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2020 – today
- 2021
[j22]Xianlong Zeng
, Simon M. Lin, Chang Liu:
Multi-View Deep Learning Framework for Predicting Patient Expenditure in Healthcare. IEEE Open J. Comput. Soc. 2: 62-71 (2021)- [c28]Xianlong Zeng, Simon M. Lin, Chang Liu:
Transformer-based unsupervised patient representation learning based on medical claims for risk stratification and analysis. BCB 2021: 17:1-17:9 - [c27]Xiang Yue, Xinliang Frederick Zhang, Ziyu Yao, Simon M. Lin, Huan Sun:
CliniQG4QA: Generating Diverse Questions for Domain Adaptation of Clinical Question Answering. BIBM 2021: 580-587 - [c26]Xinliang Frederick Zhang, Heming Sun, Xiang Yue, Simon M. Lin, Huan Sun:
COUGH: A Challenge Dataset and Models for COVID-19 FAQ Retrieval. EMNLP (1) 2021: 3759-3769 - [i9]Xianlong Zeng, Simon M. Lin, Chang Liu:
Transformer-based unsupervised patient representation learning based on medical claims for risk stratification and analysis. CoRR abs/2106.12658 (2021) - [i8]Xianlong Zeng, Simon M. Lin, Chang Liu:
Pre-training transformer-based framework on large-scale pediatric claims data for downstream population-specific tasks. CoRR abs/2106.13095 (2021) - 2020
- [j21]Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun:
Graph embedding on biomedical networks: methods, applications and evaluations. Bioinform. 36(4): 1241-1251 (2020) - [c25]Zhen Wang, Jennifer Lee, Simon M. Lin, Huan Sun:
Rationalizing Medical Relation Prediction from Corpus-level Statistics. ACL 2020: 8078-8092 - [c24]Selasi Attipoe, Yungui Huang, Sharon B. Schweikhart, Jennifer L. Hefner, Daniel M. Walker, Steven W. Rust, Jeffrey Hoffman, Simon M. Lin:
Tasks Associated With Extreme After-hours EHR Use Among Ambulatory Care Pediatricians. AMIA 2020 - [c23]Kaushik Mani, Xiang Yue, Bernal Jimenez Gutierrez, Yungui Huang, Simon M. Lin, Huan Sun:
Clinical Phrase Mining with Language Models. BIBM 2020: 1087-1090 - [c22]Manirupa Das, Juanxi Li, Eric Fosler-Lussier, Simon M. Lin, Steve Rust, Yungui Huang, Rajiv Ramnath:
Sequence-to-Set Semantic Tagging for Complex Query Reformulation and Automated Text Categorization in Biomedical IR using Self-Attention. BioNLP 2020: 14-27 - [c21]Xianlong Zeng, Yunyi Feng, Soheil Moosavinasab, Deborah Lin, Simon M. Lin, Chang Liu:
Multilevel Self-Attention Model and Its Use on Medical Risk Prediction. PSB 2020: 115-126 - [i7]Zhen Wang, Jennifer Lee, Simon M. Lin, Huan Sun:
Rationalizing Medical Relation Prediction from Corpus-level Statistics. CoRR abs/2005.00889 (2020) - [i6]Xinliang Frederick Zhang, Heming Sun, Xiang Yue, Emmett Jesrani, Simon M. Lin, Huan Sun:
COUGH: A Challenge Dataset and Models for COVID-19 FAQ Retrieval. CoRR abs/2010.12800 (2020) - [i5]Xiang Yue, Xinliang Frederick Zhang, Ziyu Yao, Simon M. Lin, Huan Sun:
CliniQG4QA: Generating Diverse Questions for Domain Adaptation of Clinical Question Answering. CoRR abs/2010.16021 (2020)
2010 – 2019
- 2019
- [j20]Alessandra C. Gasior, Carlos Reck, Victoria Lane, Richard J. Wood, Jeremy Patterson, Robert Strouse, Simon M. Lin, Jennifer N. Cooper, D. Gregory Bates, Marc A. Levitt:
Transcending Dimensions: a Comparative Analysis of Cloaca Imaging in Advancing the Surgeon's Understanding of Complex Anatomy. J. Digit. Imaging 32(5): 761-765 (2019) - [c20]Yunyi Feng, Simon M. Lin, Enju Lin, Lesley Farley, Yungui Huang, Chang Liu:
Identifying Candidates for Medical Coding Audits: Demonstration of a Data Driven Approach to Improve Medicare Severity Diagnosis-Related Group Coding Compliance. HIS 2019: 47-57 - [c19]Zhen Wang, Xiang Yue, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Huan Sun:
SurfCon: Synonym Discovery on Privacy-Aware Clinical Data. KDD 2019: 1578-1586 - [c18]Zhizhang Hu, Emre Sezgin, Simon M. Lin, Pei Zhang, Hae Young Noh, Shijia Pan:
Device-free Sleep Stage Recognition through Bed Frame Vibration Sensing. DFHS@BuildSys 2019: 39-43 - [i4]Xiang Yue, Zhen Wang, Jingong Huang, Srinivasan Parthasarathy, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Wen Zhang, Ping Zhang, Huan Sun:
Graph Embedding on Biomedical Networks: Methods, Applications, and Evaluations. CoRR abs/1906.05017 (2019) - [i3]Zhen Wang, Xiang Yue, Soheil Moosavinasab, Yungui Huang, Simon M. Lin, Huan Sun:
SurfCon: Synonym Discovery on Privacy-Aware Clinical Data. CoRR abs/1906.09285 (2019) - [i2]Xianlong Zeng, Soheil Moosavinasab, En-Ju D. Lin, Simon M. Lin, Razvan C. Bunescu, Chang Liu:
Distributed representation of patients and its use for medical cost prediction. CoRR abs/1909.07157 (2019) - [i1]Manirupa Das, Juanxi Li, Eric Fosler-Lussier, Simon M. Lin, Soheil Moosavinasab, Steve Rust, Yungui Huang, Rajiv Ramnath:
Sequence-to-Set Semantic Tagging: End-to-End Multi-label Prediction using Neural Attention for Complex Query Reformulation and Automated Text Categorization. CoRR abs/1911.04427 (2019) - 2018
- [c17]Selasi Attipoe, Yungui Huang, Sharon B. Schweikhart, Simon M. Lin:
Variation in After-hours EHR Usage among Ambulatory Care Physicians. AMIA 2018 - [c16]Syed-Amad A. Hussain, Soheil Moosavinasab, Emre Sezgin, Yungui Huang, Simon M. Lin:
Char2Vec: Learning the Semantic Embedding of Rare and Unseen Words in the Biomedical Literature. AMIA 2018 - [c15]Emre Sezgin, Monica Weiler, Anthony Weiler, Simon M. Lin:
A roadmap of transition to health independence: A patient-centered study of self-management and digital-health solutions among teens with chronic conditions. AMIA 2018 - [c14]Xianlong Zeng, Soheil Moosavinasab, Enju Lin, Yungui Huang, Chang Liu, Simon M. Lin:
DeepChild: Hospitalization Prediction via Neural Network. AMIA 2018 - [c13]David Chen, Steve Rust, En-Ju D. Lin, Simon M. Lin, Leslie Nelson, Lindsay Alfano, Linda P. Lowes:
Prediction of Clinical Outcomes of Spinal Muscular Atrophy Using Motion Tracking Data and Elastic Net Regression. BCB 2018: 474-481 - [c12]Manirupa Das, Eric Fosler-Lussier, Simon M. Lin, Soheil Moosavinasab, David Chen, Steve Rust, Yungui Huang, Rajiv Ramnath:
Phrase2VecGLM: Neural generalized language model-based semantic tagging for complex query reformulation in medical IR. BioNLP 2018: 118-128 - 2017
- [j19]Rajeswari Swaminathan, Yungui Huang, Caroline Astbury, Sara Fitzgerald-Butt, Katherine Miller, Justin Cole, Christopher W. Bartlett, Simon M. Lin:
Clinical exome sequencing reports: current informatics practice and future opportunities. J. Am. Medical Informatics Assoc. 24(6): 1184-1191 (2017) - [j18]Wei Chen, Claire Durkin, Yungui Huang, Brent Adler, Steve Rust, Simon M. Lin:
Simplified Readability Metric Drives Improvement of Radiology Reports: an Experiment on Ultrasound Reports at a Pediatric Hospital. J. Digit. Imaging 30(6): 710-717 (2017) - [c11]Tyler Gorham, Steven W. Rust, Jing Yang, James Lin, Richard Hoyt, Swan Bee Liu, Jeffrey Hoffman, Tensing Maa, Yungui Huang, Simon M. Lin:
Vitals Risk Index: A Simplified Pediatric Early Warning Index that Relies Solely on Objective Measures. AMIA 2017 - [c10]Katherine Miller, Rajeswari Swaminathan, Soheil Moosavinasab, Robert Strouse, Matthew Bailey, Yungui Huang, Simon M. Lin:
Genome Dashboard: An Interactive Tool for the Exploration of Human Genomic Variants and Phenotypic Associations. AMIA 2017 - [c9]Emre Sezgin, Koushik Jinna, Tran Bourgeois, Soheil Moosavinasab, Yungui Huang, Simon M. Lin:
DeepSuggest: Query Expansion for Clinical Notes by Deep Learning. AMIA 2017 - [c8]Rajeswari Swaminathan, Yungui Huang, Katherine Miller, Matthew Pastore, Sayaka Hashimoto, Theodora Jacobson, Danielle Mouhlas, Simon M. Lin:
Sharing exome sequencing data between Clinical Sequencing Labs and Healthcare Providers. AMIA 2017 - 2016
- [j17]Soheil Moosavinasab, Jeremy Patterson, Robert Strouse, Majid Rastegar-Mojarad, Kelly Regan, Philip R. O. Payne, Yungui Huang, Simon M. Lin:
'RE: fine drugs': an interactive dashboard to access drug repurposing opportunities. Database J. Biol. Databases Curation 2016 (2016) - [j16]Zhan Ye, Christopher Kadolph, Robert Strenn, Daniel Wall, Elizabeth McPherson, Simon M. Lin:
WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data. Comput. Biol. Medicine 68: 165-169 (2016) - [c7]Wei Chen, Soheil Moosavinasab, Steve Rust, Yungui Huang, Simon M. Lin, Anna Zemke, Ariana Prinzbach:
Evaluation of a Machine Learning Method to Rank PubMed Central Articles For Clinical Relevancy: NCH at TREC 2016 Clinical Decision Support Track. TREC 2016 - 2015
- [j15]Scott J. Hebbring, Majid Rastegar-Mojarad, Zhan Ye, John Mayer, Crystal Jacobson, Simon M. Lin:
Application of clinical text data for phenome-wide association studies (PheWASs). Bioinform. 31(12): 1981-1987 (2015) - [j14]Simon M. Lin, Marco Tomamichel:
Investigating properties of a family of quantum Rényi divergences. Quantum Inf. Process. 14(4): 1501-1512 (2015) - 2014
- [c6]Amy Webb, Aaron Albin, Zhan Ye, Majid Rastegar-Mojarad, Kun Huang, Jeffrey D. Parvin, Wolfgang Sadee, Lang Li, Simon M. Lin, Yang Xiang:
Mining massive SNP data for identifying associated SNPs and uncovering gene relationships. BCB 2014: 304-313 - [c5]Matthew Fredrikson, Eric Lantz, Somesh Jha, Simon M. Lin, David Page, Thomas Ristenpart:
Privacy in Pharmacogenetics: An End-to-End Case Study of Personalized Warfarin Dosing. USENIX Security Symposium 2014: 17-32 - 2013
- [j13]Kai Peng, Wei Xu, Jianyong Zheng, Kegui Huang, Huisong Wang, Jiansong Tong, Zhifeng Lin, Jun Liu, Wenqing Cheng, Dong Fu, Pan Du, Warren A. Kibbe, Simon M. Lin, Tian Xia:
The disease and gene annotations (DGA): an annotation resource for human disease. Nucleic Acids Res. 41(Database-Issue): 553-560 (2013) - [c4]Matthias Samwald, Robert R. Freimuth, Joanne S. Luciano, Simon M. Lin, Robert L. Powers, M. Scott Marshall, Klaus-Peter Adlassnig, Michel Dumontier, Richard D. Boyce:
An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics. MedInfo 2013: 539-542 - 2011
- [j12]Pedro Madrigal, Noa Sela, Simon M. Lin:
PLoS Computational Biology Conference Postcards from ISMB/ECCB 2011. PLoS Comput. Biol. 7(11) (2011) - 2010
- [j11]Lihua Julie Zhu, Claude Gazin, Nathan D. Lawson, Hervé Pagès, Simon M. Lin, David S. Lapointe, Michael R. Green:
ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinform. 11: 237 (2010) - [j10]Pan Du, Xiao Zhang, Chiang-Ching Huang, Nadereh Jafari, Warren A. Kibbe, Lifang Hou, Simon M. Lin:
Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinform. 11: 587 (2010)
2000 – 2009
- 2009
- [j9]Pan Du, Gang Feng, Jared Flatow, Jie Song, Michelle Holko, Warren A. Kibbe, Simon M. Lin:
From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations. Bioinform. 25(12) (2009) - 2008
- [j8]Pan Du, Warren A. Kibbe, Simon M. Lin:
lumi: a pipeline for processing Illumina microarray. Bioinform. 24(13): 1547-1548 (2008) - [j7]Pan Du, Simon M. Lin, Mary Qu Yang, Jack Y. Yang:
2009 and beyond: the decade of personalised medicine. Int. J. Comput. Biol. Drug Des. 1(4): 329-333 (2008) - [j6]Chia-Ju Lee, Dong Fu, Pan Du, Hongmei Jiang, Simon M. Lin, Warren A. Kibbe:
A divide-and-conquer strategy to solve the out-of-memory problem of processing thousands of Affymetrix microarrays. Int. J. Comput. Biol. Drug Des. 1(4): 396-405 (2008) - 2007
- [c3]Pan Du, Simon M. Lin, Warren A. Kibbe, Haihui Wang:
Application of Wavelet Transform to the MS-based Proteomics Data Preprocessing. BIBE 2007: 680-686 - 2006
- [j5]Pan Du, Warren A. Kibbe, Simon M. Lin:
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinform. 22(17): 2059-2065 (2006) - 2004
- [j4]Simon M. Lin, Patrick McConnell, Kimberly F. Johnson, Jennifer Shoemaker:
MedlineR: an open source library in R for Medline literature data mining. Bioinform. 20(18): 3659-3661 (2004) - 2002
- [j3]Patrick McConnell, Kimberly F. Johnson, Simon M. Lin:
Applications of Tree-Maps to hierarchical biological data. Bioinform. 18(9): 1278-1279 (2002) - [j2]Nilanjan Dasgupta, Simon M. Lin, Lawrence Carin:
Sequential modeling for identifying CpG island locations in human genome. IEEE Signal Process. Lett. 9(12): 407-409 (2002) - [c2]Xuejun Liao, Nilanjan Dasgupta, Simon M. Lin, Lawrence Carin:
ICA and PLS modeling for functional analysis and drug sensitivity for DNA microarray signals. ICASSP 2002: 3880-3883 - 2001
- [j1]Kimberly F. Johnson, Simon M. Lin:
Critical Assessment of Microarray Data Analysis: the 2001 challenge. Bioinform. 17(9): 857-858 (2001) - [c1]Simon M. Lin, Sumeer Dhar, Rose-Mary N. Boustany:
Extracting knowledge from gene expression data: A case study of Batten Disease. BIOKDD 2001: 2-7
Coauthor Index
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