2017

PheKnow–Cloud: A Tool for Evaluating High-Throughput Phenotype Candidates using Online Medical Literature

Jette Henderson, Ryan Bridges, Joyce C. Ho, Byron C. Wallace and Joydeep Ghosh
AMIA Joint Summits on Translational Science
pre-print


Learning Interpretable Disentangled Representations of Clinical Abstracts

Edward Banner, Iain J. Marshall and Byron C. Wallace
pre-print


"Jerk" or "Judgemental"? Patient perceptions of male versus female physicians in online reviews

Byron C Wallace and Michael J Paul
AAAI Joint Workshop on Health Intelligence (W3PHIAI)
pre-print


Retrofitting Concept Vector Representations of Medical Concepts to Improve Estimates of Semantic Similarity and Relatedness

Zhiguo Yu, Byron C. Wallace, Todd Johnson and Trevor Cohen
MEDINFO


Active Discriminative Text Representation Learning

Ye Zhang, Matt Lease and Byron C. Wallace
AAAI Conference on Artificial Intelligence (AAAI)
pre-print


OpenMEE: Intuitive, open-source software for meta-analysis in ecology and evolutionary biology

Byron C. Wallace, Marc J. Lajeunesse, George Dietz, Issa J. Dahabreh, Thomas A. Trikalinos, Christopher H. Schmid and Jessica Gurevitch
Methods in Ecology and Evolution
(forthcoming)

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Exploiting Domain Knowledge via Grouped Weight Sharing with Application to Text Categorization

Ye Zhang, Matthew Lease and Byron C. Wallace
arxiv
pre-print


2016

A Correlated Worker Model for Grouped, Imbalanced and Multitask Data

An T. Nguyen, Byron C. Wallace and Matthew Lease
Uncertainty in Artificial Intelligence (UAI)
pre-print


Systematic Review is e-Discovery in Doctor's Clothing

Matthew Lease, Gordon V. Cormack, An Thanh Nguyen, Thomas A. Trikalinos, and Byron C. Wallace
Medical Information Retrieval (MedIR) Workshop at the 39th International ACM SIGIR Conference on Research and Development in Information Retrieval
pre-print


Rationale-Augmented Convolutional Neural Networks for Text Classification

Ye Zhang, Iain Marshall and Byron C. Wallace
Empirical Methods in Natural Language Processing (EMNLP)
pre-print


Modelling Context with User Embeddings for Sarcasm Detection in Social Media

Silvio Moreira, Byron C. Wallace, Hao Lyu, Paula Carvalho and Mário J. Gaspar da Silva
The SIGNLL Conference on Computational Natural Language Learning (CoNLL)
Covered in New Scientist magazine here: https://www.newscientist.com/article/2100007-ai-reads-your-tweets-and-spots-when-youre-being-sarcastic/

pre-print


Evaluating Data Abstraction Assistant, anovel software application for dataabstraction during systematic reviews:protocol for a randomized controlled trial

Ian J Saldanha, Christopher H Schmid, Joseph Lau, Kay Dickersin, Jesse A Berlin, Jens Jap, Bryant T Smith, Simona Carini, Wiley Chan, Berry De Bruijn, Byron C Wallace, Susan M Hutfless, Ida Sim, M Hassan Murad, Sandra A Walsh, Elizabeth J Whamond and Tianjing Li
Systematic Reviews
Trial protocol

link


Probabilistic Modeling for Crowdsourcing Partially-Subjective Ratings

An T. Nguyen, Matthew Halpern, Byron C. Wallace and Matthew Lease
AAAI HCOMP
pre-print link


Using Electronic Medical Records and Physician Data to Improve Information Retrieval for Evidence-Based Care

Mengqi Jin, Hongli Li, Christopher H. Schmid and Byron C. Wallace
International Conference on Healthcare Informatics (ICHI)
pre-print


Retrofitting Word Vectors of MeSH Terms to Improve Semantic Similarity Measures

Zhiguo Yu, Trevor Cohen, Todd R. Johnson, Byron C Wallace and Elmer Bernstam
The International Workshop on Health Text Mining and Information Analysis (Co-Located with EMNLP 2016)
link


A Data-Driven Approach to Characterizing the (Perceived) Newsworthiness of Health Science Articles

Ye Zhang, Erin Willis, Michael Paul, Noémie Elhadad and Byron C. Wallace
JMIR Medical Informatics
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Leveraging coreference to identify arms in medical abstracts: An experimental study

Elisa Ferracane, Iain Marshall, Byron C. Wallace and Katrin Erk
The International Workshop on Health Text Mining and Information Analysis (Co-Located with EMNLP 2016)
pre-print


Automated Verification of Phenotypes using PubMed

Ryan Bridges, Jette Henderson, Joyce Ho, Byron C. Wallace and Joydeep Ghosh
Methods and Applications for Healthcare Analytics (MAHA) at ACM BCB
pre-print


Neural Information Retrieval: A Literature Review

Ye Zhang, Md Mustafizur Rahman, Alex Braylan, Brandon Dang, Heng-Lu Chang, Henna Kim, Quinten McNamara, Aaron Angert, Edward Banner, Vivek Khetan, Tyler McDonnell, An Thanh Nguyen, Dan Xu, Byron C. Wallace and Matthew Lease
arxiv
pre-print link


MGNC-CNN: A Simple Approach to Exploiting Multiple Word Embeddings for Sentence Classification

Ye Zhang, Stephen Roller and Byron C. Wallace
North American Chapter of the Association for Computational Linguistics (NAACL)
pre-print


Improving the Utility of MeSH terms Using the TopicalMeSH Representation

Zhiguo Yu, Elmer Bernstam, Trevor Cohen, Byron C Wallace and Todd R Johnson
Journal of Biomedical Informatics (JBI)
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Extracting PICO Sentences from Clinical Trial Reports using Supervised Distant Supervision

Byron C Wallace, Joël Kuiper, Aakash Sharma, Mingxi (Brian) Zhu and Iain J. Marshall
Journal of Machine Learning Research (JMLR)
pre-print link


2015

What Predicts Media Coverage of Health Science Articles?

Byron C Wallace, Michael J Paul and Noémie Elhadad
The International Workshop on the World Wide Web and Public Health Intelligence (W3PHI)
pre-print


RobotReviewer: Evaluation of a System for Automatically Assessing Bias in Clinical Trials

Iain J. Marshall, Joël Kuiper and Byron C. Wallace
Journal of the American Medical Informatics Association (JAMIA)
Software available @: https://robot-reviewer.vortext.systems/

pre-print link


Automating Risk of Bias Assessment for Clinical Trials

Iain J. Marshall, Joël Kuiper and Byron C. Wallace
Journal of Biomedical and Health Informatics (JBHI)
An invited journal version of our 2014 ACM-BCB paper of the same the title.

pre-print link


Reports of the AAAI 2014 Conference Workshops

Stefano V. Albrecht, André M. S. Barreto, Darius Braziunas, David L. Buckeridge, Heriberto Cuayáhuitl, Nina Dethlefs, Markus Endres, Amir-massoud Farahmand, Mark Fox, Lutz Frommberger, Sam Ganzfried, Yolanda Gil, Sébastien Guillet, Lawrence E. Hunter, Arnav Jhala, Kristian Kersting, George Konidaris, Freddy Lecue, Sheila McIlraith, Sriraam Natarajan, Zeinab Noorian, David Poole, Rémi Ronfard, Alessandro Saffiotti, Arash Shaban-Nejad, Biplav Srivastava, Gerald Tesauro, Rosario Uceda-Sosa, Guy Van den Broeck, Martijn van Otterlo, Byron C. Wallace, Paul Weng, Jenna Wiens, Jie Zhang
Artificial Intelligence Magazine
link


Combining Crowd and Expert Labels using Decision Theoretic Active Learning

An T. Nguyen, Byron C. Wallace and Matthew Lease
Conference on Human Computation & Crowdsourcing (HCOMP)
pre-print


Healthcare Data Analytics Challenge

Zhiguo Yu, Byron C. Wallace and Todd R. Johnson
International Conference on Healthcare Informatics (ICHI)
Describes our system, which won the 2015 ICHI healthcare analytics challenge.

pre-print


Graph-Sparse LDA: A Topic Model with Structured Sparsity

Finale Doshi-Velez, Byron C Wallace and Ryan P Adams
AAAI Conference on Artificial Intelligence (AAAI)
pre-print


Sparse, Contextually Informed Models for Irony Detection: Exploiting User Communities, Entities and Sentiment

Byron C Wallace, Do Kook Choe and Eugene Charniak
Association for Computational Linguistics (ACL)
pre-print link


Editorial: special issue on machine learning for health and medicine

Jenna Wiens and Byron C. Wallace
Machine Learning Journal
link


A Sensitivity Analysis of (and Practitioners' Guide to) Convolutional Neural Networks for Sentence Classification

Ye Zhang and Byron C. Wallace
arXiv
pre-print


2014

#CochraneTech: Technology and the Future of Systematic Reviews

Julian Elliott, Ida Sim, Jessica Thomas, Nancy Owens, Gordon Dooley, Jacob Riis, Byron Wallace, James Thomas, Anna Noel-Storr, Gabriel Rada, Caroline Struthers, Tracey Howe, Harriet MacLehose, Linn Brandt, Ilkka Kunnamo and Chris Mavergames
Cochrane Library Editorial
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Can Cognitive Scientists Help Computers Recognize Irony?

Byron C. Wallace and Laura Kertz
Cognitive Science Society (CogSci)
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Automating Risk of Bias Assessment for Clinical Trials

Iain J. Marshall, Joël Kuiper and Byron C. Wallace
ACM Conference on Bioinformatics, Computational Biology, and Health Informatics
Selected as the best public health paper at ACM-BCB 2014 and invited for extended journal publication.

pre-print link


Humans Require Context to Infer Ironic Intent (so Computers Probably do, too)

Byron C. Wallace, Do Kook Choe, Laura Kertz and Eugene Charniak
Association for Computational Linguistics (ACL)
pre-print link


Improving Class Probability Estimates for Imbalanced Data

Byron C. Wallace and Issa J. Dahabreh
Knowledge and Information Systems
link


Identifying Differences in Physician Communication Styles with a Log-Linear Transition Component Model

Byron C. Wallace, Issa J. Dahabreh, Thomas A. Trikalinos, M. Barton Laws, Ira Wilson and Eugene Charniak
AAAI Conference on Artificial Intelligence (AAAI)
link


Discovering Better AAAI Keywords via Clustering with Community-sourced Constraints

Kelly H. Moran, Byron C. Wallace and Carla E. Brodley
AAAI Conference on Artificial Intelligence (AAAI)
link


Spá: a web-based viewer for text mining in Evidence Based Medicine

Jöel Kuiper, Iain J. Marshall, Byron C. Wallace and Morris A. Swertz
The European Conference on Machine Learning and Principles and Practice of Knowledge Discovery in Databases (ECML-PKDD)
pre-print link


A Large-Scale Quantitative Analysis of Latent Factors and Sentiment in Online Doctor Reviews

Byron C. Wallace, Michael J. Paul, Urmimala Sarkar, Thomas A. Trikalinos and Mark Dredze
Journal of the American Medical Informatics Association (JAMIA)
pre-print link


2013

Active Literature Discovery for Scoping Evidence Reviews: How Many Needles are There?

Byron C. Wallace, Issa J. Dahabreh, Kelly H. Moran, Carla E. Brodley and Thomas A. Trikalinos
KDD Workshop on Data Mining for Healthcare (KDD-DMH)
pre-print link


Modernizing Evidence Synthesis for Evidence-Based Medicine (Book Chapter)

Byron C Wallace, Issa J Dahabreh, Christopher H Schmid, Joseph Lau and Thomas A Trikalinos
Clinical Decision Support: The Road to Broad Adoption
link


What Affects Patient (Dis)satisfaction? Analyzing Online Doctor Ratings with a Joint Topic-Sentiment Model

Michael J. Paul, Byron C. Wallace and Mark Dredze
AAAI Workshop on Expanding the Boundaries of Health Informatics Using AI (HIAI)
link


A Generative Joint, Additive, Sequential Model of Topics and Speech Acts in Patient-Doctor Communication

Byron C. Wallace, Thomas A. Trikalinos, M. Barton Laws, Ira B. Wilson and Eugene Charniak
Empirical Methods in Natural Language Processing (EMNLP)
link


Computational Irony: A Survey and new Perspectives

Byron C Wallace
Artificial Intelligence Review
link


Modernizing the systematic review process to inform comparative effectiveness: tools and methods

Byron C Wallace, Issa J Dahabreh, Christopher H Schmid, Joseph Lau and Thomas A Trikalinos
Journal of Comparative Effectiveness Research
pre-print link


Automatically Annotating Topics in Transcripts of Patient-Provider Interactions via Machine Learning

Byron C. Wallace, M. Barton Laws, Kevin Small, Ira B. Wilson and Thomas A. Trikalinos
Medical Decision Making
Highlighted in this MDM editorial.

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2012

Challenges and opportunities in applied machine learning

Carla E. Brodley, Umaa Rebbapragada, Kevin Small and Byron C Wallace
Artificial Intelligence Magazine
link


Toward modernizing the systematic review pipeline in genetics: efficient updating via data mining.

Byron C. Wallace, Kevin Small, Carla E. Brodley, Joseph Lau, Christopher H. Schmid, Lars Bertram, Christina M. Lill, Joshua T. Cohen and Thomas A. Trikalinos
Genetics in Medicine
link


Machine Learning Health Informatics: Making Better use of Domain Experts

Byron C Wallace
PhD Thesis, Tufts University
Received the runner-up for the 2012 SIGKDD 2013 Dissertation Award

link


Class Probability Estimates are Unreliable for Imbalanced Data (and How to Fix Them)

Byron C. Wallace and Issa J. Dahabreh
International Conference on Data Mining (ICDM)
Selected as one of the "best of ICDM 2012"

pre-print link


Closing the Gap between Methodologists and End-Users: R as a Computational Back-End

Byron C. Wallace, Issa J. Dahabreh, Thomas A. Trikalinos, Joseph Lau, Paul Trow and Christopher H. Schmid
Journal of Statistical Software
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Multiple narrative disentanglement: Unraveling infinite jest

Byron C. Wallace
The North American Chapter of the Association for Computational Linguistics (NAACL)
link


2011

Deploying an interactive machine learning system in an evidence-based practice center: abstrackr

Byron C Wallace, Kevin Small, Carla E Brodley, Joseph Lau and Thomas A Trikalinos
ACM SIGHIT International Health Informatics Symposium (IHI)
pre-print link


Class Imbalance, Redux

Byron C. Wallace, Kevin Small, Carla E Brodley and Thomas A Trikalinos
International Conference on Data Mining (ICDM)
link


The constrained weight space SVM: Learning with ranked features

Kevin Small, Byron C. Wallace, Carla E. Brodley and Thomas A. Trikalinos
International Conference on Machine Learning (ICML)
link


Single cell time-resolved quorum responses reveal dependence on cell density and configuration

Ragnhild D. Whitaker, Steve Pember, Byron C Wallace, Carla E Brodley and David Walt
Journal of Biological Chemistry
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Who should label what? instance allocation in multiple expert active learning

Byron C Wallace, Kevin Small, Carla E Brodley and Thomas A Trikalinos
SIAM International Conference on Data Mining (SDM)
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2010

Active learning for biomedical citation screening

Byron C Wallace, Kevin Small, Carla E Brodley and Thomas A Trikalinos
ACM SIGKDD international conference on Knowledge discovery and data mining
pre-print link


Modeling annotation time to reduce workload in comparative effectiveness reviews

Byron C Wallace, Kevin Small, Carla E Brodley and Thomas A Trikalinos
ACM International Health Informatics Symposium (IHI)
pre-print link


Semi-automated screening of biomedical citations for systematic reviews

Byron C Wallace, Thomas A Trikalinos, Joseph Lau, Carla E Brodley and Chistopher H Schmid
BMC Bioinformatics
link


2009

Meta-Analyst: software for meta-analysis of binary, continuous and diagnostic data

Byron C Wallace, Christopher H Schmid, Joseph Lau and Thomas A Trikalinos
BMC Research Methods
Highly accessed

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The COPD Genetic Association Compendium: a Comprehensive Online Database of COPD Genetic Associations

PJ Castaldi, MH Cho, M Cohn, F Langerman, S Moran, N Tarragona, H Moukhachen, R Venugopal, D Hasimja, E Kao, BC Wallace, CP Hersh, S Bagade, L Bertram, EK Silverman, TA Trikalinos
Human Molecular Genetics
link