Systematic Framework of Application Methods for Large Language Models in Language Sciences

Large Language Models (LLMs) are transforming language sciences. However, their widespread deployment currently suffers from methodological fragmentation and a lack of systematic soundness. This study proposes two comprehensive methodological frameworks designed to guide the strategic and responsible application of LLMs in language sciences. The first method-selection framework defines and systematizes three distinct, complementary approaches, each linked to a specific research goal: (1) prompt-based interaction with general-use models for exploratory analysis and hypothesis generation; (2) fine-tuning of open-source models for confirmatory, theory-driven investigation and high-quality data generation; and (3) extraction of contextualized embeddings for further quantitative analysis and probing of model internal mechanisms. We detail the technical implementation and inherent trade-offs of each method, supported by empirical case studies. Based on the method-selection framework, the second systematic framework proposed provides constructed configurations that guide the practical implementation of multi-stage research pipelines based on these approaches. We then conducted a series of empirical experiments to validate our proposed framework, employing retrospective analysis, prospective application, and an expert evaluation survey. By enforcing the strategic alignment of research questions with the appropriate LLM methodology, the frameworks enable a critical paradigm shift in language science research. We believe that this system is fundamental for ensuring reproducibility, facilitating the critical evaluation of LLM mechanisms, and providing the structure necessary to move traditional linguistics from ad-hoc utility to verifiable, robust science.

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.

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.

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.

A Knowledge-enhanced Pathology Vision-language Foundation Model for Cancer Diagnosis

Deep learning has enabled the development of highly robust foundation models for various pathological tasks across diverse diseases and patient cohorts. Among these models, vision-language pre-training, which leverages large-scale paired data to align pathology image and text embedding spaces, and provides a novel zero-shot paradigm for downstream tasks. However, existing models have been primarily data-driven and lack the incorporation of domain-specific knowledge, which limits their performance in cancer diagnosis, especially for rare tumor subtypes. To address this limitation, we establish a Knowledge-enhanced Pathology (KEEP) foundation model that harnesses disease knowledge to facilitate vision-language pre-training. Specifically, we first construct a disease knowledge graph (KG) that covers 11,454 human diseases with 139,143 disease attributes, including synonyms, definitions, and hypernym relations. We then systematically reorganize the millions of publicly available noisy pathology image-text pairs, into 143K well-structured semantic groups linked through the hierarchical relations of the disease KG. To derive more nuanced image and text representations, we propose a novel knowledge-enhanced vision-language pre-training approach that integrates disease knowledge into the alignment within hierarchical semantic groups instead of unstructured image-text pairs. Validated on 18 diverse benchmarks with more than 14,000 whole slide images (WSIs), KEEP achieves state-of-the-art performance in zero-shot cancer diagnostic tasks. Notably, for cancer detection, KEEP demonstrates an average sensitivity of 89.8% at a specificity of 95.0% across 7 cancer types. For cancer subtyping, KEEP achieves a median balanced accuracy of 0.456 in subtyping 30 rare brain cancers, indicating strong generalizability for diagnosing rare tumors.

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.

A Pipeline of Neural-Symbolic Integration to Enhance Spatial Reasoning in Large Language Models

Large Language Models (LLMs) have demonstrated impressive capabilities across various tasks. However, LLMs often struggle with spatial reasoning which is one essential part of reasoning and inference and requires understanding complex relationships between objects in space. This paper proposes a novel neural-symbolic framework that enhances LLMs' spatial reasoning abilities. We evaluate our approach on two benchmark datasets: StepGame and SparQA, implementing three distinct strategies: (1) ASP (Answer Set Programming)-based symbolic reasoning, (2) LLM + ASP pipeline using DSPy, and (3) Fact + Logical rules. Our experiments demonstrate significant improvements over the baseline prompting methods, with accuracy increases of 40-50% on StepGame} dataset and 3-13% on the more complex SparQA dataset. The "LLM + ASP" pipeline achieves particularly strong results on the tasks of Finding Relations (FR) and Finding Block (FB) questions, though performance varies across different question types. The impressive results suggest that while neural-symbolic approaches offer promising directions for enhancing spatial reasoning in LLMs, their effectiveness depends heavily on the specific task characteristics and implementation strategies. We propose an integrated, simple yet effective set of strategies using a neural-symbolic pipeline to boost spatial reasoning abilities in LLMs. This pipeline and its strategies demonstrate strong and broader applicability to other reasoning domains in LLMs, such as temporal reasoning, deductive inference etc.

AuscultaBase: A Foundational Step Towards AI-Powered Body Sound Diagnostics

Auscultation of internal body sounds is essential for diagnosing a range of health conditions, yet its effectiveness is often limited by clinicians' expertise and the acoustic constraints of human hearing, restricting its use across various clinical scenarios. To address these challenges, we introduce AuscultaBase, a foundational framework aimed at advancing body sound diagnostics through innovative data integration and contrastive learning techniques. Our contributions include the following: First, we compile AuscultaBase-Corpus, a large-scale, multi-source body sound database encompassing 11 datasets with 40,317 audio recordings and totaling 322.4 hours of heart, lung, and bowel sounds. Second, we develop AuscultaBase-Model, a foundational diagnostic model for body sounds, utilizing contrastive learning on the compiled corpus. Third, we establish AuscultaBase-Bench, a comprehensive benchmark containing 16 sub-tasks, assessing the performance of various open-source acoustic pre-trained models. Evaluation results indicate that our model outperforms all other open-source models in 12 out of 16 tasks, demonstrating the efficacy of our approach in advancing diagnostic capabilities for body sound analysis.

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.

Towards Fine-Grained Webpage Fingerprinting at Scale

Website Fingerprinting (WF) attacks can effectively identify the websites visited by Tor clients via analyzing encrypted traffic patterns. Existing attacks focus on identifying different websites, but their accuracy dramatically decreases when applied to identify fine-grained webpages, especially when distinguishing among different subpages of the same website. WebPage Fingerprinting (WPF) attacks face the challenges of highly similar traffic patterns and a much larger scale of webpages. Furthermore, clients often visit multiple webpages concurrently, increasing the difficulty of extracting the traffic patterns of each webpage from the obfuscated traffic. In this paper, we propose Oscar, a WPF attack based on multi-label metric learning that identifies different webpages from obfuscated traffic by transforming the feature space. Oscar can extract the subtle differences among various webpages, even those with similar traffic patterns. In particular, Oscar combines proxy-based and sample-based metric learning losses to extract webpage features from obfuscated traffic and identify multiple webpages. We prototype Oscar and evaluate its performance using traffic collected from 1,000 monitored webpages and over 9,000 unmonitored webpages in the real world. Oscar demonstrates an 88.6% improvement in the multi-label metric Recall@5 compared to the state-of-the-art attacks.