# SpIDER: Spatially Informed Dense Embedding Retrieval for Software Issue Localization

arXiv: https://arxiv.org/abs/2512.16956 · HTML: https://mlsanity.com/paper/2512.16956/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Software engineering coding agents, one of 16 directions in LLM agents and tool use.
- Builds on 17 of its 44 references that are in the map.
- First posted on arXiv 18 Dec 2025.

## Placed in

- LLM agents and tool use / [Software engineering coding agents](https://mlsanity.com/agents/software-engineering-coding-agents/)

## Builds on (most cited first, 17 of 17)

- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [SWE-bench: Can Language Models Resolve Real-World GitHub Issues?](https://mlsanity.com/paper/2310.06770/) (2023)
- [SWE-agent: Agent-Computer Interfaces Enable Automated Software Engineering](https://mlsanity.com/paper/2405.15793/) (2024)
- [CodeBERT: A Pre-Trained Model for Programming and Natural Languages](https://mlsanity.com/paper/2002.08155/) (2020)
- [GraphCodeBERT: Pre-training Code Representations with Data Flow](https://mlsanity.com/paper/2009.08366/) (2020)
- [Agentless: Demystifying LLM-based Software Engineering Agents](https://mlsanity.com/paper/2407.01489/) (2024)
- [RepoGraph: Enhancing AI Software Engineering with Repository-level Code Graph](https://mlsanity.com/paper/2410.14684/) (2024)
- [LocAgent: Graph-Guided LLM Agents for Code Localization](https://mlsanity.com/paper/2503.09089/) (2025)
- [SWE-PolyBench: A multi-language benchmark for repository level evaluation of coding agents](https://mlsanity.com/paper/2504.08703/) (2025)
- [RepoAgent: An LLM-Powered Open-Source Framework for Repository-level Code Documentation Generation](https://mlsanity.com/paper/2402.16667/) (2024)
- [A Quantitative and Qualitative Evaluation of LLM-Based Explainable Fault Localization](https://mlsanity.com/paper/2308.05487/) (2023)
- [CoRNStack: High-Quality Contrastive Data for Better Code Retrieval and Reranking](https://mlsanity.com/paper/2412.01007/) (2024)
- [Code Representation Learning At Scale](https://mlsanity.com/paper/2402.01935/) (2024)
- [Adaptive Re-Ranking with a Corpus Graph](https://mlsanity.com/paper/2208.08942/) (2022)
- [Issue Localization via LLM-Driven Iterative Code Graph Searching](https://mlsanity.com/paper/2503.22424/) (2025)
- [SweRank: Software Issue Localization with Code Ranking](https://mlsanity.com/paper/2505.07849/) (2025)
- [CoRet: Improved Retriever for Code Editing](https://mlsanity.com/paper/2505.24715/) (2025)

## Built on by (most cited first, 1 of 1)

- [CodeNib: A Multi-View Data System for Serving Repository Context to Coding Agents](https://mlsanity.com/paper/2607.25431/) (2026)

## Abstract (arXiv)

Retrieving code functions, classes or files relevant to a user query, bug report or feature request from large codebases is a fundamental challenge for Large Language Model (LLM)-based coding agents. Agentic approaches typically employ sparse methods like BM25 or dense embedding strategies to identify semantically relevant units. While dense embedding approaches can outperform BM25 by large margins, both ignore the graph-structured characteristics of the codebase. To address this, we propose SpIDER (Spatially Informed Dense Embedding Retrieval), a dense retrieval approach that integrates LLM-based reasoning with graph-based exploration of the codebase. We further introduce SpIDER-Bench, a graph-structured benchmark curated from SWEPolyBench, SWEBench-Verified and Multi-SWE-bench, spanning Python, Java, JavaScript and TypeScript repositories. SpIDER's graph-based candidate expansion attaches a structural reason for inclusion to each surfaced function (its seed and the edge type linking them), making the candidate set auditable while keeping the retrieval budget fixed. The graph is built from per-repository syntax trees, so it can be constructed on-demand at the start of a developer session rather than precomputed offline. Empirical results show that SpIDER consistently improves dense retrieval Recall@20 across every language and benchmark in SpIDER-Bench: by at least 13% relative (+0.05 to +0.12 absolute) along containment edges, rising to at least 27% relative (+0.11 to +0.19 absolute) once call edges are explored.