Semantic Entanglement in Vector-Based Retrieval: A Formal Framework and Context-Conditioned Disentanglement Pipeline for Agentic RAG Systems

Retrieval-augmented generation (RAG) systems must balance retrieval granularity with contextual coherence, a challenge that existing methods address through LLM-guided chunking, single-level context expansion, or hierarchical summarization. These approaches variously depend on costly LLM calls during indexing or retrieval, limit context aggregation to a single granularity level, or introduce information loss through summarization. We present SproutRAG, an attention-guided hierarchical RAG framework that addresses this trade-off by organizing sentence-level chunks into progressively larger but semantically coherent units, using learned inter-sentence attention to construct a binary chunking tree. Unlike prior approaches that rely on external LLMs, fixed context expansion, or lossy summarization, SproutRAG learns which attention heads and layers best capture semantic document structure, enabling multi-granularity retrieval without additional LLM calls or compressed summaries. At retrieval time, SproutRAG uses hierarchical beam search to retrieve candidates at multiple granularities, capturing multi-sentence relevance beyond flat retrieval. The framework is trained end-to-end with a joint objective that improves both embeddings and tree structure. Experiments across four benchmarks spanning scientific, legal, and open-domain settings demonstrate that SproutRAG improves information efficiency (IE) by 6.1% on average over the strongest baseline. Code is available on https://github.com/AmirAbaskohi/SproutRAG.

Modern retrieval-augmented generation (RAG) systems treat vector embeddings as static, context-free artifacts: an embedding has no notion of when it was created, how trustworthy its source is, or which other embeddings depend on it. This flattening of knowledge has a measurable cost: recent work on VersionRAG reports that conventional RAG achieves only 58% accuracy on versioned technical queries, because retrieval returns semantically similar but temporally invalid content. We propose SmartVector, a framework that augments dense embeddings with three explicit properties -- temporal awareness, confidence decay, and relational awareness -- and a five-stage lifecycle modeled on hippocampal-neocortical memory consolidation. A retrieval pipeline replaces pure cosine similarity with a four-signal score that mixes semantic relevance, temporal validity, live confidence, and graph-relational importance. A background consolidation agent detects contradictions, builds dependency edges, and propagates updates along those edges as graph-neural-network-style messages. Confidence is governed by a closed-form function combining an Ebbinghaus-style exponential decay, user-feedback reconsolidation, and logarithmic access reinforcement. We formalize the model, relate it to temporal knowledge graph embedding, agentic memory architectures, and uncertainty-aware RAG, and present a reference implementation. On a reproducible synthetic versioned-policy benchmark of 258 vectors and 138 queries, SmartVector roughly doubles top-1 accuracy over plain cosine RAG (62.0% vs. 31.0% on a held-out split), drops stale-answer rate from 35.0% to 13.3%, cuts Expected Calibration Error by nearly 2x (0.244 vs. 0.470), reduces re-embedding cost per single-word edit by 77%, and is robust across contradiction-injection rates from 0% to 75%.

Retrieval-Augmented Generation (RAG) systems lose retrieval accuracy when similar documents coexist in the vector database, causing unnecessary information, hallucinations, and factual errors. To alleviate this issue, we propose CHOP, a framework that iteratively evaluates chunk relevance with Large Language Models (LLMs) and progressively reconstructs documents by determining their association with specific topics or query types. CHOP integrates two key components: the CNM-Extractor, which generates compact per-chunk signatures capturing categories, key nouns, and model names, and the Continuity Decision Module, which preserves contextual coherence by deciding whether consecutive chunks belong to the same document flow. By prefixing each chunk with context-aware metadata, CHOP reduces semantic conflicts among similar documents and enhances retriever discrimination. Experiments on benchmark datasets show that CHOP alleviates retrieval confusion and provides a scalable approach for building high-quality knowledge bases, achieving a Top-1 Hit Rate of 90.77% and notable gains in ranking quality metrics.