Researchers

 

Hong Yu, PhD (Principal Investigator)

Professor and Principal Investigator UMMS BioNLP Group, Dept of Quantitative Health Sciences, University of Massachusetts Medical School Worcester; Adjunct Professor, School of Computer Science, University of Massachusetts Amherst; Research Health Scientist, VA Central Western Massachusetts.

 

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

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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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Jiaping Zheng

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's degree from Nankai University and Master's degree from University of Minnesota.

My research interests include natural language processing, information extraction, and medical informatics. My projects are: Clinical Note Aid. Providing clinical notes to patients can improve health understanding and lead to better healthcare outcome. However, the language in the clinical notes presents a challenge to the patients' comprehension. We aim to lower the barrier by providing short and easier-to-understand explanations and educational resources relevant to the clinical notes.

Discovering gaps between consumer health resources. Consumer health resources created by experts may not need the demand of the average patient. We examine online users' questions and compare them to expert curated knowledge resources. This can help guide the creation of health knowledge sources and better allocate resources to the areas that consumers are interested in.

 

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Abhyuday Narayan Jagannatha

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

 

I am an MS/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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John Lalor

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 Dr. Hong Yu in the Bio-NLP group. My research interests are in Machine Learning and Natural Language Processing.

Prior to UMass, I worked as a software developer at Eze Software in Chicago. I received my Master's Degree in Computer Science at DePaul University, where I worked on projects in Computer Science Education and Recommender Systems. I received my bachelor's degree in Information Technology Management from the University of Notre Dame, with a minor in Irish Language & Literature.

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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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Research Staff

Weisong Liu

Snr. Development Engineer, Department of Quantitative Health Sciences, UMMS

 

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 Jenny Liu Rebecca Angoff Richeek Pradhan Weisong Liu
Victoria Wang Noah Rohrer Tyler Mehegan Alex Granillo Jinying Chen
Shreya Makkapati Stephanie Carvalho Jaclyn Davis Andrew Hsu
Emily Druhl Maxwell Kruse Kevin O'Day Ricky Hansra
Asha Daiska Kathryn DeLaughter Sonali Harchandani
Yaw Opare-Sem

 

 

Alumni

    • Shashank Agarwal — Currently a Senior Data Scientist & Machine Learning Engineer at DataXu
    • YongGang Cao — Currently an SDE at Expedia, Inc
    • Brian Harrington — Currently a Lecturer at the Department of Computer and Mathematical Sciences, University of Toronto Scarborough
    • Yanpeng Li — Currently an Assistant Professor at the Dalian University of Technology and postdoc/faculty member at The Mayo Clinic
    • Zuofeng Li — Currently a Senior Scientist at Philips Research China
    • Feifan Liu — Currently an Associate Scientist (Research Faculty) at the College of Health Sciences at University of Wisconsin-Milwaukee
    • Mary Shimoyama — Currently an Assistant Professor at the Medical College of Wisconsin
    • Aurora Lin
    • Qiang Li
    • Balaji Polepalli Ramesh

    • Feifan Liu

    • Jinying Chen

    • Tsendsuren Munkhdalai

    • Richeek Pradhan

    • Victoria Wang

Administrative

Sandra Stankus, Project Coordinator

Carla McDonald, Administrative Assistant