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

Jesse Lingeman

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

 

I am a Ph.D. student in Computer Science at the University of Massachusetts Amherst. I am working with Prof. Hong Yu in the BioNLP lab. My research interests focus primarily on using machine learning to provide insights into the world around us. One of my current projects is exploring how the authors of academic publications behave, and what factors decide whether or not they work together. This is done using a time series model that explicitly models how factors relating to both an author's publications and to the network of coauthors surrounding them are changing over time.

Previously, I obtained my MS in Computer Science at New York University with Prof. Dennis Shasha, using time series models to infer gene-gene interactions from gene expression data. My masters thesis was turned into an instructional textbook for beginning bioinformaticists on how to do gene network inference, and provides an overview of many state-of-art algorithms and techniques along with simulated performance examples. During that time I also worked with Prof. Karen Adolph in the Developmental Psychology Dept, studying how infants' and non-human primates' motor skills evolve while they are first learning them. I also was lead developer on the open source data annotation program Datavyu. Before that I obtained my BA in Political Science from Western Michigan University, focusing primarily on game theory and Constitutional law.

 

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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

Subendhu Rongali

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 in collaboration with Dr. Hong Yu on safe and iterpretable machine learning in healthcare. I received my Bachelor of Technology degree in Computer Science & Engineering from India Institute of Technology Madras.

Subendhu's Linkedin

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Rumeng Li

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.

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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. 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 Whuan University, China.

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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 of biomedical text. I received both of 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

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Fei Li

Postdoc, Department of Computer Science, University of Massachusetts Lowell

 

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

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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  
  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

Administrative

Sandra Stankus, Project Coordinator

Carla McDonald, Administrative Assistant