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Ayah Zirikly

dblp:130/6419 · DBLP profile ↗
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15ranked-venue papers
3as first author
8since 2021 · last 2026
0000-0002-8441-1741ORCID · corroborated

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

Applied, interdisciplinary, general and emerging computing · 10 · 1 first-author · 4 since 2021Artificial intelligence and machine learning · 5 · 2 first-author · 4 since 2021Databases, data management, data science and information retrieval · 1 · 1 first-author

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
2 papers
Representation and self-supervised learning · 55% Trustworthy machine learning · 45%
Interdisciplinary, comprehensive, and emerging computing
1 paper
Medical and health informatics · 100%

Topics — the 6 heaviest of 7, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Machine learning › Trustworthy machine learning
interpretability
1.122022
Improving the Generalizability of Depression Detection by Leveraging Clinical Questionnaires · ACL (1) 2022
Sparse encoding for more-interpretable feature-selecting representations in probabilistic matrix factorization · ICLR 2021
Machine learning › Representation and self-supervised learning
matrix factorization
0.512021
Sparse encoding for more-interpretable feature-selecting representations in probabilistic matrix factorization · ICLR 2021
Machine learning › Representation and self-supervised learning › matrix factorization
probabilistic matrix factorization
0.512021
Sparse encoding for more-interpretable feature-selecting representations in probabilistic matrix factorization · ICLR 2021
Machine learning › Representation and self-supervised learning › representation learning › unsupervised representation learning
sparse coding
0.512021
Sparse encoding for more-interpretable feature-selecting representations in probabilistic matrix factorization · ICLR 2021
Machine learning › Trustworthy machine learning
out-of-distribution generalization
0.212022
Improving the Generalizability of Depression Detection by Leveraging Clinical Questionnaires · ACL (1) 2022
Medical and health informatics
mental health informatics
0.212022
Improving the Generalizability of Depression Detection by Leveraging Clinical Questionnaires · ACL (1) 2022

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

PHQ9 questionnaire grounding · 1.1BERT · 1.1sparse encoding · 0.5
YearPublicationVenuePosition
2026 MindSET: Advancing Mental Health Benchmarking through Large-Scale Social Media Data
abstract
Social media data has become a vital resource for studying mental health, offering real-time insights into thoughts, emotions, and behaviors that traditional methods often miss. Progress in this area has been facilitated by benchmark datasets for mental health analysis; however, most existing benchmarks have become outdated due to limited data availability, inadequate cleaning, and the inherently diverse nature of social media content (e.g., multilingual and harmful material). We present a new benchmark dataset, \textbf{MindSET}, curated from Reddit using self-reported diagnoses to address these limitations. The annotated dataset contains over \textbf{13M} annotated posts across seven mental health conditions, more than twice the size of previous benchmarks. To ensure data quality, we applied rigorous preprocessing steps, including language filtering, and removal of Not Safe for Work (NSFW) and duplicate content. We further performed a linguistic analysis using LIWC to examine psychological term frequencies across the eight groups represented in the dataset. To demonstrate the dataset utility, we conducted binary classification experiments for diagnosis detection using both fine-tuned language models and Bag-of-Words (BoW) features. Models trained on MindSET consistently outperformed those trained on previous benchmarks, achieving up to an \textbf{18-point} improvement in F1 for Autism detection. Overall, MindSET provides a robust foundation for researchers exploring the intersection of social media and mental health, supporting both early risk detection and deeper analysis of emerging psychological trends.
Saad Mankarious, Edward Kempa, Daniel Wiechmann, Elma Kerz, Yu Qiao 0005, Ayah Zirikly
LREC6
2026 Assessing genetic counseling efficiency with natural language processing
abstract
OBJECTIVE: To build natural language processing (NLP) strategies to characterize measures of genetic counseling (GC) efficiency and classify measures according to phase of GC (pre- or post-genetic testing). MATERIALS AND METHODS: This study selected and annotated 800 GC notes from 7 clinical specialties in a large academic medical center for NLP model development and validation. The NLP approaches extracted GC efficiency measures, including direct and indirect time and GC phase. The models were then applied to 24 102 GC notes collected from January 2016 through December 2023. RESULTS: NLP approaches performed well (F1 scores of 0.95 and 0.90 for direct time in GC and GC phase classification, respectively). Our findings showed median direct time in GC of 50 minutes, with significant differences in direct time distributions observed across clinical specialties, time periods (2016-2019 or 2020-2023), delivery modes (in person or telehealth), and GC phase. DISCUSSION: As referrals to GC increase, there is increasing pressure to improve efficiency. Our NLP strategy was used to generate and summarize real-world evidence of GC time for 7 clinical specialties. These approaches enable future research on the impact of interventions intended to improve GC efficiency. CONCLUSION: This work demonstrated the practical value of NLP to provide a useful and scalable strategy to generate real world evidence of GC efficiency. Principles presented in this work may also be valuable for health services research in other practice areas.
Michelle H. Nguyen, Carolyn D. Applegate, Brittney Murray, Ayah Zirikly, Crystal Tichnell, Catherine Gordon, Lisa R. Yanek, Cynthia A. James, Casey Overby Taylor
J. Am. Medical Informatics Assoc.4
2024 Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages
Natalie Wang, Sukrit Treewaree, Ayah Zirikly, Yuzhi L. Lu, Michelle H. Nguyen, Bhavik Agarwal, Jash Shah, James Michael Stevenson, Casey Overby Taylor
J. Biomed. Informatics3
2022 Improving the Generalizability of Depression Detection by Leveraging Clinical Questionnaires
abstract
Automated methods have been widely used to identify and analyze mental health conditions (e.g., depression) from various sources of information, including social media.Yet, deployment of such models in real-world healthcare applications faces challenges including poor out-of-domain generalization and lack of trust in black box models.In this work, we propose approaches for depression detection that are constrained to different degrees by the presence of symptoms described in PHQ9, a questionnaire used by clinicians in the depression screening process.In dataset-transfer experiments on three social media datasets, we find that grounding the model in PHQ9's symptoms substantially improves its ability to generalize to out-of-distribution data compared to a standard BERT-based approach.Furthermore, this approach can still perform competitively on indomain data.These results and our qualitative analyses suggest that grounding model predictions in clinically-relevant symptoms can improve generalizability while producing a model that is easier to inspect.
Thong Nguyen 0004, Andrew Yates, Ayah Zirikly, Bart Desmet, Arman Cohan
ACL (1)3
2022 Application of Natural Language Processing to Identify Social Needs from The Electronic Health Record's Free-Text Notes
Geoffrey M. Gray, Luis M. Ahumada, Ayah Zirikly, Masoud Rouhizadeh, Thomas Richards, Elham Hatef
AMIA3
2022 A Whole-Person Function Dictionary for the Mobility, Self-Care and Domestic Life Domains: a Seedset Expansion Approach
abstract
Whole-person functional limitations in the areas of mobility, self-care and domestic life affect a majority of individuals with disabilities. Detecting, recording and monitoring such limitations would benefit those individuals, as well as research on whole-person functioning and general public health. Dictionaries of terms related to whole-person function would enable automated identification and extraction of relevant information. However, no such terminologies currently exist, due in part to a lack of standardized coding and their availability mainly in free text clinical notes. In this paper, we introduce terminologies of whole-person function in the domains of mobility, self-care and domestic life, built and evaluated using a small set of manually annotated clinical notes, which provided a seedset that was expanded using a mix of lexical and deep learning approaches.
Ayah Zirikly, Bart Desmet, Julia Porcino, Jonathan Camacho, Pei-Shu Ho, Rafael Jiménez Silva, Maryanne Sacco
LREC1
2021 Sparse encoding for more-interpretable feature-selecting representations in probabilistic matrix factorization
Joshua C. Chang, Patrick Fletcher, Jungmin Han, Ted L. Chang, Shashaank Vattikuti, Bart Desmet, Ayah Zirikly, Carson C. Chow
ICLR7
2021 Ambiguity in medical concept normalization: An analysis of types and coverage in electronic health record datasets
abstract
OBJECTIVES: Normalizing mentions of medical concepts to standardized vocabularies is a fundamental component of clinical text analysis. Ambiguity-words or phrases that may refer to different concepts-has been extensively researched as part of information extraction from biomedical literature, but less is known about the types and frequency of ambiguity in clinical text. This study characterizes the distribution and distinct types of ambiguity exhibited by benchmark clinical concept normalization datasets, in order to identify directions for advancing medical concept normalization research. MATERIALS AND METHODS: We identified ambiguous strings in datasets derived from the 2 available clinical corpora for concept normalization and categorized the distinct types of ambiguity they exhibited. We then compared observed string ambiguity in the datasets with potential ambiguity in the Unified Medical Language System (UMLS) to assess how representative available datasets are of ambiguity in clinical language. RESULTS: We found that <15% of strings were ambiguous within the datasets, while over 50% were ambiguous in the UMLS, indicating only partial coverage of clinical ambiguity. The percentage of strings in common between any pair of datasets ranged from 2% to only 36%; of these, 40% were annotated with different sets of concepts, severely limiting generalization. Finally, we observed 12 distinct types of ambiguity, distributed unequally across the available datasets, reflecting diverse linguistic and medical phenomena. DISCUSSION: Existing datasets are not sufficient to cover the diversity of clinical concept ambiguity, limiting both training and evaluation of normalization methods for clinical text. Additionally, the UMLS offers important semantic information for building and evaluating normalization methods. CONCLUSIONS: Our findings identify 3 opportunities for concept normalization research, including a need for ambiguity-specific clinical datasets and leveraging the rich semantics of the UMLS in new methods and evaluation measures for normalization.
Denis Newman-Griffis, Guy Divita, Bart Desmet, Ayah Zirikly, Carolyn P. Rosé, Eric Fosler-Lussier
J. Am. Medical Informatics Assoc.4
2020 Angelfish: Building a Structurally Diverse Clinical Document Corpus
Guy Divita, Bart Desmet, Ayah Zirikly, Luke Breitfeller, Carolyn P. Rosé
AMIA3
2020 Experiences and Challenges in Manual Annotation of Functioning Information in Medical Records
Jonathan Camacho, Pei-Shu Ho, Rafael Jiménez Silva, Alex Marr, Julia Porcino, Maryanne Sacco, Ayah Zirikly, Leighton Chan, Elizabeth Rasch
AMIA7
2020 Ambiguity in Medical Concept Normalization: An Analysis of Types and Coverage in Electronic Health Record Datasets
Denis Newman-Griffis, Guy Divita, Bart Desmet, Ayah Zirikly, Carolyn P. Rosé, Eric Fosler-Lussier
AMIA4
2020 Curating Annotated Corpora for Functioning Information
Rafael Jiménez Silva, Chunxiao Zhou, Bart Desmet, Ayah Zirikly, Alex Marr, Maryanne Sacco, Pei-Shu Ho, Jonathan Camacho, Julia Porcino, Guy Divita, Elizabeth Rasch
AMIA4
2019 Automated classification of mobility activities in free text clinical narratives
Denis Newman-Griffis, Ayah Zirikly, Pei-Shu Ho, Jonathan Camacho, Maryanne Sacco, Alex Marr, Albert M. Lai, Eric Fosler-Lussier
AMIA2
2019 Bootstrapping a Mobility Dictionary from a Seed Set
Ayah Zirikly, Denis Newman-Griffis, Julia Porcino, Pei-Shu Ho, Jonathan Camacho, Maryanne Sacco, Alex Marr
AMIA1
2013 ANEAR: Automatic Named Entity Aliasing Resolution
Ayah Zirikly, Mona T. Diab
NLDB1