Researchers

 

 

Hong Yu, PhD (Principal Investigator)

Professor and Principal Investigator UMMS BioNLP Group, Dept of Computer Science, University of Massachusetts Lowell; Adjunct Professor, Dept of Medicine, University of Massachusetts Medical School Worcester; College of Information and Computer Science, University of Massachusetts Amherst; Research Health Scientist, Center for Healthcare Organization & Implementation Research, Edith Nourse Rogers Memorial Veterans Hospital.

 

I am an elected fellow of the American College of Medical Informatics. I received PhD from the Department of Biomedical Informatics at Columbia University. My research focuses on information retrieval and natural language processing and their applications to the biomedical and healthcare domain. AskHERMES is one of the few online systems that provide answers to biomedical questions. NoteAid is a system that translates electronic medical record (EMR) notes to lay language comprehensible to patients. We also mine data from EMRs for healthcare outcome studies. 

Contact

 Thumbnail: Hong Yu

Abhyuday Narayan Jagannatha

Research Assistant, School of Computer Science, University of Massachusetts Amherst

 

I am a Ph.D. Student at UMass Amherst CS. I am currently working with Prof Hong Yu in UMass BioNLP group. I am a B.Tech in Electrical Engineering from Indian Institute of Technology, Roorkee, India. And I briefly worked at Samsung before joining UMass Amherst Computer Science. 

My work primarily involves using mathematical tools to model and understand text. To this end, I mainly work with approaches borrowed from Machine Learning and Optimization. 

Some of the current projects that I am involved in are "Simplification of EMR text using Machine Translation without using a parallel corpus", and "Adverse Drug event detection". Automated Simplification of Medical Narratives through machine translation is traditionally done using a parallel corpus of complex to simple sentences. But creation of such a parallel corpus is very expensive. This is why most efforts which work on this approach use a relatively small corpus. In our work we try to replace the need for a parallel corpus by leveraging upon the regularity of the language we are using.

In our Adverse drug event project, we try to build pharmacovigilance tools which work on raw unstructured text from Medical Narratives. The goal is to have a system in place, which can detect events of Adverse drug event and then aggregate them over a large dataset to achieve meaningful information about the adverse reactions.

  

abhyuday narayan jagannatha cropped small 

Rumeng Li

Teaching and Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am a PhD student at the University of Massachusetts Amherst in the College of Information and Computer Science. I am working with Professor Hong Yu in the Bio-NLP lab. My research interests are in Natural Language Processing and Machine Learning.

I received my Master's Degree in Computer Science at Peking University, China. During which I interned at Professor Yuji Matsumoto's lab at Nara Institute of Science and Technology, Japan as a research assistant for one year working on natural language processing. I obtained BA in English Language and Literature from Beijing Sport University, China.

 

Avijit Mitra

Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am a PhD student at the University of Massachusetts Amherst in the College of Information and Computer Science. I am working with Professor Hong Yu in the Bio-NLP lab. My research focuses on the investigation and development of robust NLP pipelines, specifically for the biomedical domain. Prior to joining UMass, I received my BSc in Electrical and Electronics Engineering (EEE) from Bangladesh University of Engineering and Technology.

Avijit's Linkedin

 

 

 Pengshan_1

Zhichao Yang

Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am a MS/PhD student at the University of Massachusetts Amherst in the College of Information and Computer Science. I am working with Professor Hong Yu on biomedical text generation and knowledge graphs in the Bio-NLP lab. I received B.S. in Computer Science Engineering from the Ohio State University.

Zhichao's Linkedin

  Avijit_1

Zonghai Yao

Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am a Ph.D. student in the College of Information and Computing Sciences at the University of Massachusetts Amherst. I am working with Prof. Hong Yu in the BioNLP Laboratory. My major research interests are natural language processing and related fields. I received my Master of Science in Computer Science from Universtiy of Massachusetts Amherst.

Zonghai's Linkedin

  

Sunjae Kwon

Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am a MS/Ph.D. Student at UMASS Amherst CS. I am currently working with Prof. Hong Yu in UMass BioNLP group. I am a B.S. and M.S. in Computer Science at Sogang University. Before joining UMass, I worked at Ulsan National Institute of Science and Technology and Korea Advanced Institute of Science and Technology as an AI research scientist. 
 
I am interested in NLP and medical AI. I am involved in "Important Medical Jargon Terms Extraction with Various Medical Knowledge Resources." The goal of this project is to find difficult jargon terms from doctors' EHR notes.  For this, rather than previous methodologies to rely on statistical inference to find the terms, we are trying to use pretrained language models. Specifically, we are trying to mask and decode medical terminologies to analyze which terms are more unfamiliar. 
 

Sunjae's Linkedin

  

Huan-Yuan Chen

Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am a Ph.D. Student at UMASS Amherst CS. I am currently working with Prof. Hong Yu in UMass BioNLP group. 
 

 

  

Samuel(Sam) Osebe

Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am a MS/PhD student at the UMass Amherst CICS department. Previously, I worked at the IBM Research Lab - Africa as a Software Engineer for 5 years. During this period, I worked on diverse systems including encoding and execution of clinical guidelines, detection of adverse effects and secure exchange of medical records. Currently, I am a research student under Professor Hong Yu at the BioNLP lab. My interests are in using novel machine learning algorithms and natural language processing architectures to perform information extraction on medical domain data.
 
I received my BSc in Computer Science from the University of Nairobi, Kenya.
 

Sam's Linkedin

 

Junda Wang

Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am a PhD student at the University of Massachusetts Amherst in the College of Information and Computer Science. I am working with Professor Hong Yu in the BioNLP lab. My research focuses on healthcare, Machine Learning and causal inference. I received my MS in Computer Science at University of Rochester and BA in Applied Mathematics from Hefei University of Technology, China.

 

 
  

Hieu Tran

Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am currently a Computer Science Ph.D. student at University of Massachusetts Amherst, where I do research on Natural Language Processing with Prof. Hong Yu. Previously, I obtained my B.S. degree in Computer Science from Hanoi University of Science and Technology. My research explores mechanisms to understand human languages for computers so that computers can perform cognitive language related tasks for us. Among others, I am especially interested in distilling structured information and mining useful knowledge from massive human-written text of various domains. I am also interested in other language-related problems with deep learning, including reading comprehension, question answering, machine translation, and natural language generation.
 
 
 

Fareya Ikram

Research Assistant, College of Information and Computer Science, University of Massachusetts Amherst

 

I am an MS/Ph.D. student in the College of Information and Computing Sciences at the University of Massachusetts Amherst. I am working with Prof. Hong Yu in the BioNLP Laboratory. My research interests are applications of machine learning and natural language processing in healthcare.
 
 

Yifan Zhang

Research Assistant, Department of Computer Science, University of Massachusetts Lowell

 

I am a Ph.D. student in the Miner School of Computer & Information Sciences at the University of Massachusetts Lowell. I am currently working under the guidance of Professor Hong Yu in the Bio-NLP lab. I am interested in machine learning, natural language processing and healthcare. I received my MS in Computer Science at Brandeis University.
 
 

 

  

WonSeok Jang

Research Assistant, Department of Computer Science, University of Massachusetts Lowell

 

Hello I'm Won Seok. I am a Computer Science PhD student at the Miner School of Computer and Information Sciences at UMass Lowell. My background is nursing and I have also worked on medical data analysis during my masters at Yonsei University. My current research interest is pioneering new NLP methods for the medical field also applying analyzing medical data.
 

 

Sharmin Sultana

Research Assistant, Department of Computer Science, University of Massachusetts Lowell

 

I'm currently pursuing my MS/Ph.D. at the Richard A. Miner School of Computer & Information Sciences, University of Massachusetts Lowell. Under the guidance of Professor Hong Yu, I'm engaged in research at the Bio-NLP lab, where we explore the intersections of NLP and Machine Learning within the healthcare sector. Before embarking on this journey at UMass Lowell, I earned my undergraduate degree in Computer Science from CUET in Bangladesh.
 
 

Postdoctoral Researcher

Feiyun Ouyang

Postdoctoral Research Associate, Department of Computer Science, University of Massachusetts Lowell

 

I received PhD from the Department of Epidemiology and Medical Statistics at Central South University, China. I am now working with Professor Hong Yu in the Bio-NLP lab. My research focuses on the epidemiology and influential factors of mental health and cardiovascular diseases. 

Research Staff

Weisong Liu

Research Assistant Professor, Department of Computer Science, University of Massachusetts Lowell

 

I received my PhD in Electrical Engineering from University of Wisconsin-Milwaukee. I am interested in designing and building text mining systems using advanced NLP and data analysis tools. My experience includes information extraction, document search/retrieval, parallel computing, and clouding computing. I am currently involved in AskHERMES, ADE Repository, NoteAid, and FigureSearch projects.

 WeisongLiu12

Edgard Alex Granillo

Health Outcome Associate, Department of Quantitative Health Sciences, University of Massachusetts Medical School

 

I am physician graduated from The Evangelist University of El Salvador, currently working with Dr. Yu's BioNLP (Biomedical Natural Language Processing) group in Biomedical and health informatics. Presently I am involved in a research project focusing in building pharmacovigilance tools with the aid of BioNLP to identify adverse drug events in electronic medical records. This project involves annotation of electronic health record narratives to aid machine learning for accurately recognition of medication use and their potential adverse effects.

During the last several years I have also been involved as a part of my  research career in multiple clinical and community base surveillance  research  studies focusing in prevention on cardiovascular heart disease, all these research projects  funded by the National Institute of Health.  

Currently my research focus is in BioNLP and its applications to the biomedical and healthcare field

 AlexE 

VA Staff

Emily Druhl

Health Science Specialist, Edith Nourse Rogers Memorial Veterans Hospital



I am the research coordinator for Dr. Yu’s NoteAid project, a system to help Veterans better understand their medical records. I received my Master of Public Health from the University of New England, and my Bachelor of Science in Biology from Mt. Mercy University in Iowa. I have almost 20 years of health care experience, including deployment as a medic during Operation Iraqi Freedom.

  Emily e2

Lay Language Dictionary Contributors

 

 

Primary Contributors Curators Main Medical Reviewers Additional Medical Reviewers Computer Science
Elaine Freund Lin Boynton  Rebecca Angoff Richeek Pradhan Weisong Liu
Victoria Wang Noah Rohrer Tyler Mehegan Alex Granillo Jinying Chen
Shreya Makkapati Stephanie Carvalho Jaclyn Davis Andrew Hsu Wen Hu 
Emily Druhl Maxwell Kruse Kevin O'Day Ricky Hansra  
Asha Daiska Kathryn DeLaughter   Sonali Harchandani  
Jenni Kim Smirnova  Yaw Opare-Sem      

 
 

Alumni

    • Shashank Agarwal — Senior engineer, Google
    • YongGang Cao — Senior engineer, Amazon
    • Brian Harrington — Associate Professor at the Department of Computer and Mathematical Sciences, University of Toronto Scarborough
    • Yanpeng Li — Staff scientist, IBM
    • Zuofeng Li — Staff, Philips Research
    • Feifan Liu — Associate Professor, UMass Medical School
    • Mary Shimoyama — Professor, Medical College of Wisconsin
    • Qing Zhang — Senior engineer, Airbnb

    • Balaji Polepalli Ramesh — Scientist, Nuance

    • Jinying Chen — Assistant Professor, Boston University

    • Tsendsuren Munkhdalai — Staff scientist, Microsoft

    • Timothy Miller  — Assistant Professor, Harvard Medical School

    • Laura Dietz — Assistant Professor, University of New Hampshire
    • John Lalor — Assistant Professor, Notre Dame
    • Jiaping Zhang — Assistant Professor, Indiana University - Purdue University Indianapolis
    • Yonghao Jin — Engineer, Google Japan
    • Fei Li — Associate Professor, Wuhan University
    • Xun Wang — Scientist, Microsoft
    • Emmie Ohnuki — Software Engineer, Asana, CA
    • Bhanu Pratap Singh — Applied Scientist, Amazon
    • Pengshan Cai — Research Scientist, ASAPP
    • Prakamya Mishra — Applied Research Engineer, AMD

Administrative

Sandra Stankus, Project Coordinator

Carla McDonald, Administrative Assistant

 

 

Details