Contextual Semantic Relevance Tracks fMRI BOLD Responses During Naturalistic Speech Comprehension

Naturalistic language comprehension requires listeners to process both local probabilistic expectations and contextual semantic relations. Surprisal has been widely used to quantify local word unexpectedness, but evidence that it robustly predicts fMRI BOLD responses during continuous comprehension has been mixed. This study investigates whether contextual semantic relevance, defined as how strongly an incoming word relates to its recent semantic context, predicts BOLD responses during naturalistic speech comprehension. We analyzed two public fMRI datasets, the Alice dataset and the Moth dataset, treating them as complementary rather than identical replications. Transformed BOLD responses were modeled with generalized additive mixed models (GAMMs) and original continuous BOLD time series were tested with FIR/deconvolution analyses. In Alice, semantic relevance was significant across all 12 ROIs (region of interest), whereas surprisal was not significant after FDR correction. In Moth, semantic relevance showed consistent negative effects across all 30 ROIs, while surprisal showed no comparable pattern. These findings suggest that semantic relevance is a promising BOLD-sensitive metric of contextual semantic fit. More broadly, our findings support the view that slow hemodynamic responses during naturalistic speech comprehension may be especially sensitive to contextual semantic integration, whereas local probabilistic prediction error may be more difficult to detect reliably with fMRI. In this sense, semantic relevance extends computational models of language comprehension from prediction alone toward context-sensitive semantic integration.

Contextual Semantic Relevance and Word Surprisal Predict N400 and P600 Dynamics During Naturalistic Reading

Word surprisal is a well-established computational predictor of human neural responses during language comprehension, but it remains less clear whether local semantic fit explains neural response variation beyond lexical expectation during naturalistic reading. Using the Dublin EEG-based Reading Experiment Corpus (DERCo), this study examined whether contextual semantic relevance predicts word-locked EEG activity in the N400 and P600 windows. Contextual semantic relevance was computed as an attention-aware measure of how strongly a target word is semantically connected to its recent discourse context, and it was compared with GPT-based word surprisal. Across 22 participants and 32 EEG channels, we tested both predictors using regression-based ERP analyses and generalized additive mixed models while controlling for lexical variables and repeated observations. Both predictors were reliably associated with EEG responses, but they showed partly different temporal and scalp-level patterns. Surprisal captured expectancy-related variation, whereas contextual semantic relevance showed robust effects across N400- and P600-window mean voltages, with particularly strong explanatory support in the P600 window. Model comparisons indicated that contextual semantic relevance contributed explanatory value beyond lexical controls and surprisal. These findings suggest that naturalistic reading depends on both lexical expectation and local semantic integration, and that contextual semantic relevance offers an interpretable computational link between discourse semantic fit and ERP dynamics.

Semantic Integration and Lexical Expectation Shape N400 and P600 Dynamics During Naturalistic Reading

Word surprisal is a well-established computational predictor of human neural responses during language comprehension, but it remains less clear whether local semantic fit explains neural response variation beyond lexical expectation during naturalistic reading. Using the Dublin EEG-based Reading Experiment Corpus (DERCo), this study examined whether contextual semantic relevance predicts word-locked EEG activity in the N400 and P600 windows. Contextual semantic relevance was computed as an attention-aware measure of how strongly a target word is semantically connected to its recent discourse context, and it was compared with GPT-based word surprisal. Across 22 participants and 32 EEG channels, we tested both predictors using regression-based ERP analyses and generalized additive mixed models while controlling for lexical variables and repeated observations. Both predictors were reliably associated with EEG responses, but they showed partly different temporal and scalp-level patterns. Surprisal captured expectancy-related variation, whereas contextual semantic relevance showed robust effects across N400- and P600-window mean voltages, with particularly strong explanatory support in the P600 window. Model comparisons indicated that contextual semantic relevance contributed explanatory value beyond lexical controls and surprisal. These findings suggest that naturalistic reading depends on both lexical expectation and local semantic integration, and that contextual semantic relevance offers an interpretable computational link between discourse semantic fit and ERP dynamics.

Prior over Evidence: Stereotype-Driven Diagnosis in LLM-Based L2 Pronunciation Feedback

Large language models are increasingly deployed for written pronunciation feedback in second-language (L2) English learning, under the assumption that their diagnoses are grounded in the supplied speech evidence rather than in priors from pretraining. This assumption is tested on 1,800 L2-Arctic utterances spanning six L1 backgrounds, three audio-capable LLMs, four pronunciation dimensions, and five evidence conditions ranging from a text-only baseline to numeric acoustic features and raw audio. Each (utterance x model x condition x dimension) cell is scored on three metrics: Rating Accuracy (RA) against gold labels, Evidence Coherence (EC) assessing internal consistency without ground truth, and Grounded Correctness (GC) evaluated against gold evidence. Results show three findings across models. First, rating accuracy and grounded reasoning decouple: 39.6% of judged cells contain internally coherent reasoning that supports a wrong rating, against only 15.8% where the reasoning supports a correct rating. Second, phoneme-level feedback converges to a fixed inventory of L2-English difficulty phones that recurs across all six L1 backgrounds and all evidence conditions. Third, acoustic evidence improves the rating only when the supplied feature directly probes the target dimension: textualised F0 range raises pitch-variation grounding from (0.18-0.19) to (0.45-0.62) across all three models, while stress and phoneme correctness, which require target-to-realisation alignment, remain ungrounded. The same audio waveform without textualised F0 values does not reproduce this improvement. These findings indicate that current general-purpose LLMs are more reliable as verbalisers of externally computed pronunciation evidence than as standalone diagnostic engines.

Mimic Human Cognition, Master Multi-Image Reasoning: A Meta-Action Framework for Enhanced Visual Understanding

While Multimodal Large Language Models (MLLMs) excel at single-image understanding, they exhibit significantly degraded performance in multi-image reasoning scenarios. Multi-image reasoning presents fundamental challenges including complex inter-relationships between images and scattered critical information across image sets. Inspired by human cognitive processes, we propose the Cognition-Inspired Meta-Action Framework (CINEMA), a novel approach that decomposes multi-image reasoning into five structured meta-actions: Global, Focus, Hint, Think, and Answer which explicitly modeling the sequential cognitive steps humans naturally employ. For cold-start training, we introduce a Retrieval-Based Tree Sampling strategy that generates high-quality meta-action trajectories to bootstrap the model with reasoning patterns. During reinforcement learning, we adopt a two-stage paradigm: an exploration phase with Diversity-Preserving Strategy to avoid entropy collapse, followed by an annealed exploitation phase with DAPO to gradually strengthen exploitation. To train our model, we construct a dataset of 57k cold-start and 58k reinforcement learning instances spanning multi-image, multi-frame, and single-image tasks. We conduct extensive evaluations on multi-image reasoning benchmarks, video understanding benchmarks, and single-image benchmarks, achieving competitive state-of-the-art performance on several key benchmarks. Our model surpasses GPT-4o on the MUIR and MVMath benchmarks and notably outperforms specialized video reasoning models on video understanding benchmarks, demonstrating the effectiveness and generalizability of our human cognition-inspired reasoning framework.

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.