SEEK: Agentic Knowledge Graph Retrieval for Secure Code Generation

Large Language Models (LLMs) can generate functionally correct code that remains insecure. Security-focused fine-tuning can be expensive and is not always available, motivating inference-time approaches. Security-oriented prompting and retrieval can reduce vulnerabilities, but may also remove required behavior or apply defenses incompatible with the task. The challenge is to identify relevant security knowledge and use it to improve security without sacrificing functionality. We present SecGent, an inference-time framework that retrieves weakness context from the Common Weakness Enumeration (CWE) database and applies it to secure code generation. By connecting task specifications to relevant textual CWE records, SecGent provides task-specific security guidance without relying on retrieved vulnerable or patched code examples. Complementary functional and security tests check the resulting implementation, and their execution feedback guides repairs toward satisfying both objectives. We evaluate SecGent with four open-source LLMs and Claude Sonnet 5.5 across five programming languages on the CWEval benchmark. It achieves the highest joint functional--security success against four inference-time baselines for all five models. Across the open-weight models, mean functional-security@1 (FS@1) improves by 15.5% over RAG, with gains in both functionality and security, and by 19.8% over the strongest prompt optimizer compiled for each model. On Sonnet, FS@1 reaches 92.1%, outperforming the strongest baseline AutoGen by 4.8%. In a separate comparison, SecGent outperforms Claude Code with security-focused prompting by over 6% in FS@1. Feedback-guided repair further improves FS@1 by up to 6.7% over generation without feedback, primarily by recovering functionality while checking security.

Large language models (LLMs) are increasingly used for program synthesis, yet they often generate code that is functionally plausible but insecure. Progress in secure code generation has been hindered by benchmarks that are small, non-executable, leak mitigation details, or rely on noisy analyzers and subjective judgments, making it difficult to measure whether security improves without sacrificing correctness. We address these gaps with CodeSecEval, an execution-based benchmark for secure code generation, comprising 255 Python tasks spanning 77 CWE categories. Each task provides paired insecure and secure implementations together with executable functional and vulnerability-targeted security tests, enabling precise and reproducible evaluation of secure code generation and insecure-code repair. Building on CodeSecEval, we propose SecAwareCoder, an agent-based framework that shifts code generation toward secure-by-construction synthesis. SecAwareCoder performs task-adaptive threat modeling to identify security-sensitive regions and derive task-grounded vulnerability hypotheses, uses these hypotheses to guide both constraint-aware code generation and security-aware test synthesis, and leverages execution feedback for targeted refinement. Experiments across multiple LLM backbones show that SecAwareCoder consistently improves Pass@1 and security robustness over prompting and analyzer-driven baselines, narrowing the security--correctness gap in LLM code generation.

Large Language Models (LLMs) for code generation can replicate insecure patterns from their training data. To mitigate this, a common strategy for security hardening is to fine-tune models using supervision derived from the final transformer layer. However, this design may suffer from a final-layer bottleneck: vulnerability-discriminative cues can be distributed across layers and become less detectable near the output representations optimized for next-token prediction. To diagnose this issue, we perform layer-wise linear probing. We observe that vulnerability-related signals are most detectable in a band of intermediate-to-upper layers yet attenuate toward the final layers. Motivated by this observation, we introduce DeepGuard, a framework that leverages distributed security-relevant cues by aggregating representations from multiple upper layers via an attention-based module. The aggregated signal powers a dedicated security analyzer within a multi-objective training objective that balances security enhancement and functional correctness, and further supports a lightweight inference-time steering strategy. Extensive experiments across five code LLMs demonstrate that DeepGuard improves the secure-and-correct generation rate by an average of 11.9% over strong baselines such as SVEN. It also preserves functional correctness while exhibiting generalization to held-out vulnerability types. Our code is public at https://github.com/unknownhl/DeepGuard.