Daily Papers

Java remains central to enterprise software, and many applications outlive their original architecture. Migrating them across frameworks is a behavior-preserving refactoring spanning build configuration, dependency injection, persistence, request handling, and deployment. Existing software-engineering benchmarks cover bug fixing, feature implementation, and language or version modernization, but leave cross-framework refactoring largely unmeasured. We introduce ScarfBench, a benchmark for behavior-preserving cross-framework refactoring of enterprise Java applications. It is built from expert-written implementation triples across Spring, Jakarta EE, and Quarkus: 34 applications (29 focused single-layer, 5 whole) yielding 102 variants (~151K lines across 1946 source and test files) and 204 directed refactoring tasks. Each task gives an agent a working source application and a target framework; the agent must synthesize a target implementation preserving the source behavior. Correctness is evaluated by an application-specific executable oracle: the candidate must compile, deploy in a containerized target runtime, and pass behavioral tests over the application's observable interface. We evaluate five state-of-the-art coding agents on ScarfBench. The strongest achieves only 15.3% aggregate test pass on focused-layer migrations and 12.2% on whole applications, and only one of the 204 tasks yields a fully behaviorally equivalent target. Difficulty is asymmetric across framework directions and architectural layers: Spring<->Quarkus is the most tractable pair, and Jakarta-targeted migrations are hardest. From LLM-as-a-judge and expert adjudication of failed-task traces, we derive a taxonomy of recurring failure categories spanning build, deploy, and test stages. We release the benchmark, harness, and agent traces at https://scarfbench.info.

Multimodal molecular models often suffer from 3D conformer unreliability and modality collapse, limiting their robustness and generalization. We propose MuMo, a structured multimodal fusion framework that addresses these challenges in molecular representation through two key strategies. To reduce the instability of conformer-dependent fusion, we design a Structured Fusion Pipeline (SFP) that combines 2D topology and 3D geometry into a unified and stable structural prior. To mitigate modality collapse caused by naive fusion, we introduce a Progressive Injection (PI) mechanism that asymmetrically integrates this prior into the sequence stream, preserving modality-specific modeling while enabling cross-modal enrichment. Built on a state space backbone, MuMo supports long-range dependency modeling and robust information propagation. Across 29 benchmark tasks from Therapeutics Data Commons (TDC) and MoleculeNet, MuMo achieves an average improvement of 2.7% over the best-performing baseline on each task, ranking first on 22 of them, including a 27% improvement on the LD50 task. These results validate its robustness to 3D conformer noise and the effectiveness of multimodal fusion in molecular representation. The code is available at: github.com/selmiss/MuMo.

Recent advances in generalist multi-agent systems (MAS) have largely followed a context-engineering plus centralized paradigm, where a planner agent coordinates multiple worker agents through unidirectional prompt passing. While effective under strong planner models, this design suffers from two critical limitations: (1) strong dependency on the planner's capability, which leads to degraded performance when a smaller LLM powers the planner; and (2) limited inter-agent communication, where collaboration relies on costly prompt concatenation and context injection, introducing redundancy and information loss. To address these challenges, we propose Anemoi, a semi-centralized MAS built on the Agent-to-Agent (A2A) communication MCP server from Coral Protocol. Unlike traditional designs, Anemoi enables structured and direct inter-agent collaboration, allowing all agents to monitor progress, assess results, identify bottlenecks, and propose refinements in real time. This paradigm reduces reliance on a single planner, supports adaptive plan updates, and minimizes redundant context passing, resulting in more scalable and cost-efficient execution. Evaluated on the GAIA benchmark, Anemoi achieved 52.73% accuracy with a small LLM (GPT-4.1-mini) as the planner, surpassing the strongest open-source baseline OWL (43.63%) by +9.09% under identical LLM settings. Our implementation is publicly available at https://github.com/Coral-Protocol/Anemoi.

Instruction tuning is an effective technique to align large language models (LLMs) with human intents. In this work, we investigate how an adversary can exploit instruction tuning by injecting specific instruction-following examples into the training data that intentionally changes the model's behavior. For example, an adversary can achieve content injection by injecting training examples that mention target content and eliciting such behavior from downstream models. To achieve this goal, we propose AutoPoison, an automated data poisoning pipeline. It naturally and coherently incorporates versatile attack goals into poisoned data with the help of an oracle LLM. We showcase two example attacks: content injection and over-refusal attacks, each aiming to induce a specific exploitable behavior. We quantify and benchmark the strength and the stealthiness of our data poisoning scheme. Our results show that AutoPoison allows an adversary to change a model's behavior by poisoning only a small fraction of data while maintaining a high level of stealthiness in the poisoned examples. We hope our work sheds light on how data quality affects the behavior of instruction-tuned models and raises awareness of the importance of data quality for responsible deployments of LLMs. Code is available at https://github.com/azshue/AutoPoison.

Injecting external knowledge can improve the performance of pre-trained language models (PLMs) on various downstream NLP tasks. However, massive retraining is required to deploy new knowledge injection methods or knowledge bases for downstream tasks. In this work, we are the first to study how to improve the flexibility and efficiency of knowledge injection by reusing existing downstream models. To this end, we explore a new paradigm plug-and-play knowledge injection, where knowledge bases are injected into frozen existing downstream models by a knowledge plugin. Correspondingly, we propose a plug-and-play injection method map-tuning, which trains a mapping of knowledge embeddings to enrich model inputs with mapped embeddings while keeping model parameters frozen. Experimental results on three knowledge-driven NLP tasks show that existing injection methods are not suitable for the new paradigm, while map-tuning effectively improves the performance of downstream models. Moreover, we show that a frozen downstream model can be well adapted to different domains with different mapping networks of domain knowledge. Our code and models are available at https://github.com/THUNLP/Knowledge-Plugin.

The task of converting a natural language question into an executable SQL query, known as text-to-SQL, is an important branch of semantic parsing. The state-of-the-art graph-based encoder has been successfully used in this task but does not model the question syntax well. In this paper, we propose S^2SQL, injecting Syntax to question-Schema graph encoder for Text-to-SQL parsers, which effectively leverages the syntactic dependency information of questions in text-to-SQL to improve the performance. We also employ the decoupling constraint to induce diverse relational edge embedding, which further improves the network's performance. Experiments on the Spider and robustness setting Spider-Syn demonstrate that the proposed approach outperforms all existing methods when pre-training models are used, resulting in a performance ranks first on the Spider leaderboard.

The growing deployment of large language model (LLM) based agents that interact with external environments has created new attack surfaces for adversarial manipulation. One major threat is indirect prompt injection, where attackers embed malicious instructions in external environment output, causing agents to interpret and execute them as if they were legitimate prompts. While previous research has focused primarily on plain-text injection attacks, we find a significant yet underexplored vulnerability: LLMs' dependence on structured chat templates and their susceptibility to contextual manipulation through persuasive multi-turn dialogues. To this end, we introduce ChatInject, an attack that formats malicious payloads to mimic native chat templates, thereby exploiting the model's inherent instruction-following tendencies. Building on this foundation, we develop a persuasion-driven Multi-turn variant that primes the agent across conversational turns to accept and execute otherwise suspicious actions. Through comprehensive experiments across frontier LLMs, we demonstrate three critical findings: (1) ChatInject achieves significantly higher average attack success rates than traditional prompt injection methods, improving from 5.18% to 32.05% on AgentDojo and from 15.13% to 45.90% on InjecAgent, with multi-turn dialogues showing particularly strong performance at average 52.33% success rate on InjecAgent, (2) chat-template-based payloads demonstrate strong transferability across models and remain effective even against closed-source LLMs, despite their unknown template structures, and (3) existing prompt-based defenses are largely ineffective against this attack approach, especially against Multi-turn variants. These findings highlight vulnerabilities in current agent systems.

Large Vision-Language Models (LVLMs) suffer from serious hallucination problems, where the model-generated responses are inconsistent with the visual inputs. Existing hallucination mitigation methods are mainly based on preference alignment and require external human annotations or auxiliary models for preference data collection, which increase costs and limit sustainable improvement. To tackle these challenges, we propose Autonomous Preference Alignment via Self-Injection (APASI), a novel and generalizable method that mitigates hallucinations without external dependencies. APASI leverages the target LVLM to self-inject hallucinations into a generated response, creating a pair of responses with varying preference levels. During the self-injection process, the dis-preferred response is generated based on three key observations of hallucinations, ensuring it simulates real hallucination patterns. This fidelity offers an accurate learning signal for hallucination mitigation. Moreover, APASI incorporates an iterative alignment training strategy combined with curriculum learning to periodically update the preference data with increasing challenge, enabling stable and continuous enhancement of the LVLM. Extensive experiments across six benchmarks show that APASI not only effectively mitigates hallucinations for three baseline models but also achieves comparable or even superior performance to alignment-based methods with external dependency, thereby demonstrating its effectiveness and generalization capability. The code is available at https://github.com/davidluciolu/APASI.

In the context of newly release software frameworks, large language models (LLMs) often exhibit poor performance and a high rate of hallucination, as they are not exposed to such environments during training. Although inference-time augmentation techniques such as retrieval-augmented generation (RAG) can partially mitigate hallucinations, knowledge injection through prompting alone is insufficient to enable models to fully understand the intrinsic relationships among different components of a codebase, or to reason about the correct compositions and apply. Although explicit knowledge injection can be achieved through post-training, compared with public code domains, unseen codebases typically provide only source code and lack large volumes of high-quality, usage-oriented code that can be directly leveraged as training data. Consequently, existing data synthesis approaches are insufficient to adequately capture unseen codebases usage scenarios when restricted to source code alone. To address these challenges, we propose UCD-Training, a two-stage training framework for reasoning-aware data synthesis grounded in a code graph constructed from unseen codebases. UCD-Training first parses the source code to build a code graph, then conducts dependency-preserving continued pretraining (CPT) using file-level dependency data, followed by graph-grounded supervised fine-tuning (SFT) on three types of synthesized data augmented with explicit reasoning traces: (1) single-hop relation reasoning data, (2) compositional API reasoning data, and (3) codebase utilization data. We further introduce a new benchmark, UnseenCodeBench, for code generation on unseen codebases and conduct comprehensive experiments across multiple codebases.

Indirect prompt injection (IPI) is a major security threat to LLM-powered agents. Thus, a growing body of work have proposed a variety of defensive approaches against IPI. These can be grouped into three broad categories: 1) prompt-based (using prompting as a way to prevent agents from following malicious instructions), 2) detection-based (identifying and filtering malicious instructions), and 3) system-level (using systems insights, such as control and data isolation, for defense). However, commonly used benchmarks for evaluating defense, such as AgentDojo, are inherently static, generating a fixed distribution of IPI attacks. Consequently, static benchmarks do not usefully evaluate defense robustness to adaptive threats. We address this issue by developing AutoDojo, an adaptive extension of AgentDojo that optimizes IPI against a given defense. Using AutoDojo against state-of-the-art IPI defenses across three task suites and five target models, we make two key observations. First, many defenses offer only limited protection: a cheap, black-box adaptive attack using a frontier LLM to iteratively optimize the injection raises attack success rate (ASR) well above the level achieved by static injections against nearly all evaluated defenses. Against a filter that reduces static ASR to 0\%, AutoDojo recovers 28\% overall and 64\% on action-open tasks. Second, for prompt-level and filter-based defenses, ASR is substantially higher on action-open tasks -- where the user's request delegates the action itself to attacker-controlled content -- than on precisely specified tasks. This is a structural limit: on such tasks the injection can pose as ordinary data rather than an explicit instruction, bypassing defenses that rely on detecting instruction-like text. AutoDojo is publicly available at https://github.com/xhOwenMa/AutoDojo.

Large Language Models (LLMs) are increasingly deployed as the backend for a variety of real-world applications called LLM-Integrated Applications. Multiple recent works showed that LLM-Integrated Applications are vulnerable to prompt injection attacks, in which an attacker injects malicious instruction/data into the input of those applications such that they produce results as the attacker desires. However, existing works are limited to case studies. As a result, the literature lacks a systematic understanding of prompt injection attacks and their defenses. We aim to bridge the gap in this work. In particular, we propose a general framework to formalize prompt injection attacks. Existing attacks, which are discussed in research papers and blog posts, are special cases in our framework. Our framework enables us to design a new attack by combining existing attacks. Moreover, we also propose a framework to systematize defenses against prompt injection attacks. Using our frameworks, we conduct a systematic evaluation on prompt injection attacks and their defenses with 10 LLMs and 7 tasks. We hope our frameworks can inspire future research in this field. Our code is available at https://github.com/liu00222/Open-Prompt-Injection.

While large language models (LLMs) have shown considerable promise in code generation, real-world software development demands advanced repository-level reasoning. This includes understanding dependencies, project structures, and managing multi-file changes. However, the ability of LLMs to effectively comprehend and handle complex code repositories has yet to be fully explored. To address challenges, we introduce a hierarchical benchmark designed to evaluate repository dependency understanding (DependEval). Benchmark is based on 15,576 repositories collected from real-world websites. It evaluates models on three core tasks: Dependency Recognition, Repository Construction, and Multi-file Editing, across 8 programming languages from actual code repositories. Our evaluation of over 25 LLMs reveals substantial performance gaps and provides valuable insights into repository-level code understanding.

The widespread availability of large-scale code datasets has accelerated the development of code large language models (CodeLLMs), raising concerns about unauthorized dataset usage. Dataset poisoning offers a proactive defense by reducing the utility of such unauthorized training. However, existing poisoning methods often require full dataset poisoning and introduce transformations that break code compilability. In this paper, we introduce FunPoison, a functionality-preserving poisoning approach that injects short, compilable weak-use fragments into executed code paths. FunPoison leverages reusable statement-level templates with automatic repair and conservative safety checking to ensure side-effect freedom, while a type-aware synthesis module suppresses static analysis warnings and enhances stealth. Extensive experiments show that FunPoison achieves effective poisoning by contaminating only 10% of the dataset, while maintaining 100% compilability and functional correctness, and remains robust against various advanced code sanitization techniques.

When large language model (LLM) agents are increasingly deployed to automate tasks and interact with untrusted external data, prompt injection emerges as a significant security threat. By injecting malicious instructions into the data that LLMs access, an attacker can arbitrarily override the original user task and redirect the agent toward unintended, potentially harmful actions. Existing defenses either require access to model weights (fine-tuning), incur substantial utility loss (detection-based), or demand non-trivial system redesign (system-level). Motivated by this, we propose DataFilter, a test-time model-agnostic defense that removes malicious instructions from the data before it reaches the backend LLM. DataFilter is trained with supervised fine-tuning on simulated injections and leverages both the user's instruction and the data to selectively strip adversarial content while preserving benign information. Across multiple benchmarks, DataFilter consistently reduces the prompt injection attack success rates to near zero while maintaining the LLMs' utility. DataFilter delivers strong security, high utility, and plug-and-play deployment, making it a strong practical defense to secure black-box commercial LLMs against prompt injection. Our DataFilter model is released at https://huggingface.co/JoyYizhu/DataFilter for immediate use, with the code to reproduce our results at https://github.com/yizhu-joy/DataFilter.

Indirect Prompt Injection attacks exploit the inherent limitation of Large Language Models (LLMs) to distinguish between instructions and data in their inputs. Despite numerous defense proposals, the systematic evaluation against adaptive adversaries remains limited, even when successful attacks can have wide security and privacy implications, and many real-world LLM-based applications remain vulnerable. We present the results of LLMail-Inject, a public challenge simulating a realistic scenario in which participants adaptively attempted to inject malicious instructions into emails in order to trigger unauthorized tool calls in an LLM-based email assistant. The challenge spanned multiple defense strategies, LLM architectures, and retrieval configurations, resulting in a dataset of 208,095 unique attack submissions from 839 participants. We release the challenge code, the full dataset of submissions, and our analysis demonstrating how this data can provide new insights into the instruction-data separation problem. We hope this will serve as a foundation for future research towards practical structural solutions to prompt injection.

We present Virtual Prompt Injection (VPI) for instruction-tuned Large Language Models (LLMs). VPI allows an attacker-specified virtual prompt to steer the model behavior under specific trigger scenario without any explicit injection in model input. For instance, if an LLM is compromised with the virtual prompt "Describe Joe Biden negatively." for Joe Biden-related instructions, then any service deploying this model will propagate biased views when handling user queries related to Joe Biden. VPI is especially harmful for two primary reasons. Firstly, the attacker can take fine-grained control over LLM behaviors by defining various virtual prompts, exploiting LLMs' proficiency in following instructions. Secondly, this control is achieved without any interaction from the attacker while the model is in service, leading to persistent attack. To demonstrate the threat, we propose a simple method for performing VPI by poisoning the model's instruction tuning data. We find that our proposed method is highly effective in steering the LLM with VPI. For example, by injecting only 52 poisoned examples (0.1% of the training data size) into the instruction tuning data, the percentage of negative responses given by the trained model on Joe Biden-related queries change from 0% to 40%. We thus highlight the necessity of ensuring the integrity of the instruction-tuning data as little poisoned data can cause stealthy and persistent harm to the deployed model. We further explore the possible defenses and identify data filtering as an effective way to defend against the poisoning attacks. Our project page is available at https://poison-llm.github.io.

Large Language Models (LLMs) are attracting significant research attention due to their instruction-following abilities, allowing users and developers to leverage LLMs for a variety of tasks. However, LLMs are vulnerable to prompt-injection attacks: a class of attacks that hijack the model's instruction-following abilities, changing responses to prompts to undesired, possibly malicious ones. In this work, we introduce Jatmo, a method for generating task-specific models resilient to prompt-injection attacks. Jatmo leverages the fact that LLMs can only follow instructions once they have undergone instruction tuning. It harnesses a teacher instruction-tuned model to generate a task-specific dataset, which is then used to fine-tune a base model (i.e., a non-instruction-tuned model). Jatmo only needs a task prompt and a dataset of inputs for the task: it uses the teacher model to generate outputs. For situations with no pre-existing datasets, Jatmo can use a single example, or in some cases none at all, to produce a fully synthetic dataset. Our experiments on six tasks show that Jatmo models provide the same quality of outputs on their specific task as standard LLMs, while being resilient to prompt injections. The best attacks succeeded in less than 0.5% of cases against our models, versus over 90% success rate against GPT-3.5-Turbo. We release Jatmo at https://github.com/wagner-group/prompt-injection-defense.

LLMs show promise in transforming software development, with a growing interest in integrating them into more intelligent apps. Frameworks like LangChain aid LLM-integrated app development, offering code execution utility/APIs for custom actions. However, these capabilities theoretically introduce Remote Code Execution (RCE) vulnerabilities, enabling remote code execution through prompt injections. No prior research systematically investigates these frameworks' RCE vulnerabilities or their impact on applications and exploitation consequences. Therefore, there is a huge research gap in this field. In this study, we propose LLMSmith to detect, validate and exploit the RCE vulnerabilities in LLM-integrated frameworks and apps. To achieve this goal, we develop two novel techniques, including 1) a lightweight static analysis to examine LLM integration mechanisms, and construct call chains to identify RCE vulnerabilities in frameworks; 2) a systematical prompt-based exploitation method to verify and exploit the found vulnerabilities in LLM-integrated apps. This technique involves various strategies to control LLM outputs, trigger RCE vulnerabilities and launch subsequent attacks. Our research has uncovered a total of 20 vulnerabilities in 11 LLM-integrated frameworks, comprising 19 RCE vulnerabilities and 1 arbitrary file read/write vulnerability. Of these, 17 have been confirmed by the framework developers, with 11 vulnerabilities being assigned CVE IDs. For the 51 apps potentially affected by RCE, we successfully executed attacks on 17 apps, 16 of which are vulnerable to RCE and 1 to SQL injection. Furthermore, we conduct a comprehensive analysis of these vulnerabilities and construct practical attacks to demonstrate the hazards in reality. Last, we propose several mitigation measures for both framework and app developers to counteract such attacks.

Prompt injection defenses are often framed as semantic understanding problems and delegated to increasingly large neural detectors. For the first screening layer, however, the requirements are different: the detector runs on every request and therefore must be fast, deterministic, non-promptable, and auditable. We introduce Mirror, a data-curation design pattern that organizes prompt injection corpora into matched positive and negative cells so that a classifier learns control-plane attack mechanics rather than incidental corpus shortcuts. Using 5,000 strictly curated open-source samples -- the largest corpus supportable under our public-data validity contract -- we define a 32-cell mirror topology, fill 31 of those cells with public data, train a sparse character n-gram linear SVM, compile its weights into a static Rust artifact, and obtain 95.97\% recall and 92.07\% F1 on a 524-case holdout at sub-millisecond latency with no external model runtime dependencies. On the same holdout, our next line of defense, a 22-million-parameter Prompt Guard~2 model reaches 44.35\% recall and 59.14\% F1 at 49\,ms median and 324\,ms p95 latency. Linear models still leave residual semantic ambiguities such as use-versus-mention for later pipeline layers, but within that scope our results show that for L1 prompt injection screening, strict data geometry can matter more than model scale.

Supervised fine-tuning (SFT) is widely used to inject new knowledge into language models, but it often degrades pretrained capabilities such as reasoning and general-domain performance. We argue this forgetting arises because fine-tuning targets from humans or external systems diverge from the model's autoregressive distribution, forcing the optimizer to imitate low-probability token sequences. To address this problem, we propose MixSD, a simple external-teacher-free method for distribution-aligned knowledge injection. Instead of training on fixed targets, MixSD constructs supervision dynamically by mixing tokens from two conditionals of the base model itself: an expert conditional that observes the injected fact in context, and a naive conditional that reflects the model's original prior. The resulting supervision sequences preserve the factual learning signal while remaining substantially closer to the base model's distribution. We evaluate MixSD on two synthetic corpora that we construct to study factual recall and arithmetic function acquisition in a controlled setting, together with established benchmarks for open-domain factual question answering and knowledge editing. Across multiple model scales and settings, MixSD consistently achieves a better memorization-retention trade-off compared to SFT and on-policy self distillation baselines, retaining up to 100% of the base model's held-out capability while maintaining near-perfect training accuracy, whereas standard SFT retains as little as 1%. We further show that MixSD produces substantially lower-NLL supervision targets under the base model and reduces harmful movement along Fisher-sensitive parameter directions. These results suggest that aligning supervision with the model's native generation distribution is a simple and effective principle for knowledge injection that mitigates catastrophic forgetting.

Code generation plays a crucial role in various tasks, such as code auto-completion and mathematical reasoning. Previous work has proposed numerous methods to enhance code generation performance, including integrating feedback from the compiler. Inspired by this, we present ReflectionCoder, a novel approach that effectively leverages reflection sequences constructed by integrating compiler feedback to improve one-off code generation performance. Furthermore, we propose reflection self-distillation and dynamically masked distillation to effectively utilize these reflection sequences. Extensive experiments on three benchmarks, i.e., HumanEval (+), MBPP (+), and MultiPl-E, demonstrate that models fine-tuned with our method achieve state-of-the-art performance. Notably, ReflectionCoder-DeepSeek-Coder-33B reaches pass@1 of 82.9 (76.8) on HumanEval (+) and 84.1 (72.0) on MBPP (+), on par with GPT-3.5-Turbo and Claude-3-opus, and surpasses early GPT-4. Beyond the code domain, we believe this approach can benefit other domains that focus on final results and require long reasoning paths. Code and data are available at https://github.com/SenseLLM/ReflectionCoder.

LLM agents are evolving rapidly, powered by code execution, tools, and the recently introduced agent skills feature. Skills allow users to extend LLM applications with specialized third-party code, knowledge, and instructions. Although this can extend agent capabilities to new domains, it creates an increasingly complex agent supply chain, offering new surfaces for prompt injection attacks. We identify skill-based prompt injection as a significant threat and introduce SkillInject, a benchmark evaluating the susceptibility of widely-used LLM agents to injections through skill files. SkillInject contains 202 injection-task pairs with attacks ranging from obviously malicious injections to subtle, context-dependent attacks hidden in otherwise legitimate instructions. We evaluate frontier LLMs on SkillInject, measuring both security in terms of harmful instruction avoidance and utility in terms of legitimate instruction compliance. Our results show that today's agents are highly vulnerable with up to 80% attack success rate with frontier models, often executing extremely harmful instructions including data exfiltration, destructive action, and ransomware-like behavior. They furthermore suggest that this problem will not be solved through model scaling or simple input filtering, but that robust agent security will require context-aware authorization frameworks. Our benchmark is available at https://www.skill-inject.com/.

Multi-modal large language model (MLLM)-based web agents interact with webpage environments by generating actions based on screenshots of the webpages. In this work, we propose WebInject, a prompt injection attack that manipulates the webpage environment to induce a web agent to perform an attacker-specified action. Our attack adds a perturbation to the raw pixel values of the rendered webpage. After these perturbed pixels are mapped into a screenshot, the perturbation induces the web agent to perform the attacker-specified action. We formulate the task of finding the perturbation as an optimization problem. A key challenge in solving this problem is that the mapping between raw pixel values and screenshot is non-differentiable, making it difficult to backpropagate gradients to the perturbation. To overcome this, we train a neural network to approximate the mapping and apply projected gradient descent to solve the reformulated optimization problem. Extensive evaluation on multiple datasets shows that WebInject is highly effective and significantly outperforms baselines.

Experience internalization converts contextual experience from past interactions into reusable parametric capability, offering a promising path toward continual learning in large language models (LLMs). While prior work has predominantly focused on single-iteration transfer, we discover that under multi-iteration experience learning, existing methods suffer from a progressive capability collapse rather than compounding improvement. We systematically examine this failure through three vital dimensions of experience internalization: (1) Experience Granularity: We find that principle-level experience is more durable than instance-level experience, as it effectively abstracts transferable strategies away from trajectory-specific details. (2) Experience Injection Pattern: Our analysis reveals that step-wise injection significantly outperforms global injection by aligning experience with intermediate decision states, a property that is critical for long-horizon tool use. (3) Internalization Regime: We demonstrate that off-policy context-distillation on high-quality teacher trajectories provides a substantially more stable training signal than on-policy context-distillation, which is inherently limited by local corrections on student-induced flawed states. Together, these insights yield a simple yet robust recipe for stable and sustainable experience internalization, providing concrete guidance for engineering self-evolving and continually learning LLMs.

Source code is rarely written in isolation. It depends significantly on the programmatic context, such as the class that the code would reside in. To study this phenomenon, we introduce the task of generating class member functions given English documentation and the programmatic context provided by the rest of the class. This task is challenging because the desired code can vary greatly depending on the functionality the class provides (e.g., a sort function may or may not be available when we are asked to "return the smallest element" in a particular member variable list). We introduce CONCODE, a new large dataset with over 100,000 examples consisting of Java classes from online code repositories, and develop a new encoder-decoder architecture that models the interaction between the method documentation and the class environment. We also present a detailed error analysis suggesting that there is significant room for future work on this task.

We present RepoST, a scalable method to construct environments that provide execution feedback for repository-level code generation for both training and evaluation. Unlike existing works that aim to build entire repositories for execution, which is challenging for both human and LLMs, we provide execution feedback with sandbox testing, which isolates a given target function and its dependencies to a separate script for testing. Sandbox testing reduces the complexity of external dependencies and enables constructing environments at a large scale. We use our method to construct RepoST-Train, a large-scale train set with 7,415 functions from 832 repositories. Training with the execution feedback provided by RepoST-Train leads to a performance gain of 5.5% Pass@1 on HumanEval and 3.5% Pass@1 on RepoEval. We also build an evaluation dataset, RepoST-Eval, and benchmark 12 code generation models.

Vision-Language Model (VLM) based Web Agents represent a significant step towards automating complex tasks by simulating human-like interaction with websites. However, their deployment in uncontrolled web environments introduces significant security vulnerabilities. Existing research on adversarial environmental injection attacks often relies on unrealistic assumptions, such as direct HTML manipulation, knowledge of user intent, or access to agent model parameters, limiting their practical applicability. In this paper, we propose AdInject, a novel and real-world black-box attack method that leverages the internet advertising delivery to inject malicious content into the Web Agent's environment. AdInject operates under a significantly more realistic threat model than prior work, assuming a black-box agent, static malicious content constraints, and no specific knowledge of user intent. AdInject includes strategies for designing malicious ad content aimed at misleading agents into clicking, and a VLM-based ad content optimization technique that infers potential user intents from the target website's context and integrates these intents into the ad content to make it appear more relevant or critical to the agent's task, thus enhancing attack effectiveness. Experimental evaluations demonstrate the effectiveness of AdInject, attack success rates exceeding 60% in most scenarios and approaching 100% in certain cases. This strongly demonstrates that prevalent advertising delivery constitutes a potent and real-world vector for environment injection attacks against Web Agents. This work highlights a critical vulnerability in Web Agent security arising from real-world environment manipulation channels, underscoring the urgent need for developing robust defense mechanisms against such threats. Our code is available at https://github.com/NicerWang/AdInject.

Large Language Model (LLM) agents increasingly rely on long-term memory and Retrieval-Augmented Generation (RAG) to persist experiences and refine future performance. While this experience learning capability enhances agentic autonomy, it introduces a critical, unexplored attack surface, i.e., the trust boundary between an agent's reasoning core and its own past. In this paper, we introduce MemoryGraft. It is a novel indirect injection attack that compromises agent behavior not through immediate jailbreaks, but by implanting malicious successful experiences into the agent's long-term memory. Unlike traditional prompt injections that are transient, or standard RAG poisoning that targets factual knowledge, MemoryGraft exploits the agent's semantic imitation heuristic which is the tendency to replicate patterns from retrieved successful tasks. We demonstrate that an attacker who can supply benign ingestion-level artifacts that the agent reads during execution can induce it to construct a poisoned RAG store where a small set of malicious procedure templates is persisted alongside benign experiences. When the agent later encounters semantically similar tasks, union retrieval over lexical and embedding similarity reliably surfaces these grafted memories, and the agent adopts the embedded unsafe patterns, leading to persistent behavioral drift across sessions. We validate MemoryGraft on MetaGPT's DataInterpreter agent with GPT-4o and find that a small number of poisoned records can account for a large fraction of retrieved experiences on benign workloads, turning experience-based self-improvement into a vector for stealthy and durable compromise. To facilitate reproducibility and future research, our code and evaluation data are available at https://github.com/Jacobhhy/Agent-Memory-Poisoning.

Recent advances in Large Language Models (LLMs) enable exciting LLM-integrated applications, which perform text-based tasks by utilizing their advanced language understanding capabilities. However, as LLMs have improved, so have the attacks against them. Prompt injection attacks are an important threat: they trick the model to deviate from the original application's instructions and instead follow user directives. These attacks rely on the LLM's ability to follow instructions and inability to separate the prompts and user data. We introduce structured queries, a general approach to tackle this problem. Structured queries separate prompts and data into two channels. We implement a system that supports structured queries. This system is made of (1) a secure front-end that formats a prompt and user data into a special format, and (2) a specially trained LLM that can produce high-quality outputs from these inputs. The LLM is trained using a novel fine-tuning strategy: we convert a base (non-instruction-tuned) LLM to a structured instruction-tuned model that will only follow instructions in the prompt portion of a query. To do so, we augment standard instruction tuning datasets with examples that also include instructions in the data portion of the query, and fine-tune the model to ignore these. Our system significantly improves resistance to prompt injection attacks, with little or no impact on utility. Our code is released at https://github.com/Sizhe-Chen/PromptInjectionDefense.

Repository-level code generation has attracted growing attention in recent years. Unlike function-level code generation, it requires the model to understand the entire repository, reasoning over complex dependencies across functions, classes, and modules. However, existing approaches such as retrieval-augmented generation (RAG) or context-based function selection often fall short: they primarily rely on surface-level similarity and struggle to capture the rich dependencies that govern repository-level semantics. In this paper, we introduce InlineCoder, a novel framework for repository-level code generation. InlineCoder enhances the understanding of repository context by inlining the unfinished function into its call graph, thereby reframing the challenging repository understanding as an easier function-level coding task. Given a function signature, InlineCoder first generates a draft completion, termed an anchor, which approximates downstream dependencies and enables perplexity-based confidence estimation. This anchor drives a bidirectional inlining process: (i) Upstream Inlining, which embeds the anchor into its callers to capture diverse usage scenarios; and (ii) Downstream Retrieval, which integrates the anchor's callees into the prompt to provide precise dependency context. The enriched context, combining draft completion with upstream and downstream perspectives, equips the LLM with a comprehensive repository view.

While Large Language Models (LLMs) acquire vast knowledge during pre-training, they often lack domain-specific, new, or niche information. Continual pre-training (CPT) attempts to address this gap but suffers from catastrophic forgetting and inefficiencies in low-data regimes. We introduce Knowledge-Instruct, a novel approach to efficiently inject knowledge from limited corpora through pure instruction-tuning. By generating information-dense synthetic instruction data, it effectively integrates new knowledge while preserving general reasoning and instruction-following abilities. Knowledge-Instruct demonstrates superior factual memorization, minimizes catastrophic forgetting, and remains scalable by leveraging synthetic data from relatively small language models. Additionally, it enhances contextual understanding, including complex multi-hop reasoning, facilitating integration with retrieval systems. We validate its effectiveness across diverse benchmarks, including Companies, a new dataset that we release to measure knowledge injection capabilities.

Identifiers, such as method and variable names, form a large portion of source code. Therefore, low-quality identifiers can substantially hinder code comprehension. To support developers in using meaningful identifiers, several (semi-)automatic techniques have been proposed, mostly being data-driven (e.g. statistical language models, deep learning models) or relying on static code analysis. Still, limited empirical investigations have been performed on the effectiveness of such techniques for recommending developers with meaningful identifiers, possibly resulting in rename refactoring operations. We present a large-scale study investigating the potential of data-driven approaches to support automated variable renaming. We experiment with three state-of-the-art techniques: a statistical language model and two DL-based models. The three approaches have been trained and tested on three datasets we built with the goal of evaluating their ability to recommend meaningful variable identifiers. Our quantitative and qualitative analyses show the potential of such techniques that, under specific conditions, can provide valuable recommendations and are ready to be integrated in rename refactoring tools. Nonetheless, our results also highlight limitations of the experimented approaches that call for further research in this field.

Large Language Models (LLMs) are increasingly used in a variety of important applications, yet their safety and reliability remain as major concerns. Various adversarial and jailbreak attacks have been proposed to bypass the safety alignment and cause the model to produce harmful responses. We introduce Self-supervised Prompt INjection (SPIN) which can detect and reverse these various attacks on LLMs. As our self-supervised prompt defense is done at inference-time, it is also compatible with existing alignment and adds an additional layer of safety for defense. Our benchmarks demonstrate that our system can reduce the attack success rate by up to 87.9%, while maintaining the performance on benign user requests. In addition, we discuss the situation of an adaptive attacker and show that our method is still resilient against attackers who are aware of our defense.

With the availability of various instruction datasets, a pivotal challenge is how to effectively select and integrate these instructions to fine-tune large language models (LLMs). Previous research mainly focuses on selecting individual high-quality instructions. However, these works overlooked the joint interactions and dependencies between different categories of instructions, leading to suboptimal selection strategies. Moreover, the nature of these interaction patterns remains largely unexplored, let alone optimize the instruction set with regard to them. To fill these gaps, in this paper, we: (1) systemically investigate interaction and dependency patterns between different categories of instructions, (2) manage to optimize the instruction set concerning the interaction patterns using a linear programming-based method, and optimize the learning schema of SFT using an instruction dependency taxonomy guided curriculum learning. Experimental results across different LLMs demonstrate improved performance over strong baselines on widely adopted benchmarks.

Prompt injection is one of the most critical vulnerabilities in LLM agents; yet, effective automated attacks remain largely unexplored from an optimization perspective. Existing methods heavily depend on human red-teamers and hand-crafted prompts, limiting their scalability and adaptability. We propose AutoInject, a reinforcement learning framework that generates universal, transferable adversarial suffixes while jointly optimizing for attack success and utility preservation on benign tasks. Our black-box method supports both query-based optimization and transfer attacks to unseen models and tasks. Using only a 1.5B parameter adversarial suffix generator, we successfully compromise frontier systems including GPT 5 Nano, Claude Sonnet 3.5, and Gemini 2.5 Flash on the AgentDojo benchmark, establishing a stronger baseline for automated prompt injection research.

With the recent advancement of Large Language Models (LLMs), generating functionally correct code has become less complicated for a wide array of developers. While using LLMs has sped up the functional development process, it poses a heavy risk to code security. Code generation with proper security measures using LLM is a significantly more challenging task than functional code generation. Security measures may include adding a pair of lines of code with the original code, consisting of null pointer checking or prepared statements for SQL injection prevention. Currently, available code repair LLMs generate code repair by supervised fine-tuning, where the model looks at cross-entropy loss. However, the original and repaired codes are mostly similar in functionality and syntactically, except for a few (1-2) lines, which act as security measures. This imbalance between the lines needed for security measures and the functional code enforces the supervised fine-tuned model to prioritize generating functional code without adding proper security measures, which also benefits the model by resulting in minimal loss. Therefore, in this work, for security hardening and strengthening of generated code from LLMs, we propose a reinforcement learning-based method for program-specific repair with the combination of semantic and syntactic reward mechanisms that focus heavily on adding security and functional measures in the code, respectively.

In recent years, the rapid development of large language models (LLMs) has brought new vitality to the various domains and generated substantial social and economic benefits. However, the swift advancement of LLMs has introduced new security vulnerabilities. Jailbreak, a form of attack that induces LLMs to output harmful content through carefully crafted prompts, poses a challenge to the safe and trustworthy development of LLMs. Previous jailbreak attack methods primarily exploited the internal capabilities of the model. Among them, one category leverages the model's implicit capabilities for jailbreak attacks, where the attacker is unaware of the exact reasons for the attack's success. The other category utilizes the model's explicit capabilities for jailbreak attacks, where the attacker understands the reasons for the attack's success. For example, these attacks exploit the model's abilities in coding, contextual learning, or understanding ASCII characters. However, these earlier jailbreak attacks have certain limitations, as they only exploit the inherent capabilities of the model. In this paper, we propose a novel jailbreak method, SQL Injection Jailbreak (SIJ), which utilizes the construction of input prompts by LLMs to inject jailbreak information into user prompts, enabling successful jailbreak of the LLMs. Our SIJ method achieves nearly 100\% attack success rates on five well-known open-source LLMs in the context of AdvBench, while incurring lower time costs compared to previous methods. More importantly, SIJ reveals a new vulnerability in LLMs that urgently needs to be addressed. To this end, we propose a defense method called Self-Reminder-Key and demonstrate its effectiveness through experiments. Our code is available at https://github.com/weiyezhimeng/SQL-Injection-Jailbreak{https://github.com/weiyezhimeng/SQL-Injection-Jailbreak}.

Large language models (LLMs) increasingly rely on retrieving information from external corpora. This creates a new attack surface: indirect prompt injection (IPI), where hidden instructions are planted in the corpora and hijack model behavior once retrieved. Previous studies have highlighted this risk but often avoid the hardest step: ensuring that malicious content is actually retrieved. In practice, unoptimized IPI is rarely retrieved under natural queries, which leaves its real-world impact unclear. We address this challenge by decomposing the malicious content into a trigger fragment that guarantees retrieval and an attack fragment that encodes arbitrary attack objectives. Based on this idea, we design an efficient and effective black-box attack algorithm that constructs a compact trigger fragment to guarantee retrieval for any attack fragment. Our attack requires only API access to embedding models, is cost-efficient (as little as $0.21 per target user query on OpenAI's embedding models), and achieves near-100% retrieval across 11 benchmarks and 8 embedding models (including both open-source models and proprietary services). Based on this attack, we present the first end-to-end IPI exploits under natural queries and realistic external corpora, spanning both RAG and agentic systems with diverse attack objectives. These results establish IPI as a practical and severe threat: when a user issued a natural query to summarize emails on frequently asked topics, a single poisoned email was sufficient to coerce GPT-4o into exfiltrating SSH keys with over 80% success in a multi-agent workflow. We further evaluate several defenses and find that they are insufficient to prevent the retrieval of malicious text, highlighting retrieval as a critical open vulnerability.

Enabling continual learning in LLMs remains a key unresolved research challenge. In a recent announcement, a frontier LLM company made a step towards this by introducing Agent Skills, a framework that equips agents with new knowledge based on instructions stored in simple markdown files. Although Agent Skills can be a very useful tool, we show that they are fundamentally insecure, since they enable trivially simple prompt injections. We demonstrate how to hide malicious instructions in long Agent Skill files and referenced scripts to exfiltrate sensitive data, such as internal files or passwords. Importantly, we show how to bypass system-level guardrails of a popular coding agent: a benign, task-specific approval with the "Don't ask again" option can carry over to closely related but harmful actions. Overall, we conclude that despite ongoing research efforts and scaling model capabilities, frontier LLMs remain vulnerable to very simple prompt injections in realistic scenarios. Our code is available at https://github.com/aisa-group/promptinject-agent-skills.

Instruction following evaluates large language models (LLMs) on their ability to generate outputs that adhere to user-defined constraints. However, existing benchmarks often rely on templated constraint prompts, which lack the diversity of real-world usage and limit fine-grained performance assessment. To fill this gap, we propose a multi-dimensional constraint framework encompassing three constraint patterns, four constraint categories, and four difficulty levels. Building on this framework, we develop an automated instruction generation pipeline that performs constraint expansion, conflict detection, and instruction rewriting, yielding 1,200 code-verifiable instruction-following test samples. We evaluate 19 LLMs across seven model families and uncover substantial variation in performance across constraint forms. For instance, average performance drops from 77.67% at Level I to 32.96% at Level IV. Furthermore, we demonstrate the utility of our approach by using it to generate data for reinforcement learning, achieving substantial gains in instruction following without degrading general performance. In-depth analysis indicates that these gains stem primarily from modifications in the model's attention modules parameters, which enhance constraint recognition and adherence. Code and data are available in https://github.com/Junjie-Ye/MulDimIF.

LLMs have demonstrated significant potential in code generation tasks, achieving promising results at the function or statement level across various benchmarks. However, the complexities associated with creating code artifacts like classes, particularly within the context of real-world software repositories, remain underexplored. Prior research treats class-level generation as an isolated task, neglecting the intricate dependencies & interactions that characterize real-world software environments. To address this gap, we introduce RepoClassBench, a comprehensive benchmark designed to rigorously evaluate LLMs in generating complex, class-level code within real-world repositories. RepoClassBench includes "Natural Language to Class generation" tasks across Java, Python & C# from a selection of repositories. We ensure that each class in our dataset not only has cross-file dependencies within the repository but also includes corresponding test cases to verify its functionality. We find that current models struggle with the realistic challenges posed by our benchmark, primarily due to their limited exposure to relevant repository contexts. To address this shortcoming, we introduce Retrieve-Repotools-Reflect (RRR), a novel approach that equips LLMs with static analysis tools to iteratively navigate & reason about repository-level context in an agent-based framework. Our experiments demonstrate that RRR significantly outperforms existing baselines on RepoClassBench, showcasing its effectiveness across programming languages & under various settings. Our findings emphasize the critical need for code-generation benchmarks to incorporate repo-level dependencies to more accurately reflect the complexities of software development. Our work shows the benefits of leveraging specialized tools to enhance LLMs' understanding of repository context. We plan to make our dataset & evaluation harness public.

While Large Language Models (LLMs) have achieved remarkable success in code generation, they often struggle with the deep, long-horizon reasoning required for complex software engineering. We attribute this limitation to the nature of standard pre-training data: static software repositories represent only the terminal state of an intricate intellectual process, abstracting away the intermediate planning, debugging, and iterative refinement. To bridge this gap, we propose a novel paradigm: understanding via reconstruction. We hypothesize that reverse-engineering the latent agentic trajectories -- the planning, reasoning, and debugging steps -- behind static repositories provides a far richer supervision signal than raw code alone. To operationalize this, we introduce a framework that synthesizes these trajectories using a multi-agent simulation. This process is grounded in the structural realities of the source repositories (e.g., dependency graphs and file hierarchies) to ensure fidelity. Furthermore, to guarantee the logical rigor of the synthetic data, we employ a search-based optimization technique that iteratively refines the Chain-of-Thought (CoT) reasoning to maximize the likelihood of the ground-truth code. Empirical results demonstrate that continuous pre-training on these reconstructed trajectories significantly enhances Llama-3-8B's performance across diverse benchmarks, including long-context understanding, coding proficiency, and agentic capabilities.

Recently, an increasing number of AI-driven programming assistants powered by code LLMs have been integrated into various real-world software development environments, significantly boosting developer productivity. However, existing code generation benchmarks primarily focus on general-purpose scenarios, leaving the code generation performance of LLMs for specific application domains largely unknown. In this paper, we introduce a new benchmark, MultiCodeBench, to fill this gap. MultiCodeBench comprises 2,400 programming tasks, covering 12 popular software development domains and 15 programming languages. Specifically, we perform in-depth research to identify these 12 application domains. Given that each domain may involve multiple technical frameworks, and that different frameworks present distinct challenges in the coding process, we categorize the commonly used frameworks and platforms within each domain. We then sample programming problems from GitHub repositories related to these subdomains. To ensure the quality of the tasks and mitigate data leakage issues, we invite annotators to rewrite the docstrings for each task in MultiCodeBench. Additionally, we build a static analysis-based dependency parsing tool to extract the dependencies in the ground truth for each task, enabling deeper performance analysis. Through extensive experiments on MultiCodeBench with eleven representative mainstream LLMs, we reveal the code generation performance of the LLMs across different application domains, providing practical insights for developers in downstream fields when selecting LLMs. Furthermore, we analyze the reasons behind the models' failures in completing software application development tasks, offering guidance for model developers to enhance domain-specific code generation capabilities.

Recent code large language models (LLMs) have shown promising performance in generating standalone functions but face limitations in repository-level code generation due to their lack of awareness of repository-level dependencies (e.g., user-defined attributes), resulting in dependency errors such as undefined-variable and no-member errors. In this work, we introduce ToolGen, an approach that integrates autocompletion tools into the code LLM generation process to address these dependencies. ToolGen comprises two main phases: Trigger Insertion and Model Fine-tuning (Offline), and Tool-integrated Code Generation (Online). During the offline phase, ToolGen augments functions within a given code corpus with a special mark token, indicating positions to trigger autocompletion tools. These augmented functions, along with their corresponding docstrings, are then used to fine-tune a selected code LLM. In the online phase, ToolGen iteratively generates functions by predicting tokens step-by-step using the fine-tuned LLM. Whenever a mark token is encountered, ToolGen invokes the autocompletion tool to suggest code completions and selects the most appropriate one. We conduct comprehensive experiments to evaluate ToolGen's effectiveness in repository-level code generation. To facilitate this evaluation, we create a benchmark comprising 680 real-world code repositories and introduce two new repository-level metrics: Dependency Coverage and Static Validity Rate. The results demonstrate that ToolGen significantly improves Dependency Coverage by 15.2% to 45.8% and Static Validity Rate by 10.9% to 42.2% across three distinct code LLMs, while maintaining competitive performance in widely-recognized similarity metrics. Furthermore, our generalizability evaluation confirms ToolGen's consistent performance when applied to diverse code LLMs, including various model architectures and scales.

Locating the files and functions requiring modification in large open-source software (OSS) repositories is challenging due to their scale and structural complexity. Existing large language model (LLM)-based methods typically treat this as a repository-level retrieval task and rely on multiple auxiliary tools, which overlook code execution logic and complicate model control. We propose RepoNavigator, an LLM agent equipped with a single execution-aware tool-jumping to the definition of an invoked symbol. This unified design reflects the actual flow of code execution while simplifying tool manipulation. RepoNavigator is trained end-to-end via Reinforcement Learning (RL) directly from a pretrained model, without any closed-source distillation. Experiments demonstrate that RL-trained RepoNavigator achieves state-of-the-art performance, with the 7B model outperforming 14B baselines, the 14B model surpassing 32B competitors, and even the 32B model exceeding closed-source models such as Claude-3.7. These results confirm that integrating a single, structurally grounded tool with RL training provides an efficient and scalable solution for repository-level issue localization.

Large Language Models (LLMs) have seen rapid adoption in recent years, with industries increasingly relying on them to maintain a competitive advantage. These models excel at interpreting user instructions and generating human-like responses, leading to their integration across diverse domains, including consulting and information retrieval. However, their widespread deployment also introduces substantial security risks, most notably in the form of prompt injection and jailbreak attacks. To systematically evaluate LLM vulnerabilities -- particularly to external prompt injection -- we conducted a series of experiments on eight commercial models. Each model was tested without supplementary sanitization, relying solely on its built-in safeguards. The results exposed exploitable weaknesses and emphasized the need for stronger security measures. Four categories of attacks were examined: direct injection, indirect (external) injection, image-based injection, and prompt leakage. Comparative analysis indicated that Claude 3 demonstrated relatively greater robustness; nevertheless, empirical findings confirm that additional defenses, such as input normalization, remain necessary to achieve reliable protection.

Prompt injection attacks pose a critical threat to large language models (LLMs), enabling goal hijacking and data leakage. Prompt guard models, though effective in defense, suffer from over-defense -- falsely flagging benign inputs as malicious due to trigger word bias. To address this issue, we introduce NotInject, an evaluation dataset that systematically measures over-defense across various prompt guard models. NotInject contains 339 benign samples enriched with trigger words common in prompt injection attacks, enabling fine-grained evaluation. Our results show that state-of-the-art models suffer from over-defense issues, with accuracy dropping close to random guessing levels (60%). To mitigate this, we propose InjecGuard, a novel prompt guard model that incorporates a new training strategy, Mitigating Over-defense for Free (MOF), which significantly reduces the bias on trigger words. InjecGuard demonstrates state-of-the-art performance on diverse benchmarks including NotInject, surpassing the existing best model by 30.8%, offering a robust and open-source solution for detecting prompt injection attacks. The code and datasets are released at https://github.com/SaFoLab-WISC/InjecGuard.

Instruction tuning is a supervised fine-tuning approach that significantly improves the ability of large language models (LLMs) to follow human instructions. We propose SelfCodeAlign, the first fully transparent and permissive pipeline for self-aligning code LLMs without extensive human annotations or distillation. SelfCodeAlign employs the same base model for inference throughout the data generation process. It first extracts diverse coding concepts from high-quality seed snippets to generate new tasks. It then samples multiple responses per task, pairs each with test cases, and validates them in a sandbox environment. Finally, passing examples are selected for instruction tuning. In our primary experiments, we use SelfCodeAlign with CodeQwen1.5-7B to generate a dataset of 74k instruction-response pairs. Finetuning on this dataset leads to a model that achieves a 67.1 pass@1 on HumanEval+, surpassing CodeLlama-70B-Instruct despite being ten times smaller. Across all benchmarks, this finetuned model consistently outperforms the original version trained with OctoPack, the previous state-of-the-art method for instruction tuning without human annotations or distillation. Additionally, we show that SelfCodeAlign is effective across LLMs of various sizes, from 3B to 33B, and that the base models can benefit more from alignment with their own data distribution. We further validate each component's effectiveness in our pipeline, showing that SelfCodeAlign outperforms both direct distillation from GPT-4o and leading GPT-3.5-based distillation methods, such as OSS-Instruct and Evol-Instruct. SelfCodeAlign has also led to the creation of StarCoder2-Instruct, the first fully transparent, permissively licensed, and self-aligned code LLM that achieves state-of-the-art coding performance.

Although multimodal large language models (MLLMs) are increasingly deployed in real-world applications, their instruction-following behavior leaves them vulnerable to prompt injection attacks. Existing prompt injection methods predominantly rely on textual prompts or perceptible visual prompts that are observable by human users. In this work, we study imperceptible visual prompt injection against powerful closed-source MLLMs, where adversarial instructions are embedded in the visual modality. Our method adaptively embeds the malicious prompt into the input image via a bounded text overlay to provide semantic guidance. Meanwhile, the imperceptible visual perturbation is iteratively optimized to align the feature representation of the attacked image with those of the malicious visual and textual targets at both coarse- and fine-grained levels. Specifically, the visual target is instantiated as a text-rendered image and progressively refined during optimization to more faithfully represent the desired semantics and improve transferability. Extensive experiments on two multimodal understanding tasks across multiple closed-source MLLMs demonstrate the superior performance of our approach compared to existing methods.

Large Language Models (LLMs), renowned for their superior proficiency in language comprehension and generation, stimulate a vibrant ecosystem of applications around them. However, their extensive assimilation into various services introduces significant security risks. This study deconstructs the complexities and implications of prompt injection attacks on actual LLM-integrated applications. Initially, we conduct an exploratory analysis on ten commercial applications, highlighting the constraints of current attack strategies in practice. Prompted by these limitations, we subsequently formulate HouYi, a novel black-box prompt injection attack technique, which draws inspiration from traditional web injection attacks. HouYi is compartmentalized into three crucial elements: a seamlessly-incorporated pre-constructed prompt, an injection prompt inducing context partition, and a malicious payload designed to fulfill the attack objectives. Leveraging HouYi, we unveil previously unknown and severe attack outcomes, such as unrestricted arbitrary LLM usage and uncomplicated application prompt theft. We deploy HouYi on 36 actual LLM-integrated applications and discern 31 applications susceptible to prompt injection. 10 vendors have validated our discoveries, including Notion, which has the potential to impact millions of users. Our investigation illuminates both the possible risks of prompt injection attacks and the possible tactics for mitigation.

This paper presents a pioneering methodology, termed StructTuning, to efficiently transform foundation Large Language Models (LLMs) into domain specialists. It significantly minimizes the training corpus requirement to a mere 0.3% while achieving an impressive 50% of traditional knowledge injection performance. Our method is inspired by the educational processes for human students, particularly how structured domain knowledge from textbooks is absorbed and then applied to tackle real-world challenges through specific exercises. Based on this, we propose a novel two-stage knowledge injection strategy: Structure-aware Continual Pre-Training (SCPT) and Structure-aware Supervised Fine-Tuning (SSFT). In the SCPT phase, we organize the training data into an auto-generated taxonomy of domain knowledge, enabling LLMs to effectively memorize textual segments linked to specific expertise within the taxonomy's architecture. Subsequently, in the SSFT phase, we explicitly prompt models to reveal the underlying knowledge structure in their outputs, leveraging this structured domain insight to address practical problems adeptly. Our ultimate method has undergone extensive evaluations across model architectures and scales, using closed-book question-answering tasks on LongBench and MMedBench datasets. Remarkably, our method matches 50% of the improvement displayed by the state-of-the-art MMedLM2 on MMedBench, but with only 0.3% quantity of the training corpus. This breakthrough showcases the potential to scale up our StructTuning for stronger domain-specific LLMs. Code will be made public soon.

Language models of code (LMs) work well when the surrounding code in the vicinity of generation provides sufficient context. This is not true when it becomes necessary to use types or functionality defined in another module or library, especially those not seen during training. LMs suffer from limited awareness of such global context and end up hallucinating, e.g., using types defined in other files incorrectly. Recent work tries to overcome this issue by retrieving global information to augment the local context. However, this bloats the prompt or requires architecture modifications and additional training. Integrated development environments (IDEs) assist developers by bringing the global context at their fingertips using static analysis. We extend this assistance, enjoyed by developers, to the LMs. We propose a notion of monitors that use static analysis in the background to guide the decoding. Unlike a priori retrieval, static analysis is invoked iteratively during the entire decoding process, providing the most relevant suggestions on demand. We demonstrate the usefulness of our proposal by monitoring for type-consistent use of identifiers whenever an LM generates code for object dereference. To evaluate our approach, we curate PragmaticCode, a dataset of open-source projects with their development environments. On models of varying parameter scale, we show that monitor-guided decoding consistently improves the ability of an LM to not only generate identifiers that match the ground truth but also improves compilation rates and agreement with ground truth. We find that LMs with fewer parameters, when guided with our monitor, can outperform larger LMs. With monitor-guided decoding, SantaCoder-1.1B achieves better compilation rate and next-identifier match than the much larger text-davinci-003 model. The datasets and code will be released at https://aka.ms/monitors4codegen .

Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) systems are increasingly integrated into clinical workflows; however, prompt injection attacks can steer these systems toward clinically unsafe or misleading outputs. We introduce the Medical Prompt Injection Benchmark (MPIB), a dataset-and-benchmark suite for evaluating clinical safety under both direct prompt injection and indirect, RAG-mediated injection across clinically grounded tasks. MPIB emphasizes outcome-level risk via the Clinical Harm Event Rate (CHER), which measures high-severity clinical harm events under a clinically grounded taxonomy, and reports CHER alongside Attack Success Rate (ASR) to disentangle instruction compliance from downstream patient risk. The benchmark comprises 9,697 curated instances constructed through multi-stage quality gates and clinical safety linting. Evaluating MPIB across a diverse set of baseline LLMs and defense configurations, we find that ASR and CHER can diverge substantially, and that robustness depends critically on whether adversarial instructions appear in the user query or in retrieved context. We release MPIB with evaluation code, adversarial baselines, and comprehensive documentation to support reproducible and systematic research on clinical prompt injection. Code and data are available at GitHub (code) and Hugging Face (data).

Autonomous coding agents are increasingly integrated into software development workflows, offering capabilities that extend beyond code suggestion to active system interaction and environment management. OpenClaw, a representative platform in this emerging paradigm, introduces an extensible skill ecosystem that allows third-party developers to inject behavioral guidance through lifecycle hooks during agent initialization. While this design enhances automation and customization, it also opens a novel and unexplored attack surface. In this paper, we identify and systematically characterize guidance injection, a stealthy attack vector that embeds adversarial operational narratives into bootstrap guidance files. Unlike traditional prompt injection, which relies on explicit malicious instructions, guidance injection manipulates the agent's reasoning context by framing harmful actions as routine best practices. These narratives are automatically incorporated into the agent's interpretive framework and influence future task execution without raising suspicion.We construct 26 malicious skills spanning 13 attack categories including credential exfiltration, workspace destruction, privilege escalation, and persistent backdoor installation. We evaluate them using ORE-Bench, a realistic developer workspace benchmark we developed. Across 52 natural user prompts and six state-of-the-art LLM backends, our attacks achieve success rates from 16.0% to 64.2%, with the majority of malicious actions executed autonomously without user confirmation. Furthermore, 94% of our malicious skills evade detection by existing static and LLM-based scanners. Our findings reveal fundamental tensions in the design of autonomous agent ecosystems and underscore the urgent need for defenses based on capability isolation, runtime policy enforcement, and transparent guidance provenance.

The ability of CodeLLMs to generate executable and functionally correct code at the repository-level scale remains largely unexplored. We introduce RepoExec, a novel benchmark for evaluating code generation at the repository-level scale. RepoExec focuses on three main aspects: executability, functional correctness through automated test case generation with high coverage rate, and carefully crafted cross-file contexts to accurately generate code. Our work explores a controlled scenario where developers specify necessary code dependencies, challenging the model to integrate these accurately. Experiments show that while pretrained LLMs outperform instruction-tuned models in correctness, the latter excel in utilizing provided dependencies and demonstrating debugging capabilities. We also introduce a new instruction-tuned dataset that focuses on code dependencies and demonstrate that CodeLLMs fine-tuned on our dataset have a better capability to leverage these dependencies effectively. RepoExec aims to provide a comprehensive evaluation of code functionality and alignment with developer intent, paving the way for more reliable and applicable CodeLLMs in real-world scenarios. The dataset and source code can be found at~https://github.com/FSoft-AI4Code/RepoExec.

Prompt injection remains a central obstacle to the safe deployment of large language models, particularly in multi-agent settings where intermediate outputs can propagate or amplify malicious instructions. Building on earlier work that introduced a four-metric Total Injection Vulnerability Score (TIVS), this paper extends the evaluation framework with semantic similarity-based caching and a fifth metric (Observability Score Ratio) to yield TIVS-O, investigating how defence effectiveness interacts with transparency in a HOPE-inspired Nested Learning architecture. The proposed system combines an agentic pipeline with Continuum Memory Systems that implement semantic similarity-based caching across 301 synthetically generated injection-focused prompts drawn from ten attack families, while a fourth agent performs comprehensive security analysis using five key performance indicators. In addition to traditional injection metrics, OSR quantifies the richness and clarity of security-relevant reasoning exposed by each agent, enabling an explicit analysis of trade-offs between strict mitigation and auditability. Experiments show that the system achieves secure responses with zero high-risk breaches, while semantic caching delivers substantial computational savings, achieving a 41.6% reduction in LLM calls and corresponding decreases in latency, energy consumption, and carbon emissions. Five TIVS-O configurations reveal optimal trade-offs between mitigation strictness and forensic transparency. These results indicate that observability-aware evaluation can reveal non-monotonic effects within multi-agent pipelines and that memory-augmented agents can jointly maximize security robustness, real-time performance, operational cost savings, and environmental sustainability without modifying underlying model weights, providing a production-ready pathway for secure and green LLM deployments.

Large Language Models (LLMs) are increasingly deployed in agentic systems that interact with an external environment; this makes them susceptible to prompt injections when dealing with untrusted data. To overcome this limitation, we propose SIC (Soft Instruction Control)-a simple yet effective iterative prompt sanitization loop designed for tool-augmented LLM agents. Our method repeatedly inspects incoming data for instructions that could compromise agent behavior. If such content is found, the malicious content is rewritten, masked, or removed, and the result is re-evaluated. The process continues until the input is clean or a maximum iteration limit is reached; if imperative instruction-like content remains, the agent halts to ensure security. By allowing multiple passes, our approach acknowledges that individual rewrites may fail but enables the system to catch and correct missed injections in later steps. Although immediately useful, worst-case analysis shows that SIC is not infallible; strong adversary can still get a 15% ASR by embedding non-imperative workflows. This nonetheless raises the bar.

Pre-trained models (PTMs) are machine learning models that have been trained in advance, often on large-scale data, and can be reused for new tasks, thereby reducing the need for costly training from scratch. Their widespread adoption introduces a new class of software dependency, which we term Software Dependencies 2.0, extending beyond conventional libraries to learned behaviors embodied in trained models and their associated artifacts. The integration of PTMs as software dependencies in real projects remains unclear, potentially threatening maintainability and reliability of modern software systems that increasingly rely on them. Objective: In this study, we investigate Software Dependencies 2.0 in open-source software (OSS) projects by examining the reuse of PTMs, with a focus on how developers manage and integrate these models. Specifically, we seek to understand: (1) how OSS projects structure and document their PTM dependencies; (2) what stages and organizational patterns emerge in the reuse pipelines of PTMs within these projects; and (3) the interactions among PTMs and other learned components across pipeline stages. We conduct a mixed-methods analysis of a statistically significant random sample of 401 GitHub repositories from the PeaTMOSS dataset (28,575 repositories reusing PTMs from Hugging Face and PyTorch Hub). We quantitatively examine PTM reuse by identifying patterns and qualitatively investigate how developers integrate and manage these models in practice.

Large Language Models (LLMs) have demonstrated remarkable success in various tasks such as natural language understanding, text summarization, and machine translation. However, their general-purpose nature often limits their effectiveness in domain-specific applications that require specialized knowledge, such as healthcare, chemistry, or legal analysis. To address this, researchers have explored diverse methods to enhance LLMs by integrating domain-specific knowledge. In this survey, we provide a comprehensive overview of these methods, which we categorize into four key approaches: dynamic knowledge injection, static knowledge embedding, modular adapters, and prompt optimization. Each approach offers unique mechanisms to equip LLMs with domain expertise, balancing trade-offs between flexibility, scalability, and efficiency. We discuss how these methods enable LLMs to tackle specialized tasks, compare their advantages and disadvantages, evaluate domain-specific LLMs against general LLMs, and highlight the challenges and opportunities in this emerging field. For those interested in delving deeper into this area, we also summarize the commonly used datasets and benchmarks. To keep researchers updated on the latest studies, we maintain an open-source at: https://github.com/abilliyb/Knowledge_Injection_Survey_Papers, dedicated to documenting research in the field of specialized LLM.

Large Language Models (LLMs) can interact with the real world by connecting with versatile external APIs, resulting in better problem-solving and task automation capabilities. Previous research primarily focuses on APIs with limited arguments from a single source or overlooks the complex dependency relationship between different APIs. However, it is essential to utilize multiple APIs collaboratively from various sources (e.g., different Apps in the iPhone), especially for complex user instructions. In this paper, we introduce AppBench, the first benchmark to evaluate LLMs' ability to plan and execute multiple APIs from various sources in order to complete the user's task. Specifically, we consider two significant challenges in multiple APIs: 1) graph structures: some APIs can be executed independently while others need to be executed one by one, resulting in graph-like execution order; and 2) permission constraints: which source is authorized to execute the API call. We have experimental results on 9 distinct LLMs; e.g., GPT-4o achieves only a 2.0\% success rate at the most complex instruction, revealing that the existing state-of-the-art LLMs still cannot perform well in this situation even with the help of in-context learning and finetuning. Our code and data are publicly available at https://github.com/ruleGreen/AppBench.

Supervised Fine-Tuning (SFT) is essential for training large language models (LLMs), significantly enhancing critical capabilities such as instruction following and in-context learning. Nevertheless, creating suitable training datasets tailored for specific domains remains challenging due to unique domain constraints and data scarcity. In this paper, we propose SearchInstruct, an innovative method explicitly designed to construct high quality instruction datasets for SFT. Our approach begins with a limited set of domain specific, human generated questions, which are systematically expanded using a large language model. Subsequently, domain relevant resources are dynamically retrieved to generate accurate and contextually appropriate answers for each augmented question. Experimental evaluation demonstrates that SearchInstruct enhances both the diversity and quality of SFT datasets, leading to measurable improvements in LLM performance within specialized domains. Additionally, we show that beyond dataset generation, the proposed method can also effectively facilitate tasks such as model editing, enabling efficient updates to existing models. To facilitate reproducibility and community adoption, we provide full implementation details, the complete set of generated instruction response pairs, and the source code in a publicly accessible Git repository: [https://github.com/mostafaamiri/SearchInstruct](https://github.com/mostafaamiri/SearchInstruct)

Code generation with large language models (LLMs), often termed vibe coding, is increasingly adopted in production but fails to ensure code quality, particularly in security (e.g., SQL injection vulnerabilities) and maintainability (e.g., missing type annotations). Existing methods, such as supervised fine-tuning and rule-based post-processing, rely on labor-intensive annotations or brittle heuristics, limiting their scalability and effectiveness. We propose REAL, a reinforcement learning framework that incentivizes LLMs to generate production-quality code using program analysis-guided feedback. Specifically, REAL integrates two automated signals: (1) program analysis detecting security or maintainability defects and (2) unit tests ensuring functional correctness. Unlike prior work, our framework is prompt-agnostic and reference-free, enabling scalable supervision without manual intervention. Experiments across multiple datasets and model scales demonstrate that REAL outperforms state-of-the-art methods in simultaneous assessments of functionality and code quality. Our work bridges the gap between rapid prototyping and production-ready code, enabling LLMs to deliver both speed and quality.

Large Language Models (LLMs) are increasingly being integrated into various applications. The functionalities of recent LLMs can be flexibly modulated via natural language prompts. This renders them susceptible to targeted adversarial prompting, e.g., Prompt Injection (PI) attacks enable attackers to override original instructions and employed controls. So far, it was assumed that the user is directly prompting the LLM. But, what if it is not the user prompting? We argue that LLM-Integrated Applications blur the line between data and instructions. We reveal new attack vectors, using Indirect Prompt Injection, that enable adversaries to remotely (without a direct interface) exploit LLM-integrated applications by strategically injecting prompts into data likely to be retrieved. We derive a comprehensive taxonomy from a computer security perspective to systematically investigate impacts and vulnerabilities, including data theft, worming, information ecosystem contamination, and other novel security risks. We demonstrate our attacks' practical viability against both real-world systems, such as Bing's GPT-4 powered Chat and code-completion engines, and synthetic applications built on GPT-4. We show how processing retrieved prompts can act as arbitrary code execution, manipulate the application's functionality, and control how and if other APIs are called. Despite the increasing integration and reliance on LLMs, effective mitigations of these emerging threats are currently lacking. By raising awareness of these vulnerabilities and providing key insights into their implications, we aim to promote the safe and responsible deployment of these powerful models and the development of robust defenses that protect users and systems from potential attacks.

Diffusion-based large language models (dLLMs) have recently emerged as a powerful alternative to autoregressive LLMs, offering faster inference and greater interactivity via parallel decoding and bidirectional modeling. However, despite strong performance in code generation and text infilling, we identify a fundamental safety concern: existing alignment mechanisms fail to safeguard dLLMs against context-aware, masked-input adversarial prompts, exposing novel vulnerabilities. To this end, we present DIJA, the first systematic study and jailbreak attack framework that exploits unique safety weaknesses of dLLMs. Specifically, our proposed DIJA constructs adversarial interleaved mask-text prompts that exploit the text generation mechanisms of dLLMs, i.e., bidirectional modeling and parallel decoding. Bidirectional modeling drives the model to produce contextually consistent outputs for masked spans, even when harmful, while parallel decoding limits model dynamic filtering and rejection sampling of unsafe content. This causes standard alignment mechanisms to fail, enabling harmful completions in alignment-tuned dLLMs, even when harmful behaviors or unsafe instructions are directly exposed in the prompt. Through comprehensive experiments, we demonstrate that DIJA significantly outperforms existing jailbreak methods, exposing a previously overlooked threat surface in dLLM architectures. Notably, our method achieves up to 100% keyword-based ASR on Dream-Instruct, surpassing the strongest prior baseline, ReNeLLM, by up to 78.5% in evaluator-based ASR on JailbreakBench and by 37.7 points in StrongREJECT score, while requiring no rewriting or hiding of harmful content in the jailbreak prompt. Our findings underscore the urgent need for rethinking safety alignment in this emerging class of language models. Code is available at https://github.com/ZichenWen1/DIJA.

The proliferation of agentic AI coding assistants, including Claude Code, GitHub Copilot, Cursor, and emerging skill-based architectures, has fundamentally transformed software development workflows. These systems leverage Large Language Models (LLMs) integrated with external tools, file systems, and shell access through protocols like the Model Context Protocol (MCP). However, this expanded capability surface introduces critical security vulnerabilities. In this Systematization of Knowledge (SoK) paper, we present a comprehensive analysis of prompt injection attacks targeting agentic coding assistants. We propose a novel three-dimensional taxonomy categorizing attacks across delivery vectors, attack modalities, and propagation behaviors. Our meta-analysis synthesizes findings from 78 recent studies (2021--2026), consolidating evidence that attack success rates against state-of-the-art defenses exceed 85\% when adaptive attack strategies are employed. We systematically catalog 42 distinct attack techniques spanning input manipulation, tool poisoning, protocol exploitation, multimodal injection, and cross-origin context poisoning. Through critical analysis of 18 defense mechanisms reported in prior work, we identify that most achieve less than 50\% mitigation against sophisticated adaptive attacks. We contribute: (1) a unified taxonomy bridging disparate attack classifications, (2) the first systematic analysis of skill-based architecture vulnerabilities with concrete exploit chains, and (3) a defense-in-depth framework grounded in the limitations we identify. Our findings indicate that the security community must treat prompt injection as a first-class vulnerability class requiring architectural-level mitigations rather than ad-hoc filtering approaches.

Instruction-following made modern large language models (LLMs) helpful assistants. However, the key to taming LLMs on complex instructions remains mysterious, for that there are huge gaps between models trained by open-source community and those trained by leading companies. To bridge the gap, we propose a simple and scalable approach UltraIF for building LLMs that can follow complex instructions with open-source data. UltraIF first decomposes real-world user prompts into simpler queries, constraints, and corresponding evaluation questions for the constraints. Then, we train an UltraComposer to compose constraint-associated prompts with evaluation questions. This prompt composer allows us to synthesize complicated instructions as well as filter responses with evaluation questions. In our experiment, for the first time, we successfully align LLaMA-3.1-8B-Base to catch up with its instruct version on 5 instruction-following benchmarks without any benchmark information, using only 8B model as response generator and evaluator. The aligned model also achieved competitive scores on other benchmarks. Moreover, we also show that UltraIF could further improve LLaMA-3.1-8B-Instruct through self-alignment, motivating broader use cases for the method. Our code will be available at https://github.com/kkk-an/UltraIF.

Transformer-based large language models (LLMs) provide a powerful foundation for natural language tasks in large-scale customer-facing applications. However, studies that explore their vulnerabilities emerging from malicious user interaction are scarce. By proposing PromptInject, a prosaic alignment framework for mask-based iterative adversarial prompt composition, we examine how GPT-3, the most widely deployed language model in production, can be easily misaligned by simple handcrafted inputs. In particular, we investigate two types of attacks -- goal hijacking and prompt leaking -- and demonstrate that even low-aptitude, but sufficiently ill-intentioned agents, can easily exploit GPT-3's stochastic nature, creating long-tail risks. The code for PromptInject is available at https://github.com/agencyenterprise/PromptInject.