Researchers
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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. |
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Feifan Liu, PhD(Co-Investigator) Assistant Professor at UMMS BioNLP Group, Department of Quantitative Health Sciences and Department of Radiology, University of Massachusetts Medical
School Worcester. I received Ph.D from the Institute of Automation, Chinese Academy of Sciences. I was a senior research scientist in healthcare division at Nuance Communications Inc. before joining UMMS. My research interests include natural language processing and machine learning, especially focusing on applying them towards next generation biomedical intelligence. |
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Jinying Chen Postdoctoral Research Scientist, Department of Quantitative Health Sciences, UMMS I am a postdoctoral research scientist, working at Dr. Hong Yu’s BioNLP group. I received my PhD from the Department of Computer and Information Science at the University of Pennsylvania. My research focuses on new algorithms and models for biomedical information extraction (literature and EHR) by leveraging natural language processing (NLP) and machine learning technologies. Ongoing projects include relation extraction for bio entities, open domain word sense disambiguation, active learning for clinical NER. My previous research projects include word sense disambiguation, information extraction, machine translation, and image document analysis. |
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Tsendsuren Munkhdalai Postdoctoral Associate, Department of Quantitative Health Sciences, UMMS
I am a postdoctoral associate at Prof. Hong’s BioNLP group at UMass Medical School. I received my Ph.D. from Database & Bioinformatics Laboratory at Chungbuk National University, South Korea. My research focuses on semi-supervised learning, representation learning and deep learning for text mining and natural language processing. In particular, I develop methods to leverage large unlabeled data and to improve performance on NLP related tasks, namely named entity recognition, and event and complex relation extraction. |
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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. |
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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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Gowtham R Raman
I am a Master's student (CS) at the University of Massachusetts, Amherst. My interests lie in machine learning and NLP. I am currently working in the Bio NLP lab under Prof. Hong on using deep-learning techniques to model Electronic Health Records and predict ICD codes. Prior to this, I interned at Yahoo! where I worked on building deep learning based Named Entity Recognition system. Before joining UMass, I was working with Ittiam systems in Bangalore. I completed my bachelors in Electronics and Communication Engineering from NIT, Trichy (India).
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Richeek Pradhan Research Assistant, Graduate School of Biomedical Sciences, UMass Medical School
I am a PhD student in the Graduate School of Biomedical Sciences in the UMass Medical School working under Dr. Hong Yu. I received my MD from the West Bengal University of Health Sciences, India, and completed my residency in Clinical Pharmacology, also under the same university. I briefly taught in a medical school in India and worked as a medical advisor to Novo Nordisk before I joined Dr. Yu’s lab as a PhD candidate. I am interested in adverse drug event detection from electronic health records utilizing natural language processing, and using this technology in the area of diabetes to detect unstructured hypoglycemia events from medical records. I am also interested in observational studies exploring issues in drug safety.
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Research Staff |
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Elaine Freund Program Director, Department of Quantitative Health Sciences, UMMS I received my PhD from University of Southern California Dept. of Molecular Biology. My experience spans academics, business, consulting and government environments. I have deep experience managing large scale, big data projects and working with multi-disciplinary scientific and technical teams. I participated in development of annotation tooling and have managed life-sciences annotation teams. Current projects involve annotation of electronic health record narratives to aid machine learning for identification of medication exposures and adverse events. |
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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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Matthew Cornell Senior Development Engineer, Department of Quantitative Health Sciences, UMMS
I am a research software engineer writing all sorts of programs for the lab (tools, applications, databases, NLP, and so on). I have a B.S. in Electrical Engineering, and an M.S. in Computer Science from UMass/Amherst. Before grad school I worked for NASA launching space ships early in the Shuttle program at the Kennedy Space Center. Since then I've worked for decades in various AI research labs, learning and utilizing whatever tool/language/system works the best for the project. I specialize in the Extreme Programming software development methodology.
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Victoria Wang Clinical Research Assistant, Department of Quantitative Health Sciences, UMMS
My work includes the annotating of medical records with MedDRA for Adverse Events, PHI, and other medical attributes. I evaluate synonym and curate lay-language definitions for medical terminologies and jargon. I work closely with other annotators and Elaine to manage organizational tasks for annotation and curation projects. I am also involved in the statistical analysis of the annotation data. |
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Nadya Frid Annotation Editor
I received my M.A. in Theoretical and Computational Linguistics from the Russian University for the Humanities, Moscow. Experienced in both academic and corporate environments. My expertise includes but is not limited to corpus linguistics, information extraction, ontology development, dictionary acquisition, machine translation, research on semantics, syntax, pragmatics and discourse. |
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Heather Keating Annotation Editor
I received my PhD in Cell and Molecular Biology from Purdue University and post-doctoral training in Genetics at University of Wisconsin-Madison. I have experience creating and editing content for many biological and biomedical databases, including ctdbase.org, a database examining relationships between human health, genes and chemical exposure. Currently I work as a senior editor developing annotation practices for electronic health records, contributing biomedical domain expertise to aid in machine learning and adverse drug event detection.
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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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Raelene Goodwin Annotator
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Brian Corner Annotator
I received my PhD in Biochemistry from University of Otago, New Zealand and postdoctoral training in Genetics at University of Washington, Monash University, and University of Minnesota. I have taught college classes in biology, and have experience creating and editing content for several biological/biomedical databases. I’m particularly interested in the application of emerging genetic technologies and artificial intelligence to healthcare. Currently I work as an annotator of electronic health records, focusing on adverse drug event detection.
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VA Staff |
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Emily Druhl
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Lay Language Dictionary Contributors |
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Alumni
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Administrative Sandra Stankus, Project Coordinator Carla McDonald, Administrative Assistant |
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