Kun Sun

Jiangkai Long, Yanran Zhu, Chang Tang et al.

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.

Xinda Wang, Shu Wang, Pengbin Feng et al.

With the increasing usage of open-source software (OSS) components, vulnerabilities embedded within them are propagated to a huge number of underlying applications. In practice, the timely application of security patches in downstream software is challenging. The main reason is that such patches do not explicitly indicate their security impacts in the documentation, which would be difficult to recognize for software maintainers and users. However, attackers can still identify these "secret" security patches by analyzing the source code and generate corresponding exploits to compromise not only unpatched versions of the current software, but also other similar software packages that may contain the same vulnerability due to code cloning or similar design/implementation logic. Therefore, it is critical to identify these secret security patches to enable timely fixes. To this end, we propose a deep learning-based defense system called PatchRNN to automatically identify secret security patches in OSS. Besides considering descriptive keywords in the commit message (i.e., at the text level), we leverage both syntactic and semantic features at the source-code level. To evaluate the performance of our system, we apply it on a large-scale real-world patch dataset and conduct a case study on a popular open-source web server software - NGINX. Experimental results show that the PatchRNN can successfully detect secret security patches with a low false positive rate.

Kun Sun, Rong Wang

The development of different theories of discourse structure has led to the establishment of discourse corpora based on these theories. However, the existence of discourse corpora established on different theoretical bases creates challenges when it comes to exploring them in a consistent and cohesive way. This study has as its primary focus the conversion of PDTB annotations into dependency structures. It employs refined BERT-based discourse parsers to test the validity of the dependency data derived from the PDTB-style corpora in English, Chinese, and several other languages. By converting both PDTB and RST annotations for the same texts into dependencies, this study also applies ``dependency distance'' metrics to examine the correlation between RST dependencies and PDTB dependencies in English. The results show that the PDTB dependency data is valid and that there is a strong correlation between the two types of dependency distance. This study presents a comprehensive approach for analyzing and evaluating discourse corpora by employing discourse dependencies to achieve unified analysis. By applying dependency representations, we can extract data from PDTB, RST, and SDRT corpora in a coherent and unified manner. Moreover, the cross-linguistic validation establishes the framework's generalizability beyond English. The establishment of this comprehensive dependency framework overcomes limitations of existing discourse corpora, supporting a diverse range of algorithms and facilitating further studies in computational discourse analysis and language sciences.

Rong Wang, Kun Sun, Jonas Kuhn

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.

Brian Choi, Shu Wang, Isabelle Choi et al.

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.

Rong Wang, Kun Sun

The traditional personality models only yield binary results. This paper presents a novel approach for training personality detection models that produce continuous output values, using mixed strategies. By leveraging the PANDORA dataset, which includes extensive personality labeling of Reddit comments, we developed models that predict the Big Five personality traits with high accuracy. Our approach involves fine-tuning a RoBERTa-base model with various strategies such as Multi-Layer Perceptron (MLP) integration, and hyperparameter tuning. The results demonstrate that our models significantly outperform traditional binary classification methods, offering precise continuous outputs for personality traits, thus enhancing applications in AI, psychology, human resources, marketing and health care fields.

Jiaming Mu, Binghui Wang, Qi Li et al.

Graph Neural Networks (GNNs) have achieved state-of-the-art performance in various graph structure related tasks such as node classification and graph classification. However, GNNs are vulnerable to adversarial attacks. Existing works mainly focus on attacking GNNs for node classification; nevertheless, the attacks against GNNs for graph classification have not been well explored. In this work, we conduct a systematic study on adversarial attacks against GNNs for graph classification via perturbing the graph structure. In particular, we focus on the most challenging attack, i.e., hard label black-box attack, where an attacker has no knowledge about the target GNN model and can only obtain predicted labels through querying the target model.To achieve this goal, we formulate our attack as an optimization problem, whose objective is to minimize the number of edges to be perturbed in a graph while maintaining the high attack success rate. The original optimization problem is intractable to solve, and we relax the optimization problem to be a tractable one, which is solved with theoretical convergence guarantee. We also design a coarse-grained searching algorithm and a query-efficient gradient computation algorithm to decrease the number of queries to the target GNN model. Our experimental results on three real-world datasets demonstrate that our attack can effectively attack representative GNNs for graph classification with less queries and perturbations. We also evaluate the effectiveness of our attack under two defenses: one is well-designed adversarial graph detector and the other is that the target GNN model itself is equipped with a defense to prevent adversarial graph generation. Our experimental results show that such defenses are not effective enough, which highlights more advanced defenses.

Fengting Li, Xuankai Liu, Xiaoli Zhang et al.

Deep neural networks (DNNs) have been applied in a wide range of applications,e.g.,face recognition and image classification; however,they are vulnerable to adversarial examples. By adding a small amount of imperceptible perturbations,an attacker can easily manipulate the outputs of a DNN. Particularly,the localized adversarial examples only perturb a small and contiguous region of the target object,so that they are robust and effective in both digital and physical worlds. Although the localized adversarial examples have more severe real-world impacts than traditional pixel attacks,they have not been well addressed in the literature. In this paper,we propose a generic defense system called TaintRadar to accurately detect localized adversarial examples via analyzing critical regions that have been manipulated by attackers. The main idea is that when removing critical regions from input images,the ranking changes of adversarial labels will be larger than those of benign labels. Compared with existing defense solutions,TaintRadar can effectively capture sophisticated localized partial attacks, e.g.,the eye-glasses attack,while not requiring additional training or fine-tuning of the original model's structure. Comprehensive experiments have been conducted in both digital and physical worlds to verify the effectiveness and robustness of our defense.

Shu Wang, Jiahao Cao, Xu He et al.

Automatic speech recognition (ASR) systems have been widely deployed in modern smart devices to provide convenient and diverse voice-controlled services. Since ASR systems are vulnerable to audio replay attacks that can spoof and mislead ASR systems, a number of defense systems have been proposed to identify replayed audio signals based on the speakers' unique acoustic features in the frequency domain. In this paper, we uncover a new type of replay attack called modulated replay attack, which can bypass the existing frequency domain based defense systems. The basic idea is to compensate for the frequency distortion of a given electronic speaker using an inverse filter that is customized to the speaker's transform characteristics. Our experiments on real smart devices confirm the modulated replay attacks can successfully escape the existing detection mechanisms that rely on identifying suspicious features in the frequency domain. To defeat modulated replay attacks, we design and implement a countermeasure named DualGuard. We discover and formally prove that no matter how the replay audio signals could be modulated, the replay attacks will either leave ringing artifacts in the time domain or cause spectrum distortion in the frequency domain. Therefore, by jointly checking suspicious features in both frequency and time domains, DualGuard can successfully detect various replay attacks including the modulated replay attacks. We implement a prototype of DualGuard on a popular voice interactive platform, ReSpeaker Core v2. The experimental results show DualGuard can achieve 98% accuracy on detecting modulated replay attacks.