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Alona Fyshe

dblp:30/3660 · DBLP profile ↗
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21ranked-venue papers
4as first author
9since 2021 · last 2025
0000-0003-4367-0306ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 17 · 3 first-author · 7 since 2021Applied, interdisciplinary, general and emerging computing · 4 · 1 first-author · 3 since 2021Graphics, computer vision, multimedia, augmented reality and games · 3Databases, data management, data science and information retrieval · 1

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Artificial intelligence
8 papers
Reinforcement learning · 23% Optimization for machine learning · 20% Representation and self-supervised learning · 19%
Interdisciplinary, comprehensive, and emerging computing
6 papers
Bioinformatics and computational biology · 83% Medical and health informatics · 17%
Network and information security
1 paper
Cryptographic primitives and cryptanalysis · 100%

Topics — the 24 heaviest of 29, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Machine learning › Representation and self-supervised learning
multimodal representation learning
0.912025
Finding Shared Decodable Concepts and their Negations in the Brain · ICLR 2025
Bioinformatics and computational biology › neuroscience › neuroinformatics
brain decoding
0.912025
Finding Shared Decodable Concepts and their Negations in the Brain · ICLR 2025
Bioinformatics and computational biology
computational neuroscience
0.912025
Finding Shared Decodable Concepts and their Negations in the Brain · ICLR 2025
Machine learning › Transfer learning and domain adaptation › domain shift
covariate shift
0.612022
Resonance in Weight Space: Covariate Shift Can Drive Divergence of SGD with Momentum · ICLR 2022
Machine learning › Deep learning architectures and training › training dynamics
optimization dynamics
0.612022
Resonance in Weight Space: Covariate Shift Can Drive Divergence of SGD with Momentum · ICLR 2022
Machine learning › Optimization for machine learning
stochastic gradient descent
0.612022
Resonance in Weight Space: Covariate Shift Can Drive Divergence of SGD with Momentum · ICLR 2022
Machine learning › Optimization for machine learning › stochastic gradient descent
stochastic gradient descent with momentum
0.612022
Resonance in Weight Space: Covariate Shift Can Drive Divergence of SGD with Momentum · ICLR 2022
Machine learning › Reinforcement learning › value-based reinforcement learning
q-learning
0.412020
Maxmin Q-learning: Controlling the Estimation Bias of Q-learning · ICLR 2020
Machine learning › Reinforcement learning
value-based reinforcement learning
0.412020
Maxmin Q-learning: Controlling the Estimation Bias of Q-learning · ICLR 2020
Medical and health informatics
cognitive neuroscience
0.212016
BrainBench: A Brain-Image Test Suite for Distributional Semantic Models · EMNLP 2016
Cryptographic primitives and cryptanalysis › symmetric cryptography
substitution cipher
0.212016
Poet Admits // Mute Cypher: Beam Search to find Mutually Enciphering Poetic Texts · EMNLP 2016
Cryptographic primitives and cryptanalysis › symmetric cryptography
symmetric ciphers
0.212016
Poet Admits // Mute Cypher: Beam Search to find Mutually Enciphering Poetic Texts · EMNLP 2016
Medical and health informatics
mental health informatics
0.212023
Language and Mental Health: Measures of Emotion Dynamics from Text as Linguistic Biosocial Markers · EMNLP 2023
Machine learning › Representation and self-supervised learning › representation learning › distributed representation learning
semantic vector representation
0.212014
Interpretable Semantic Vectors from a Joint Model of Brain- and Text- Based Meaning · ACL (1) 2014
Bioinformatics and computational biology › neuroscience
neuroinformatics
0.212014
Good-enough brain model: challenges, algorithms and discoveries in multi-subject experiments · KDD 2014
Bioinformatics and computational biology › protein function prediction
protein subcellular localization prediction
0.112008
Improving subcellular localization prediction using text classification and the gene ontology · Bioinform. 2008
Natural language and speech › Language models and text generation › text generation
constrained text generation
0.112016
Poet Admits // Mute Cypher: Beam Search to find Mutually Enciphering Poetic Texts · EMNLP 2016
Natural language and speech › Information extraction and text analysis › distributional semantics
distributional semantic models
0.112016
BrainBench: A Brain-Image Test Suite for Distributional Semantic Models · EMNLP 2016
Natural language and speech › Language models and text generation
text generation
0.112016
Poet Admits // Mute Cypher: Beam Search to find Mutually Enciphering Poetic Texts · EMNLP 2016
Machine learning › Trustworthy machine learning
interpretability
0.112006
Visual Explanation of Evidence with Additive Classifiers · AAAI 2006
Visualization and visual analytics › explainable AI › explainable machine learning
explanation visualization
0.112006
Visual Explanation of Evidence with Additive Classifiers · AAAI 2006
Bioinformatics and computational biology
protein function prediction
0.112005
The Proteome Analyst Suite of Automated Function Prediction Tools · AAAI 2005
Bioinformatics and computational biology
proteomics
0.112005
The Proteome Analyst Suite of Automated Function Prediction Tools · AAAI 2005
Bioinformatics and computational biology › knowledge representation in biology › biomedical ontology
gene ontology
0.012008
Improving subcellular localization prediction using text classification and the gene ontology · Bioinform. 2008

Methods — techniques the papers use, named apart from their topics

contrastive learning · 1.7DBSCAN clustering · 1.7CLIP · 1.7emotion dynamics metrics · 1.3stochastic gradient descent with momentum · 0.6benchmark construction · 0.5beam search · 0.5maxmin q-learning · 0.4ensemble · 0.4probabilistic modeling · 0.4multi-subject inference · 0.4n-gram models · 0.2n-gram model · 0.2text classification · 0.1synonym expansion · 0.1GO hierarchy · 0.1additive model · 0.1automated function prediction · 0.1
YearPublicationVenuePosition
2025 Finding Shared Decodable Concepts and their Negations in the Brain
abstract
Prior work has offered evidence for functional localization in the brain; different anatomical regions preferentially activate for certain types of visual input. For example, the fusiform face area preferentially activates for visual stimuli that include a face. However, the spectrum of visual semantics is extensive, and only a few semantically-tuned patches of cortex have so far been identified in the human brain. Using a multimodal (natural language and image) neural network architecture (CLIP, \cite{CLIP}, we train a highly accurate contrastive model that maps brain responses during naturalistic image viewing to CLIP embeddings. We then use a novel adaptation of the DBSCAN clustering algorithm to cluster the parameters of these participant-specific contrastive models. This reveals what we call Shared Decodable Concepts (SDCs): clusters in CLIP space that are decodable from common sets of voxels across multiple participants. Examining the images most and least associated with each SDC cluster gives us additional insight into the semantic properties of each SDC. We note SDCs for previously reported visual features (e.g. orientation tuning in early visual cortex) as well as visual semantic concepts such as faces, places and bodies. In cases where our method finds multiple clusters for a visuo-semantic concept, the least associated images allow us to dissociate between confounding factors. For example, we discovered two clusters of food images, one driven by color, the other by shape. We also uncover previously unreported areas with visuo-semantic sensitivity such as regions of extrastriate body area (EBA) tuned for legs/hands and sensitivity to numerosity in right intraparietal sulcus, sensitivity associated with visual perspective (close/far) and more. Thus, our contrastive-learning methodology better characterizes new and existing visuo-semantic representations in the brain by leveraging multimodal neural network representations and a novel adaptation of clustering algorithms.
Cory Efird, Alex Murphy, Joel Zylberberg, Alona Fyshe
ICLR4
2024 DISTO: Textual Distractors for Multiple Choice Reading Comprehension Questions using Negative Sampling
Bilal Ghanem, Alona Fyshe
EDM2
2024 Exploring Temporal Sensitivity in the Brain Using Multi-timescale Language Models: An EEG Decoding Study
abstract
Abstract The brain’s ability to perform complex computations at varying timescales is crucial, ranging from understanding single words to grasping the overarching narrative of a story. Recently, multi-timescale long short-term memory (MT-LSTM) models (Mahto et al. 2020; Jain et al. 2020) have been introduced, which use temporally tuned parameters to induce sensitivity to different timescales of language processing (i.e., related to near/distant words). However, there has not been an exploration of the relationship between such temporally tuned information processing in MT-LSTMs and the brain’s processing of language using high temporal resolution recording modalities, such as electroencephalography (EEG). To bridge this gap, we used an EEG dataset recorded while participants listened to Chapter 1 of “Alice in Wonderland” and trained ridge regression models to predict the temporally tuned MT-LSTM embeddings from EEG responses. Our analysis reveals that EEG signals can be used to predict MT-LSTM embeddings across various timescales. For longer timescales, our models produced accurate predictions within an extended time window of ±2 s around word onset, while for shorter timescales, significant predictions are confined to a narrower window ranging from −180 ms to 790 ms. Intriguingly, we observed that short timescale information is not only processed in the vicinity of word onset but also at more distant time points. These observations underscore the parallels and discrepancies between computational models and the neural mechanisms of the brain. As word embeddings are used more as in silico models of semantic representation in the brain, a more explicit consideration of timescale-dependent processing enables more targeted explorations of language processing in humans and machines.
Sijie Ling, Alex Murphy, Alona Fyshe
Comput. Linguistics3
2023 Weakly-Supervised Questions for Zero-Shot Relation Extraction
abstract
Zero-Shot Relation Extraction (ZRE) is the task of Relation Extraction where the training and test sets have no shared relation types.This very challenging domain is a good test of a model's ability to generalize.Previous approaches to ZRE reframed relation extraction as Question Answering (QA), allowing for the use of pre-trained QA models.However, this method required manually creating gold question templates for each new relation.Here, we do away with these gold templates and instead learn a model that can generate questions for unseen relations.Our technique can successfully translate relation descriptions into relevant questions, which are then leveraged to generate the correct tail entity.On tail entity extraction, we outperform the previous state-of-the-art by more than 16 F1 points without using gold question templates.On the RE-QA dataset where no previous baseline for relation extraction exists, our proposed algorithm comes within 0.7 F1 points of a system that uses gold question templates.Our model also outperforms the stateof-the-art ZRE baselines on the FewRel and WikiZSL datasets, showing that QA models no longer need template questions to match the performance of models specifically tailored to the ZRE task.Our implementation is available
Saeed Najafi, Alona Fyshe
EACL2
2023 Language and Mental Health: Measures of Emotion Dynamics from Text as Linguistic Biosocial Markers
abstract
Research in psychopathology has shown that, at an aggregate level, the patterns of emotional change over time-emotion dynamics-are indicators of one's mental health.One's patterns of emotion change have traditionally been determined through self-reports of emotions; however, there are known issues with accuracy, bias, and ease of data collection.Recent approaches to determining emotion dynamics from one's everyday utterances addresses many of these concerns, but it is not yet known whether these measures of utterance emotion dynamics (UED) correlate with mental health diagnoses.Here, for the first time, we study the relationship between tweet emotion dynamics and mental health disorders.We find that each of the UED metrics studied varied by the user's self-disclosed diagnosis.For example: average valence was significantly higher (i.e., more positive text) in the control group compared to users with ADHD, MDD, and PTSD.Valence variability was significantly lower in the control group compared to ADHD, depression, bipolar disorder, MDD, PTSD, and OCD but not PPD.Rise and recovery rates of valence also exhibited significant differences from the control.This work provides important early evidence for how linguistic cues pertaining to emotion dynamics can play a crucial role as biosocial markers for mental illnesses and aid in the understanding, diagnosis, and management of mental health disorders.
Daniela Teodorescu, Tiffany Cheng, Alona Fyshe, Saif M. Mohammad
EMNLP3
2022 Predicting Reading Comprehension Scores of Elementary School Students
Yuyang Nie, Helene Deacon, Alona Fyshe, Carrie Demmans Epp
EDM3
2022 Resonance in Weight Space: Covariate Shift Can Drive Divergence of SGD with Momentum
Kirby Banman, Liam Peet-Pare, Nidhi Hegde 0001, Alona Fyshe, Martha White
ICLR4
2021 Which acoustic features support the language-cognition link in infancy: A machine-learning approach
Joseph C. Y. Lau, Alona Fyshe, Sandra Waxman
CogSci2
2021 Words as a window: Using word embeddings to explore the learned representations of Convolutional Neural Networks
Dhanush Dharmaretnam, Chris Foster, Alona Fyshe
Neural Networks3
2020 Maxmin Q-learning: Controlling the Estimation Bias of Q-learning
Qingfeng Lan, Yangchen Pan, Alona Fyshe, Martha White
ICLR3
2020 Improved object recognition using neural networks trained to mimic the brain's statistical properties
Callie Federer, Haoyan Xu, Alona Fyshe, Joel Zylberberg
Neural Networks3
2018 Decoding Music in the Human Brain Using EEG Data
abstract
Semantic vectors, or language embeddings, are used in computational linguistics to represent language for a variety of machine related tasks including translation, speech to text, and natural language understanding. These semantic vectors have also been extensively studied in correlation with human brain data, showing evidence that the representation of language in the human brain can be modeled through these vectors with high correlation. Further, various attempts have been made to study how the human brain represents and understands music. For example, it has been shown that EEG data of subjects listening to music can be used for tempo detection and singer gender recognition. We propose studying the relationship between the EEG data of subjects listening to audio and the audio feature vectors modeled after the semantic vectors in computational linguistics. This could provide new insight into how the brain processes and understands music.
Chris Foster, Dhanush Dharmaretnam, Haoyan Xu, Alona Fyshe, George Tzanetakis
MMSP4
2016 Poet Admits // Mute Cypher: Beam Search to find Mutually Enciphering Poetic Texts
abstract
The Xenotext Experiment implants poetry into an extremophile's DNA, and uses that DNA to generate new poetry in a protein form.The molecular machinery of life requires that these two poems encipher each other under a symmetric substitution cipher.We search for ciphers which permit writing under the Xenotext constraints, incorporating ideas from cipher-cracking algorithms, and using n-gram data to assess a cipher's "writability".Our algorithm, Beam Verse, is a beam search which uses new heuristics to navigate the cipher-space.We find thousands of ciphers which score higher than successful ciphers used to write Xenotext constrained texts.
Cole Peterson, Alona Fyshe
EMNLP2
2016 BrainBench: A Brain-Image Test Suite for Distributional Semantic Models
abstract
The brain is the locus of our language ability, and so brain images can be used to ground linguistic theories.Here we introduce Brain-Bench, a lightweight system for testing distributional models of word semantics.We compare the performance of several models, and show that the performance on brain-image tasks differs from the performance on behavioral tasks.We release our benchmark test as part of a web service.
Haoyan Xu, Brian Murphy, Alona Fyshe
EMNLP3
2015 A Compositional and Interpretable Semantic Space
abstract
Alona Fyshe, Leila Wehbe, Partha P. Talukdar, Brian Murphy, Tom M. Mitchell. Proceedings of the 2015 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2015.
Alona Fyshe, Leila Wehbe, Partha P. Talukdar, Brian Murphy, Tom M. Mitchell
HLT-NAACL1
2014 Interpretable Semantic Vectors from a Joint Model of Brain- and Text- Based Meaning
abstract
Vector space models (VSMs) represent word meanings as points in a high dimensional space. VSMs are typically created using a large text corpora, and so represent word semantics as observed in text. We present a new algorithm (JNNSE) that can incorporate a measure of semantics not previously used to create VSMs: brain activation data recorded while people read words. The resulting model takes advantage of the complementary strengths and weaknesses of corpus and brain activation data to give a more complete representation of semantics. Evaluations show that the model 1) matches a behavioral measure of semantics more closely, 2) can be used to predict corpus data for unseen words and 3) has predictive power that generalizes across brain imaging technologies and across subjects. We believe that the model is thus a more faithful representation of mental vocabularies.
Alona Fyshe, Partha P. Talukdar, Brian Murphy, Tom M. Mitchell
ACL (1)1
2014 Good-enough brain model: challenges, algorithms and discoveries in multi-subject experiments
abstract
Given a simple noun such as {\em apple}, and a question such as "is it edible?", what processes take place in the human brain? More specifically, given the stimulus, what are the interactions between (groups of) neurons (also known as functional connectivity) and how can we automatically infer those interactions, given measurements of the brain activity? Furthermore, how does this connectivity differ across different human subjects?
Evangelos E. Papalexakis, Alona Fyshe, Nicholas D. Sidiropoulos, Partha P. Talukdar, Tom M. Mitchell, Christos Faloutsos
KDD2
2013 Documents and Dependencies: an Exploration of Vector Space Models for Semantic Composition
Alona Fyshe, Brian Murphy, Partha P. Talukdar, Tom M. Mitchell
CoNLL1
2008 Improving subcellular localization prediction using text classification and the gene ontology
abstract
MOTIVATION: Each protein performs its functions within some specific locations in a cell. This subcellular location is important for understanding protein function and for facilitating its purification. There are now many computational techniques for predicting location based on sequence analysis and database information from homologs. A few recent techniques use text from biological abstracts: our goal is to improve the prediction accuracy of such text-based techniques. We identify three techniques for improving text-based prediction: a rule for ambiguous abstract removal, a mechanism for using synonyms from the Gene Ontology (GO) and a mechanism for using the GO hierarchy to generalize terms. We show that these three techniques can significantly improve the accuracy of protein subcellular location predictors that use text extracted from PubMed abstracts whose references are recorded in Swiss-Prot.
Alona Fyshe, Yifeng Liu 0001, Duane Szafron, Russell Greiner, Paul Lu
Bioinform.1
2006 Visual Explanation of Evidence with Additive Classifiers
Brett Poulin, Roman Eisner, Duane Szafron, Paul Lu, Russell Greiner, David S. Wishart, Alona Fyshe, Brandon Pearcy, John Anvik
AAAI7
2005 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
AAAI7