2018

Machine Learning for Identifying Randomized Controlled Trials: an evaluation and practitioner’s guide

Iain Marshall, Anna Noel Storr, Joël Kuiper, James Thomas and Byron C. Wallace
Research Synthesis Methods
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An Interpretable Joint Graphical Model for Fact-Checking from Crowds

An Thanh Nguyen, Aditya Kharosekar, Matthew Lease and Byron C. Wallace
Proceedings of the Thirty-Second AAAI Conference on Artificial Intelligence (AAAI-18)
pre-print


Living systematic reviews: 2. Combining human and machine effort

J Thomas, A Noel-Storr, I Marshall, BC Wallace, S McDonale, C Mavergames, P Glasziou, I Shemilt, A Synnot, T Turner and J Elliot
Journal of Clinical Epidemiology
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Neural Information Retrieval: At the End of the Early Years

KD Onal, Y Zhang, IS Altingovde, M Rahman, P Karagoz, A Braylan, B Dang, HL Chang, H Kim, Q McNamara, A Angert, E Banner, V Khetan, T McDonnell, AT Nguyen, D Xu, BC Wallace, M Rijke, and M Lease
Information Retrieval
pre-print link


2017

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

Ye Zhang and Byron C. Wallace
International Joint Conference on Natural Language Processing (IJCNLP)
pre-print


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
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Aggregating and Predicting Sequence Labels from Crowd Annotations

An Thanh Nguyen, Byron C. Wallace, Junyi Jessy Li, Ani Nenkova and Matthew Lease
Association for Computational Linguistics (ACL)
pre-print


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
Recipient of the 2017 Distinguished Clinical Research Informatics Paper Award

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


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

Ye Zhang, Matthew Lease and Byron C. Wallace
Association for Computational Linguistics (ACL)
pre-print


Quantifying Mental Health from Social Media with Neural User Embeddings

Silvio Amir, Glen Coppersmith, Paula Carvalho, Mário J. Silva and Byron C. Wallace
Machine Learning in Health Care (MLHC)
pre-print


An Exploration of Crowdsourcing Citation Screening for Systematic Reviews

Michael L. Mortensen, Gaelen P. Adam, Thomas A. Trikalinos, Tim Kraska and Byron C. Wallace
Research Synthesis Methods
pre-print


Automating Biomedical Evidence Synthesis: RobotReviewer

Iain Marshall, Joël Kuiper, Edward Banner and Byron C. Wallace
Association for Computational Linguistics (ACL)
Demo paper

pre-print


Identifying diagnostic test accuracy publications using a deep model

Gaurav Singh, Iain Marshall, James Thomas and Byron C. Wallace
CLEF eHealth


Identifying Reports of Randomized Controlled Trials (RCTs) via a Hybrid Machine Learning and Crowdsourcing Approach

Byron C. Wallace, Anna Noel-Storr, Iain J Marshall, Aaron M. Cohen, Neil R. Smalheiser and James Thomas
Journal of the American Medical Informatics Association (JAMIA)
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A Neural Candidate-Selector Architecture for Automatic Structured Clinical Text Annotation

Gaurav Singh, Iain Marshall, James Thomas, John Shawe-Taylor and Byron C. Wallace
International Conference on Information and Knowledge Management (CIKM)
pre-print


Detecting Twitter posts with Adverse Drug Reactions using Convolutional Neural Networks

Sarthak Jain, Xun Peng and Byron C. Wallace
Media Mining for Health Applications Workshop & Shared Task at AMIA 2017
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2016

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


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

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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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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


Probabilistic Modeling for Crowdsourcing Partially-Subjective Ratings

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


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)
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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


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


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


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


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


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


2015

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


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


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


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


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


Editorial: special issue on machine learning for health and medicine

Jenna Wiens and Byron C. Wallace
Machine Learning Journal
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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
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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


2014

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


#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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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)
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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


Improving Class Probability Estimates for Imbalanced Data

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


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


2013

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
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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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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


Computational Irony: A Survey and new Perspectives

Byron C Wallace
Artificial Intelligence Review
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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)
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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


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)
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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
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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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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
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Multiple narrative disentanglement: Unraveling infinite jest

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


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

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2011

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)
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Class Imbalance, Redux

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


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)
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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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


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
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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


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
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