Portfolio

My research interests include multi-view learning, network-based analysis, social data mining and biomedical informatics. I’ve been mostly working on integrating multi-view data using network-based approaches for both social media and bioinformatics area.

Experience

Assistant Professor September 2021 - Present
- Department of Artificial Intelligence, Ajou University, Suwon, Korea
Postdoctoral Researcher January 2020 - August 2021
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
- Department of Digital Health, SAIHST, Sungkyunkwan University, Samsung Medical Center, Seoul, Korea
- Research area: Bioinformatics, Cancer analysis
Visiting Graduate Student April 2019 - December 2020
- Kim Lab at Univerisity of Pennsylvania, Philadelphia, PA, USA
- Advised by Professor Dokyoon Kim
- Research area: Bioinformatics, Multi-omics data integration, Network-based analysis, Cancer analysis
Ph.D. Student August 2014 - December 2020
- Learning and Mining from data(LAMDA) lab at Ajou University, Suwon, Korea
- Advised by Professor Kyung-Ah Sohn
- Research area: Bioinformatics, Social data mining, Multi-view learning, Multi-omics data integration, Network-based analysis
Teaching Assistant
- Advanced Data Mining (Autumn 2016)
- Data Mining (Autumn 2014; Autumn 2015; Autumn 2016; Spring 2017)
- Algorithms (Spring 2015)

Education

Ajou University
- Ph.D., Computer Engineering, 2014 - 2020
  - Thesis: Network-based machine learning approach for aggregating multi-modal data [Slides]
  - Course works: Computational Biology, Bioinformatics, Biomedical and Healthcare Informatics, Computer Vision, Parallel and Distributed Systems, Advanced Algorithms, Advanced Data Mining
- B.S., Computer Engineering, 2009 - 2014
  - Course works: Data Mining, Algorithms, Data Structure, Database, Probability and Statistics

Publications

Hang-Rai Kim, Sang-Hyuk Jung, Jaeho Kim, Hyemin Jang, Sung Hoon Kang, Song Hwangbo, Jun Pyo Kim, So Yeon Kim, Beomsu Kim, Soyeon Kim, Jee Hyang Jeong, Soo Jin Yoon, Kyung Won Park, Eun-Joo Kim, Bora Yoon, Jae-Won Jang, Jin Yong Hong, Seong Hye Choi, Young Noh, Ko Woon Kim, Si Eun Kim, Jin San Lee, Na-Yeon Jung, Juyoun Lee, Byeong C. Kim, Sang Joon Son, Chang Hyung Hong, Duk L. Na, Sang Won Seo, Hong-Hee Won, Hee Jin Kim. (2021) Identifying novel genetic variants for brain amyloid deposition: a genome-wide association study in the Korean population. Alzheimer’s Research & Therapy, 13:117 [Paper]
So Yeon Kim, Eun Kyung Choe, Manu Shivakumar, Dokyoon Kim* and Kyung-Ah Sohn*. (2021) Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer. Bioinformatics, 37(16):2405-2413. [Paper] [Code]
Eun Kyung Choe, Sangwoo Lee, So Yeon Kim, Manu Shivakumar, Kyu Joo Park, Young Jun Chai, Dokyoon Kim*. (2021) Prognostic effect of inflammatory genes on stage I-III colorectal cancer - integrative analysis of TCGA data. Cancers, 13(4):751 [Paper]
Sangwoo Lee, Eun Kyung Choe, So Yeon Kim, Hua Sun Kim, Kyu Joo Park* and Dokyoon Kim*. (2020) Liver imaging features by convolutional neural network to predict the metachronous liver metastasis in stage I-III colorectal cancer patients based on preoperative abdominal CT scan. BMC Bioinformatics, 14(1): 8 (presented at the 18th Asia Pacific Bioinformatics Conference(APBC 2020), Seoul, Korea) [Paper]
So Yeon Kim, Hyun-Hwan Jeong, Jaesik Kim, Jeong-Hyeon Moon and Kyung-Ah Sohn*. (2019) Robust Pathway-based Multi-Omics Data Integration using Directed Random Walk for Survival Prediction in Multiple Cancer Studies. Biology Direct, 14(1): 8 (presented at the 17th Annual International Conference on Critical Assessment of Massive Data Analysis (CAMDA 2018, ISMB COSI track), Chicago, USA) [Paper] [Slides]
So Yeon Kim, Tae Rim Kim, Hyun-Hwan Jeong and Kyung-Ah Sohn*. (2018) Integrative Pathway based Survival Prediction utilizing Interaction between Gene Expression and DNA Methylation in Breast Cancer. BMC Medical Genomics, 11(Suppl 3):68 (presented at Translational Bioinformatics Conference (TBC 2017), Los Angeles, USA) [Paper] [Slides]
So Yeon Kim and Kyung-Ah Sohn*. (2017) Multi-view network-based social-tagged landmark image clustering. 2017 IEEE International Conference on Image Processing (ICIP 2017), Beijing, China [Paper] [Poster]
Garam Lee, Lisa Bang, So Yeon Kim, Dokyoon Kim* and Kyung-Ah Sohn*. (2017) Identifying subtype-specific associations between gene expression and DNA methylation profiles in breast cancer. BMC medical genomics, 10(1), 28 [Paper]
Moon Soo Cha, So Yeon Kim, Jae Hee Ha, Min-June Lee, Young-June Choi and Kyung-Ah Sohn*. (2016) Topic Model based Approach for Improved Indexing in Content based Document Retrieval. International Journal of Networked and Distributed Computing, 4(1), 55-64 [Paper]
Hyun-hwan Jeong, So Yeon Kim, Kyubum Wee and Kyung-Ah Sohn*. (2015) Investigating the utility of clinical outcome-guided mutual information network in network-based Cox regression. BMC systems biology, 9(Suppl 1), S8 [Paper]
So Yeon Kim and Kyung-Ah Sohn*. (2015) Graph-Based Spam Image Detection for Mobile Phone Spam Image Filtering. International Journal of Software Innovation 3(4):72-86 [Paper]
Sungdo Gu, So Yeon Kim, Hyun-hwan Jeong and Kyung-Ah Sohn*. (2015) Constructing and Exploiting Software Metrics Networks for Software Quality Assessment. the 5th International Conference on IT Convergence and Security (ICITCS 2015), Kuala Lumpur, Malaysia [Paper]
So Yeon Kim, Sungdo Gu, Hyun-hwan Jeong and Kyung-Ah Sohn*. (2015) A Network Clustering Based Software Attribute Selection for Identifying Fault-Prone Modules. the 5th International Conference on IT Convergence and Security (ICITCS 2015), Kuala Lumpur, Malaysia [Paper] [Slides]
So Yeon Kim and Kyung-Ah Sohn*. (2015) Mobile phone spam image detection based on graph partitioning with Pyramid Histogram of Visual Words image descriptor. the IEEE/ACIS 14th International Conference on Computer and Information Science (ICIS 2015), Las Vegas, USA [Paper] [Slides]
Moon Soo Cha, So Yeon Kim, Jae Hee Ha, Min-June Lee, Young-June Choi and Kyung-Ah Sohn*. (2015) CBDIR: Fast and effective content based document Information Retrieval system. the IEEE/ACIS 14th International Conference on Computer and Information Science (ICIS 2015), Las Vegas, USA [Paper]
So Yeon Kim, Yenewondim Biadgie and Kyung-Ah Sohn*. (2015) Investigating the Effectiveness of E-mail Spam Image Data for Phone Spam Image Detection Using Scale Invariant Feature Transform Image Descriptor. Information Science and Applications, LNEE 339:591-598 (presented at the 6th International Conference on Information Science and Applications (ICISA 2015), Pattaya, Thailand) [Paper] [Slides]
Seung Woo Cho, Moon Soo Cha, So Yeon Kim, Joo Cheol Song and Kyung-Ah Sohn*. (2014) Investigating temporal and spatial trends of brand images using Twitter opinion mining. the 5th International Conference on Information Science and Applications (ICISA 2014) * Undergraduate Research Awards at Ajou University [Paper]