1 citations · 1 across the 12 of their papers we have counts for
14 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…
Hierarchical and Permutation-Invariant Feature Transformation Learning via Policy-Guided Embedding Search
Rui Liu, Tao Zhe, Yanyong Huang +5
Feature transformation improves predictive performance on tabular data by constructing informative abstractions from raw features. Recent generative approaches encode transformatio…
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…
Import What You Need: Learning When and How to Augment EHR Graphs with External Knowledge
Chen Chen, Mohsen Nayebi Kerdabadi, Dongjie Wang +2
Longitudinal prediction from electronic health records (EHRs) is limited by the sparsity and irregularity in patient trajectories, and knowledge augmentation with external knowledg…
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…
Neural Structure Embedding for Symbolic Regression via Continuous Structure Search and Coefficient Optimization
Fateme Memar, Tao Zhe, Dongjie Wang
Symbolic regression aims to discover human-interpretable equations that explain observational data. However, existing approaches rely heavily on discrete structure search (e.g., ge…
Robust and Efficient Tool Orchestration via Layered Execution Structures with Reflective Correction
Tao Zhe, Haoyu Wang, Bo Luo +6
Tool invocation is a core capability of agentic systems, yet failures often arise not from individual tool calls but from how multiple tools are organized and executed together. Ex…
City Editing: Hierarchical Agentic Execution for Dependency-Aware Urban Geospatial Modification
Rui Liu, Steven Jige Quan, Zhong-Ren Peng +6
Urban renewal requires incremental modifications to existing geospatial plans, yet manually updating complex layouts under spatial constraints is labor-intensive and error-prone. T…
From Queries to Insights: Agentic LLM Pipelines for Spatio-Temporal Text-to-SQL
Manu Redd, Tao Zhe, Dongjie Wang
Natural-language-to-SQL (NL-to-SQL) systems hold promise for democratizing access to structured data, allowing users to query databases without learning SQL. Yet existing systems s…
Constraint-Aware Route Recommendation from Natural Language via Hierarchical LLM Agents
Tao Zhe, Rui Liu, Fateme Memar +5
Route recommendation aims to provide users with optimal travel plans that satisfy diverse and complex requirements. Classical routing algorithms (e.g., shortest-path and constraint…
Permutation-Invariant Representation Learning for Robust and Privacy-Preserving Feature Selection
Rui Liu, Tao Zhe, Yanjie Fu +3
Feature selection eliminates redundancy among features to improve downstream task performance while reducing computational overhead. Existing methods often struggle to capture intr…
Multi-Ontology Integration with Dual-Axis Propagation for Medical Concept Representation
Mohsen Nayebi Kerdabadi, Arya Hadizadeh Moghaddam, Dongjie Wang +1
Medical ontology graphs map external knowledge to medical codes in electronic health records via structured relationships. By leveraging domain-approved connections (e.g., parent-c…