circuits and Systems Conference (BioCAS), pp. 619-622, Atlanta, Georgia, USA, October 2015.
paper  link

Wearable and Wireless Measurement System for Evaluating Penile Tumescence

Sungwoon Choi, Seijoon Kim, Jae Young Park, and Sungroh Yoon, in Proceedings of IEEE Biomedical Circuits and Systems Conference (BioCAS), pp. 37-40, Atlanta, Georgia, USA, October 2015.
paper  link

Computational Prediction of Competitive Endogenous RNA

Seunghyun Park, Soowon Kang, Hyeyoung Min, and Sungroh Yoon, in Proceedings of IEEE Biomedical Circuits and Systems Conference (BioCAS), pp. 382-385, Atlanta, Georgia, USA, October 2015.
paper  link

Boosted Categorical Restricted Boltzmann Machine for Computational Prediction of Splice Junctions

Taehoon Lee and Sungroh Yoon, in Proceedings of International Conference on Machine Learning (ICML), Lille, France, July 2015.
paper  link

Execution Time Modeling for Heterogeneous Computing System

Hyeokjun Seo, Eui-Young Chung, and Sungroh Yoon,  in Proceedings of the 30th International Technical Conference on Circuits/Systems, Computers and Communications, Seoul, Korea, June 2015.

Journal

Automated band annotation for RNA structure probing experiments with numerous capillary electrophoresis profiles

Seungmyung Lee, Hanjoo Kim, Siqi Tan, Taehoon Lee, Sungroh Yoon, and Rhiju Das, Bioinformatics, vol. 31, no. 17, pp. 2808-2815, September 2015.
paper  link  suppl

Multi-threaded Hierarchical Clustering by Parallel Nearest-Neighbor Chaining

Yongkweon Jeon and Sungroh Yoon, IEEE Transactions on Parallel and Distributed Systems, vo. 26, no. 9, pp. 2534-2548, September 2015.
paper  link  suppl

Genome-wide detection of allelic genetic variation to predict biochemical recurrence after radical prostatectomy among prostate cancer patients using an exome SNP chip

Jong Jin Oh, Seunghyun Park, Sang Eun Lee, Sung Kyu Hong, Sangchul Lee, Hak Min Lee, Jung Keun Lee, Jin-Nyoung Ho, Sungroh Yoon, and Seok-Soo Byun, Journal of Cancer Research and Clinical Oncology, vol. 141, no. 8, pp. 1493-1501, August 2015.
paper  link

High-dimensional Fused Lasso Regression using Majorization-Minimization and Parallel Processing

Donghyeon Yu, Joong-Ho Won, Taehoon Lee, Johan Lim, and Sungroh Yoon, Journal of Computational and Graphical Statistics, vol. 24, no. 1, pp. 121-153, March 2015.
paper  link

Design Trade-Offs of SSDs: from Energy Consumption’s Perspective

Seokhei Cho, Changhyun Park, Youjip Won, Sooyong Kang, Jaehyuk Cha, Sungroh Yoon, and Jongmoo Choi, ACM Transactions on Storage, vol. 11, no. 2, article 8, March 2015.
paper  link

Google unveils a glimpse of allergic rhinitis in the real world

Min-Gyu Kang, Woo-Jung Song, Sungwoon Choi, Hanjoo Kim, Heonseok Ha, Sae-Hoon Kim, Sang-Heon Cho, Kyung-Up Min, Sungroh Yoon, and Yoon-Seok Chang, Allergy, vol. 70, no. 1, pp. 124-128, January 2015.
paper  link

2014

Conference

Analytical Model of SSD Parallelism

Jinsoo Yoo, Youjip Won, Sooyong Kang, Jongmoo Choi, Sungroh Yoon, and Jaehyuk Cha, in Proceedings of 4th International Conference on Simulation and Modeling Methodologies, Technologies, and Applications (SIMULTECH 2014) , Vienna, Austria, August 2014.

CASPER: Context-Aware Scheme for Paired-End Read from High-Throughput Short-Read Amplicon Sequencing

Sunyoung Kwon, Byunghan Lee, and Sungroh Yoon, in Proceedings of 2014 RECOMB-Seq (Massively Parallel Sequencing) , Pittsburgh, USA, March 2014. [full paper published in BMC Bioinformatics]

Ensemble Learning for Robust Prediction of microRNA-mRNA Interactions

Seunghak Yu, Juho Kim, Hyeyoung Min, and Sungroh Yoon, in Proceedings of the 2014 International Conference on Big Data and Smart Computing, Bangkok, Thailand, January 2014.

Ensemble Algorithms for DNA Motif Finding

Juho Kim, Seunghak Yu, and Sungroh Yoon, in Proceedings of the 2014 International Conference on Electronics, Information and Communication, Kota Kinabalu, Malaysia, January 2014.

Journal

IO Workload Characterization Revisited: A Data-Mining Approach

Bumjoon Seo, Sooyong Kang, Jongmoo Choi, Jaehyuk Cha, Youjip Won, and Sungroh Yoon, IEEE Transactions on Computers, vol. 63, no. 12, pp. 3026-3038, December 2014.
paper  link

Ensemble learning can significantly improve human microRNA target prediction

Seunghak Yu, Juho Kim, Hyeyoung Min, and Sungroh Yoon, Methods, vol. 69, no. 3, pp. 220-229, October 2014.
paper  link

CASPER: Context-Aware Scheme for Paired-End Read from High-Throughput Short-Read Amplicon Sequencing

Sunyoung Kwon, Byunghan Lee, and Sungroh Yoon, BMC Bioinformatics , vol. 15, no. suppl 9, p. S10, September 2014.
paper  link

The Use of Exome Genotyping to Predict Pathological Gleason Score Upgrade after Radical Prostatectomy in Low-Risk Prostate Cancer Patients

Jong Jin Oh, Seunghyun Park, Sang Eun Lee, Sung Kyu Hong, Sangchul Lee, Gheeyoung Choe, Sungroh Yoon, and Seok-soo Byun, PLOS ONE, vol. 9, no. 8, e104146, August 2014.
paper  link

Macro and Small over Micro: Macromolecules and Small Molecules that Regulate microRNAs

Soowon Kang, Kyungtaek Im, Jihae Baek, Sungroh Yoon, and Hyeyoung Min, ChemBioChem, vol. 15, no. 8, pp. 1071-1078, May 2014.
paper  link

Standardization of RNA chemical mapping experiments

Wipapat Kladwang, Thomas H. Mann, Alex Becka, Siqi Tian, Hanjoo Kim, Sungroh Yoon, and Rhiju Das, Biochemistry, vol. 53, no. 19, pp. 3063-3065, April 2014.
paper  link

Design of a Bitmap-based QoS-aware Memory Controller for a Packet Memory

Seunghak Yu, Sungroh Yoon, Eui-Young Chung, and Hyuk-Jun Lee, Electronics Express, vol. 11, no. 5, pp. 1-12, March 2014.
paper  link

RNA Design Rules from a Massive Open Laboratory

Jeehyung Lee, Wipapat Kladwang, Minjae Lee, Daniel Cantu, Martin Azizyan, Hanjoo Kim, Alex Limpaecher, Snehal Gaikwad, Sungroh Yoon, Adrien Treuille, and Rhiju Das, Proceedings of the National Academy of Sciences of the United States of America (PNAS), vol. 111, no. 6, pp. 2122-2127, February 2014.
paper  link

Selected Papers (2004~2013)

2013

Conference

In-Depth Analysis of Interrelation between Quality Scores and Real Errors in Illumina Reads

Sunyoung Kwon, Seunghyun Park, Byunghan Lee, and Sungroh Yoon, in Proceedings of IEEE 35th Annual International Conference on Engineering in Medicine and Biology, Osaka, Japan, July 2013.
paper  link

Robust Classification of DNA Damage Patterns in Single Cell Gel Electrophoresis

Taehoon Lee, Sungmin Lee, Woo Young Sim, Yu Mi Jung, Sunmi Han, Chanil CHung, Jay Junkeun Chang, Hyeyoung Min, and Sungroh Yoon, in Proceedings of IEEE 35th Annual International Conference on Engineering in Medicine and Biology, Osaka, Japan, July 2013.

Graph-Based Binning Method for Clustering 16s rRNA Sequences into OTUs

Hyun-Soo Choi, Seunghyun Park, Chulwoo Kim, and Sungroh Yoon, in Proceedings of the 28th International Technical Conference on Circuits/Systems, Computers and Communications, Yeosu, Korea, July 2013.

Tree-Based Comparison and Classification of RNA Secondary Structure

Hanjoo Kim, Sungwoon Choi, Chulwoo Kim, and Sungroh Yoon, in Proceedings of the 28th International Technical Conference on Circuits/Systems, Computers and Communications, Yeosu, Korea, July 2013.

VSSIM: Virtual Machine Based SSD Simulator

Jinsoo Yoo, Youjip Won, Joongwoo Hwang, Sooyong Kang, Jongmoo Choi, Sungroh Yoon, and Jaehyuk Cha, in Proceedings of the 2013 Conference on Mass Storage Systems and Technologies (MSST13), Long Beach, USA, May 2013.

Journal

GPU-Based Acceleration of an RNA Tertiary Structure Prediction Algorithm

Yongkweon Jeon, Eesuk Jung, Hyeyoung Min, Eui-Young Chung, and Sungroh Yoon, Computers in Biology and Medicine, vol. 43, no. 8, pp. 1011-1022, September 2013.
paper  link

HiTRACE-Web: an Online Tool for Robust Analysis of High-Throughput Capillary Electrophoresis

Hanjoo Kim, Pablo Cordero, Rhiju Das, and Sungroh Yoon, Nucleic Acids Research, vol. 41, no. W1, pp. W492-498, July 2013.
paper  link  server

Massively Parallel Energy Space Exploration for Uncluttered Visualization of Vascular Structures

Yongkweon Jeon, Joong-Ho Won and Sungroh Yoon, IEEE Transactions on Biomedical Engineering, vol. 60, no. 1, pp. 240-244, Jaunary 2013.
paper  link

Entropy-Based Analysis and Bioinformatics-Inspired Integration of Global Economic Information Transfer

Jinkyu Kim, Gunn Kim, Sungbae An, Young-Kyun Kwon and Sungroh Yoon, PLOS ONE, vol. 8, no. 1, e51986, January 2013.
paper  link

Uncluttered Single-Image Visualization of Vascular Structures using GPU and Integer Programming

Joong-Ho Won, Yongkweon Jeon, Jarrett Rosenberg, Sungroh Yoon, Geoffrey D. Rubin and Sandy Napel, IEEE Transactions on Visualization and Computer Graphics, vol. 19, no. 1, pp. 81-93, January 2013.
paper  link  suppl

2012

Conference

Rapid and Robust Denoising of Pyrosequenced Amplicons for Metagenomics

Byunghan Lee, Joonhong Park, and Sungroh Yoon, in Proceedings of IEEE International Conference on Data Mining (ICDM 2012), Brussels, Belgium, December 2012.
paper  link

Influence of Number of Channels and FTL on SSD Power Consumption

Seokhei Cho, Youjip Won, Sooyong Kang, Jaehyuk Cha, Jongmoo Choi and Sungroh Yoon, in Proceedings of 2012 International Conference of Electrical, Computer, Electronics and Biomedical Engineering (ICECEBE2012), Bangkok, Thailand, December 2012.

Deduplication in SSDs: Model and Quantitative Analysis

Jonghwa Kim, ChoongHyun Lee, Ikjoon Son, Jongmoo Choi, Sungroh Yoon, Hu-ung Lee, Sooyong Kang, Youjip Won and Jaehyuk Cha, in Proceedings of the 2012 Conference on Mass Storage Systems and Technologies (MSST12), Pacific Grove, USA, April 2012.

Journal

Application-Support Particle Filter for Dynamic Voltage Scaling of Multimedia Applications

Jae-Beom Lee, Myoung-Jin Kim, Sungroh Yoon, and Eui-Young Chung, IEEE Transactions on Computers, vol. 61, no. 9, pp. 1256-1269, September 2012.
paper  link

Can the Prostate Risk Calculator Based on Western Population be Applied to Asian Population?

Duck Ki Yoon, Jae Young Park, Sungroh Yoon, Man Sik Park, Du Geon Moon, and Fritz H. Schröder, The Prostate, vol. 72, no. 7, pp. 721-729, May 2012.
paper  link  server

vHoT: a Database for Predicting Inter-Species Iteractions between Viral microRNA and Host Genomes

Hanjoo Kim, Seunghyun Park, Hyeyoung Min, and Sungroh Yoon, Archives of Virology, vol. 157, no. 3, pp. 497-501, March 2012.
paper  link  server

2011

Conference

SSD Characterization: From Energy Consumption’s Perspective

Balgeun Yoo, Youjip Won, Seokhei Cho, Sooyong Kang, Jongmoo Choi and Sungroh Yoon, in Proceedings of 3rd USENIX Workshop on Hot Topics in Storage and File Systems (HotStorage ’11), Portland, USA, June 2011.
paper  link

Journal

HiTRACE: High-throughput robust analysis for capillary electrophoresis

Sungroh Yoon, Jinkyu Kim, Justine Hum, Hanjoo Kim, Seunghyun Park, Wipapat Kladwang and Rhiju Das, Bioinformatics, vol. 27, no. 13, pp. 1798-1805, July 2011.
paper  link  code  suppl

Buffer Controller Based Multiple Processing Element Utilization for Dataflow Synthesis

Woohyung Chun, Sungroh Yoon and Sangjin Hong, IEEE Transactions on Very Large Scale Integration Systems, vol. 19, no. 7, pp. 1249-1262, July 2011.
paper  link

Verification Methodology for the IMT-Advanced Channel Simulator

Kyung-Won Kim, Jae-Joon Park, Sungroh Yoon and Seong-Jun Oh, Electronics Express, vol. 8, no. 13, pp. 994-1000, July 2011.
paper  link

Energy-Aware Interconnect Resource Reduction through Buffer Access Manipulation for Data-Centric Applications

Woohyung Chun, Sungroh Yoon and Sangjin Hong, IEEE Transactions on Very Large Scale Integration Systems, vol. 19, no. 5, pp. 818-831, May 2011.
paper  link

Constructing Accurate Contact Maps for Hydroxyl Radical Cleavage Based High-Throughput RNA Structure Inference

Jinkyu Kim, Hanjoo Kim, Hyeyoung Min and Sungroh Yoon, IEEE Transactions on Biomedical Engineering, vol. 58, no. 5, pp. 1347-1355, May 2011.
paper  link  suppl

Initial biopsy outcome prediction in Korean patients – comparison of a noble web-based Korean prostate cancer risk calculator versus prostate-specific antigen testing

Jae Young Park, Sungroh Yoon, Man Sik Park, Dae-Yeon Cho, Hong-Seok Park, Du Geon Moon and Duck Ki Yoon, JKMS, vol. 26, no. 1, pp. 85-91, January 2011.
paper  link  server

Fast sort of floating-point data for data engineering

Changsoo Kim, Sungroh Yoon and Dongseung Kim, Advances in Engineering Software, vol. 42, no. 1-2, pp. 50-54, January-February 2011.
paper  link

2010

Conference

Exploiting Multiple Switch Libraries in Topology Synthesis of On-Chip Interconnection Network

Minje Jun, Sungroh Yoon and Eui-Young Chung, in Proceedings of Design, Automation and Test in Europe (DATE), pp. 1390-1395, Dresden, Germany, March 2010.

Journal

Application of maximin correlation analysis to classifying protein environments for function prediction

Taehoon Lee, Hyeyoung Min, Seung Jean Kim and Sungroh Yoon, Biochemical and Biophysical Research Communications, vol. 400, no. 2, pp. 219-224, September 2010.
paper  link  suppl

Support vector machine based classification of 3-dimensional protein physicochemical environments for automated function annotation

Hyeyoung Min, Seunghak Yu, Taehoon Lee and Sungroh Yoon, Archives of Pharmacal Research, vol. 33, no. 9, pp. 1451-1459, September 2010.
paper  link

Concurrent simulation platform for energy-aware smart metering systems

Seunghyun Park, Hanjoo Kim, Hichan Moon, Jun Heo and Sungroh Yoon, IEEE Transactions on Consumer Electronics, vol. 56, no. 3, pp. 1918-1926, August 2010.
paper  link

Architecture Exploration of High-Performance PCs with a Solid-State Disk

Dong Kim, Kwanhu Bang, Seung-Hwan Ha, Sungroh Yoon and Eui-Young Chung, IEEE Transactions on Computers, vol. 59, no. 7, pp. 878-890, July 2010.
paper  link

Got target?: Computational methods for microRNA target prediction and their extension

Hyeyoung Min and Sungroh Yoon, Experimental and Molecular Medicine, vol. 42, no. 4, pp. 234-244, April 2010.
paper  link

Numerically Efficient Algorithm for Modified Trellis Approaches

Hichan Moon and Sungroh Yoon, IEEE Transactions on Communications, vol. 58, no. 2, pp. 385-389, February 2010.
paper  link

2009

Conference

Performance Analysis of Network Coding with Rapter Codes for Multimedia Broadcast Services

Kwangseok Noh, Sungroh Yoon and Jun Heo, in Proceedings of International Conference on Consumer Electronics, pp. 1-2, Las Vegas, USA, January 2009.

Journal

Stochastic Modeling and Concurrent Simulation of the Game of Golf

Sungroh Yoon, Seil Lee and Seong-Jun Oh, ETRI Journal, vol. 31, no. 6, pp. 809-811, December 2009.
paper  link

Nonlinear Preprocessing Method for Detecting Peaks from Gas Chromatograms

Byonghyo Shim, Hyeyoung Min and Sungroh Yoon, BMC Bioinformatics, vol. 10, no. 1, p. 378, November 2009.
paper  link  code

Good Puncturing Scheme for Rate Compatible Low-Density Parity-Check Codes

Sunghoon Choi, Sungroh Yoon, Wonjin Sung, Hongkyu Kwon and Jun Heo, Journal of Communications and Networks, vol. 11, no. 5, pp. 456-464, October 2009.
paper  link

High-Speed Post-Layout Logic Simulation Using Quasi-Static Clock Event Evaluation

Myeong-Jin Kim, Eui-Young Chung and Sungroh Yoon, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 28, no. 8, pp. 1274-1278, August 2009.
paper  link

A Robust Peak Detection Method for RNA Structure Inference by High-Throughput Contact Mapping

Jinkyu Kim, Seunghak Yu, Byonghyo Shim, Hanjoo Kim, Hyeyoung Min, Eui-Young Chung, Rhiju Das and Sungroh Yoon, Bioinformatics, vol. 25, no. 9, pp. 1137-1144, May 2009. paper  link  suppl  code

Performance Analysis of Network Coding with Raptor Codes for IPTV

Kwangseok Noh, Sungroh Yoon and Jun Heo, IEEE Transactions on Consumer Electronics, vol. 55, no. 1, pp. 83-87, February 2009.
paper  link

Run-Time Adaptive Workload Estimation for Dynamic Voltage Scaling

Sung-Yong Bang, Kwanhu Bang, Sungroh Yoon and Eui-Young Chung, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 28, no. 9, pp. 1334-1347, September 2009.
paper  link

K-Maximin Clustering: A Maximin Correlation Approach to Partition-Based Clustering

Taehoon Lee, Seung Jean Kim, Eui-Young Chung and Sungroh Yoon, Electronics Express, vol. 6, no. 17, pp. 1205-1211, September 2009.
paper  link

2004 – 2008

Conference

Parallel External Sort of Floating-Point Data by Integer Conversion

Changsoo Kim, Sungroh Yoon and Dongseung Kim, in Proceedings of Applied Computing Conference, pp. 120-123, Istanbul, Turkey, May 2008.

Exploiting Binary Abstractions in Deciphering Gene Interactions

Sungroh Yoon, Abhishek Garg, Eui-Young Chung, Hyun Seok Park, Woong Yang Park and Giovanni De Micheli, in Proceedings of IEEE 28th Annual International Conference of IEEE Engineering in Medicine and Biology, pp. 5858-5863, New York City, USA, September 2006.

Clustering Protein Microenvironments for Automated Function Prediction

Sungroh Yoon, Jessica Ebert, and Russ B. Altman, in Proceedings of the Second Automated Function Prediction Meeting, San Diego, USA, August 2006.

Mining Gene Sets for Measuring Similarities

Christine Nardini, Daniele Masotti, Sungroh Yoon, Enrico Macii, Michael D. Kuo, Giovanni De Micheli and Luca Benini, in Proceedings of IEEE Symposium on Computers and Communications, pp. 227-232, Pula-Cagliari, Sardinia, Italy, June 2006.

Clinical Bioimaging and Functional Genomics

Elisa Ficarra, Sungroh Yoon, Luca Benini, Enrico Macii and Giovanni De Micheli, in Proceedings of I FIMA International Conference on Models and Methods for Human Genomics, Ayas-Champoluc, Aosta Valley, Italy, January 2006.

Bioimaging and Functional Genomics

Elisa Ficarra, Giovanni De Micheli, Sungroh Yoon, Luca Benini and Enrico Macii, in Proceedings of pHealth 2006, International Workshop on Wearable Micro- and Nanosystems for Personalized Health, Luzern, Switzerland, January 2006.

Prediction and Analysis of Human microRNA Regulatory Modules

Sungroh Yoon and Giovanni De Micheli, in Proceedings of IEEE 27th Annual International Conference of IEEE Engineering in Medicine and Biology, pp. 4799-4802, Shanghai, China, September 2005.

Finding Co-clusters of Genes and Clinical Parameters

Sungroh Yoon, Luca Benini and Giovanni De Micheli, in Proceedings of IEEE 27th Annual International Conference of IEEE Engineering in Medicine and Biology, pp. 906-912, Shanghai, China, September 2005.

An Application of Zero-suppressed Binary Decision Diagrams to Clustering Analysis of DNA Microarray Data

Sungroh Yoon and Giovanni De Micheli, in Proceedings of IEEE 26th Annual International Conference of IEEE Engineering in Medicine and Biology, pp. 2925-2928, San Francisco, USA, September 2004.

Enhanced pClustering and Its Applications to Gene Expression Data

Sungroh Yoon, Christine Nardini, Luca Benini and Giovanni De Micheli, in Proceedings of IEEE 4th Symposium on Bioinformatics and Bioengineering, pp. 275-282, Taichung, Taiwan, May 2004.

Journal

Joint Co-clustering: Co-clustering of Genomic and Clinical Bioimaging Data

Elisa Ficarra, Giovanni De Micheli, Sungroh Yoon, Luca Benini and Enrico Macii, Computers and Mathematics with Applications, vol. 55, no. 5, pp. 938-949, March 2008.
paper  link

Co-clustering: A Versatile Tool for Data Analysis in Biomedical Informatics

Sungroh Yoon, Luca Benini and Giovanni De Micheli, IEEE Transactions on Information Technology in Biomedicine, vol. 11, no. 4, pp. 493-494, July 2007.
paper  link

Clustering Protein Microenvironments for Function Prediction: Finding PROSITE motifs in 3D

Sungroh Yoon, Jessica Ebert, Eui-Young Chung, Giovanni De Micheli and Russ B. Altman,  BMC Bioinformatics, 2007, vol. 8, Suppl 4:S10, May 2007.
paper  link

A Variability-Insensitive Scheme for NAND Flash Memory Interfaces

Chang-Il Sohn, Sungroh Yoon, Sung-Woo Chung, Chan-Ik Park and Eui-Young Chung, Electronics Letters, vol. 42, no. 23, pp. 1335-1337, November 2006.
paper  link

Computational Methods for Identifying MicroRNAs and Their Targets

Sungroh Yoon and Giovanni De Micheli, Birth Defects Research, vol. 78, no. 2, pp. 118-128, June 2006.
paper  link

A Pattern Mining Method for High-throughput Lab-on-a-Chip Data Analysis

Sungroh Yoon, Luca Benini and Giovanni De Micheli, IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 25, no. 2, pp. 358-377, February 2006.
paper  link

Discovering Coherent Biclusters from Gene Expression Data Using Zero-suppressed Binary Decision Diagrams

Sungroh Yoon, Christine Nardini, Luca Benini and Giovanni De Micheli, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 4, pp. 339-354, October-December 2005.
paper  link

Prediction of Regulatory Modules Comprising microRNAs and Target Genes

Sungroh Yoon and Giovanni De Micheli, Bioinformatics, vol. 21, ii93-ii100, September 2005.
paper  link

Others

A High-Performance Solid-State Disk with Double-Data-Rate NAND Flash Memory

Eui-Young Chung, Chang-Il Son, Kwanhu Bang, Dong Kim, and Sungroh Yoon, arXiv:1502.02239v1 [cs.AR], February 2015.
paper  link

FRAME: Fast and Realistic Attacker Modeling and Evaluation for Temporal Logic Correlation in Static Noise

Sungroh Yoon, Nahmsuk Oh, Peivand Tehrani, Eui-Young Chung, and Giovanni De Micheli, arXiv:1502.02236v1 [cs.OH], February 2015.
paper  link

Technologies and Analysis Methods for Detecting Gene Expression by DNA Microarrays

Sungroh Yoon, IEEE Technology Survey, September 2006.
link

A Pattern Mining Method for High-throughput Lab-on-a-chip Data Analysis

Sungroh Yoon, Luca Benini and Giovanni De Micheli, in Krishnendu Chakrabarty and Jun Zeng, Editors, Design Automation Methods and Tools for Microfluidics-Based Biochips, Springer-Verlag, New York, 2006.
link

Defects vs. Faults: Some Data from the ELF35 and Murphy Chips

Edward J. McCluskey, Ahmad Al-Yamani, James Chien-mo Li, Chao-wen Tseng, Erik Volkerink, Sungroh Yoon, Francois-Fabien Ferhani, Edward Li and Subhasish Mitra, Center for Reliable Computing Technical Report, Stanford University, October 2002.

Testable Design of ELF13: 0.13μm Digital CMOS Circuits

Sungroh Yoon, James Chien-mo Li and Edward J. McCluskey, Center for Reliable Computing Technical Report, Stanford University, May 2002.