8 papers
SoftGene: Protein Language Model-Enhanced Soft Prompting for Interpretable Gene Set Annotation
Drew Ross, Arya Hadizadeh Moghaddam, Dongjie Wang +2
Gene set analysis is a cornerstone of functional genomics, yet it remains labor-intensive and heavily dependent on manual curation and expert biological interpretation. While Large…
RASPER: Reward-Aligned Summarization of Clinical Notes for EHR Outcome Prediction
Arya Hadizadeh Moghaddam, Mohsen Nayebi Kerdabadi, Chen Chen +2
Unstructured discharge notes in Electronic Health Records (EHRs) often carry signal complementary to structured medical codes, holding patient-specific evidence that standardized c…
REFINE: LLM Refinement over Budgeted Text-Attributed Graphs for Personalized Medical Concept Representation
Mohsen Nayebi Kerdabadi, Arya Hadizadeh Moghaddam, Dongjie Wang +1
Learning rich medical concept representations is essential for EHR prediction. Text-attributed knowledge graphs (TKGs) provide a natural foundation by organizing heterogeneous medi…
Text-Attributed Knowledge Graph Enrichment with Large Language Models for Medical Concept Representation
Mohsen Nayebi Kerdabadi, Arya Hadizadeh Moghaddam, Chen Chen +2
In electronic health record (EHR) mining, learning high-quality representations of medical concepts (e.g., standardized diagnosis, medication, and procedure codes) is fundamental f…
RePrompT: Recurrent Prompt Tuning for Integrating Structured EHR Encoders with Large Language Models
Arya Hadizadeh Moghaddam, Drew Ross, Mohsen Nayebi Kerdabadi +2
Large Language Models (LLMs) have shown strong promise for mining Electronic Health Records (EHRs) by reasoning over longitudinal clinical information to capture context-rich patie…
User-Adaptive Meta-Learning for Cold-Start Medication Recommendation with Uncertainty Filtering
Arya Hadizadeh Moghaddam, Mohsen Nayebi Kerdabadi, Dongjie Wang +2
Large-scale Electronic Health Record (EHR) databases have become indispensable in supporting clinical decision-making through data-driven treatment recommendations. However, existi…
SurvAttack: Black-Box Attack On Survival Models through Ontology-Informed EHR Perturbation
Mohsen Nayebi Kerdabadi, Arya Hadizadeh Moghaddam, Bin Liu +2
Survival analysis (SA) models have been widely studied in mining electronic health records (EHRs), particularly in forecasting the risk of critical conditions for prioritizing high…
Meta-Learning on Augmented Gene Expression Profiles for Enhanced Lung Cancer Detection
Arya Hadizadeh Moghaddam, Mohsen Nayebi Kerdabadi, Cuncong Zhong +1
Gene expression profiles obtained through DNA microarray have proven successful in providing critical information for cancer detection classifiers. However, the limited number of s…