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Duanyu Feng

Duanyu Feng contributes to research discovery and scholarly infrastructure.

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Machine Learning Information Retrieval

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preprint2026arXiv

Advancing Edge Classification through High-Dimensional Causal Modeling of Node-Edge Interplay

Edge classification, a crucial task for graph applications, remains relatively under-explored compared to link prediction. Current methods often overlook the potential causal influences of node features on edge features, leading to a loss of relevant prior information. In this work, we present an empirical exploration using the Causal Edge Classification Framework (CECF). Unlike conventional causal inference methods, CECF is the first framework to apply causal inference principles to the edge classification task and to explore modeling edge features as a high-dimensional treatment within a causal framework. Based on the node embedding of Graph Neural Network (GNN), CECF seeks to learn a balanced representation of high-dimensional edge features by mitigating the potential influence of node features. Then, a cross-attention network captures the complex dependencies between node and edge features for final edge classification. Extensive experiments demonstrate that CECF not only achieves superior performance but also serves as a flexible, plug-and-play enhancement for existing methods. We also provide empirical analyses, offering insights into when and how this high-dimensional causal modeling framework works for the edge classification.

preprint2026arXiv

Concordia: Self-Improving Synthetic Tables for Federated LLMs

Federated learning (FL) enables training large language models (LLMs) without sharing raw data, but adapting LLMs under strict data isolation and non-IID client distributions remains challenging in practice. Synthetic data offers a natural privacy-preserving surrogate for local training, yet existing federated pipelines typically treat synthetic generation as static or loosely coupled with downstream optimization, leading to rapidly diminishing utility under heterogeneous clients. We study federated adaptation of LLMs on tabular tasks where raw records and validation data cannot be shared, and local training must rely entirely on synthetic tables. We propose Concordia, a tri-level optimization framework that aligns synthetic data generation with federated validation utility despite these constraints. At the client level, models are adapted via parameter-efficient LoRA training on synthetic tables. Clients additionally learn lightweight utility scorers from private validation feedback to reweight synthetic samples during local training. At the outer level, each client refines its own synthetic table generator using group-relative policy optimization (GRPO), guided by an ensemble of heterogeneous scorers shared across clients, without aggregating generator parameters or exposing validation data. Experiments on privacy-sensitive tabular benchmarks from finance and healthcare demonstrate that Concordia consistently improves federated performance, cross-client stability, and robustness to distribution shift compared to static and decoupled synthetic-data baselines.

preprint2026arXiv

Unlocking Biological Workflows for Robust Protein-Text Question Answering: A Dual-Dimensional RAG Framework

Protein-Text Question Answering (QA) is crucial for interpreting biological sequences through natural language. The integration of Large Language Models (LLMs) with Retrieval-Augmented Generation (RAG) that efficiently leverages biological databases and facilitates reasoning offers a potent approach for it. However, constrained by the standard RAG pipeline, these models often rely on curated, static datasets instead of expert-proven biological workflows, lacking the fine-grained information processing and struggling to generalize to novel (OOD) proteins. To bridge this gap, we propose 2D-ProteinRAG, a novel framework that empowers LLMs to operate within the gold-standard biological research workflow (BLAST). To further extract high-quality information from noisy retrieval contexts, we introduce a dual-dimensional (2D) filtering strategy following the expert analytical paradigms. Horizontal Fine-grained Attribute Alignment utilizes a lightweight, intent-aware discriminative filter to prune irrelevant metadata and align database entries with specific user queries. Vertical Homology-based Semantic Denoising resolves functional contradictions and redundancy across multiple homologs via hierarchical clustering. Extensive evaluations on both In-Distribution and diverse biological OOD benchmarks demonstrate that 2D-ProteinRAG consistently achieves state-of-the-art performance, outperforming fine-tuned baselines and other RAG methods. Our results validate the framework's robustness and scalability, providing a practical solution for interpreting protein functions in real-world scientific scenarios.

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