Graph-Based Retrieval

Retrieval-Augmented Generation (RAG) is widely used to ground answers in documents. For complex technical documentation, however, the primary bottleneck is often not model reasoning but a mismatch between a query and the way knowledge is organized for retrieval. This mismatch is pronounced in Electronic Design Automation (EDA) documentation, where the information needed for an answer is scattered across heterogeneous yet tightly coupled artifacts. We therefore redesign the basic retrieval unit of RAG. Instead of operating on isolated chunks or binary relations, we collect typed artifacts into EDA functional units. Each unit is recorded as a hyperedge with links to its source chunks. We then train an encoder to align queries with functional units and combine unit retrieval with direct chunk retrieval. After mapping the selected units back to their sources, a unified reranker chooses the evidence given to the generator. On the newly constructed EDADocEval-QA dataset, our method improves ROUGE-L by 37.1% over Chunk RAG and 55.6% over the strongest graph baseline. On the public ORD-MMBench benchmark, it improves ROUGE-L by 30.0% over the strongest baseline. These results support function-aware evidence organization in the evaluated EDA documentation settings.

Large language models (LLMs) have demonstrated strong capabilities in question answering, yet they still frequently suffer from hallucinations on knowledge-intensive tasks. Knowledge graphs (KGs) provide LLMs with structured, interpretable, and updatable factual grounding, making them a promising external knowledge source for reliable reasoning. However, existing LLM-guided graph reasoning methods typically rely on hop-wise greedy or beam-style pruning during evidence retrieval. Such local decision processes are inherently myopic: evidence that appears weak near the source may become crucial only after deeper graph context is explored, causing answer-critical branches to be discarded prematurely and making the reasoning chain difficult to recover. To address this limitation, we propose Foresight-over-Graph (FoG), a foresight-aware evidence retrieval framework for knowledge base question answering (KBQA). FoG iteratively constructs a question-relevant evidence subgraph and uses far-to-near feedback to guide path exploration, and maintains a compact memory subgraph to support continued exploration. Extensive experiments on widely used KBQA benchmarks demonstrate that FoG achieves state-of-the-art performance, with a particularly large improvement of 16.58% in Hit on CWQ, while also reducing LLM calls and token usage. Our code is available at https://github.com/yhong7/FoG .

Clinical questions often depend on linking a patient's multimodal evidence to external biomedical knowledge, yet existing predictive systems rarely represent such links explicitly, so they can neither be traced to their evidence sources nor removed to measure their contributions. We present MM-KG (Multimodal Knowledge Graph), which represents heterogeneous, multimodal patient observations and biomedical concepts as separate layers in one typed graph, joined by explicit alignment edges. First, modality-specific harmonizers convert EHR text, imaging, genomic, and biospecimen data into typed observations mapped to UMLS concepts, which a route-prioritized aligner links to a biomedical knowledge graph. Query-conditioned retrieval then selects a compact subgraph for downstream use by a large language model or a graph neural network. We build MM-KGs for MIMIC-IV and ADNI, and evaluate them with a 2x2 design that separates patient evidence, biomedical knowledge, and their interaction. On questions that require both sources, neither source alone performs far above chance, whereas their combination yields a drug-controlled AUROC interaction of +0.194 on MIMIC and +0.299 on ADNI. On held-out five-candidate ranking, MM-KG outperforms MindMap by +0.131 Hits@1 and leads an adapted GraphCare on the items that require consulting the patient, and deleting the single answer-bearing relation from the retrieved packet returns Hits@1 to the no-knowledge baseline. Finally, query-conditioned retrieval reaches 0.731 AUROC with 6.8x less context than the strongest generic policy, whereas static knowledge graph context gives no consistent gain on ordinary outcome prediction. Knowledge graphs thus benefit clinical LLMs not as background context but as explicit links between multimodal patient evidence and the relation a question requires, and MM-KG makes these links retrievable, traceable, and testable.

Skill Retrieval (SR) aims to identify the most relevant skills from external skill libraries, and becomes increasingly challenging as libraries grow in scale and diversity. Existing methods either rank skills independently or rely on predefined graph propagation and hierarchical routing, making them vulnerable to semantic distractors, local trapping, and early routing errors. We formulate SR as an adaptive information-foraging process that coordinates region-level navigation with skill-level selection according to the utility and uncertainty observed during search. Based on this formulation, we propose SkillGATE, a graph-guided hierarchical retrieval framework with Gate-Aware Monte Carlo Tree Search (MCTS). SkillGATE constructs a graph-preserving hierarchical index and performs adaptive retrieval through selection, expansion, simulation, and backpropagation. G-PUCT guides action selection, expansion explores new regions, simulation evaluates candidate skills, and backpropagation updates search statistics. Experiments on six SR benchmarks show that SkillGATE consistently improves diverse retrieval and reranking backbones, achieving a 16.3% improvement in overall R@1 over the strongest retriever-based baseline. Our code is available at https://github.com/Edwinbe/SkillGATE-v1/.

Patent search requires processing documents routinely exceeding tens of thousands of tokens. Most neural retrieval approaches operate on truncated inputs, limiting their effectiveness. Graph-based retrieval addresses this by representing each patent as a structured invention graph, but constructing these graphs relies on brittle rule-based parsers. We present the neural parser, which adapts biaffine attention from dependency parsing to predict invention graphs directly from patent text. Our local biaffine attention restricts pairwise scoring to a sliding window, reducing complexity from $O(n^2)$ to $O(n \cdot w)$. Since local and global scoring share the same weights, the model trains on short sequences and deploys on documents exceeding 40,000 tokens without retraining. Distilled from 1 million rule-parsed documents, it surpasses its teacher at 3$\times$ lower inference cost: neural graphs improve citation recall by 0.5% on short queries and 1.1% on full documents in a downstream Graph Transformer retrieval system.

Retrieving the right tables is a prerequisite for Text-to-SQL over realistic databases. Dense table retrievers rank schema elements independently, but this ignores a key source of evidence: some required tables are not mentioned in the question and become identifiable only through their join relationships to already relevant tables. We introduce JOINGR, a join-aware table retrieval method that treats the database join graph as the retrieval space. Columns are represented as graph nodes, while intra-table and foreign-key relationships are represented as typed edges. Given a question, JOINGR selects semantically similar anchor tables, traverses join edges with a query-conditioned scorer, and aggregates the resulting edge deposits into table scores. The scorer is a lightweight MLP on top of frozen query, node, and edge embeddings, trained with a pairwise margin loss over gold tables. On BIRD and Spider datasets, JOINGR is competitive with the strongest retrieval baselines. On BEAVER, a challenging enterprise benchmark with multi-hop table requirements, JOINGR substantially improves recall over dense retrieval and re-ranking baselines. Cross-domain experiments show that the learned scorer transfers across benchmarks, indicating that the method captures reusable joingraph traversal behavior.

Long-term memory lets LLM agents recall past interactions and remain consistent across sessions, but memory systems are hard to compare because they often vary in representation, indexing, retrieval, and evaluation. We present a controlled evaluation framework based on shared 5W-style conversational memories. Localized graph configurations traverse a common base graph; AdaptiveGraph adds chronological edges and Personalized PageRank diffusion. We also evaluate BM25 over the same extracted notes and OpenClaw as a raw-input external reference. Retrieval rankings vary across memory settings. On LongMemEval-S, AdaptiveGraph is the strongest graph configuration at 0.844 MRR, but BM25 reaches 0.867 and OpenClaw 0.880. On ATANT Core, localized graph traversal outperforms diffusion and BM25, whereas BM25 leads the stress rounds. Reducing LongMemEval-S within the tested range does not reproduce the ATANT diffusion penalty, but the smallest tested store remains larger than ATANT Core, so store size cannot be ruled out. The penalty also persists under a permissive content-match criterion. Vocabulary normalization and extraction quality substantially affect graph retrieval, and missing extraction tags are common among top-five misses. Retrieval strategies should therefore be evaluated jointly with the memory setting and against strong lexical baselines.

Graph-based retrieval-augmented generation supports multi-hop retrieval by organizing corpus information into graphs. However, existing relation-free graph retrieval methods rely primarily on query-sentence similarity to search for evidence. This can exclude useful bridging evidence with low query similarity and activate incidental entities unrelated to the reasoning chain. In this paper, we propose a simple and effective approach called NexusRAG, which augments the relation-free Tri-Graph with a corpus-level entity neighborhood structure derived from joint entity co-occurrence and semantic similarity. NexusRAG employs this structure to guide two complementary propagation paths: neighborhood-constrained semantic propagation through sentences identifies the query-relevant entity frontier, while direct structural propagation between neighboring entities expands that frontier to structurally related entities. The propagated entity weights also inform neighborhood-aware passage initialization for Personalized PageRank. Experiments on three multi-hop QA benchmarks and a domain-specific subset of GraphRAG-Bench show that NexusRAG consistently outperforms existing approaches. On the GraphRAG-Bench subset, NexusRAG achieves the highest evidence recall in all question categories, exceeding baselines by 4.2-8.1 points. The implementation code is available at https://github.com/Jacob-biu/NexusRAG.

Answering questions and completing tasks over large document collections often requires connecting evidence spread across multiple documents, such as a project's approval recorded in one, its requirements in another, and its latest status in a third. Recent LLM agents approach this by iteratively searching the full corpus rather than reading only a fixed set of top-ranked documents. However, when the corpus is exposed only as a flat collection of files, a relevant document gives no indication of how it relates to others, so the agent must rediscover these relationships for every query, often missing complementary evidence while simultaneously consuming substantial additional tokens. To address this, we introduce CorpusMap, a navigation layer that organizes the corpus around its recurring entities, which are identifiable from the documents themselves and can link a single document to many others across sources. Specifically, CorpusMap represents each recurring entity as an Entity Page that aggregates information about it and links to every document that refers to it, forming a graph between entities and documents that the agent can traverse to gather otherwise disconnected evidence. Moreover, since CorpusMap is constructed offline by resolving mentions of the same entity across documents, its links are shared across queries rather than rediscovered repeatedly at inference time. Using 7 different models with 3 benchmark datasets, we show that CorpusMap improves both evidence discovery and answer quality over raw-corpus agentic search while using fewer tokens on average, and further outperforms 4 alternative navigation layers, suggesting that entities serve as effective anchors for navigating large document collections.

Graph-based approximate nearest neighbor search (ANNS) is widely used for large-scale semantic search. Its indices are constructed primarily based on geometric relationships among embeddings of an input dataset (e.g., documents or images), rather than explicitly optimizing for semantic relevance. However, when using these indices for downstream query retrieval, performance is evaluated based on the semantic relevance of the retrieved results to the query. This creates a fundamental "geometry-semantic" mismatch between how the indices are constructed and how their retrieval results are evaluated. While existing LLM-based reranking methods can partially mitigate this mismatch at query time, they leave this underlying structural problem in the graph unresolved. We therefore propose LLM-Guided Graph Pruning (LGP), a general framework that addresses this mismatch directly by leveraging LLM reasoning to refine an existing ANN graph index itself. LGP identifies structurally "low-value" neighbors of nodes and replaces them with LLM-selected alternatives that provide useful semantic information while retaining desired geometric structures of the original graph, including sparsity and efficient navigability. Experiments on representative semantic retrieval benchmarks show that LGP consistently improves end-to-end retrieval performance over both vanilla greedy graph search and LLM-based reranking across widely used graph-based ANN indices such as DiskANN and HNSW.

Understanding how two entities are connected often requires tracing multi-hop relations across documents to identify intermediate entities and supporting evidence that explain a connection. This is a task that appears frequently in scientific research and other knowledge-intensive analyses. We formalise this setting as multi-hop relation inference: given two known endpoint entities, we aim to recover the bridge entities and evidence-grounded reasoning chains that connect them across a document corpus, and to generate an explanation grounded in the retrieved evidence. Existing multi-hop RAG systems typically seek an unknown answer entity rather than explicitly recovering the connection between two known endpoints and graph-based approaches often rely on costly LLM-extracted knowledge graphs that limit scalability to large document collections. We introduce ConRAG, which builds a lightweight entity-document graph from entity co-occurrence and LLM-based entity filtering. Its connective retrieval infers and semantically ranks paths between two endpoints. On MuSiQue and 2WikiMultiHopQA, ConRAG consistently improves bridge entity and reasoning chain recovery over strong RAG baselines, while reducing graph-indexing token cost by up to roughly 1.5 orders of magnitude. Our results show that endpoint-constrained path retrieval provides an effective and index-efficient approach to evidence-grounded relation discovery.

Multi-hop retrieval-augmented generation requires a retriever to connect evidence distributed across documents while preserving a concise, faithful generation context. Existing indexes leave two complementary gaps: chunk-based RAG can break cross-passage evidence chains, whereas an unlabeled pairwise projection without generating-topic provenance cannot jointly preserve topic-level co-participation and per-occurrence entity descriptions. We propose STITCH-RAG, a hypergraph-based framework with three coupled components. First, a semi-merged topic hypergraph encodes multi-entity co-participation as topic-summary hyperedges while retaining per-chunk entity states linked by canonical-name equivalence. Second, spatio-temporal influence bridging propagation (STIBP) combines topic-space propagation with deterministic chunk-index linkage across name-equivalent states under frequency-adaptive decay. Third, continuous STIBP scores replace binary entity-match seeds in localized Personalized PageRank (PPR). We characterize the condition under which this prior assigns more PPR mass to ground-truth evidence than a binary prior. Under the reported protocol, STITCH-RAG attains the highest reported Contain-Acc and LLM-Acc point estimates among the compared methods on HotpotQA and 2WikiMultiHopQA, and higher Recall@8 than the methods included in the standardized retrieval comparison. Results on the mixed-domain benchmark remain auxiliary preference-based evidence because only LLM-judged accuracy is available.

Multi-source knowledge graphs (KGs) need query mechanisms that expose reliability and exploit domain structure. This paper presents TCMaster, a property-graph query substrate for confidence-aware traversal and workload-guided physical design over Traditional Chinese Medicine KGs. TCMaster integrates pharmacopoeias, prescriptions, molecular databases, and LLM-extracted micro-semantics into a KG with approximately 221K entities and 723K base edges. It annotates edges with provenance-level confidence, rewrites Cypher queries with confidence predicates, ranks multi-hop paths under PRODUCT, MIN, or weighted-average policies, and uses ontology skew through direction selection, herb-attribute bitmaps, and materialized shortcut edges. On Neo4j, direction selection improves attribute lookup by a factor of 1.47, shortcuts accelerate high-fanout target counting by a factor of 4.42, confidence filtering removes 39.3 percent of low-quality heterogeneous paths, and KG retrieval improves TCMbench QA accuracy by 20.0 percentage points.

An advanced retrieval-augmented generation pipeline is typically assembled from three or four independently operated systems: an approximate nearest-neighbour index, a full-text search engine, a graph database, and a relational document store. Each contributes its own deployment surface, configuration model, and failure modes, and the integration logic that binds them is written anew in every project. In this work, we present \textsc{Quanta}, an open-source Python library, which unifies dense vector search over 4-bit quantised embeddings, BM25 full-text retrieval, and knowledge-graph traversal behind a single retrieval API. Quanta makes two design commitments, which distinguish it from existing hybrid retrieval stacks. First, signals are combined by \emph{weighted reciprocal rank fusion} rather than by normalising heterogeneous scores onto a shared range, which we argue is ill-posed because such normalisations are query-dependent. Second, the graph is a \emph{candidate expander and not a relevance scorer}: traversal widens the candidate pool, and the newly admitted documents are re-scored by the dense indexes under an identifier allowlist, so structural adjacency determines what is considered while content evidence determines how it ranks.

Graph-based retrieval-augmented generation (RAG) can help answer questions that require information from many documents. However, building a graph often requires many language-model calls during ingestion. It is therefore important to ask whether its quality gains justify the additional cost. We present EffiRAG, a graph-based RAG system designed to reduce this cost. It uses the graph to locate relevant passages and generates answers from the original text. This design preserves source information while keeping graph construction and query processing lightweight. We evaluate EffiRAG on UltraDomain, which contains 120 open-ended questions from four domains. Compared with LightRAG-hybrid, EffiRAG produces the preferred answer on 93 questions. LightRAG is preferred on 7, and the remaining 20 are splits. EffiRAG also reduces total system cost by 57 percent, from USD 0.952 to USD 0.408. The cost includes language-model calls during ingestion and querying. The advantage remains as the corpus grows. At 10 and 20 documents per domain, EffiRAG uses a lightweight, non-LLM filter to skip low-salience chunks. It remains preferred over LightRAG-hybrid. It costs 4.2 times and 4.5 times less, respectively. The comparisons identify different quality-cost trade-offs. Graph-based RAG systems should therefore be evaluated by both answer quality and cost. The results favor graph structure that locates and preserves source evidence.

Complete suffix prediction is challenging in sequential decision settings, where the same prefix can remain compatible with several plausible suffixes. We propose a graphbased metric-learning framework that reformulates complete suffix prediction as latent retrieval over process graphs. Prefixes and suffixes are represented as directed attributed graphs and encoded by edge-conditioned graph neural networks, allowing event-level activities and transition-level durations to be modelled jointly. Prefix representations are projected into the latent suffix space through a predictor trained with a joint reconstruction and contrastive objective strengthened using process-aware hard negatives. To stabilise the learned retrieval geometry, spectral normalisation, and retrieval robustness, spectral normalisation is applied to enforce a Lipschitz constraint on both encoders and predictor. Experiments on two real-life process datasets demonstrate that the proposed framework achieves the best overall results across nearly all evaluated criteria. It improves semantic suffix accuracy measured by normalized Damerau-Levenshtein distance, yields strong retrieval quality through Recall@1, Recall@5, and MRR@5, and maintains temporal plausibility according to Mean Absolute Error. These results show that graph-based latent retrieval is an effective alternative to sequential suffix prediction for recommendation-oriented process monitoring under structural and KPI-related constraints.

Graph Retrieval-Augmented Generation (GraphRAG) can connect evidence distributed across a corpus graph, but most systems use largely shared exploration procedures across queries. This creates a structural mismatch: direct facts may need compact local neighborhoods, comparisons need balanced coverage of multiple targets, and mediated questions may require deeper paths through weakly related connectors. We present Mosaic, a training-free framework that formulates GraphRAG retrieval as a per-query control problem. An LLM analyzer converts query-specific evidence requirements into a bounded policy over seed selection, graph traversal, stopping, and evidence selection, while the corpus graph, indexes, scoring functions, grounding procedure, and answer generator remain shared. On GraphRAG-Bench, Mosaic achieves query-weighted Answer Correctness of 76.97 on Medical and 64.33 on Novel, improving over the strongest previously reported overall results by 5.13 and 4.43 points. On Medical, it reaches 95.1 Evidence Recall and 86.1 Context Relevancy. Controlled comparisons on an identical graph and generator show that no fixed narrow, medium, or wide policy is consistently optimal; Mosaic improves by 9.96 points over the strongest canonical fixed policy. Relative to Fixed Wide, it evaluates 81.9% fewer paths and retains 47.2% fewer evidence items. Transfer experiments on HotpotQA, MuSiQue, and 2WikiMultiHopQA further show that the policy interface can be applied without benchmark-specific retriever training.

Graph-based retrieval can improve multi-hop question answering, but existing approaches often incur high query-time costs and produce diffuse, oversized contexts that reduce generation efficiency. We present LiteRAG, a graph-based retrieval method that replaces expensive retrieval-time LLM control with query-conditioned algorithmic exploration and reasoning-chain context construction. On DistComp, a benchmark for multi-hop retrieval over distributed-systems papers, LiteRAG attains the highest overall quality among the evaluated methods (0.798) while reducing per-query latency by over 100$\times$ and cost by over 99% relative to GraphRAG Global and DRIFT. On UltraDomain, it matches LinearRAG on overall quality while using about 14$\times$ fewer tokens. An ablation study indicates that LiteRAG's query-adaptive thresholding and community-aware hub penalization are the main drivers of its token-efficiency gains.

LLM agents use large libraries of reusable skills. At thousands of skill entries, retrieval becomes the bottleneck. Graph-of-Skills (GoS) retrieves dependency-aware bundles from a typed skill graph, and SkillDAG shows that such a graph can accumulate execution-backed structure online. Neither asks whether execution traces can be distilled into a better retrieval graph that generalizes to unseen tasks. We present \textbf{Self-Evolving Graph-of-Skills (SE-GoS)}, which treats the retrieval graph as an index rather than a learned representation: the graph is maintained from execution traces while the retrieval pipeline, the skill library, and the model stay fixed. SE-GoS applies three updates: (1) \textbf{topology}, which induces relations from execution evidence and retracts an avoid edge only after repeated successful co-use; (2) \textbf{edge-weight}, which softly attenuates unsupported semantic edges and reinforces incoming edges to used skills; and (3) \textbf{node-description}, which updates retrieval-facing descriptions stored on graph nodes ranked too low. On SkillsBench, one evolution round lifts average reward from 52.4% to 59.4%, above full-library loading, vector retrieval, static GoS, and SkillDAG, and this ordering repeats on all three backbones. Retrieval over the evolved graph spends about two-thirds of the input tokens that loading the full library costs. Repeating the round does not help. The same graph improves a held-out split it never saw from 52.9% to 58.3%, so what it accumulates transfers rather than memorizes traces. Skill graphs can therefore be improved from execution experience without model training, retrieval-algorithm changes, skill-content modifications, or a model judging which skills are related.

Large language model question answering over power-grid models must respect a fixed context budget. We introduce seed-anchored graph rendering, a deterministic method that prioritizes query-local graph evidence without adding method-specific tuned or learned parameters beyond the shared hop bound and context budget. The method provides a checkable condition under which predefined seed-local answer-bearing render units are preserved in a greedy bounded-context prefix. We evaluate the approach on Common Information Model (CIM) network models exchanged through the Common Grid Model Exchange Standard (CGMES). On two budget-binding CGMES encodings, naive descriptions-first rendering retains local evidence for every single-hop item but only 0.12 and 0.00 of multi-hop items, whereas seed-anchored rendering retains all such evidence. On a preregistered fresh 100-item bank from the SmallGrid topology family, accuracy rises from 0.450 to 0.970 under a fixed 8,000-character context budget. Under a common retrieval and rendering pipeline, the standards-native seed-anchored graph matches or exceeds extracted graph representations produced by LightRAG, Microsoft GraphRAG, and HippoRAG, while avoiding LLM graph-construction tokens. The results are specific to the evaluated CIM/CGMES models, reader, and context budget; they concern budget-bounded retrieval rather than general question answering.

This article presents SSAKG 2.0, an open-source software package for constructing and operating Structural Sequential Associative Knowledge Graphs (SSAKGs). An SSAKG represents objects as graph vertices and ordered sequences as structural patterns of graph connections. The resulting sparse graph is used as an associative memory in which complete sequences can be reconstructed from a partial, unordered context. Version 2.0 introduces new algorithms that exploit individual bits of computer memory to efficiently search graph connections. The package is implemented in Python, while performance-critical graph operations are implemented in C and exposed through a Python interface. This hybrid implementation provides a flexible high-level programming environment while reducing the memory and computational overhead associated with large sparse graphs. The algorithms were evaluated using randomly generated numerical sequences, sequences derived from sentences in the NLTK corpus, and mRNA sequences. The experiments demonstrate the ability of the package to store and reconstruct sequences from partial contexts and provide a basis for evaluating the effects of graph density, sequence length, and memory size on retrieval performance. SSAKG 2.0 is distributed under the Apache 2.0 open-source license. The package includes documentation and reproducible examples and is publicly available through GitHub and the Python Package Index (PyPI).

Hierarchical Knowledge graph (KG)-based retrieval augmented generation (RAG) has emerged as a powerful approach for supporting large language models with structured knowledge. However, there are primary challenges: (i) the lack of methods for automatic KG construction using ontology expansion for low-resource languages such as Vietnamese, (ii) the absence of systematic evaluation for knowledge retrieval strategies leveraging the hierarchical structures. In this paper, we propose an end-to-end pipeline for KG construction and retrieval strategies evaluation. In the KG construction, we employ a three-phase hybrid relation extraction pipeline: intra-batch deduplication via Union-Find, approximate cross-batch search, and LLM extraction with a centroid filter that reduces prompts combined with a five-step dual-LLM validator to prevent bloated ontology. A two-tier architecture consists of unmergeable structural nodes to preserve the document structure and mergeable content nodes. The retrieval evaluation consists of three graph traversal strategies: Top-Down, Horizontal, and Bottom-Up, which are evaluated on a synthetically generated benchmark of 1,210 Vietnamese queries from 109 subgraphs, categorized by five query directions. In this paper, we construct the tree knowledge graph from Vietnamese high school History textbooks (nearly 400 pages) to produce 750 nodes and 4,341 semantic edges with controlled ontology growth from 40 to 41 types. Among experimental graph traversal strategies, the Top-Down strategy with structure surpasses the vector baseline by 4.7 percentage points in NDCG@10. As a result, tree-structural information provides valuable information beyond flat cosine similarity but degrades performance when the query does not require structural context.

Retrieval-Augmented Generation (RAG) mitigates large language models (LLMs) hallucinations, yet conventional dense retrieval struggles with the complex reasoning paths of multi-hop question answering (QA). Graph-based RAG captures multi-step relationships but suffers from severe semantic drift and high online latency due to noisy global graph traversals. Thus, we propose ISO-RAG (ISOperimetric Retrieval-Augmented Generation), a geometry-aware RAG framework. By projecting the underlying knowledge graph into a hyperbolic Poincare ball to precompute node-wise isoperimetric profiles, ISO-RAG prunes spurious edges during retrieval, restricting the search space to a strictly localized subgraph. This topological purification regulates Personalized PageRank (PPR) diffusion driving the retrieval process, ensuring exact and low-latency convergence. Experiments on multi-hop QA benchmarks demonstrate that ISO-RAG outperforms state-of-the-art baselines by average absolute gains of 10.0% in retrieval recall and 4.3% in downstream exact match, achieving a superior accuracy-efficiency trade-off by fundamentally eliminating the latency bottleneck of global traversals. Our source code is available at https://github.com/ZaiizaiZHANG/ISO-RAG.

Large language models extracting knowledge graphs from text capture only explicitly stated facts, often leaving semantically related entities disconnected across documents. We present an additive, engine-neutral second pass that discovers these latent ties without altering extracted facts. Each document is chunked and embedded once; top-k nearest- neighbor queries across existing chunks yield candidate node pairs via entity membership maps. Candidate pairs are scored using Shepard inverse-distance weighting with a rescaled chord distance metric, avoiding the threshold-collapsing flaw of affine cosine scoring behind a k-NN gate. Un-gated per-pair accumulators form a commutative monoid, ensuring the pipeline is strictly order-independent and scales incrementally without recomputing prior documents. Implemented across FalkorDB, Kinetica, ArangoDB, and Neo4j, our method shows that 768- and 240-dimensional embeddings retain 92% and 72% edge fidelity against a 3072-D baseline while achieving a 25x faster top-k formulation.

Path-finding over knowledge graphs has become an effective way to ground LLM reasoning on multi-hop questions. However, biomedical QA introduces two distinct challenges that general-domain methods are not designed for: (i) queries do not expose intermediate reasoning and can be answered through multiple valid pathways, and (ii) biomedical knowledge graphs are densely connected, so path-finding methods easily take wrong turns. To address these challenges, we propose AdaPath, a path-finding framework that retrieves query-adaptive meta-paths from Path-Bank, which captures both query semantics and biomedical knowledge graph structure. AdaPath provides the missing cues in biomedical queries while effectively pruning dense knowledge graph neighborhoods during multi-hop reasoning. We further release BioStrat-QA, a biomedical KGQA benchmark that stratifies multi-hop queries by how much intermediate reasoning they expose. Across biomedical KGQA benchmarks, AdaPath consistently outperforms baselines, sustaining meaningful path-finding even when multi-hop queries expose less surface information. The source code is available at https://github.com/Jun-Hyeong-Kim/AdaPath.

GNN-based Knowledge Graph Question Answering (KGQA) pipelines process queries through four discrete stages: entity linking, subgraph retrieval, GNN reasoning, and answer generation. Standard robustness evaluations conflate stage-level failures into a single end-to-end metric, obscuring both the source of brittleness and the appropriate mitigation target. We ask which stage fails, and why, when the pipeline is subjected to adversarial perturbations on the input question. We introduce a stage-isolation protocol with two answer-preserving adversarial perturbations verified against the knowledge graph: Compositional Restructuring (CR) and Relation Synonym Swap (RS) target distinct stages while leaving entity seeds intact. Evaluated across ComplexWebQuestions and WebQSP, the results run counter to prevailing assumptions: the GNN reasoning stage retains near-baseline accuracy when the subgraph is intact, while subgraph construction accounts for over 99% of the end-to-end collapse under CR, occurring even when the gold answer is present in 74% of retrieved subgraphs. This exposes a fundamental distinction between answer presence and answer reachability that end-to-end metrics cannot detect, and places the mitigation target firmly at the subgraph construction stage rather than the reasoning model. Perturbed datasets and evaluation infrastructure are released at https://anonymous.4open.science/r/atkgrag-E85C .

Multi-hop retrieval must recover passages that provide sufficient evidence together. An initial passage often resolves an entity or relation implicit in the question, making the missing evidence easier to describe only after retrieval begins. Graph retrieval improves access to related evidence through stored corpus structure, but its retrieval signal is commonly derived from the original question. Complementary evidence must then be reached through stored relations even when an observed passage provides a more direct semantic cue. We introduce EviReform, which separates revising the retrieval request from aggregating evidence in the graph. Retrieved source passages formulate residual queries for the unresolved information need. The original and residual retrieval signals are normalized separately, combined, and propagated between propositions that share entities. On 2WikiMultiHopQA, HotpotQA, and MuSiQue, EviReform exceeds the strongest baseline by up to 5.59 Recall@5 points and 4.50 F1 points. These results show that observed evidence can guide graph retrieval toward the part of a supporting chain left underspecified by the original question. Code is available at https://github.com/XrazyMee/EviReform.

While retrieval-augmented generation (RAG) has proven effective at giving LLMs access to external knowledge, mainstream dense-retrieval implementations remain inherently limited in handling structured constraints and multi-hop reasoning. Graph-based methods address this by constructing knowledge graphs offline, but they often fragment semantics, incur high maintenance, and complicate incremental updates. We propose SAG (SQL-Retrieval Augmented Generation), a structured retrieval architecture that organizes documents into an event-entity index without building a global knowledge graph. SAG represents each chunk as a semantically complete event paired with its entities, forming a latent hyperedge that preserves n-ary relations without decomposing them into triples. At query time, SAG treats shared entities as join keys to connect related chunks. This dynamically yields a query-scoped neighborhood of events, and yet every piece of evidence remains the original chunk throughout. Experiments on HotpotQA, 2WikiMultiHopQA, and MuSiQue show that SAG achieves the best retrieval and end-to-end QA performance on every benchmark, with gains that widen as reasoning-chain complexity increases. On MuSiQue, where multi-hop evidence chaining is most demanding, SAG reaches 80.36% Recall@5, outperforming the strongest baseline by 11.52 points. This work paves the way for knowledge infrastructure that enables LLM agents to retrieve and reason over continually growing organizational knowledge.

Agents backed by large skill libraries must decide which skills to load and in what order. Loading the entire library into context is expensive and provides no structure for autonomous sequencing. We study two systems for this problem over a corpus of 690 skills: a hybrid ranker combining lexical and dense-embedding retrieval for sparse, on-demand loading, and a typed knowledge graph encoding workflow relations such as prerequisites, data flow, and ordering. On a set of 117 realistic, non-echoing queries, the hybrid ranker retrieves the correct skill within the top five in 73.5% +/- 8.0 of cases, leaving roughly a quarter of queries unserved. When used as the design intended (substituting graph neighbours for additional ranked results at matched token budget), the graph is significantly worse (-11.2 points, p = 0.0007). Its LLM-generated edge layer adds nothing over neighbours obtained free from a local embedding pass, and 73% of the queries the ranker misses are not reachable through the graph at all. We attribute this to a pre-filter topology bound. Because the graph's candidate edges are drawn from the same embedding neighbourhood the ranker already searches, 98.6% of typed edges connect skills the ranker had already surfaced together. The graph can enrich relation semantics but cannot extend retrieval reach. We further show that evaluating on author-written queries overstates hit@5 by up to 44 points, which would have hidden these results entirely. Our contribution is a mechanistic account of why added structure does not improve retrieval over a strong ranker, and identify the conditions under which adding structural interdependence into the retrieval is optimal.

Fifteen years ago, Low proposed that pun translators should stop searching for equivalent words and instead search for new points of contact between sound and meaning. In this paper, we investigate that idea computationally. We model pun translation as a process of discovery, exploration, and selection. A retrieval system searches semantic and phonological neighborhoods for target-language affordances: sound-meaning bridges that may support new wordplay. Multiple language models then explore these opportunities by generating competing translations, while a multi-perspective generate-and-rank architecture selects among them. Beyond system development, our primary contribution is an analysis of how retrieved affordances propagate through the translation process. We find that generators actively exploit retrieved opportunities, evaluators progressively concentrate around stronger sound-meaning bridges, and exact phonological collisions are selected at disproportionately high rates when available. At the same time, many puns still yield no usable affordances, suggesting that retrieval remains the central bottleneck in computational pun translation. The resulting picture is remarkably close to the process envisioned by Low. Successful pun translation emerges not from preserving source-language words, but from discovering new places in the target language where sound and meaning collide.