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.

 

 

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Bhanu Pratap Singh

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

I am a Ph.D. student at University of Massachusetts, Amherst. I'm working with Prof. Hong Yu. I received my Bachelor of Technology degree from Malaviya National Institute of Technology Jaipur.

Bhanu's Linkedin

bsinghpratap (Bhanu Pratap Singh) · GitHub

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.

Pengshan Cai

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. I study natural language processing, with a specific focus on its application in medical domain. I received my MS in Computer Science at Institute of Computing Technology, Chinese Academy of Sciences and BA in Computer Science from Wuhan University, China.

Alice

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

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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

Hiba Ahsan

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

 

I am an MS/PhD student at the University of Massachusetts Amherst, currently being advised by Professor Hong Yu. My interest lies in mining knowledge from clinical text using NLP.

Hiba's Linkedin

 Zhichao_2

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

 

Vijeta Deshpande

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

 

I am a Ph.D. student at the University of Massachusetts Lowell and working under the guidance of Prof. Hong Yu in the BioNLP lab.

I completed my M.S. in Operations Research from UMass Amherst where I worked on modeling non-communicable diseases (as a stochastic process) and finding optimal intervention strategies for the prevention and control of the disease. This work was done under the guidance of Prof. Chaitra Gopalappa in the Disease Modeling Lab. After graduation, I worked at Massachussetts General Hospital on evaluating the effectiveness of preventive interventions for HIV and COVID-19, under the guidance of Dr. Kennth Freedberg and Dr. Pooyan Kazemian (research group: MPEC).

I am very interested in improving medical decision-making through machine  learning, and at BioNLP I will focus on leveraging Natural Language Processing to understand unstructured data, to improve medical decision making.

Vijeta'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. 
 

Huan-Yuan's Linkedin

 

 

Samuel(Sam) Kovaly

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

 

I am a MS Student at UMASS Amherst CS. I am currently working with Prof. Hong Yu in UMass BioNLP group. I obtained B.S. in Computer Science at UMass Lowell. 
 

Sam's Linkedin

 

 

Minhwa Lee

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

 

I am a MS Studentn studying Computer Science at University of Massachusetts Amherst. I am currently working with Prof. Hong Yu in UMass BioNLP group.
Before joining UMass Amherst, I earned my BA degree at The Colledge of Wooster, Ohio, where I double-majored in Computer Science and Mathematics and minored in Statistical & Data Sciences as well. My research interests lie in the intersection of machine learning and natural language processing in healthcare domains.
 

Minhwa's Linkedin

 

 

Yi Cao

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

 

I am a MS student at the University of Massachusetts Amherst in the College of Information and Computing Sciences. I am currently working with Prof. Hong Yu in UMass BioNLP group. My interests are NLP and game development.
 

Yi's Linkedin

Emmie Ohnuki

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

 

I’m an undergraduate student at UMass Amherst majoring in Computer Science and minoring in mathematical computation and computational linguistics. I’m currently working under Professor Hong Yu in the BioNLP lab. My interests lie in NLP and ML.     

 

Guanghao(Gary) Wei

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

 

I am pursuing my bachelor's degree in Mathematics and Computer Science at UMass Amherst. I'm a developer interested in Artificial Intelligence, Cybersecurity, IoT, and Game Development. I'm currently working with Prof. Hong Yu at BioNLP Lab. My vision is to do something noble, and I'm still on the road to learning.
 

Gary's Linkedin

 

 

Xun Wang

Postdoc, Department of Computer Science, University of Massachusetts Lowell

 

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.

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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.

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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 — Assistant 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, UMass Medical School

    • 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
    • Abhyuday Jagannatha 

Administrative

Sandra Stankus, Project Coordinator

Carla McDonald, Administrative Assistant