arXiv subjects

Kun Sun

Publications and source records attributed to Kun Sun.

At least 37 records · Page 2Linked to original sources

arXiv2025

When Genes Speak: A Semantic-Guided Framework for Spatially Resolved Transcriptomics Data Clustering

Spatial transcriptomics enables gene expression profiling with spatial context, offering unprecedented insights into the tissue microenvironment. However, most computational models treat genes as isolated numerical features, ignoring the rich biological semantics encoded in their symbols. This prevents a truly deep understanding of critical biological characteristics. To overcome this limitation, we present SemST, a semantic-guided deep learning framework for spatial transcriptomics data clustering. SemST leverages Large Language Models (LLMs) to enable genes to "speak" through their symbolic meanings, transforming gene sets within each tissue spot into biologically informed embeddings. These embeddings are then fused with the spatial neighborhood relationships captured by Graph Neural Networks (GNNs), achieving a coherent integration of biological function and spatial structure. We further introduce the Fine-grained Semantic Modulation (FSM) module to optimally exploit these biological priors. The FSM module learns spot-specific affine transformations that empower the semantic embeddings to perform an element-wise calibration of the spatial features, thus dynamically injecting high-order biological knowledge into the spatial context. Extensive experiments on public spatial transcriptomics datasets show that SemST achieves state-of-the-art clustering performance. Crucially, the FSM module exhibits plug-and-play versatility, consistently improving the performance when integrated into other baseline methods.

cs.LG↗

arXiv2025

NeuroDeX: Unlocking Diverse Support in Decompiling Deep Neural Network Executables

On-device deep learning models have extensive real world demands. Deep learning compilers efficiently compile models into executables for deployment on edge devices, but these executables may face the threat of reverse engineering. Previous studies have attempted to decompile DNN executables, but they face challenges in handling compilation optimizations and analyzing quantized compiled models. In this paper, we present NeuroDeX to unlock diverse support in decompiling DNN executables. NeuroDeX leverages the semantic understanding capabilities of LLMs along with dynamic analysis to accurately and efficiently perform operator type recognition, operator attribute recovery and model reconstruction. NeuroDeX can recover DNN executables into high-level models towards compilation optimizations, different architectures and quantized compiled models. We conduct experiments on 96 DNN executables across 12 common DNN models. Extensive experimental results demonstrate that NeuroDeX can decompile non-quantized executables into nearly identical high-level models. NeuroDeX can recover functionally similar high-level models for quantized executables, achieving an average top-1 accuracy of 72%. NeuroDeX offers a more comprehensive and effective solution compared to previous DNN executables decompilers.

cs.LG↗

arXiv2025

PathFix: Automated Program Repair with Expected Path

Automated program repair (APR) techniques are effective in fixing inevitable defects in software, enhancing development efficiency and software robustness. However, due to the difficulty of generating precise specifications, existing APR methods face two main challenges: generating too many plausible patch candidates and overfitting them to partial test cases. To tackle these challenges, we introduce a new APR method named PathFix, which leverages path-sensitive constraints extracted from correct execution paths to generate patches for repairing buggy code. It is based on one observation: if a buggy program is repairable, at least one expected path is supposed to replace the fault path in the patched program. PathFix operates in four main steps. First, it traces fault paths reaching the fault output in the buggy program. Second, it derives expected paths by analyzing the desired correct output on the control flow graph, where an expected path defines how a feasible patch leads to the correct execution. Third, PathFix generates and evaluates patches by solving state constraints along the expected path. Fourth, we validate the correctness of the generated patch. To further enhance repair performance and mitigate scalability issues introduced by path-sensitive analysis, we integrate a large language model (LLM) into our framework. Experimental results show that PathFix outperforms existing solutions, particularly in handling complex program structures such as loops and recursion.

cs.SE↗

arXiv2025

Scaling Law in LLM Simulated Personality: More Detailed and Realistic Persona Profile Is All You Need

This research focuses on using large language models (LLMs) to simulate social experiments, exploring their ability to emulate human personality in virtual persona role-playing. The research develops an end-to-end evaluation framework, including individual-level analysis of stability and identifiability, as well as population-level analysis called progressive personality curves to examine the veracity and consistency of LLMs in simulating human personality. Methodologically, this research proposes important modifications to traditional psychometric approaches (CFA and construct validity) which are unable to capture improvement trends in LLMs at their current low-level simulation, potentially leading to remature rejection or methodological misalignment. The main contributions of this research are: proposing a systematic framework for LLM virtual personality evaluation; empirically demonstrating the critical role of persona detail in personality simulation quality; and identifying marginal utility effects of persona profiles, especially a Scaling Law in LLM personality simulation, offering operational evaluation metrics and a theoretical foundation for applying large language models in social science experiments.

cs.CY↗

arXiv2025

The fragility of "cultural tendencies" in LLMs

In a recent study, Lu, Song, and Zhang (2025) (LSZ) propose that large language models (LLMs), when prompted in different languages, display culturally specific tendencies. They report that the two models (i.e., GPT and ERNIE) respond in more interdependent and holistic ways when prompted in Chinese, and more independent and analytic ways when prompted in English. LSZ attribute these differences to deep-seated cultural patterns in the models, claiming that prompt language alone can induce substantial cultural shifts. While we acknowledge the empirical patterns they observed, we find their experiments, methods, and interpretations problematic. In this paper, we critically re-evaluate the methodology, theoretical framing, and conclusions of LSZ. We argue that the reported "cultural tendencies" are not stable traits but fragile artifacts of specific models and task design. To test this, we conducted targeted replications using a broader set of LLMs and a larger number of test items. Our results show that prompt language has minimal effect on outputs, challenging LSZ's claim that these models encode grounded cultural beliefs.

cs.CL↗

arXiv2025

Conceptual Design Report of Super Tau-Charm Facility: The Accelerator

Electron-positron colliders operating in the GeV region of center-of-mass energies or the Tau-Charm energy region, have been proven to enable competitive frontier research, due to its several unique features. With the progress of high energy physics in the last two decades, a new-generation Tau-Charm factory, Super Tau Charm Facility (STCF) has been actively promoting by the particle physics community in China. STCF holds great potential to address fundamental questions such as the essence of color confinement and the matter-antimatter asymmetry in the universe in the next decades. The main design goals of STCF are with a center-of-mass energy ranging from 2 to 7 GeV and a peak luminosity surpassing 5*10^34 cm^-2s^-1 that is optimized at a center-of-mass energy of 4 GeV, which is about 50 times that of the currently operating Tau-Charm factory - BEPCII. The STCF accelerator is composed of two main parts: a double-ring collider with the crab-waist collision scheme and an injector that provides top-up injections for both electron and positron beams. As a typical third-generation electron-positron circular collider, the STCF accelerator faces many challenges in both accelerator physics and technology. In this paper, the conceptual design of the STCF accelerator complex is presented, including the ongoing efforts and plans for technological R&D, as well as the required infrastructure. The STCF project aims to secure support from the Chinese central government for its construction during the 15th Five-Year Plan (2026-2030) in China.

physics.acc-ph↗

arXiv2025

Off-Path TCP Exploits: PMTUD Breaks TCP Connection Isolation in IP Address Sharing Scenarios

Path MTU Discovery (PMTUD) and IP address sharing are integral aspects of modern Internet infrastructure. In this paper, we investigate the security vulnerabilities associated with PMTUD within the context of prevalent IP address sharing practices. We reveal that PMTUD is inadequately designed to handle IP address sharing, creating vulnerabilities that attackers can exploit to perform off-path TCP hijacking attacks. We demonstrate that by observing the path MTU value determined by a server for a public IP address (shared among multiple devices), an off-path attacker on the Internet, in collaboration with a malicious device, can infer the sequence numbers of TCP connections established by other legitimate devices sharing the same IP address. This vulnerability enables the attacker to perform off-path TCP hijacking attacks, significantly compromising the security of the affected TCP connections. Our attack involves first identifying a target TCP connection originating from the shared IP address, followed by inferring the sequence numbers of the identified connection. We thoroughly assess the impacts of our attack under various network configurations. Experimental results reveal that the attack can be executed within an average time of 220 seconds, achieving a success rate of 70%.Case studies, including SSH DoS, FTP traffic poisoning, and HTTP injection, highlight the threat it poses to various applications. Additionally, we evaluate our attack across 50 real-world networks with IP address sharing--including public Wi-Fi, VPNs, and 5G--and find 38 vulnerable. Finally, we responsibly disclose the vulnerabilities, receive recognition from organizations such as IETF, Linux, and Cisco, and propose our countermeasures.

cs.CR↗

arXiv2025

TraceRAG: A LLM-Based Framework for Explainable Android Malware Detection and Behavior Analysis

Sophisticated evasion tactics in malicious Android applications, combined with their intricate behavioral semantics, enable attackers to conceal malicious logic within legitimate functions, underscoring the critical need for robust and in-depth analysis frameworks. However, traditional analysis techniques often fail to recover deeply hidden behaviors or provide human-readable justifications for their decisions. Inspired by advances in large language models (LLMs), we introduce TraceRAG, a retrieval-augmented generation (RAG) framework that bridges natural language queries and Java code to deliver explainable malware detection and analysis. First, TraceRAG generates summaries of method-level code snippets, which are indexed in a vector database. At query time, behavior-focused questions retrieve the most semantically relevant snippets for deeper inspection. Finally, based on the multi-turn analysis results, TraceRAG produces human-readable reports that present the identified malicious behaviors and their corresponding code implementations. Experimental results demonstrate that our method achieves 96\% malware detection accuracy and 83.81\% behavior identification accuracy based on updated VirusTotal (VT) scans and manual verification. Furthermore, expert evaluation confirms the practical utility of the reports generated by TraceRAG.

cs.SE↗

arXiv2025

Boosting Pathology Foundation Models via Few-shot Prompt-tuning for Rare Cancer Subtyping

Rare cancers comprise 20-25% of all malignancies but face major diagnostic challenges due to limited expert availability-especially in pediatric oncology, where they represent over 70% of cases. While pathology vision-language (VL) foundation models show promising zero-shot capabilities for common cancer subtyping, their clinical performance for rare cancers remains limited. Existing multi-instance learning (MIL) methods rely only on visual features, overlooking cross-modal knowledge and compromising interpretability critical for rare cancer diagnosis. To address this limitation, we propose PathPT, a novel framework that fully exploits the potential of vision-language pathology foundation models through spatially-aware visual aggregation and task-specific prompt tuning. Unlike conventional MIL, PathPT converts WSI-level supervision into fine-grained tile-level guidance by leveraging the zero-shot capabilities of VL models, thereby preserving localization on cancerous regions and enabling cross-modal reasoning through prompts aligned with histopathological semantics. We benchmark PathPT on eight rare cancer datasets(four adult and four pediatric) spanning 56 subtypes and 2,910 WSIs, as well as three common cancer datasets, evaluating four state-of-the-art VL models and four MIL frameworks under three few-shot settings. Results show that PathPT consistently delivers superior performance, achieving substantial gains in subtyping accuracy and cancerous region grounding ability. This work advances AI-assisted diagnosis for rare cancers, offering a scalable solution for improving subtyping accuracy in settings with limited access to specialized expertise.

cs.CV↗

arXiv2025

ChainMarks: Securing DNN Watermark with Cryptographic Chain

With the widespread deployment of deep neural network (DNN) models, dynamic watermarking techniques are being used to protect the intellectual property of model owners. However, recent studies have shown that existing watermarking schemes are vulnerable to watermark removal and ambiguity attacks. Besides, the vague criteria for determining watermark presence further increase the likelihood of such attacks. In this paper, we propose a secure DNN watermarking scheme named ChainMarks, which generates secure and robust watermarks by introducing a cryptographic chain into the trigger inputs and utilizes a two-phase Monte Carlo method for determining watermark presence. First, ChainMarks generates trigger inputs as a watermark dataset by repeatedly applying a hash function over a secret key, where the target labels associated with trigger inputs are generated from the digital signature of model owner. Then, the watermarked model is produced by training a DNN over both the original and watermark datasets. To verify watermarks, we compare the predicted labels of trigger inputs with the target labels and determine ownership with a more accurate decision threshold that considers the classification probability of specific models. Experimental results show that ChainMarks exhibits higher levels of robustness and security compared to state-of-the-art watermarking schemes. With a better marginal utility, ChainMarks provides a higher probability guarantee of watermark presence in DNN models with the same level of watermark accuracy.

cs.CR↗

arXiv2025

SentinelAgent: Graph-based Anomaly Detection in Multi-Agent Systems

The rise of large language model (LLM)-based multi-agent systems (MAS) introduces new security and reliability challenges. While these systems show great promise in decomposing and coordinating complex tasks, they also face multi-faceted risks across prompt manipulation, unsafe tool usage, and emergent agent miscoordination. Existing guardrail mechanisms offer only partial protection, primarily at the input-output level, and fall short in addressing systemic or multi-point failures in MAS. In this work, we present a system-level anomaly detection framework tailored for MAS, integrating structural modeling with runtime behavioral oversight. Our approach consists of two components. First, we propose a graph-based framework that models agent interactions as dynamic execution graphs, enabling semantic anomaly detection at node, edge, and path levels. Second, we introduce a pluggable SentinelAgent, an LLM-powered oversight agent that observes, analyzes, and intervenes in MAS execution based on security policies and contextual reasoning. By bridging abstract detection logic with actionable enforcement, our method detects not only single-point faults and prompt injections but also multi-agent collusion and latent exploit paths. We validate our framework through two case studies, including an email assistant and Microsoft's Magentic-One system, demonstrating its ability to detect covert risks and provide explainable root-cause attribution. Our work lays the foundation for more trustworthy, monitorable, and secure agent-based AI ecosystems.

cs.AI↗

arXiv2025

A Generalist Audio Foundation Model for Comprehensive Body Sound Auscultation

Accurate and efficient auscultation-based diagnostics are vital for early disease detection, especially in resource-limited settings where specialized clinical expertise is scarce. Traditional auscultation, which heavily depends on clinician experience, suffers from significant inter-observer variability, while existing AI models often falter due to the limitations of non-representative training data. In this study, we introduce AuscultaBase, a novel AI-driven diagnostic framework that harnesses self-supervised and contrastive learning techniques alongside large-scale, multi-source data integration to advance body sound analysis. By generating robust feature representations, AuscultaBase markedly enhances performance in abnormality detection, disease classification, and activity recognition tasks. Comprehensive evaluations on our newly established benchmark, AuscultaBench, demonstrate that AuscultaBase consistently outperforms state-of-the-art methods across key performance metrics, underscoring its potential as a scalable and cost-effective tool for clinical screening and early disease intervention. The code and model checkpoint has been released in https://github.com/applewpj/AuscultaBase.

cs.SD↗

arXiv2025

TYPEPULSE: Detecting Type Confusion Bugs in Rust Programs

Rust supports type conversions and safe Rust guarantees the security of these conversions through robust static type checking and strict ownership guidelines. However, there are instances where programmers need to use unsafe Rust for certain type conversions, especially those involving pointers. Consequently, these conversions may cause severe memory corruption problems. Despite extensive research on type confusion bugs in C/C++, studies on type confusion bugs in Rust are still lacking. Also, due to Rust's new features in the type system, existing solutions in C/C++ cannot be directly applied to Rust. In this paper, we develop a static analysis tool called TYPEPULSE to detect three main categories of type confusion bugs in Rust including misalignment, inconsistent layout, and mismatched scope. TYPEPULSE first performs a type conversion analysis to collect and determine trait bounds for type pairs. Moreover, it performs a pointer alias analysis to resolve the alias relationship of pointers. Following the integration of information into the property graph, it constructs type patterns and detects each type of bug in various conversion scenarios. We run TYPEPULSE on the top 3,000 Rust packages and uncover 71 new type confusion bugs, exceeding the total number of type confusion bugs reported in RUSTSEC over the past five years. We have received 32 confirmations from developers, along with one CVE ID and six RUSTSEC IDs.

cs.CR↗

arXiv2024

Dspy-based Neural-Symbolic Pipeline to Enhance Spatial Reasoning in LLMs

Large Language Models (LLMs) have demonstrated remarkable capabilities across various tasks, yet they often struggle with spatial reasoning. This paper presents a novel neural-symbolic framework that enhances LLMs' spatial reasoning abilities through iterative feedback between LLMs and Answer Set Programming (ASP). We evaluate our approach on two benchmark datasets: StepGame and SparQA, implementing three distinct strategies: (1) direct prompting baseline, (2) Facts+Rules prompting, and (3) DSPy-based LLM+ASP pipeline with iterative refinement. Our experimental results demonstrate that the LLM+ASP pipeline significantly outperforms baseline methods, achieving an average 82% accuracy on StepGame and 69% on SparQA, marking improvements of 40-50% and 8-15% respectively over direct prompting. The success stems from three key innovations: (1) effective separation of semantic parsing and logical reasoning through a modular pipeline, (2) iterative feedback mechanism between LLMs and ASP solvers that improves program rate, and (3) robust error handling that addresses parsing, grounding, and solving failures. Additionally, we propose Facts+Rules as a lightweight alternative that achieves comparable performance on complex SparQA dataset, while reducing computational overhead.Our analysis across different LLM architectures (Deepseek, Llama3-70B, GPT-4.0 mini) demonstrates the framework's generalizability and provides insights into the trade-offs between implementation complexity and reasoning capability, contributing to the development of more interpretable and reliable AI systems.

cs.AI↗

arXiv2024

ReDAN: An Empirical Study on Remote DoS Attacks against NAT Networks

In this paper, we conduct an empirical study on remote DoS attacks targeting NAT networks. We show that Internet attackers operating outside local NAT networks can remotely identify a NAT device and subsequently terminate TCP connections initiated from the identified NAT device to external servers. Our attack involves two steps. First, we identify NAT devices on the Internet by exploiting inadequacies in the PMTUD mechanism within NAT specifications. This deficiency creates a fundamental side channel that allows Internet attackers to distinguish if a public IPv4 address serves a NAT device or a separate IP host, aiding in the identification of target NAT devices. Second, we launch a remote DoS attack to terminate TCP connections on the identified NAT devices. While recent NAT implementations may include protective measures, such as packet legitimacy validation to prevent malicious manipulations on NAT mappings, we discover that these safeguards are not widely adopted in real world. Consequently, attackers can send crafted packets to deceive NAT devices into erroneously removing innocent TCP connection mappings, thereby disrupting the NATed clients to access remote TCP servers. Our experimental results reveal widespread security vulnerabilities in existing NAT devices. After testing 8 types of router firmware and 30 commercial NAT devices from 14 vendors, we identify vulnerabilities in 6 firmware types and 29 NAT devices. Moreover, our measurements reveal a stark reality: 166 out of 180 (over 92%) tested real-world NAT networks, comprising 90 4G LTE/5G networks, 60 public Wi-Fi networks, and 30 cloud VPS networks, are susceptible to exploitation. We responsibly disclosed the vulnerabilities to affected vendors and received a significant number of acknowledgments. Finally, we propose our countermeasures against the identified DoS attack.

cs.CR↗

arXiv2024

Exploiting Cross-Layer Vulnerabilities: Off-Path Attacks on the TCP/IP Protocol Suite

After more than 40 years of development, the fundamental TCP/IP protocol suite, serving as the backbone of the Internet, is widely recognized for having achieved an elevated level of robustness and security. Distinctively, we take a new perspective to investigate the security implications of cross-layer interactions within the TCP/IP protocol suite caused by ICMP error messages. Through a comprehensive analysis of interactions among Wi-Fi, IP, ICMP, UDP, and TCP due to ICMP errors, we uncover several significant vulnerabilities, including information leakage, desynchronization, semantic gaps, and identity spoofing. These vulnerabilities can be exploited by off-path attackers to manipulate network traffic stealthily, affecting over 20% of popular websites and more than 89% of public Wi-Fi networks, thus posing risks to the Internet. By responsibly disclosing these vulnerabilities to affected vendors and proposing effective countermeasures, we enhance the robustness of the TCP/IP protocol suite, receiving acknowledgments from well-known organizations such as the Linux community, the OpenWrt community, the FreeBSD community, Wi-Fi Alliance, Qualcomm, HUAWEI, China Telecom, Alibaba, and H3C.

cs.CR↗

arXiv2024

Differential contributions of machine learning and statistical analysis to language and cognitive sciences

Data-driven approaches have revolutionized scientific research, with machine learning and statistical analysis being commonly used methodologies. Despite their widespread use, these approaches differ significantly in their techniques, objectives and implementations. Few studies have systematically applied both methods to identical datasets to highlight potential differences, particularly in language and cognitive sciences. This study employs the Buckeye Speech Corpus to illustrate how machine learning and statistical analysis are applied in data-driven research to obtain distinct insights on language production. We demonstrate the theoretical differences, implementation steps, and unique objectives of each approach through a comprehensive, tutorial-like comparison. Our analysis reveals that while machine learning excels at pattern recognition and prediction, statistical methods provide deeper insights into relationships between variables. The study highlights how semantic relevance, a novel metric measuring contextual influence on target words, contributes to understanding word duration in speech. We also systematically compare the differences between regression models used in machine learning and statistical analysis, particularly focusing on the training and fitting processes. Additionally, we clarify several common misconceptions that contribute to the confusion between these two approaches. Overall, by elucidating the complementary strengths of machine learning and statistics, this research enhances our understanding of diverse data-driven strategies in language and cognitive sciences, offering researchers valuable guidance on when and how to effectively apply these approaches in different research contexts.

cs.CL↗

arXiv2024

The Roles of Contextual Semantic Relevance Metrics in Human Visual Processing

Semantic relevance metrics can capture both the inherent semantics of individual objects and their relationships to other elements within a visual scene. Numerous previous research has demonstrated that these metrics can influence human visual processing. However, these studies often did not fully account for contextual information or employ the recent deep learning models for more accurate computation. This study investigates human visual perception and processing by introducing the metrics of contextual semantic relevance. We evaluate semantic relationships between target objects and their surroundings from both vision-based and language-based perspectives. Testing a large eye-movement dataset from visual comprehension, we employ state-of-the-art deep learning techniques to compute these metrics and analyze their impacts on fixation measures on human visual processing through advanced statistical models. These metrics could also simulate top-down and bottom-up processing in visual perception. This study further integrates vision-based and language-based metrics into a novel combined metric, addressing a critical gap in previous research that often treated visual and semantic similarities separately. Results indicate that all metrics could precisely predict fixation measures in visual perception and processing, but with distinct roles in prediction. The combined metric outperforms other metrics, supporting theories that emphasize the interaction between semantic and visual information in shaping visual perception/processing. This finding aligns with growing recognition of the importance of multi-modal information processing in human cognition. These insights enhance our understanding of cognitive mechanisms underlying visual processing and have implications for developing more accurate computational models in fields such as cognitive science and human-computer interaction.

cs.CV↗