Trellis Driver: Distributing a Java Workflow across a Network of Workstations. - Nicholas Lamb; Paul Lu; Alona Fyshe (ICPP Workshops, 2004)

Proteome Analyst: custom predictions with explanations in a web-based tool for high-throughput proteome annotations. - Duane Szafron; Paul Lu; Russell Greiner; David S. Wishart; Brett Poulin; Roman Eisner; Zhiyong Lu; John Anvik; Cam Macdonell; Alona Fyshe; David Meeuwis (Nucleic Acids Res., 2004)

The Proteome Analyst Suite of Automated Function Prediction Tools. - Brett Poulin; Duane Szafron; Paul Lu; Russell Greiner; David S. Wishart; Roman Eisner; Alona Fyshe; Brandon Pearcy; Luca Pireddu (AAAI, 2005)

PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization. - Paul Lu; Duane Szafron; Russell Greiner; David S. Wishart; Alona Fyshe; Brandon Pearcy; Brett Poulin; Roman Eisner; Danny Ngo; Nicholas Lamb (Nucleic Acids Res., 2005)

Visual Explanation of Evidence with Additive Classifiers. - Brett Poulin; Roman Eisner; Duane Szafron; Paul Lu; Russell Greiner; David S. Wishart; Alona Fyshe; Brandon Pearcy; Cam Macdonell; John Anvik (AAAI, 2006)

Term Generalization and Synonym Resolution for Biological Abstracts: Using the Gene Ontology for Subcellular Localization Prediction. - Alona Fyshe; Duane Szafron (BioNLP@NAACL-HLT, 2006)

Improving subcellular localization prediction using text classification and the gene ontology. - Alona Fyshe; Yifeng Liu 001; Duane Szafron; Russell Greiner; Paul Lu (Bioinform., 2008)

Hierarchical Latent Dictionaries for Models of Brain Activation. - Alona Fyshe; Emily B. Fox; David B. Dunson; Tom M. Mitchell (AISTATS, 2012)

Tracking neural coding of perceptual and semantic features of concrete nouns. - Gustavo P. Sudre; Dean Pomerleau; Mark Palatucci; Leila Wehbe; Alona Fyshe; Riitta Salmelin; Tom M. Mitchell (NeuroImage, 2012)

Documents and Dependencies: an Exploration of Vector Space Models for Semantic Composition. - Alona Fyshe; Brian Murphy; Partha Pratim Talukdar; Tom M. Mitchell (CoNLL, 2013)

Interpretable Semantic Vectors from a Joint Model of Brain- and Text- Based Meaning. - Alona Fyshe; Partha Pratim Talukdar; Brian Murphy; Tom M. Mitchell (ACL (1), 2014)

Good-enough brain model: challenges, algorithms and discoveries in multi-subject experiments. - Evangelos E. Papalexakis; Alona Fyshe; Nicholas D. Sidiropoulos; Partha Pratim Talukdar; Tom M. Mitchell; Christos Faloutsos (KDD, 2014)

Good-Enough Brain Model: Challenges, Algorithms, and Discoveries in Multisubject Experiments. - Evangelos E. Papalexakis; Alona Fyshe; Nicholas D. Sidiropoulos; Partha Pratim Talukdar; Tom M. Mitchell; Christos Faloutsos (Big Data, 2014)

A Compositional and Interpretable Semantic Space. - Alona Fyshe; Leila Wehbe; Partha Pratim Talukdar; Brian Murphy; Tom M. Mitchell (HLT-NAACL, 2015)

Poet Admits // Mute Cypher: Beam Search to find Mutually Enciphering Poetic Texts. - Cole Peterson; Alona Fyshe (EMNLP, 2016)

BrainBench: A Brain-Image Test Suite for Distributional Semantic Models. - Haoyan Xu; Brian Murphy; Alona Fyshe (EMNLP, 2016)

Ensemble Methods for Native Language Identification. - Sophia Chan; Maryam Honari Jahromi; Benjamin Benetti; Aazim Lakhani; Alona Fyshe (BEA@EMNLP, 2017)

Social and Emotional Correlates of Capitalization on Twitter. - Sophia Chan; Alona Fyshe (PEOPLES@NAACL-HTL, 2018)

Interpreting Word-Level Hidden State Behaviour of Character-Level LSTM Language Models. - Avery Hiebert; Cole Peterson; Alona Fyshe; Nishant A. Mehta (BlackboxNLP@EMNLP, 2018)

Decoding Music in the Human Brain Using EEG Data. - Chris Foster; Dhanush Dharmaretnam; Haoyan Xu; Alona Fyshe; George Tzanetakis (MMSP, 2018)

The Emergence of Semantics in Neural Network Representations of Visual Information. - Dhanush Dharmaretnam; Alona Fyshe (NAACL-HLT (2), 2018)

Training neural networks to have brain-like representations improves object recognition performance. - Callie Federer; Haoyan Xu; Alona Fyshe; Joel Zylberberg (CoRR, 2019)

From Language to Language-ish: How Brain-Like is an LSTM's Representation of Atypical Language Stimuli? - Maryam Hashemzadeh; Greta Kaufeld; Martha White; Andrea E. Martin; Alona Fyshe (EMNLP (Findings), 2020)

Maxmin Q-learning: Controlling the Estimation Bias of Q-learning. - Qingfeng Lan; Yangchen Pan; Alona Fyshe; Martha White (ICLR, 2020)

From Language to Language-ish: How Brain-Like is an LSTM's Representation of Nonsensical Language Stimuli? - Maryam Hashemzadeh; Greta Kaufeld; Martha White; Andrea E. Martin; Alona Fyshe (CoRR, 2020)

Improved object recognition using neural networks trained to mimic the brain's statistical properties. - Callie Federer; Haoyan Xu; Alona Fyshe; Joel Zylberberg (Neural Networks, 2020)

Which acoustic features support the language-cognition link in infancy: A machine-learning approach. - Joseph C. Y. Lau; Alona Fyshe; Sandra Waxman (CogSci, 2021)

Predictive Representation Learning for Language Modeling. - Qingfeng Lan; Luke Kumar; Martha White; Alona Fyshe (CoRR, 2021)

Words as a window: Using word embeddings to explore the learned representations of Convolutional Neural Networks. - Dhanush Dharmaretnam; Chris Foster; Alona Fyshe (Neural Networks, 2021)

Question Generation for Reading Comprehension Assessment by Modeling How and What to Ask. - Bilal Ghanem; Lauren Lutz Coleman; Julia Rivard Dexter; Spencer McIntosh von der Ohe; Alona Fyshe (ACL (Findings), 2022)

Predicting Reading Comprehension Scores of Elementary School Students. - Yuyang Nie; Helene Deacon; Alona Fyshe; Carrie Demmans Epp (EDM, 2022)

Resonance in Weight Space: Covariate Shift Can Drive Divergence of SGD with Momentum. - Kirby Banman; Liam Peet-Pare; Nidhi Hegde 001; Alona Fyshe; Martha White (ICLR, 2022)

Discriminative Models Can Still Outperform Generative Models in Aspect Based Sentiment Analysis. - Dhruv Mullick; Alona Fyshe; Bilal Ghanem (CoRR, 2022)

Long Term Fairness for Minority Groups via Performative Distributionally Robust Optimization. - Liam Peet-Pare; Nidhi Hegde 001; Alona Fyshe (CoRR, 2022)

Different Spectral Representations in Optimized Artificial Neural Networks and Brains. - Richard C. Gerum; Cassidy Pirlot; Alona Fyshe; Joel Zylberberg (CoRR, 2022)

Improving the Accuracy and Robustness of CNNs Using a Deep CCA Neural Data Regularizer. - Cassidy Pirlot; Richard C. Gerum; Cory Efird; Joel Zylberberg; Alona Fyshe (CoRR, 2022)

No More Pesky Hyperparameters: Offline Hyperparameter Tuning for RL. - Han Wang; Archit Sakhadeo; Adam M. White; James Bell 004; Vincent Liu; Xutong Zhao; Puer Liu; Tadashi Kozuno; Alona Fyshe; Martha White (Trans. Mach. Learn. Res., 2022)

Weakly-Supervised Questions for Zero-Shot Relation Extraction. - Saeed Najafi; Alona Fyshe (EACL, 2023)

Language and Mental Health: Measures of Emotion Dynamics from Text as Linguistic Biosocial Markers. - Daniela Teodorescu; Tiffany Cheng; Alona Fyshe; Saif M. Mohammad (EMNLP, 2023)

Utterance Emotion Dynamics in Children's Poems: Emotional Changes Across Age. - Daniela Teodorescu; Alona Fyshe; Saif M. Mohammad (WASSA@ACL, 2023)

DISTO: Evaluating Textual Distractors for Multi-Choice Questions using Negative Sampling based Approach. - Bilal Ghanem; Alona Fyshe (CoRR, 2023)

Identifying Shared Decodable Concepts in the Human Brain Using Image-Language Foundation Models. - Cory Efird; Alex Murphy; Joel Zylberberg; Alona Fyshe (CoRR, 2023)

Better Handling Coreference Resolution in Aspect Level Sentiment Classification by Fine-Tuning Language Models. - Dhruv Mullick; Bilal Ghanem; Alona Fyshe (CoRR, 2023)

RIFF: Learning to Rephrase Inputs for Few-shot Fine-tuning of Language Models. - Saeed Najafi; Alona Fyshe (ACL (Findings), 2024)

SoftSkillQG: Robust Skill-Targeted Reading Comprehension Question Generation Using Soft-prompts. - Spencer McIntosh von der Ohe; Alona Fyshe (Canadian AI, 2024)

DISTO: Textual Distractors for Multiple Choice Reading Comprehension Questions using Negative Sampling. - Bilal Ghanem; Alona Fyshe (EDM, 2024)

Characterizing Human and Zero-Shot GPT-3.5 Object-Similarity Judgments. - D. McKnight; Alona Fyshe (NAACL-HLT (Findings), 2024)

Exploring Temporal Sensitivity in the Brain Using Multi-timescale Language Models: An EEG Decoding Study. - Sijie Ling; Alex Murphy; Alona Fyshe (Comput. Linguistics, 2024)

Correcting Biased Centered Kernel Alignment Measures in Biological and Artificial Neural Networks. - Alex Murphy; Joel Zylberberg; Alona Fyshe (CoRR, 2024)

What's the Opposite of a Face? Finding Shared Decodable Concepts and their Negations in the Brain. - Cory Efird; Alex Murphy; Joel Zylberberg; Alona Fyshe (CoRR, 2024)

Its Not a Modality Gap: Characterizing and Addressing the Contrastive Gap. - Abrar Fahim; Alex Murphy; Alona Fyshe (CoRR, 2024)

Exploring Curriculum Learning for Vision-Language Tasks: A Study on Small-Scale Multimodal Training. - Rohan Saha; Abrar Fahim; Alona Fyshe; Alex Murphy (CoRR, 2024)

Finding Shared Decodable Concepts and their Negations in the Brain. - Cory Daniel Efird; Alex Murphy; Joel Zylberberg; Alona Fyshe (ICLR, 2025)

Neural Network Sparsity in Brain-Body-Machine Interfaces. - Laura C. Petrich; Samuel Neumann; Patrick M. Pilarski; Alona Fyshe (ICORR, 2025)