A Comprehensive Survey in LLM(-Agent) Full Stack Safety: Data, Training and Deployment

The remarkable success of Large Language Models (LLMs) has illuminated a promising pathway toward achieving Artificial General Intelligence for both academic and industrial communities, owing to their unprecedented performance across various applications. As LLMs continue to gain prominence in both research and commercial domains, their security and safety implications have become a growing concern, not only for researchers and corporations but also for every nation. Currently, existing surveys on LLM safety primarily focus on specific stages of the LLM lifecycle, e.g., deployment phase or fine-tuning phase, lacking a comprehensive understanding of the entire "lifechain" of LLMs. To address this gap, this paper introduces, for the first time, the concept of "full-stack" safety to systematically consider safety issues throughout the entire process of LLM training, deployment, and eventual commercialization. Compared to the off-the-shelf LLM safety surveys, our work demonstrates several distinctive advantages: (I) Comprehensive Perspective. We define the complete LLM lifecycle as encompassing data preparation, pre-training, post-training, deployment and final commercialization. To our knowledge, this represents the first safety survey to encompass the entire lifecycle of LLMs. (II) Extensive Literature Support. Our research is grounded in an exhaustive review of over 800+ papers, ensuring comprehensive coverage and systematic organization of security issues within a more holistic understanding. (III) Unique Insights. Through systematic literature analysis, we have developed reliable roadmaps and perspectives for each chapter. Our work identifies promising research directions, including safety in data generation, alignment techniques, model editing, and LLM-based agent systems. These insights provide valuable guidance for researchers pursuing future work in this field.

Prejudge-Before-Think: Enhancing Large Language Models at Test-Time by Process Prejudge Reasoning

In this paper, we introduce a new \emph{process prejudge} strategy in LLM reasoning to demonstrate that bootstrapping with process prejudge allows the LLM to adaptively anticipate the errors encountered when advancing the subsequent reasoning steps, similar to people sometimes pausing to think about what mistakes may occur and how to avoid them, rather than relying solely on trial and error. Specifically, we define a prejudge node in the rationale, which represents a reasoning step, with at least one step that follows the prejudge node that has no paths toward the correct answer. To synthesize the prejudge reasoning process, we present an automated reasoning framework with a dynamic tree-searching strategy. This framework requires only one LLM to perform answer judging, response critiquing, prejudge generation, and thought completion. Furthermore, we develop a two-phase training mechanism with supervised fine-tuning (SFT) and reinforcement learning (RL) to further enhance the reasoning capabilities of LLMs. Experimental results from competition-level complex reasoning demonstrate that our method can teach the model to prejudge before thinking and significantly enhance the reasoning ability of LLMs. Code and data is released at https://github.com/wjn1996/Prejudge-Before-Think.

3DAffordSplat: Efficient Affordance Reasoning with 3D Gaussians

3D affordance reasoning is essential in associating human instructions with the functional regions of 3D objects, facilitating precise, task-oriented manipulations in embodied AI. However, current methods, which predominantly depend on sparse 3D point clouds, exhibit limited generalizability and robustness due to their sensitivity to coordinate variations and the inherent sparsity of the data. By contrast, 3D Gaussian Splatting (3DGS) delivers high-fidelity, real-time rendering with minimal computational overhead by representing scenes as dense, continuous distributions. This positions 3DGS as a highly effective approach for capturing fine-grained affordance details and improving recognition accuracy. Nevertheless, its full potential remains largely untapped due to the absence of large-scale, 3DGS-specific affordance datasets. To overcome these limitations, we present 3DAffordSplat, the first large-scale, multi-modal dataset tailored for 3DGS-based affordance reasoning. This dataset includes 23,677 Gaussian instances, 8,354 point cloud instances, and 6,631 manually annotated affordance labels, encompassing 21 object categories and 18 affordance types. Building upon this dataset, we introduce AffordSplatNet, a novel model specifically designed for affordance reasoning using 3DGS representations. AffordSplatNet features an innovative cross-modal structure alignment module that exploits structural consistency priors to align 3D point cloud and 3DGS representations, resulting in enhanced affordance recognition accuracy. Extensive experiments demonstrate that the 3DAffordSplat dataset significantly advances affordance learning within the 3DGS domain, while AffordSplatNet consistently outperforms existing methods across both seen and unseen settings, highlighting its robust generalization capabilities.

PathVLM-R1: A Reinforcement Learning-Driven Reasoning Model for Pathology Visual-Language Tasks

The diagnosis of pathological images is often limited by expert availability and regional disparities, highlighting the importance of automated diagnosis using Vision-Language Models (VLMs). Traditional multimodal models typically emphasize outcomes over the reasoning process, compromising the reliability of clinical decisions. To address the weak reasoning abilities and lack of supervised processes in pathological VLMs, we have innovatively proposed PathVLM-R1, a visual language model designed specifically for pathological images. We have based our model on Qwen2.5-VL-7B-Instruct and enhanced its performance for pathological tasks through meticulously designed post-training strategies. Firstly, we conduct supervised fine-tuning guided by pathological data to imbue the model with foundational pathological knowledge, forming a new pathological base model. Subsequently, we introduce Group Relative Policy Optimization (GRPO) and propose a dual reward-driven reinforcement learning optimization, ensuring strict constraint on logical supervision of the reasoning process and accuracy of results via cross-modal process reward and outcome accuracy reward. In the pathological image question-answering tasks, the testing results of PathVLM-R1 demonstrate a 14% improvement in accuracy compared to baseline methods, and it demonstrated superior performance compared to the Qwen2.5-VL-32B version despite having a significantly smaller parameter size. Furthermore, in out-domain data evaluation involving four medical imaging modalities: Computed Tomography (CT), dermoscopy, fundus photography, and Optical Coherence Tomography (OCT) images: PathVLM-R1's transfer performance improved by an average of 17.3% compared to traditional SFT methods. These results clearly indicate that PathVLM-R1 not only enhances accuracy but also possesses broad applicability and expansion potential.

Regretful Decisions under Label Noise

Machine learning models are routinely used to support decisions that affect individuals -- be it to screen a patient for a serious illness or to gauge their response to treatment. In these tasks, we are limited to learning models from datasets with noisy labels. In this paper, we study the instance-level impact of learning under label noise. We introduce a notion of regret for this regime which measures the number of unforeseen mistakes due to noisy labels. We show that standard approaches to learning under label noise can return models that perform well at a population level while subjecting individuals to a lottery of mistakes. We present a versatile approach to estimate the likelihood of mistakes at the individual level from a noisy dataset by training models over plausible realizations of datasets without label noise. This is supported by a comprehensive empirical study of label noise in clinical prediction tasks. Our results reveal how failure to anticipate mistakes can compromise model reliability and adoption, and demonstrate how we can address these challenges by anticipating and avoiding regretful decisions.

Adaptive Bounded Exploration and Intermediate Actions for Data Debiasing

The performance of algorithmic decision rules is largely dependent on the quality of training datasets available to them. Biases in these datasets can raise economic and ethical concerns due to the resulting algorithms' disparate treatment of different groups. In this paper, we propose algorithms for sequentially debiasing the training dataset through adaptive and bounded exploration in a classification problem with costly and censored feedback. Our proposed algorithms balance between the ultimate goal of mitigating the impacts of data biases -- which will in turn lead to more accurate and fairer decisions, and the exploration risks incurred to achieve this goal. Specifically, we propose adaptive bounds to limit the region of exploration, and leverage intermediate actions which provide noisy label information at a lower cost. We analytically show that such exploration can help debias data in certain distributions, investigate how {algorithmic fairness interventions} can work in conjunction with our proposed algorithms, and validate the performance of these algorithms through numerical experiments on synthetic and real-world data.

PINP: Physics-Informed Neural Predictor with latent estimation of fluid flows

Accurately predicting fluid dynamics and evolution has been a long-standing challenge in physical sciences. Conventional deep learning methods often rely on the nonlinear modeling capabilities of neural networks to establish mappings between past and future states, overlooking the fluid dynamics, or only modeling the velocity field, neglecting the coupling of multiple physical quantities. In this paper, we propose a new physics-informed learning approach that incorporates coupled physical quantities into the prediction process to assist with forecasting. Central to our method lies in the discretization of physical equations, which are directly integrated into the model architecture and loss function. This integration enables the model to provide robust, long-term future predictions. By incorporating physical equations, our model demonstrates temporal extrapolation and spatial generalization capabilities. Experimental results show that our approach achieves the state-of-the-art performance in spatiotemporal prediction across both numerical simulations and real-world extreme-precipitation nowcasting benchmarks.

Skywork R1V: Pioneering Multimodal Reasoning with Chain-of-Thought

We introduce Skywork R1V, a multimodal reasoning model extending the an R1-series Large language models (LLM) to visual modalities via an efficient multimodal transfer method. Leveraging a lightweight visual projector, Skywork R1V facilitates seamless multimodal adaptation without necessitating retraining of either the foundational language model or the vision encoder. To strengthen visual-text alignment, we propose a hybrid optimization strategy that combines Iterative Supervised Fine-Tuning (SFT) with Group Relative Policy Optimization (GRPO), significantly enhancing cross-modal integration efficiency. Additionally, we introduce an adaptive-length Chain-of-Thought distillation approach for reasoning data generation. This approach dynamically optimizes reasoning chain lengths, thereby enhancing inference efficiency and preventing excessive reasoning overthinking. Empirical evaluations demonstrate that Skywork R1V, with only 38B parameters, delivers competitive performance, achieving a score of 69.0 on the MMMU benchmark and 67.5 on MathVista. Meanwhile, it maintains robust textual reasoning performance, evidenced by impressive scores of 72.0 on AIME and 94.0 on MATH500. The Skywork R1V model weights have been publicly released to promote openness and reproducibility.

To Give or Not to Give? The Impacts of Strategically Withheld Recourse

Individuals often aim to reverse undesired outcomes in interactions with automated systems, like loan denials, by either implementing system-recommended actions (recourse), or manipulating their features. While providing recourse benefits users and enhances system utility, it also provides information about the decision process that can be used for more effective strategic manipulation, especially when the individuals collectively share such information with each other. We show that this tension leads rational utility-maximizing systems to frequently withhold recourse, resulting in decreased population utility, particularly impacting sensitive groups. To mitigate these effects, we explore the role of recourse subsidies, finding them effective in increasing the provision of recourse actions by rational systems, as well as lowering the potential social cost and mitigating unfairness caused by recourse withholding.

Efficient Dynamic Clustering-Based Document Compression for Retrieval-Augmented-Generation

Retrieval-Augmented Generation (RAG) has emerged as a widely adopted approach for knowledge integration during large language model (LLM) inference in recent years. However, current RAG implementations face challenges in effectively addressing noise, repetition and redundancy in retrieved content, primarily due to their limited ability to exploit fine-grained inter-document relationships. To address these limitations, we propose an \textbf{E}fficient \textbf{D}ynamic \textbf{C}lustering-based document \textbf{C}ompression framework (\textbf{EDC\textsuperscript{2}-RAG}) that effectively utilizes latent inter-document relationships while simultaneously removing irrelevant information and redundant content. We validate our approach, built upon GPT-3.5, on widely used knowledge-QA and hallucination-detected datasets. The results show that this method achieves consistent performance improvements across various scenarios and experimental settings, demonstrating strong robustness and applicability. Our code and datasets can be found at https://github.com/Tsinghua-dhy/EDC-2-RAG.