Dense sentence embeddings are fundamental to modern Retrieval-Augmented Generation (RAG) systems but suffer from a lack of interpretability due to feature superposition. This opacity hinders the alignment of retrieval processes with human intent, as the entangled representations are difficult to analyze or control. In this work, we propose a method to disentangle the dense representations of sentence transformers (e.g., E5) into human-interpretable concepts using Top-k Sparse Autoencoders (SAEs). We demonstrate that these disentangled features align with specific semantic, syntactic, and pragmatic categories. Furthermore, we introduce an activation steering mechanism that allows for precise intervention in the retrieval process. By clamping specific latent features, we show that it is possible to re-rank search results to better align with user constraints without retraining the backbone model. Our findings suggest that SAE-based decomposition offers a viable path toward transparent and steerable neural information retrieval.
Explaining why dense retrievers assign high relevance scores remains challenging because retrieval decisions are made through opaque high-dimensional embeddings. Existing explanations often focus on surface signals, such as lexical matches, token alignments, or post-hoc textual rationales, and thus provide limited insight into the latent factors that shape dense retrieval behavior at the embedding level. We propose \textit{Xetrieval}, an embedding-level mechanistic framework for explaining dense retrieval. \textit{Xetrieval} first introduces a lightweight reasoning internalizer that approximates Chain-of-Thought reasoning directly in the embedding space with a single forward pass, enriching sentence embeddings with reasoning-oriented information while avoiding expensive autoregressive generation. It then decomposes these reasoning-enhanced embeddings into sparse, human-interpretable features, each associated with a coherent natural language description. By aggregating sparse feature overlaps across multiple document-side views, \textit{Xetrieval} provides feature-level explanations of individual retrieval decisions. Experiments on diverse retrievers and benchmarks show that \textit{Xetrieval} uncovers coherent interpretable features, yields stronger pair-level intervention effects, and supports task-level feature steering. The project page and source code are available at https://hihiczx.github.io/Xetrieval .
Retrieval-Augmented Generation (RAG) systems depend on the geometric properties of vector representations to retrieve contextually appropriate evidence. When source documents interleave multiple topics within contiguous text, standard vectorization produces embedding spaces in which semantically distinct content occupies overlapping neighborhoods. We term this condition semantic entanglement. We formalize entanglement as a model-relative measure of cross-topic overlap in embedding space and define an Entanglement Index (EI) as a quantitative proxy. We argue that higher EI constrains attainable Top-K retrieval precision under cosine similarity retrieval. To address this, we introduce the Semantic Disentanglement Pipeline (SDP), a four-stage preprocessing framework that restructures documents prior to embedding. We further propose context-conditioned preprocessing, in which document structure is shaped by patterns of operational use, and a continuous feedback mechanism that adapts document structure based on agent performance. We evaluate SDP on a real-world enterprise healthcare knowledge base comprising over 2,000 documents across approximately 25 sub-domains. Top-K retrieval precision improves from approximately 32% under fixed-token chunking to approximately 82% under SDP, while mean EI decreases from 0.71 to 0.14. We do not claim that entanglement fully explains RAG failure, but that it captures a distinct preprocessing failure mode that downstream optimization cannot reliably correct once encoded into the vector space.
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.
Amirhossein Abaskohi, Issam H. Laradji, Peter West +1