2022
Combining Feature and Instance Attribution to Detect Artifacts
Pouya Pezeshkpour, Sarthak Jain, Sameer Singh and Byron C. Wallace
Evaluating Factuality in Text Simplification
Ashwin Devaraj, William Berkeley Sheffield, Byron C Wallace and Junyi Jessy Li
Accuracy and Efficiency of Machine Learning–Assisted Risk-of-Bias Assessments in “Real-World” Systematic Reviews
Anneliese Arno, James Thomas, Byron C. Wallace, Iain J. Marshall, Joanne E. McKenzie, and Julian H. Elliott
2021
Interpretability Analysis for Named Entity Recognition to Understand System Predictions and How They Can Improve
Oshin Agarwal, Yinfei Yang, Byron C. Wallace, and Ani Nenkova
Generating (Factual?) Narrative Summaries of RCTs: Experiments with Neural Multi-Document Summarization
Byron C. Wallace, Sayantan Saha, Frank Soboczenski and Iain J. Marshall
Understanding Clinical Trial Reports: Extracting Medical Entities and Their Relations
Benjamin E. Nye, Jay DeYoung, Eric Lehman, Ani Nenkova, Iain J. Marshall, and Byron C. Wallace
An Empirical Comparison of Instance Attribution Methods for NLP
Pouya Pezeshkpour, Sarthak Jain, Byron C. Wallace and Sameer Singh
Paragraph-level Simplification of Medical Texts
Ashwin Devaraj, Iain J. Marshall, Byron C. Wallace and Junjy Jessy Li
Does BERT Pretrained on Clinical Notes Reveal Sensitive Data?
Eric Lehman, Sarthak Jain, Karl Pichotta, Yoav Goldberg and Byron C. Wallace
On the Impact of Random Seeds on the Fairness of Clinical Classifiers
Silvio Amir, Jan-Willem van de Meent and Byron C. Wallace
State of the evidence: a survey of global disparities in clinical trials
Iain J Marshall, Veline L'Esperance, Rachel Marshall, James Thomas, Anna Noel-Storr, Frank Soboczenski, Benjamin Nye, Ani Nenkova, Byron C. Wallace
Biomedical Interpretable Entity Representations
Diego Garcia-Olano, Yasumasa Onoe, Ioana Baldini, Joydeep Ghosh, Byron C. Wallace and Kush Varzney
Unsupervised Data Augmentation with Naive Augmentation and without Unlabeled Data
David Lowell, Brian Howard, Zachary C. Lipton. Byron C. Wallace
Disentangling Representations of Text by Masking Transformers
Xiongyi Zhang, Jan-Willem van de Meent and Byron C. Wallace
What Would it Take to get Biomedical QA Systems into Practice?
Gregory Kell, Iain Marshall, Byron C. Wallace and Andre Jaun
2020
Towards a Computational Framework for Automating Substance Use Counseling with Virtual Agents
Stefan Olafsson, Byron C. Wallace, and Timothy Bickmore
Semi-Automated Evidence Synthesis in Health Psychology: Current Methods and Future Prospects
Iain Marshall, Blair T. Johnson, Zigeng Wang, Sanguthevar Rajasekaran and Byron C. Wallace
MMiDaS-AE: Multi-modal Missing Data aware Stacked Autoencoder for Biomedical Abstract Screening
Eric Lee, Byron C. Wallace, Karla Galaviz, and Joyce C. Ho
ERASER: A Benchmark to Evaluate Rationalized NLP Models
Jay DeYoung, Sarthak Jain, Nazneen Fatema Rajani, Eric Lehman, Caiming Xiong, Richard Socher, and Byron C. Wallace
Explaining Black Box Predictions and Unveiling Data Artifacts through Influence Functions
Xiaochuang Han, Byron C. Wallace, and Yulia Tsvetkov
Learning to Faithfully Rationalize by Construction
Sarthak Jain, Sarah Wiegreffe, Yuval Pinter, and Byron C. Wallace
Trialstreamer: Mapping and Browsing Medical Evidence in Real-Time
Benjamin Nye, Ani Nenkova, Iain J. Marshall, and Byron C. Wallace
Evidence Inference 2.0: More Data, Better Models
Jay DeYoung and Eric Lehman and Benjamin Nye and Iain Marshall and Byron C. Wallace
Semi-Automating Knowledge Base Construction for Cancer Genetics
Somin Wadhwa, Kanhua Yin, Kevin S. Hughes, and Byron C. Wallace
Query-Focused EHR Summarization to Aid Imaging Diagnosis
Denis Jered McInerney, Borna Dabiri, Anne-Sophie Touret, Geoffrey Young, Jan-Willem van de Meent and Byron C. Wallace
Trialstreamer: a living, automatically updated database of clinical trial reports
Iain J. Marshall, Benjamin Nye, Joël Kuiper, Anna Noel-Storr, Rachel Marshall, Rory Maclean, Frank Soboczenski, Ani Nenkova, James Thomas, and Byron C. Wallace
Predicting unplanned readmissions following a hip or knee arthroplasty
Ramin Mohammadi, Sarthak Jain, Amir T Namin, Melissa Scholem Heller, Ramya Palacholla, Sagar Kamarthi, and Byron C. Wallace
2019
Learning to Identify Patients at Risk of Uncontrolled Hypertension Using Electronic Health Records Data
Ramin Mohammadi, Sarthak Jain, Stephen Agboola, Ramya Palacholla, Sagar Kamarthi and Byron C. Wallace
Explainable Modeling of Annotations in Crowdsourcing
An Thanh Nguyen, Matthew Lease and Byron C. Wallace
Structured Representations for Reviews: Aspect-Based Variational Hidden Factor Models
Babak Esmaeili, Hongyi Huang, Byron C. Wallace, and Jan-Willem van de Meent
Rapid reviews may produce different results to systematic reviews: a meta-epidemiological study
Iain J. Marshall, Rachel Marshall, Byron C. Wallace, Jon Brassey, and James Thomas
Attention is not Explanation
Sarthak Jain and Byron C. Wallace
Inferring Which Medical Treatments Work from Reports of Clinical Trials
Eric Lehman, Jay DeYoung, Regina Barzilay, and Byron C. Wallace
Predicting Annotation Difficulty to Improve Task Routing and Model Performance for Biomedical Information Extraction
Yinfei Yang, Oshin Agarwal, Chris Tar, Byron C. Wallace, and Ani Nenkova
MASH: software tools for developing interactive and transparent machine learning systems
An Thanh Nguyen, Matthew Lease, and Byron C. Wallace
Browsing Health: Information Extraction to Support New Interfaces for Accessing Medical Evidence
Soham Parikh, Elizabeth Conrad, Oshin Agarwal, Iain Marshall, Byron C. Wallace and Ani Nenkova
An Analysis of Attention over Clinical Notes for Predictive Tasks
Sarthak Jain and Byron C. Wallace
Machine learning to help researchers evaluate biases in clinical trials: a prospective, randomized user study
Frank Soboczenski, Thomas A Trikalinos, Joël Kuiper, Randolph G Bias, Byron C Wallace and Iain J Marshall
Practical Obstacles to Deploying Active Learning
David Lowell, Zachary Lipton and Byron C. Wallace
Are Online Reviews of Physicians Biased Against Female Providers?
Avijit Thawani, Michael J. Paul, Urmimala Sarkar, and Byron C. Wallace
Toward systematic review automation: a practical guide to using machine learning tools in research synthesis
Iain Marshall and Byron C. Wallace
2018
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
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
An Interpretable Joint Graphical Model for Fact-Checking from Crowds
An Thanh Nguyen, Aditya Kharosekar, Matthew Lease and Byron C. Wallace
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
Syntactic Patterns Improve Information Extraction for Medical Search
Roma Patel, Yinfei Yang, Iain Marshall, Ani Nenkova, and Byron C. Wallace.
PIVET: A scaled phenotype evidence generation framework using online medical literature
Jette Henderson, Junyuan Ke, Joyce C. Ho, Joydeep Ghosh, and Byron C. Wallace
A Corpus with Multi-Level Annotations of Patients, Interventions and Outcomes to Support Language Processing for Medical Literature
Ben Nye, Junyi Jessy Li, Roma Patel, Yinfei Yang, Iain Marshall, Ani Nenkova and Byron C. Wallace
Believe it or not: Designing a Human-AI Partnership for Mixed-Initiative Fact-Checking
An T. Nguyen, Aditya Kharosekar, Saumyaa Krishnan, Siddhesh Krishnan, Elizabeth Tate, Byron C. Wallace and Matthew Lease
Learning Disentangled Representations of Texts with Application to Biomedical Abstracts
Sarthak Jain, Edward Banner, Jan-Willem van de Meent, Jan-Willem, Iain J. Marshall and Byron C. Wallace
Structured Multi-Label Biomedical Text Tagging via Attentive Neural Tree Decoding
Gaurav Singh, James Thomas, Iain J. Marshall, John Shawe-Taylor and Byron C. Wallace
2017
A Sensitivity Analysis of (and Practitioners' Guide to) Convolutional Neural Networks for Sentence Classification
Ye Zhang and Byron C. Wallace
Active Discriminative Text Representation Learning
Ye Zhang, Matt Lease and Byron C. Wallace
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
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
Exploiting Domain Knowledge via Grouped Weight Sharing with Application to Text Categorization
Ye Zhang, Matthew Lease and Byron C. Wallace
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
Aggregating and Predicting Sequence Labels from Crowd Annotations
An Thanh Nguyen, Byron C. Wallace, Junyi Jessy Li, Ani Nenkova and Matthew Lease
Automating Biomedical Evidence Synthesis: RobotReviewer
Iain Marshall, Joël Kuiper, Edward Banner and Byron C. Wallace
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
Quantifying Mental Health from Social Media with Neural User Embeddings
Silvio Amir, Glen Coppersmith, Paula Carvalho, Mário J. Silva and Byron C. Wallace
An Exploration of Crowdsourcing Citation Screening for Systematic Reviews
Michael L. Mortensen, Gaelen P. Adam, Thomas A. Trikalinos, Tim Kraska and Byron C. Wallace
Identifying diagnostic test accuracy publications using a deep model
Gaurav Singh, Iain Marshall, James Thomas and Byron C. Wallace
A Neural Candidate-Selector Architecture for Automatic Structured Clinical Text Annotation
Gaurav Singh, Iain Marshall, James Thomas, John Shawe-Taylor and Byron C. Wallace
Detecting Twitter posts with Adverse Drug Reactions using Convolutional Neural Networks
Sarthak Jain, Xun Peng and Byron C. Wallace
2016
MGNC-CNN: A Simple Approach to Exploiting Multiple Word Embeddings for Sentence Classification
Ye Zhang, Stephen Roller and Byron C. Wallace
Improving the Utility of MeSH terms Using the TopicalMeSH Representation
Zhiguo Yu, Elmer Bernstam, Trevor Cohen, Byron C Wallace and Todd R Johnson
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
A Correlated Worker Model for Grouped, Imbalanced and Multitask Data
An T. Nguyen, Byron C. Wallace and Matthew Lease
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
Rationale-Augmented Convolutional Neural Networks for Text Classification
Ye Zhang, Iain Marshall and Byron C. Wallace
Systematic Review is e-Discovery in Doctor's Clothing
Matthew Lease, Gordon V. Cormack, An Thanh Nguyen, Thomas A. Trikalinos, and Byron C. Wallace
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
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
Automated Verification of Phenotypes using PubMed
Ryan Bridges, Jette Henderson, Joyce Ho, Byron C. Wallace and Joydeep Ghosh
Probabilistic Modeling for Crowdsourcing Partially-Subjective Ratings
An T. Nguyen, Matthew Halpern, Byron C. Wallace and Matthew Lease
Leveraging coreference to identify arms in medical abstracts: An experimental study
Elisa Ferracane, Iain Marshall, Byron C. Wallace and Katrin Erk
Retrofitting Word Vectors of MeSH Terms to Improve Semantic Similarity Measures
Zhiguo Yu, Trevor Cohen, Todd R. Johnson, Byron C Wallace and Elmer Bernstam
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
2015
Graph-Sparse LDA: A Topic Model with Structured Sparsity
Finale Doshi-Velez, Byron C Wallace and Ryan P Adams
What Predicts Media Coverage of Health Science Articles?
Byron C Wallace, Michael J Paul and Noémie Elhadad
RobotReviewer: Evaluation of a System for Automatically Assessing Bias in Clinical Trials
Iain J. Marshall, Joël Kuiper and Byron C. Wallace
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
Sparse, Contextually Informed Models for Irony Detection: Exploiting User Communities, Entities and Sentiment
Byron C Wallace, Do Kook Choe and Eugene Charniak
Automating Risk of Bias Assessment for Clinical Trials
Iain J. Marshall, Joël Kuiper and Byron C. Wallace
Combining Crowd and Expert Labels using Decision Theoretic Active Learning
An T. Nguyen, Byron C. Wallace and Matthew Lease
Healthcare Data Analytics Challenge
Zhiguo Yu, Byron C. Wallace and Todd R. Johnson
Editorial: special issue on machine learning for health and medicine
Jenna Wiens and Byron C. Wallace
2014
Improving Class Probability Estimates for Imbalanced Data
Byron C. Wallace and Issa J. Dahabreh
Humans Require Context to Infer Ironic Intent (so Computers Probably do, too)
Byron C. Wallace, Do Kook Choe, Laura Kertz and Eugene Charniak
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
Discovering Better AAAI Keywords via Clustering with Community-sourced Constraints
Kelly H. Moran, Byron C. Wallace and Carla E. Brodley
Spá: a web-based viewer for text mining in Evidence Based Medicine
Jöel Kuiper, Iain J. Marshall, Byron C. Wallace and Morris A. Swertz
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
#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
Automating Risk of Bias Assessment for Clinical Trials
Iain J. Marshall, Joël Kuiper and Byron C. Wallace
Can Cognitive Scientists Help Computers Recognize Irony?
Byron C. Wallace and Laura Kertz
2013
Computational Irony: A Survey and new Perspectives
Byron C Wallace
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
What Affects Patient (Dis)satisfaction? Analyzing Online Doctor Ratings with a Joint Topic-Sentiment Model
Michael J. Paul, Byron C. Wallace and Mark Dredze
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
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
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
Modernizing Evidence Synthesis for Evidence-Based Medicine (Book Chapter)
Byron C Wallace, Issa J Dahabreh, Christopher H Schmid, Joseph Lau and Thomas A Trikalinos
2012
Challenges and opportunities in applied machine learning
Carla E. Brodley, Umaa Rebbapragada, Kevin Small and Byron C Wallace
Machine Learning Health Informatics: Making Better use of Domain Experts
Byron C Wallace
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
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
Multiple narrative disentanglement: Unraveling infinite jest
Byron C. Wallace
Class Probability Estimates are Unreliable for Imbalanced Data (and How to Fix Them)
Byron C. Wallace and Issa J. Dahabreh
2011
Who should label what? instance allocation in multiple expert active learning
Byron C Wallace, Kevin Small, Carla E Brodley and Thomas A Trikalinos
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
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
Class Imbalance, Redux
Byron C. Wallace, Kevin Small, Carla E Brodley and Thomas A Trikalinos
The constrained weight space SVM: Learning with ranked features
Kevin Small, Byron C. Wallace, Carla E. Brodley and Thomas A. Trikalinos
2010
Modeling annotation time to reduce workload in comparative effectiveness reviews
Byron C Wallace, Kevin Small, Carla E Brodley and Thomas A Trikalinos
Semi-automated screening of biomedical citations for systematic reviews
Byron C Wallace, Thomas A Trikalinos, Joseph Lau, Carla E Brodley and Chistopher H Schmid
Active learning for biomedical citation screening
Byron C Wallace, Kevin Small, Carla E Brodley and Thomas A Trikalinos
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
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