Retrieval-Augmented Generation Systems

Retrieval-Augmented Generation (RAG) improves the factual accuracy of large language model (LLM) outputs by grounding generation in external knowledge. Recent agentic RAG systems extend this paradigm with critical agents to evaluate model responses and iteratively refine outputs. However, most prior work implicitly assumes reliable critic feedback and focuses on planning strategies, while paying limited attention to the robustness of the error-correction process itself, which can be impacted by misaligned error categories and ineffective or incorrect corrections. Here, we hypothesize that RAG performance can be improved without explicit error categorization. We propose RePAIR, a response-action learning paradigm that directly maps flawed RAG outputs to error-mitigating action plans without relying on fine-grained error taxonomies and explicit critic supervision. Across multiple benchmarks, RePAIR consistently improves agentic RAG performance.

Clinical value set authoring -- the task of identifying all codes in a standardized vocabulary that define a clinical concept -- is a recurring bottleneck in clinical quality measurement and phenotyping. A natural approach is to prompt a large language model (LLM) to generate the required codes directly, but structured clinical vocabularies are large, version-controlled, and not reliably memorized during pretraining. We propose Retrieval-Augmented Set Completion (RASC): retrieve the $K$ most similar existing value sets from a curated corpus to form a candidate pool, then apply a classifier to each candidate code. Theoretically, retrieve-and-select can reduce statistical complexity by shrinking the effective output space from the full vocabulary to a much smaller retrieved candidate pool. We demonstrate the utility of RASC on 11,803 publicly available VSAC value sets, constructing the first large-scale benchmark for this task. A cross-encoder fine-tuned on SAPBert achieves AUROC0.852 and value-set-level F10.298, outperforming a simpler three-layer Multilayer Perceptron (AUROC0.799, F10.250) and both reduce the number of irrelevant candidates per true positive from 12.3 (retrieval-only) to approximately 3.2 and 4.4 respectively. Zero-shot GPT-4o achieves value-set-level F1~0.105, with 48.6% of returned codes absent from VSAC entirely. This performance gap widens with increasing value set size, consistent with RASC's theoretical advantage. We observe similar performance gains across two other classifier model types, namely a cross-encoder initialized from pre-trained SAPBert and a LightGBM model, demonstrating that RASC's benefits extend beyond a single model class. The code to download and create the benchmark dataset, as well as the model training code is available at: \href{https://github.com/mukhes3/RASC}{https://github.com/mukhes3/RASC}.

This position paper argues that Retrieval-Augmented Generation (RAG) systems exhibit a factual bias-optimizing for epistemic uncertainty reduction while ignoring the aleatoric uncertainty inherent in opinion-rich content. This misalignment demands a paradigm shift in RAG system design. A survey of 34 major RAG benchmarks reveals that only one addresses opinion synthesis, confirming that the bias is structural and embedded in datasets, retrieval-generation objectives, and evaluation metrics alike. Beyond technical limitations, this bias poses risks to transparent and accountable AI. Namely, echo chamber effects that amplify dominant viewpoints, which can lead to opinion manipulation and under-representation of minority voices. We formalize the problem through the lens of uncertainty quantification, showing that factual queries should minimize posterior entropy while opinion queries must preserve it. We derive a unified objective over coverage, fidelity, and fairness using the Wasserstein distance. As an existence proof, we present Opinion-Aware RAG (O-RAG), an architecture featuring LLM-based opinion extraction and entity-linked opinion metadata. We evaluate it across two domains -- e-commerce seller forums and public hotel reviews. Experiments demonstrate 18-48% reduction in Wasserstein distance to corpus-level sentiment distributions, +26.8% sentiment diversity, and +42.7% entity match rate. Human evaluators preferred opinion-enriched generation 79.2% of the time. We propose a research agenda and argue that as RAG systems increasingly mediate access to information, their ability to represent diverse perspectives is of the essence.

Rerankers play a pivotal role in refining retrieval results for Retrieval-Augmented Generation. However, current reranking models are typically optimized on static human annotated relevance labels in isolation, decoupled from the downstream generation process. This isolation leads to a fundamental misalignment: documents identified as topically relevant by information retrieval metrics often fail to provide the actual utility required by the LLM for precise answer generation. To bridge this gap, we introduce ReRanking Preference Optimization (RRPO), a reinforcement learning framework that directly aligns reranking with the LLM's generation quality. By formulating reranking as a sequential decision-making process, RRPO optimizes for context utility using LLM feedback, thereby eliminating the need for expensive human annotations. To ensure training stability, we further introduce a reference-anchored deterministic baseline. Extensive experiments on knowledge-intensive benchmarks demonstrate that RRPO significantly outperforms strong baselines, including the powerful list-wise reranker RankZephyr. Further analysis highlights the versatility of our framework: it generalizes seamlessly to diverse readers (e.g., GPT-4o), integrates orthogonally with query expansion modules like Query2Doc, and remains robust even when trained with noisy supervisors.

Drug recommendation requires a deep understanding of individual patient context, especially for complex conditions like Parkinson's disease. While LLMs possess broad medical knowledge, they fail to capture the subtle nuances of actual prescribing patterns. Existing RAG methods also struggle with these complexities because guideline-based retrieval remains too generic and similar-patient retrieval often replicates majority patterns without accounting for the unique clinical nuances of individual patients. To bridge this gap, we propose PACE-RAG (Patient-Aware Contextual and Evidence-Constrained RAG). Rather than directly copying frequent medications from retrieved patients, PACE-RAG personalizes recommendations by first extracting patient-specific clinical features, retrieving cases around these features, and then refining the final prescription using the patient's current symptoms, active medication history, and focus-specific prescribing tendencies. By analyzing treatment patterns tailored to specific clinical features, PACE-RAG generates patient-specific medication recommendations along with an explainable clinical summary. PACE-RAG achieved the strongest performance among the evaluated inference-only LLM-based methods, reaching F1 scores of 80.84% and 47.22% on the Parkinson's disease and MIMIC-IV cohorts, respectively. Our code is available at: https://github.com/ChaeYoungHuh/PACE-RAG.

Retrieval-augmented generation (RAG) enhances zero-shot time series (TS) forecasting by leveraging external knowledge bases, yet existing approaches overlook input-level relevance when fusing retrieved samples with the query. We argue that not all retrievals are equally useful, and irrelevant ones can degrade performance. To this end, we propose Cross-RAG, a zero-shot RAG-based forecasting framework that selectively attends to query-relevant retrieved samples via query--retrieval cross-attention. By modeling input-level relevance between the query and retrieved samples, Cross-RAG jointly incorporates three sources of information: 1) the query itself, 2) the retrieved samples, and 3) their relational interactions. In particular, this input-aware design enables Cross-RAG to remain stable as the number of retrieved samples $k$ grows, whereas prior methods without cross-attention require careful $k$ tuning to avoid degradation from irrelevant retrievals. Extensive experiments demonstrate that Cross-RAG consistently improves zero-shot forecasting performance across multiple TSFM backbones and various RAG methods, with additional analyses confirming its effectiveness across various retrieval scenarios. Code is available at https://github.com/seunghan96/cross-rag/.

With the rapid advancement of agent-based methods in recent years, Agentic RAG has undoubtedly become an important research direction. Multi-hop reasoning, which requires models to engage in deliberate thinking and multi-step interaction, serves as a critical testbed for assessing such capabilities. However, existing benchmarks typically provide only final questions and answers, while lacking the intermediate hop-level questions that gradually connect atomic questions to the final multi-hop query. This limitation prevents researchers from analyzing at which step an agent fails and restricts more fine-grained evaluation of model capabilities. Moreover, most current benchmarks are manually constructed, which is both time-consuming and labor-intensive, while also limiting scalability and generalization. To address these challenges, we introduce AgenticRAGTracer, the first Agentic RAG benchmark that is primarily constructed automatically by large language models and designed to support step-by-step validation. Our benchmark spans multiple domains, contains 1,305 data points, and has no overlap with existing mainstream benchmarks. Extensive experiments demonstrate that even the best large language models perform poorly on our dataset. For instance, GPT-5 attains merely 22.6% EM accuracy on the hardest portion of our dataset. Hop-aware diagnosis reveals that failures are primarily driven by distorted reasoning chains -- either collapsing prematurely or wandering into over-extension. This highlights a critical inability to allocate steps consistent with the task's logical structure, providing a diagnostic dimension missing in traditional evaluations. We believe our work will facilitate research in Agentic RAG and inspire further meaningful progress in this area. Our code and data are available at https://github.com/YqjMartin/AgenticRAGTracer.

Long-context LLMs and Retrieval-Augmented Generation defer state tracking and evidence consolidation to query time, which is brittle when facts evolve and answers depend on latent states. We introduce Unified Memory Agent (UMA) for a one-to-many setting: query-agnostic external memory is constructed once from a stream and reused across multiple future QA sessions. A single policy maintains a structured Memory Bank through CRUD operations and answers using both the Memory Bank and raw context. Task-Stratified GRPO uses the mean reward of QA trajectories branching from each sampled memory state to supervise memory maintenance, while normalizing memory and per-question QA groups separately. We also introduce Ledger-QA, a diagnostic benchmark for long-horizon state tracking over accumulated updates. At the 16k budget, UMA-Generalist achieves the highest average score among compared methods across the test-time-learning and accurate-retrieval benchmarks and transfers to Ledger-QA without task-specific training; UMA-Specialist further improves long-horizon tracking after task adaptation. These results support learned proactive memory management for long-context reasoning.

Retrieval-Augmented Generation (RAG) systems combine dense retrievers and language models to ground their outputs in external documents. However, the interaction between these components remains opaque, creating challenges for deployment in high-stakes domains. We present RAG-E, an end-to-end explainability framework that quantifies retriever-generator alignment through mathematically grounded attribution methods. Our approach adapts Integrated Gradients for retriever analysis, proposes a Monte Carlo-stabilized Shapley Value approximation for generator attribution, and introduces the Weighted Attribution-Relevance Gap (WARG) metric to measure how closely the generator's document usage aligns with retriever rankings. Experiments on PopQA, QAMPARI, and TREC CAST datasets reveal substantial misalignment: depending on the model and setting, generators often ignore top-ranked documents and rely on documents ranked as less relevant. We show that WARG captures retriever-generator alignment better than Pearson and Spearman correlations and can serve as an indicator of RAG performance. RAG-E and WARG provide a practical framework for auditing this interaction, enabling more reliable and transparent RAG systems.

When answering user queries, LLMs often retrieve knowledge from external sources stored in retrieval-augmented generation (RAG) databases. These are often populated from unvetted sources, e.g. the open web, and can contain maliciously crafted data. This paper studies attacks that can manipulate the context retrieved by LLMs from such RAG databases. Prior work on such context manipulation primarily injects false or toxic content, which can often be detected by fact-checking or linguistic analysis. A more subtle threat, which we call epistemic bias injection (EBI), is where adversaries inject factually correct yet epistemically biased passages that systematically favor one side of an open-ended issue. Although linguistically coherent and truthful, such adversarial passages effectively crowd out alternative viewpoints during retrieval from the RAG and push LLM outputs towards an attack-desired stance. As a core contribution, we propose a novel characterization of the problem: We give a geometric metric that quantifies stance polarity and epistemic bias. This metric can be computed directly on embeddings of text passages. Leveraging it, we construct EBI attacks and develop a lightweight prototype defense called BiasDef for them. We evaluate them both on a comprehensive benchmark constructed from public question answering datasets. Our results show that: (1) the proposed attack induces significant stance polarity shifts, effectively evading existing retrieval-based sanitization defenses, and (2) BiasDef substantially reduces adversarial retrieval and epistemic bias in LLM's answers. Overall, this demonstrates the new threat as well as the ease of employing epistemic bias metrics for filtering in RAG-enabled LLMs.

Recent advances in large language models (LLMs) have led to a surge of interest in query augmentation for information retrieval (IR). Two main approaches have emerged. The first prompts LLMs to generate answers or pseudo-documents that serve as new queries, relying purely on the model's parametric knowledge or contextual information. The second applies reinforcement learning (RL) to fine-tune LLMs for query rewriting, directly optimizing retrieval metrics. While having respective advantages and limitations, the two approaches have not been compared under consistent experimental conditions. In this work, we present the first systematic comparison of prompting-based and RL-based query augmentation across diverse benchmarks, including evidence-seeking, ad hoc, and tool retrieval. Our key finding is that under a compute-aware comparison setting, simple, training-free query augmentation often performs on par with, or even surpasses, more expensive RL-based counterparts, especially when using powerful LLMs. Motivated by this discovery, we introduce a novel hybrid method, On-policy Pseudo-document Query Expansion (OPQE), in which the LLM policy learns to generate a pseudo-document that maximizes retrieval performance, rather than rewriting the query, thus merging the flexibility and generative structure of prompting with the targeted optimization of RL. We show OPQE outperforms both standalone prompting and RL-based rewriting, demonstrating that a synergistic approach yields the best results. We open source our implementation to facilitate reproducibility.

Existing data poisoning attacks on retrieval-augmented generation (RAG) systems scale poorly because they require costly optimization of poisoned documents for each target phrase. We introduce Eyes-on-Me, a modular attack that decomposes an adversarial document into reusable Attention Attractors and Focus Regions. Attractors are optimized to direct attention to the Focus Region. Attackers can then insert semantic baits for the retriever or malicious instructions for the generator, adapting to new targets at near zero cost. This is achieved by steering a small subset of attention heads that we empirically identify as strongly correlated with attack success. Across 18 end-to-end RAG settings (3 datasets $\times$ 2 retrievers $\times$ 3 generators), Eyes-on-Me raises average attack success rates from 21.9 to 57.8 (+35.9 points, 2.6$\times$ over prior work). A single optimized attractor transfers to unseen black box retrievers and generators without retraining. Our findings establish a scalable paradigm for RAG data poisoning and show that modular, reusable components pose a practical threat to modern AI systems. They also contribute to interpretability research by revealing a strong link between attention concentration and model outputs.

We present a lightweight, model-agnostic temporal layer for RAG and use cybersecurity data to separate two problems that are usually conflated. For freshness, a half-life recency prior surfaces the newest relevant item where a cosine-only baseline scores 0.00; on a hard NVD CVE test, where the freshest item is not the most similar, it reaches Latest@10 of 0.60 versus 0.20 for a semantic-then-newest baseline, but stays partial and parameter-sensitive. For topic evolution, a heuristic tracker's low 0.08 macro-F1 is driven by the labeling rule, not the clusterer (HDBSCAN: 0.10; fixing the rule alone reaches 0.49, and 0.96 without clustering noise). We contribute a reproducible decoupling of the two, with honest real-data scope and a reference implementation.

Retrieval-Augmented Generation (RAG) systems are increasingly deployed in high-stakes domains, where safety depends not only on how a system answers, but also on whether a query should be answered given a knowledge base (KB). Out-of-domain (OOD) queries can cause dense retrieval to surface weakly related context and lead the generator to produce fluent but unjustified responses. We study lightweight, KB-aligned OOD detection as an always-on gate for RAG systems. Our approach applies PCA to KB embeddings and scores queries in a compact subspace selected either by explained-variance retention (EVR) or by a separability-driven t-test ranking. We evaluate geometric semantic-search rules and lightweight classifiers across 16 domains, including high-stakes COVID-19 and Substance Use KBs, and stress-test robustness using both LLM-generated attacks and an in-the-wild 4chan attack. We find that low-dimensional detectors achieve competitive OOD performance while being faster, cheaper, and more interpretable than prompted LLM-based judges. Finally, human and LLM-based evaluations show that OOD queries primarily degrade the relevance of RAG outputs, showing the need for efficient external OOD detection to maintain safe, in-scope behavior.

Retrieval-Augmented Generation (RAG) equips large language models with external knowledge and is central to knowledge-intensive tasks. As RAG systems enter real-world use, generators must reliably leverage retrieved evidence. Recent fine-tuning methods improve adaptation to RAG scenarios, but optimization remains challenging because retrieval may return incomplete, fragmented, noisy, or conflicting contexts. Complex tasks further require fine-grained evidence dependencies. These challenges make high-quality supervision costly and limit generalization. We present KARE-RAG (Knowledge-Aware Refinement and Enhancement for RAG), a training-time scaffolded alignment framework. It uses structured knowledge representations as temporary scaffolds to expose evidence organization, support localized factual refinement, and construct fine-grained preference pairs. In our main implementation, an expert LLM refines a lightweight graph-structured evidence sketch. The generator is optimized with token-weighted Dense Direct Preference Optimization (DDPO), which focuses learning on edited scaffold regions. Scaffolds are used only for data construction and training supervision. At inference time, the model runs as standard Vanilla RAG without graph construction, extra retrieval, or latency overhead. Experiments show that KARE improves transfer across the evaluated QA and relation extraction datasets with limited training data, while leaving general capabilities largely unchanged. KARE can also complement existing RAG training objectives as an additional alignment stage.

Large language models (LLMs) integrated with retrieval-augmented generation (RAG) have improved factuality by grounding outputs in external evidence. However, they remain susceptible to unfaithful generation, where outputs contradict retrieved context despite its relevance and accuracy. Existing approaches aiming to improve faithfulness primarily focus on enhancing the utilization of external context, but often overlook the persistent influence of internal parametric knowledge during generation. In this work, we investigate the internal mechanisms behind unfaithful generation and identify a subset of mid-to-deep feed-forward networks (FFNs) that are disproportionately activated in such cases. Building on this insight, we propose Parametric Knowledge Muting through FFN Suppression (ParamMute), a framework that improves contextual faithfulness by suppressing the activation of unfaithfulness-associated FFNs and calibrating the model toward retrieved knowledge. To evaluate our approach, we introduce CoFaithfulQA, a benchmark specifically designed to evaluate faithfulness in scenarios where internal knowledge conflicts with accurate external evidence. Experimental results show that ParamMute significantly enhances faithfulness across both CoFaithfulQA and the established ConFiQA benchmark, achieving substantial reductions in reliance on parametric memory. These findings underscore the importance of mitigating internal knowledge dominance and provide a new direction for improving LLM trustworthiness in RAG. All codes are available at https://github.com/OpenBMB/ParamMute.

Retrieval-augmented generation (RAG) synergizes the retrieval of pertinent data with the generative capabilities of Large Language Models (LLMs), ensuring that the generated output is not only contextually relevant but also accurate and current. We introduce XRAG, an open-source, modular codebase that facilitates exhaustive evaluation of the performance of foundational components of advanced RAG modules. These components are systematically categorized into four core phases: pre-retrieval, retrieval, post-retrieval, and generation. We systematically analyse them across reconfigured datasets, providing a comprehensive benchmark for their effectiveness. As the complexity of RAG systems continues to escalate, we underscore the critical need to identify potential failure points in RAG systems. We formulate a suite of experimental methodologies and diagnostic testing protocols to dissect the failure points inherent in RAG engineering. Subsequently, we proffer bespoke solutions aimed at bolstering the overall performance of these modules. Our work thoroughly evaluates the performance of advanced core components in RAG systems, providing insights into optimizations for prevalent failure points.

In customer contact centers, human agents often struggle with long average handling times (AHT) due to the need to manually interpret queries and retrieve relevant knowledge base (KB) articles. While retrieval augmented generation (RAG) systems using large language models (LLMs) have been widely adopted in industry to assist with such tasks, RAG faces challenges in real-time conversations, such as inaccurate query formulation and redundant retrieval of frequently asked questions (FAQs). To address these limitations, we propose a decision support system that can look beyond RAG by first identifying customer questions in real time. If the query matches an FAQ, the system retrieves the answer directly from the FAQ database; otherwise, it generates answers via RAG. Our approach reduces reliance on manual queries, providing responses to agents within 2 seconds. Deployed in AI-powered human-agent assist solution at Minerva CQ, this system improves efficiency, reduces AHT, and lowers operational costs. We also introduce an automated LLM-agentic workflow to identify FAQs from historical transcripts when no predefined FAQs exist.

Novice math teachers often encounter students' mistakes that are difficult to diagnose and remediate. Misconceptions are especially challenging because teachers must explain what went wrong and how to solve them. Although many existing large language model (LLM) platforms can assist in generating instructional feedback, these LLMs loosely connect pedagogical knowledge and student mistakes, which might make the guidance less actionable for teachers. To address this gap, we propose MisEdu-RAG, a dual-hypergraph-based retrieval-augmented generation (RAG) framework that organizes pedagogical knowledge as a concept hypergraph and real student mistake cases as an instance hypergraph. Given a query, MisEdu-RAG performs a two-stage retrieval to gather connected evidence from both layers and generates a response grounded in the retrieved cases and pedagogical principles. We evaluate on \textit{MisstepMath}, a dataset of math mistakes paired with teacher solutions, as a benchmark for misconception-aware retrieval and response generation across topics and error types. Evaluation results on \textit{MisstepMath} show that, compared with baseline models, MisEdu-RAG improves token-F1 by 10.95% and yields up to 15.3% higher five-dimension response quality, with the largest gains on \textit{Diversity} and \textit{Empowerment}. To verify its applicability in practical use, we further conduct a pilot study through a questionnaire survey of 221 teachers and interviews with 6 novices. The findings suggest that MisEdu-RAG provides diagnosis results and concrete teaching moves for high-demand misconception scenarios. Overall, MisEdu-RAG demonstrates strong potential for scalable teacher training and AI-assisted instruction for misconception handling. Our code is available on GitHub: https://github.com/GEMLab-HKU/MisEdu-RAG.