Towards Trustworthy and Cost-Efficient Data Integration: From Naïve RAG to Agentic RAG

Large language models (LLMs) and AI agents have demonstrated strong potential for data integration in zero-shot and few-shot settings. However, they continue to face significant accuracy and cost challenges in enterprise environments due to a persistent knowledge gap. This paper envisions trustworthy, scalable, and cost-efficient integration through knowledge-grounded LLMs and agents operating within a retrieval-augmented generation (RAG) workflow. Here, trustworthiness refers to evidence-grounded, verifiable reasoning, where integration decisions are transparently supported by retrieved knowledge, robust against hallucination, and consistent across tasks. We trace the evolution from classic RAG to GraphRAG and KG-RAG (knowledge graph-based RAG), highlighting how these paradigms bridge parametric and contextual knowledge. Building on this trajectory, we explore the shift toward Agentic RAG, where autonomous multi-agent systems adaptively plan, retrieve, refine, and reason for complex integration tasks. We examine optimization strategies for cost-efficient integration, addressing computational bottlenecks in large-scale enterprise settings. Finally, we outline open challenges and future directions toward building reliable, explainable, and scalable knowledge-grounded integration systems.

FeLoG: Scalable and Efficient Distributed Graph Embedding with Feedback Loop Mechanism

Graph embedding maps graph nodes into low-dimensional vectors to support applications such as recommendation, fraud detection, and graph-based retrieval-augmented generation (GraphRAG). As graphs scale to billions of edges, scalable and efficient graph embedding has become increasingly important. Existing frameworks commonly adopt a sampling-training paradigm, in which mini-batches are constructed by sampling nodes and their neighbors. However, sampling is typically decoupled from evolving embedding quality, causing redundant exploration of well-trained regions while under-sampling undertrained nodes. At the system level, such decoupling further leads to excessive communication, serialized execution, and low resource utilization in distributed environments. We present FeLoG, a feedback loop-driven system for scalable distributed graph embedding. (1) FeLoG introduces feedback-coupled sampling and training, dynamically prioritizing undertrained nodes according to real-time embedding-quality feedback, thereby reducing redundant computation and accelerating convergence. (2) It employs activity-aware communication that compresses frequently occurring node sequences to reduce intra-machine PCIe traffic and selectively synchronizes frequently updated embeddings to reduce inter-machine communication. (3) It adopts a round-interleaved pipeline that overlaps next-round sampling with current-round training to improve CPU-GPU utilization. Experiments against six state-of-the-art baselines on large-scale graphs show that FeLoG achieves an average speedup of 27.9x, reduces communication cost by more than 53.1%, and sustains over 80% CPU-GPU utilization.

Informative Missingness to Generate Irregular Clinical Time Series

Laboratory tests in electronic health records are collected irregularly, and the absence of a test order can be as informative as the measurement itself. Such missingness reflects clinicians' decisions and patient physiology, making it important to model it directly rather than treat it as a preprocessing artifact. Here we present a diffusion-based approach for generating clinical time series that jointly models laboratory values and their observation patterns using the public Data Analytics Challenge on Missing Data Imputation (DACMI) benchmark derived from MIMIC-III. To preserve realistic sampling, we align chart times into 4-hour intervals and segment admissions into 7-day windows, producing trajectories that pair each lab value with a corresponding observation indicator. Standard transformations and normalization are applied to stabilize training. Our method extends the TimeDiff framework to learn continuous lab values and discrete missingness patterns through complementary diffusion objectives. Experiments show that the generated data closely match real patient trajectories across individual lab distributions and joint value-missingness embeddings, demonstrating that diffusion models can capture clinically meaningful dependencies between patient physiology and clinicians' testing behavior under MNAR-like (missing-not-at-random) missingness. These preliminary results indicate that our model can serve as an initial component toward developing clinical foundation models. By producing synthetic priors that preserve key physiology-missingness relationships, this work motivates the subsequent training of Prior-Data Fitted Networks capable of leveraging informative missingness, which we will investigate in the extended work.

LLMs+Graphs: Toward Graph-Native, Synergistic AI Systems

Large Language Models (LLMs) have advanced rapidly, but their limitations in structured and multi-hop reasoning underscore the need for graph-native, synergistic artificial intelligence (AI) systems. Graph-structured data underpins critical applications across social, biological, financial, transportation, web, and knowledge domains, making it essential to understand how LLMs can leverage graph computation for grounded, context-rich inference. Three complementary synergies are emerging: LLMs augmented with graph computation for retrieval and reasoning; bidirectional integration between LLMs and knowledge graphs (KGs), where LLMs support KG construction and curation while KGs enforce semantic constraints and factual consistency; and AI agents strengthened by graph algorithms for planning, decision making, and multi-step reasoning. In parallel, LLMs introduce new capabilities for graph data management and graph machine learning (ML) through natural language interfaces and hybrid LLM-graph neural network (GNN) pipelines. This tutorial synthesizes the algorithms, systems, and design principles driving these converging directions, offering data science and data mining researchers a unified perspective on integrating LLMs, graph data management, graph mining, graph ML, and agentic computation into next-generation graph-native AI systems.

LLM+Graph@VLDB'2025 Workshop Summary

The integration of large language models (LLMs) with graph-structured data has become a pivotal and fast evolving research frontier, drawing strong interest from both academia and industry. The 2nd LLM+Graph Workshop, co-located with the 51st International Conference on Very Large Data Bases (VLDB 2025) in London, focused on advancing algorithms and systems that bridge LLMs, graph data management, and graph machine learning for practical applications. This report highlights the key research directions, challenges, and innovative solutions presented by the workshop's speakers.

Tipping the Balance: Impact of Class Imbalance Correction on the Performance of Clinical Risk Prediction Models

Objective: ML-based clinical risk prediction models are increasingly used to support decision-making in healthcare. While class-imbalance correction techniques are commonly applied to improve model performance in settings with rare outcomes, their impact on probabilistic calibration remains insufficiently understood. This study evaluated the effect of widely used resampling strategies on both discrimination and calibration across real-world clinical prediction tasks. Methods: Ten clinical datasets spanning diverse medical domains and including 605,842 patients were analyzed. Multiple machine-learning model families, including linear models and several non-linear approaches, were evaluated. Models were trained on the original data and under three commonly used 1:1 class-imbalance correction strategies (SMOTE, RUS, ROS). Performance was assessed on held-out data using discrimination and calibration metrics. Results: Across all datasets and model families, resampling had no positive impact on predictive performance. Changes in the Receiver Operating Characteristic Area Under Curve (ROC-AUC) relative to models trained on the original data were small and inconsistent (ROS: -0.002, p<0.05; RUS: -0.004, p>0.05; SMOTE: -0.01, p<0.05), with no resampling strategy demonstrating a systematic improvement. In contrast, resampling in general degraded the calibration performance. Models trained using imbalance correction exhibited higher Brier scores (0.029 to 0.080, p<0.05), reflecting poorer probabilistic accuracy, and marked deviations in calibration intercept and slope, indicating systematic distortions of predicted risk despite preserved rank-based performance. Conclusion: In a diverse set of real-world clinical prediction tasks, commonly used class-imbalance correction techniques did not provide generalizable improvements in discrimination and were associated with degraded calibration.

ATEX-CF: Attack-Informed Counterfactual Explanations for Graph Neural Networks

Counterfactual explanations offer an intuitive way to interpret graph neural networks (GNNs) by identifying minimal changes that alter a model's prediction, thereby answering "what must differ for a different outcome?". In this work, we propose a novel framework, ATEX-CF that unifies adversarial attack techniques with counterfactual explanation generation-a connection made feasible by their shared goal of flipping a node's prediction, yet differing in perturbation strategy: adversarial attacks often rely on edge additions, while counterfactual methods typically use deletions. Unlike traditional approaches that treat explanation and attack separately, our method efficiently integrates both edge additions and deletions, grounded in theory, leveraging adversarial insights to explore impactful counterfactuals. In addition, by jointly optimizing fidelity, sparsity, and plausibility under a constrained perturbation budget, our method produces instance-level explanations that are both informative and realistic. Experiments on synthetic and real-world node classification benchmarks demonstrate that ATEX-CF generates faithful, concise, and plausible explanations, highlighting the effectiveness of integrating adversarial insights into counterfactual reasoning for GNNs.

Cost-Efficient RAG for Entity Matching with LLMs: A Blocking-based Exploration

Retrieval-augmented generation (RAG) enhances LLM reasoning in knowledge-intensive tasks, but existing RAG pipelines incur substantial retrieval and generation overhead when applied to large-scale entity matching. To address this limitation, we introduce CE-RAG4EM, a cost-efficient RAG architecture that reduces computation through blocking-based batch retrieval and generation. We also present a unified framework for analyzing and evaluating RAG systems for entity matching, focusing on blocking-aware optimizations and retrieval granularity. Extensive experiments suggest that CE-RAG4EM can achieve comparable or improved matching quality while substantially reducing end-to-end runtime relative to strong baselines. Our analysis further reveals that key configuration parameters introduce an inherent trade-off between performance and overhead, offering practical guidance for designing efficient and scalable RAG systems for entity matching and data integration.

Finding Counterfactual Evidences for Node Classification

Counterfactual learning is emerging as an important paradigm, rooted in causality, which promises to alleviate common issues of graph neural networks (GNNs), such as fairness and interpretability. However, as in many real-world application domains where conducting randomized controlled trials is impractical, one has to rely on available observational (factual) data to detect counterfactuals. In this paper, we introduce and tackle the problem of searching for counterfactual evidences for the GNN-based node classification task. A counterfactual evidence is a pair of nodes such that, regardless they exhibit great similarity both in the features and in their neighborhood subgraph structures, they are classified differently by the GNN. We develop effective and efficient search algorithms and a novel indexing solution that leverages both node features and structural information to identify counterfactual evidences, and generalizes beyond any specific GNN. Through various downstream applications, we demonstrate the potential of counterfactual evidences to enhance fairness and accuracy of GNNs.

Generating Skyline Explanations for Graph Neural Networks

This paper proposes a novel approach to generate subgraph explanations for graph neural networks GNNs that simultaneously optimize multiple measures for explainability. Existing GNN explanation methods often compute subgraphs (called ``explanatory subgraphs'') that optimize a pre-defined, single explainability measure, such as fidelity or conciseness. This can lead to biased explanations that cannot provide a comprehensive explanation to clarify the output of GNN models. We introduce skyline explanation, a GNN explanation paradigm that aims to identify k explanatory subgraphs by simultaneously optimizing multiple explainability measures. (1) We formulate skyline explanation generation as a multi-objective optimization problem, and pursue explanations that approximate a skyline set of explanatory subgraphs. We show the hardness for skyline explanation generation. (2) We design efficient algorithms with an onion-peeling approach that strategically removes edges from neighbors of nodes of interests, and incrementally improves explanations as it explores an interpretation domain, with provable quality guarantees. (3) We further develop an algorithm to diversify explanations to provide more comprehensive perspectives. Using real-world graphs, we empirically verify the effectiveness, efficiency, and scalability of our algorithms.