[Jun 2017] My PhD Thesis awarded the inaugural Doctoral Dissertation Award Honorable Mention by AMIA
[Apr 2017] Welcome incoming post-doctoral associates: Dr. Chengsheng Mao and Dr. Yuan Zhao
[Apr 2017] Our biomedical relation extraction paper was recommended by F1000Prime.
[Mar 2017] Our SANTF paper was selected into the 2016 IMIA Yearbook of Medical Informatics as one of the five best NLP works in the year.
[Nov 2016] Computational Phenotyping Tutorial [slides] at AMIA 2016 (with Fei Wang, Jimeng Sun, Xiaoqian Jiang)
[Sept 2016] Seminar at Amazon Research
Yuan holds a Ph.D. from MIT, with a Computer Science major and a Mathematics minor. He completed the GEMS (Graduate Education in Medical Sciences) certificate program by MIT IMES (Institute for Medical Engineering and Science) to gain exposure to general medicine. His advisors are Prof. Peter Szolovits and Prof. Ozlem Uzuner. He also works(ed) with Prof. Andrew Lo, Prof. Sam Madden, Dr. Ephraim Hochberg, Dr. Aliyah R. Sohani, Dr. Jason Baron, Dr. Anand Dighe, Dr. Alal Eran and Dr. Issac Kohane.
Machine learning, natural language processing, time series analysis, computational genomics and big data analytics, with a focus on medical and clinical applications including but not limited to lymphoma, breast cancer, cardiovascular disease, and kidney diseases.
Journal Submission Preprints
* indicates corresponding author
Segment convolutional neural networks (Seg-CNNs) for classifying relations in clinical notes
Luo, Y; Cheng, Y; Uzuner, O; Szolovits, P; Starren, J.
Journal of the American Medical Informatics Association (JAMIA) 2017 doi: 10.1093/jamia/ocx090.
Recurrent neural networks for classifying relations in clinical notes
Journal of Biomedical Informatics, 2017, 72: 85-95.
Natural Language Processing for EHR-Based Pharmacovigilance: A Structured Review
Luo, Y; Thompson, WK; Herr, TM; Zeng, Z; Berendsen MA; Jonnalagadda, S; Starren, J.
Drug Safety, 2017 doi: 10.1007/s40264-017-0558-6.
Tensor factorization for precision medicine in heart failure with preserved ejection fraction
Luo, Y; Ahmad, F; Sha, S.
Journal of Cardiovascular Translational Research, 2017, 10(3): 305-312.
Efficient Queries of Stand-off Annotations for Natural Language Processing on Electronic Medical Records
Luo, Y; Szolovits, P.
Biomedical Informatics Insights 2016:8 29-38, doi: 10.4137/BII.S38916.
Tensor Factorization towards Precision Medicine
Luo, Y; Wang, F; Szolovits, P.
Briefings in Bioinformatics 2016, doi: 10.1093/bib/bbw026.
Bridging Semantics and Syntax with Graph Algorithms - State-of-the-Art of Extracting Biomedical Relations
Luo, Y; Uzuner, O; Szolovits, P.
Briefings in Bioinformatics 2016, doi: 10.1093/bib/bbw001.
Using Machine Learning to Predict Laboratory Test Results
Luo, Y; Szolovits, P; Dighe, A; Baron, J.
American Journal of Clinical Pathology 2016, doi: http://dx.doi.org/10.1093/ajcp/aqw064.
Subgraph Augmented Non-Negative Tensor Factorization (SANTF) for Modeling Clinical Text
Luo, Y; Xin, Y; Hochberg, E; Joshi, R; Uzuner, O; Szolovits, P.
Journal of the American Medical Informatics Association (JAMIA) 2015 doi: 10.1093/jamia/ocv016.
Selected into the 2016 IMIA Yearbook of Medical Informatics as one of the five best NLP works in the year.
MIT News "How a computer can help your doctor better diagnose cancer"
Boston Magazine "Can a Computer Diagnose Cancer?"
Gizmodo "MIT Is Developing an AI Cancer Diagnosis System"
SD Times "MIT researchers are developing software to better diagnose cancer"
Text Mining in Cancer Gene and Pathway Prioritization [pdf]
Luo, Y; Riedlinger, G; Szolovits, P.
Cancer Informatics 2014 13(S1): 69-79.
Automatic Lymphoma Classification with Sentence Subgraph Mining from Pathology Reports [pdf]
Luo, Y; Sohani, AR; Hochberg, E; Szolovits, P.
Journal of the American Medical Informatics Association (JAMIA) 2014 21(5):824-832.
A De-Identifier for Medical Discharge Summaries [pdf]
Uzuner, Ö; Sibanda, T; Luo, Y; Szolovits, P.
Artificial intelligence in medicine 2008 42(1): 13-35.
Identifying patient smoking status from medical discharge records [pdf]
Uzuner Ö; Goldstein, I; Luo, Y; Kohane, I.
Journal of the American Medical Informatics Association (JAMIA) 2008 15(1): 14-24.
Evaluating the state-of-the-art in automatic de-identification. [pdf]
Uzuner, Ö; Luo, Y; Szolovits, P.
Journal of the American Medical Informatics Association (JAMIA) 2007 14(5): 550-563..
* indicates corresponding author
Contralateral Breast Cancer Event Detection Using Nature Language Processing [pdf]
Zeng, Z; Li, X; Espino, S; Roy, A; Kitsch, K; Clare, S; Khan, S; Luo, Y*.
AMIA Annual Symposium 2017 (Full Paper, Podium Presentation).
Predicting ICU Mortality Risk by Grouping Temporal Trends from a Multivariate Panel of Physiologic Measurements [pdf]
Luo, Y; Xin, Yu; Joshi, R; Celi, L; Szolovits, P.
AAAI Conference on Artificial Intelligence 2016.
Efficient Algebraic Interval Queries on Biomedical Sequence Annotations [abstract]
Luo, Y; Szolovits, P.
AMIA Joint Summits on Translational Science 2014 (Abstract, Podium Presentation), full paper in preparation.
Semi-Supervised Learning to Identify UMLS Semantic Relations [pdf]
Luo, Y; Uzuner Ö.
AMIA Joint Summits on Translational Science 2014 (Full Paper, Podium Presentation).
A Study on Expert Sourcing Enterprise Question Collection and Classification [pdf]
Luo, Y; Boucher, T; Oral, T; Osofsky, D; Weber, S.
Language Resources and Evaluation Conference (LREC) 2014.
Unsupervised Learning in Clinical Narrative Text and Physiological Time Series Using Tensor Factorization
Luo, Y; Xin, Y; Joshi, R; Szolovits, P.
NIPS Workshop on Machine Learning for Clinical Data Analysis and Healthcare 2013.
Extending CyDAS's Karyotype Parser to Understand in Situ Hybridization
AMIA Annual Symposium 2012 (Poster).
Honors And Awards
- AAAS/Science Program for Excellence in Science (1/2014)
- First prize in AMIA 2013 Natural Language Processing Doctoral Consortium (11/2013)
- Weilun Fund Fellowship, Tsinghua University (2002-2004)
- First Prizes in China National Olympiad in Chemistry and Mathematics (2000-2001)
09/2015 - Present, Course Director/Co-Instructor, HSIP 441, HSIP 42 Methods in Health and Biomedical Informatics (Graduate) Northwestern
Role: covering materials on non-parametric Bayesian statistics, Graph Mining, Machine Learning
01/2013 - 05/2013, Teaching Assistant, 6.830/6.814 Database Systems (Graduate/Undergraduate) MIT
Supervisor: Prof. Sam Madden
09/2007 - 05/2008, Teaching Assistant, CS564 Database Management Systems (Undergraduate) UW-Madison
Supervisors: Prof. Anhai Doan, Prof. David DeWitt
Selected Professional Services
- Program Committee Member, ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) 2017
- Scientific Program Committee Member, AMIA Joint Summits on Translational Science 2017
- Program Committee Member, Conference on Information and Knowledge Management (CIKM) 2015
- Member of the 2014-2015 Student Editorial Board for Journal of the American Medical Informatics Association (JAMIA)
- Session chairs for AMIA Annual Symposium (2014 and 2015)
- Chair for the session of Clinical Data Repositories, in 2014 AMIA Joint Summits on Translational Science
- Member of AAAI, AAAS, AMIA
Reviewer for the following journals: Journal of the American Medical Informatics Association (JAMIA), Journal of Biomedical Informatics, BMC Bioinformatics, BMC Medical Informatics and Decision Making, PLOS One, Biomed Research International, IEEE Transaction on Image Processing (TIP)
Reviewer for American Medical Informatics Association (AMIA) Annual Symposium, and AMIA Joint Summits on Translational Science
05/2011 - 08/2011, 12/2011 - 02/2012, 05/2012 - 08/2012, intern at CIO Lab, IBM, MA
Supervisors: Tolga Oral, Sara Weber
- Leader of a group of three interns researching on adapting the Watson DeepQA system that won the Jeopardy! Challenge to support question and answering in IBM's sales domain.
- Developed an enterprise question classification system with question classification guidelines. Developed candidate answer generators for multiple enterprise question classes. Worked in content ingestion across various IBM repositories as well as enterprise ontology creation.
05/2008 - 08/2008, intern at Server Manageability Group, Oracle, CA
Supervisors: Leonidas Galanis, Karl Dias
- Research on topics in synthetic and real database workload clustering, with workload features such as read/write table, OCI type etc, or user customized features.
- Developed a workload clustering system that enhanced Oracle Database Replay (a real application testing tool) to more intelligent testing, enabling test on both hardware change and application change.
Last modified: Sept. 2016