Huan He
hehuan2112@gmail.com
Department of Biomedical Informatics and Data Science, Yale University School of Medicine
100 College St, New Haven, CT 06510
NEWS
Jul. 2024: One year in New Haven, CT completed! Forward to the next chapter!
Jun. 2024: Congratulations to Dr. Lin for winning the Best Paper Award in industry track in IEEE ICHI 2024! Congratulations to Dr. Fu for the paper acceptance in JAMIA! I gave a presentation about visual analytics and applications in the Yale NLP/LLM interest group meeting!
May 2024: ASCO 2024 is a great conference! Thousands of posters and many interesting talks and exhibitions! Looking forward to the next year!
Apr. 2024: We presented our data visualization + LLM work at YSM Cushing/Whitney Medical Library!
Mar. 2024: Happy to meet friends at Boston in AMIA Informatics Summit 2024! And congratulations to Dr. Raja's presentation A Study of Biomedical Relation Extraction Using GPT Models!
Feb. 2024: Our latest visualization project and MeLLaMA LLM project at Yale AI in Medicine Symposium
Jan. 2024: 2024! New start! New aims!
Dec. 2023: Goodbye 2023, hello 2024! Happy New Year! Hope all the projects will be successful in 2024!
Oct. 2023: VAHC 2023 workshop at IEEE VIS 2023!
Sep. 2023: Explored the beautiful campus of Yale University! The Sterling Memorial Library is amazing! And the Yale University Art Gallery is also a must-see place!
Aug. 2023: There are many beautiful places in New Haven, CT! East Rock, Wesk Rock, and Farmington Canal Heritage Trail~
Jul. 2023: Two posters are accepted by AMIA Annual Symposium 2023! And congratulations to Taylor Hawkins and Kurt Miller for the acceptance of their student papers! Congratulations to Andrew Wen for the acceptance of the JAMIA and npj Digital Medicine!
Jun. 2023: Relocated to New Haven, CT for my new role as a Research Scientist in the Department of Biomedical Informatics and Data Science at Yale University School of Medicine!
May 2023: Congratulations to Dr. Moon for the acceptance of two JMIR papers!
Mar. 2023: AMIA IS 2023 @Seattle! Sleepless in Seattle (due to deadlines and two oral presentations :)! Nice city, people, and food!
Feb. 2023: Congratulations to Dr. Liu for the Established Investigator Award!
Jan. 2023: Happy new year! Updated the data structure and layout of my website with Pelican!
Dec. 2022: Congratulations to Dr. Riaz and Syed Arsalan Ahmed Naqvi for the paper acceptance of JAMA Oncology! And, my podium, system demo, and poster are accepted by AMIA IS 2023!
Nov. 2022: Enjoy AMIA 2022 and serve as paper co-chair for VAHC 2022 @Washington D.C.! And congratulations to Dr. Moon for her Distinguished Paper Award in AMIA 2022! And my poster and co-author paper are accepted by IEEE BIBM 2022!
Oct. 2022: Meet friends in IEEE VIS 2022 @Oklahoma City!
Aug. 2022: Our team 'COVID-19 Predictive Analytics Task Force' received Mayo Clinic Team Science Award.
Jul. 2022: Two posters are accepted in IEEE VIS 2022!
Jun. 2022: Our papers, podiums, and posters are accepted in AMIA 2022! And serve as the Web Chair for IEEE ICHI 2022.
Mar. 2022: AMIA IS 2022 @Chicago!
Feb. 2022: Congratulations to Dr. Riaz and Syed Arsalan Ahmed Naqvi for the ASCO Merit Award!
Dec. 2021: Submissions are accepted by AMIA IS 2022 and Bioinformatics!
Nov. 2021: Nice trip to San Diego for AMIA 2021! So many people!
Oct. 2021: IEEE VIS 2021 Virtual ... Hope to be hybrid or offline next year in Oklahoma!
Jul. 2021: Two posters are accepted in IEEE VIS 2021!
Jun. 2021: One oral presentation and two posters are accepted in AMIA 2021!
Mar. 2021: Still work from home ... submitted our works to VIS and AMIA! Keep coding!
Nov. 2020: Virtual AMIA 2020! So many events, wow...
Oct. 2020: Virtual VIS20 is also great! Got Best Poster Award of IEEE VIS 2020! Happy!
Aug. 2020: Two posters are accepted by IEEE VIS 2020! Congratulations to Yating on the acceptance of her FIRST TVCG track paper!
Jul. 2020: Two posters are accepted by AMIA 2020!
Mar. 2020: Start work from home ... work hard!
Oct. 2019: Meet people at VIS19 in Vancouver! 3 papers are accepted in IEEE BigData 2019! Congratulations to Rongzhe and Yingchao!
Aug. 2019: Mayo Clinic Orientation!
Jul. 2019: PhD defense passed! A paper is accepted in VAST'19!
Jun. 2019: PhD Dissertation submitted!
May 2019: An IJCAI demo has been accepted!
Apr. 2019: My first SCI paper has been accepted!
Feb. 2019: Two demos are accepted in WWW'19 demonstration track!
Dec. 2018: The paper of VUC is accepted in CompEd'19!
Oct. 2018: VIS18 is exciting! Impressive trip to Berlin.
Jul. 2018: VUSphere has been accepted in VAST 2018 Conference Track! So happy!
Mar. 2018: My FIRST first author international conference paper has been accepted by Edutainment'18! So excited!
I'm a Research Scientist working at the Department of Biomedical Informatics and Data Science of Yale University School of Medicine, working with Dr. Hua Xu. I was a research fellow in the Department of AI and Informatics of Mayo Clinic, working with Dr. Hongfang Liu. I received my Ph.D at the School of Electronic and Information Engineering, Xi'an Jiaotong University supervised by Dr. Qinghua Zheng. I obtained my master degree and bachelor degreen in software engineering from Xi'an Jiaotong University. My research interest mainly focuses on applying data visualization, visual analytics, and machine learning techniques in addressing real-world clinical challenges.
2024
Journal of the American Medical Informatics Association, Volume 31, Issue 7, May 14, 2024
38742455 10.1093/jamia/ocae101 Cite
IEEE 12th International Conference on Healthcare Informatics (ICHI 2024) Best Paper Award in industry track, Orlando, FL, Jun 4, 2024
Abstract IEEE Xplore 10.1109/ICHI61247.2024.00072 Cite
2023
Journal of the American Medical Informatics Association, August 14, 2023
37555837 10.1093/jamia/ocad134 Cite
npj Digital Medicine, July 21, 2023
37479735 PMC10362064 10.1038/s41746-023-00878-9 Cite
JMIR AI, June 20, 2023
10.2196/41818 Cite
JAMA Oncology, March 2, 2023
36862387 PMC9982744 10.1001/jamaoncol.2022.7762 Cite
npj Digital Medicine, April 13, 2023
37368483 PMC10337517 10.2196/48072 Cite
AMIA 2023 Informatics Summit, Seattle, WA, March 13-17, 2023
Podium Abstract Slide Cite
AMIA 2023 Informatics Summit, Seattle, WA, March 13-17, 2023
Podium Abstract Cite
AMIA 2023 Informatics Summit, Seattle, WA, March 13-17, 2023
Podium Abstract Cite
AMIA 2023 Informatics Summit, Seattle, WA, March 13-17, 2023
Podium Abstract Cite
2022
AMIA 2022 Annual Symposium, Washington, D.C., Nov 5 - 9, 2022
PDF PDF (AMIA Knowledge Center) Cite
AMIA 2022 Annual Symposium, Washington, D.C., Nov 5 - 9, 2022
PDF (AMIA Knowledge Center Link) Cite
2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 3280-3286, Washington, D.C., Dec 6-8, 2022
IEEE Xplore 10.1109/BIBM55620.2022.9995620 Cite
Clinical and Translational Science, 07 December 2022
36478394 10.1111/cts.13463 Cite
The 64th ASH Annual Meeting and Exposition (Oral and Poster), New Orleans, Louisiana, , Dec. 10 - 13, 2022
Paper Link Poster Cite
OHDSI Symposium 2022, Rockville, MD, Oct. 14 - 16, 2022
Showcase Link PDF Poster Cite
IEEE VIS 2022, Oklahoma City, OK, Oct. 16 - 21, 2022
PDF Poster Demo: https://ohnlp.github.io/MedTator/ Cite
IEEE VIS 2022, Oklahoma City, OK, Oct. 16 - 21, 2022
PDF Poster Poster for AMIA 2022 Demo: https://ohnlp.github.io/Meta.js/ Cite
Annals of Oncology (2022) 33 (suppl_7): S616-S652 (ESMO Congress 2022), Sep. 9 - 13, 2022
Poster Living SRMA Cite
JCO Clinical Cancer Informatics, 6:e2200006, 2022 July
PDF 35917480 10.1200/CCI.22.00006 Cite
IEEE 10th International Conference on Healthcare Informatics (ICHI 2022), Rochester, MN, June 11 - 14, 2022
IEEE Xplore 10.1109/ICHI54592.2022.00017 Cite
Journal of Clinical Oncology 40, no. 16_suppl (June 01, 2022) e24070-e24070 (2022 ASCO Annual Meeting), Chicago, IL, June 3-7, 2022
Poster Link 10.1200/JCO.2022.40.16_suppl.e24070 Cite
AMIA Informatics Summit 2022, Chicago, IL, March 21 - 24, 2022
PDF PDF (AMIA Knowledge Center) Poster Cite
AMIA Informatics Summit 2022, Chicago, IL, March 21 - 24, 2022
PDF PDF (AMIA Knowledge Center) Slide Demo Poster on ICHI 2022 Cite
Critical Reviews in Oncology Hematology. 103706 Epub, 2022 May 07
35537621 10.1016/j.critrevonc.2022.103706 Living SRMA Cite
Bioinformatics, Volume 38, Issue 6, Pages 1776-1778, 15 March 2022
PDF Supplementary File 34983060 10.1093/bioinformatics/btab880 Demo GitHub Cite
2021
IEEE VIS 2021 Virtual, Virtual, Oct. 24 - 29, 2021
PDF Poster PDF (for AMIA 21) Poster (for AMIA 21) Demo Cite
Mayo Clinic Proceedings. 2022 Feb;97(2):308-324, 2021 Jun 22
34172290 10.1016/j.mayocp.2020.10.041 Cite
AMIA 2021 Annual Symposium, San Diego, CA, Oct. 26 - Nov 3, 2021
PDF (AMIA Knowledge Center) Cite
JCO Clinical Cancer Informatics. 2021 May;5:588-599, 2021 May
34043431 10.1200/CCI.21.00035 Living SRMA Cite
European Urology, Volume 80, Issue 6, Pages 712-723, December 2021
33824031 10.1016/j.eururo.2021.03.016 Living SRMA Cite
2020
JMIR Medical Informatics. 2020 Nov 16;8(11):e18659. doi: 10.2196/18659., 2020 Nov
33108311 10.2196/18659 Cite
2019
IEEE Big Data 2019, Los Angeles, CA, Dec. 9-12, 2019
PDF 10.1109/BigData47090.2019.9005656 Cite
IEEE Big Data 2019, Dec. 9-12, 2019
PDF 10.1109/BigData47090.2019.9006325 Cite
IEEE Big Data 2019, Los Angeles, CA, Dec. 9-12, 2019
PDF 10.1109/BigData47090.2019.9006526 Cite
Ph.D Dissertation, at Xi'an Jiaotong Univeristy, July, 29, 2019
PDF (Image Compressed) Slide (Image Compressed) Cite
IEEE VIS 2019, Vancouver, Canada, Oct 20-25, 2019
PDF 10.1109/VISUAL.2019.8933778 Cite
The 28th International Joint Conference on Artificial Intelligence Demo Track (IJCAI 2019), Macao, China, August 10-16, 2019
PDF 10.24963/ijcai.2019/964 Cite
IEEE Access, 2019
PDF Slide 10.1109/ACCESS.2019.2910589 Cite
2019 The Web Conference Demonstration Track (WWW 2019), San Francisco, CA, May 13-17, 2019
PDF 10.1145/3308558.3314140 Video Demo Cite
2019 The Web Conference Demonstration Track (WWW 2019), San Francisco, CA, May 13-17, 2019
10.1145/3308558.3314144 Video Cite
2019 ACM Global Computing Education Conference (CompEd 2019), Chengdu, China, May 17-19, 2019
PDF 10.1145/3300115.3309514 Demo Cite
2018
IEEE VIS 2018, Berlin, Germany, Oct 21-26, 2018
PDF VIDEO (Fast Forward) TALK VIDEO (VIMEO) Slides Slides(58.9MB) 10.1109/VAST.2018.8802383 Cite
IEEE 18th International Conference on Advanced Learning Technologies (ICALT 2018), Mumbai, India, July 9-13, 2018
PDF Slide 10.1109/ICALT.2018.00053 Cite
12th International Conference on E-learning and Games (Edutainment), Xi'an, China, June 28-30, 2018
PDF Slide 10.1007/978-3-030-23712-7_54 Cite
Before 2018
2015 IEEE Trustcom/BigDataSE/ISPA, Helsinki, Finland, Aug 20 - 22, 2015
PDF DEMO Slides 10.1109/Trustcom.2015.572 Cite
IEEE 11th International Conference on e-Business Engineering (ICEBE 2014), Guangzhou, China, November 5-7, 2014
PDF 10.1109/ICEBE.2014.51 Cite
The Chinese Journal of ICT in Education (中国教育信息化), 2012 (3) : 57-60, 2012
PDF 1673-8454(2012)03-0057-04 Cite
Experimental Technology and Management (实验技术与管理) 2011 (5) :229-231, 2011
PDF 1002-4956(2011)05-0229-03 Cite
Experimental Technology and Management (实验技术与管理) 2011 (5) :216-218, 2011
PDF 1002-4956(2011)05-0216-03 Cite
Projects
Multi-site Collaboration, Rochester, MN, USA / Phoenix, AZ, USA / Boston, MA, USA / Karachi, Pakistan
To create and maintain living interactive systematic reviews and meta-analysis (SRMA), we proposed a living evidence synthesis framework (LIvE), which continually updates, incorporate relevant new evidence as it becomes available. The LIvE framework has been suggested as a solution to address the challenge of synthesizing evidence in fields with rapidly moving evidence. I designed the multi-layer system architecture and developed all the modules which cover the whole evidence synthesis workflow from end to end, including data collection, screening, extraction, meta-analysis, and visualization. Several living SRMAs have been released and kept updated based on this framework.
Links: Meta.js Living SRMA First-line Treatment of Metastatic Renal Cell Carcinoma Direct Oral Anti-Coagulants compared to Dalteparin for treatment of Cancer Associated Thrombosis Adjuvant Treatment Options in Renal Cell Carcinoma Metastatic Castration Sensitive Prostate CancerMayo Clinic, Rochester, MN, USA
I proposed, designed, and developed MedTator, a lightweight serverless web-based application for corpus development, which implements text annotation, corpus statistics, inter-annotator agreement evaluation, error analysis, corpus visualization, and format conversion to facilitate the creation of gold standard corpus for building natural language processing and machine learning models. In addition to the annotation tool itself, I also developed several scripts to enable further usage of the annotated files for practice uses, such as training named entity recognition / relation identification models, format convertion, and text embeddings.
Links: Paper MedTator DemoMayo Clinic, Rochester, MN, USA
I designed the system architecture and implemented both the data pipeline and frontend of the Mayo Clinic's Coronavirus Map tracking tool, which has county-by-county information on COVID-19 cases and trends nationwide and predictive modeling that forecasts where hot spots will emerge over the next 14 days.
Links: NewsMayo Clinic, Rochester, MN, USA
As the clinical studies increase, it's hard to find those studies that focus on specific rare disease topics in our internal IRB system. To address this issue, I design and developed the Rare Disease Study Identification (RDSI) system, which aims to promote the exploration of rare disease studies in existing study repositories by using natural language processing and data visualization techniques. The RDSI system is based on several open-source tools, such as MetaMapLite and MedTagger.
Links: PosterSchool of e-Learning, Xi'an Jiaotong University, Xi'an, Shaanxi, China
A tool embbeded in learning management system. In this tool, I proposed a calendar-like model to encode the temporal attributes of interactions in the long-term learning process. Based on a trained simplified CNN model with learning process data, this tool can predict students' grade point based on their engagement history. We believe that it can help students understand their learning process of multiple courses in a semester, and support instructors to analyze the temporal patterns.
Links: DemoSchool of e-Learning, Xi'an Jiaotong University, Xi'an, Shaanxi, China
To understand the video utilization patterns and the enrollment across the country, I designed and implemented this visual analytic system called VUSphere. It has three linked views: an overview with a spherical layout to show the overall video utilization, a detailed statistics view with 4 panels with 9 tabs, and a comparison view to examine different elements.
Links: VideoWonderTek Inc., Shanghai, China
To facilitate the efficiency and scalability of small files reading and writing, we designed and implemented a basic file system based on FUSE and MongoDB with refer to prior work in our team. With the characteristics of the MongoDB database, I designed a algorithm and a data structure for mapping from the tree directory structure to the key-value structure and implemented the operations specified by FUSE, such as getattr, create, write, flush, etc. In addition, I visualized the detailed r/w operation sequences to improve the performance.
Links:MOOC2U.com, Open Edutaiment Inc., Beijing, China
An educational data analysis system for MOOC China platform. I designed the architecture of this system and developed most of the modules, including behavior capturer, log collector, analyzer based on Apache Spark, and the visualization. We integrated several common used charts, such as bar chart, map, heatmap, etc., to show how students interacts with this platform. The statistical results of learning log are visualized to gain insights into the learning patterns and trends in MOOC China platform.
Links:Network and Information Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China
In order to connnect isolated information islands between information systems of many departments, such as graduate school, department of archives, finance office, employment center etc., I designed and developed this system based on Serice-Oriented-Architecture (SOA) approach and technologies. Data in each isolated system can be synced without modification to existing systems.
Links:Network and Information Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China
During the freshmen enrollment of each year, taking a photo for ID was a very time-consuming part, especially when there are about 4,000 - 5,000 students enrolled in two days. It takes about 2-3 minutes for each part-time photographer to take a photo that meets standard. As a result, students had to wait in a long queue. To address this issue, I developed a semi-automatic camera system that integrates campus card service, standard PC camera and student information system based on OpenCV and SOA technologies. An intern student can take a good photo within 15 seconds with just 3 mouse clicks, which greatly improves the efficiency and significantly shorten the queue length.
Links:Network and Information Center, Xi'an Jiaotong University, Xi'an, Shaanxi, China
At that time, the process of paying various fees required manual services (e.g., network fee, entry fee, etc.), which were not only time-consuming but also cumbersome. I developed a desktop software and a web-based application to help students self-pay on the terminals. The detailed design and are included in my master thesis.
Links: MASTER THESIS PDFTools
A visualization tool for understanding the migration of virtual machines among the physical machines.
Link: Homepage | Repository
A tool for searching the recommended journals by colleges of XJTU
Link: Homepage | Repository
Generating a year calendar of A4-size page with the deadlines of conference in one year I am concerned.
Link: Homepage | Repository
Patents
ZL201410328449.0
一种面向MapReduce框架的地理归属信息查询方法 / Xi'an Jiaotong University
Weizhan Zhang, Huan He, Ni Xue, Qinghua Zheng, Bo Dong
ZL201310298976.7
一种基于HBase的构建和检索增量索引的方法 / Xi'an Jiaotong University
Qinghua Zheng, Bo Dong, Huan He, Kailei Song, Haipeng Xu, Tian Ma, Yaxing Chen
ZL201410840805.7
一种基于DOM的网页关键内容抽取方法 / Xi'an Jiaotong University
Bo Dong, Ni Xue, Huan He, Qinghua Zheng, Tian Ma
ZL201410658492.3
一种基于HBase的税收统计报表存储与计算的方法 / Xi'an Jiaotong University
Qinghua Zheng, Tian Ma, Bing Li, Huan He, Jianfei Ruan, Zhenchao Zhang, Jiansheng Shi, Peiyong Wang, Yunhui Qian
ZL201310272890.7
基于重叠点识别的网络重叠社团检测方法 / Xi'an Jiaotong University
Jun Liu, Haipeng Xu, Bo Dong, Qinghua Zheng, Tian Ma, Huan He, Bing Li
ZL201410344242.2
基于主从架构的MapReduce任务跨数据中心调度系统及方法 / Xi'an Jiaotong University
Weizhan Zhang, Jianfei Ruan, Qinghua Zheng, Bo Dong, Hanning Zhang, Huan He
Work Experience
Community Services
- The Visual Computer
- Journal of Biomedical Informatics (JBI)
- Journal of Medical Internet Research (JMIR)
- PloS one
- The International Review of Research in Open and Distributed Learning
- IEEE Access
- International conferences, including AMIA Annual Symposium 2022-2023, VAHC 2022, IEEE VIS 2023, IEEE ICHI 2022, IEEE BIBM 2022, IEEE PacificVis 2022, and AAAI 2018
- Paper co-chair of the workshop on Visual Analytics in Healthcare (VAHC) 2022, 2024
- Web co-chair for the workshop on Visual Analytics in Healthcare (VAHC) 2023, 2024
- Web chair for the 10th IEEE International Conference on Healthcare Informatics (ICHI) 2022
- Director of Art and UI, BMY BBS of Xi'an Jiaotong Univeristy (2007 - 2012)
Awards
Mayo Clinic, Rochester, MN, USA
IEEE VIS 2020, Virtual
Shaanxi Provincial Key Lab of Big Data Knowledge Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, China
Ministry of Education of the People's Republic of China, Xi'an, Shaanxi, China
Xi'an Jiaotong University, Xi'an, Shaanxi, China
Minister of Education, Xi'an, Shaanxi, China
China Society for Industrial and Applied Mathematics (CSIAM), Beijing, China
Xi'an Jiaotong University, Xi'an, Shaanxi, China