SemanticST: Spatially Informed Semantic Graph Learning for Clustering, Integration, and Scalable Analysis of Spatial Transcriptomics

Spatial transcriptomics (ST) technologies enable gene expression profiling with spatial resolution, offering unprecedented insights into tissue organization and disease heterogeneity. However, current analysis methods often struggle with noisy data, limited scalability, and inadequate modelling of complex cellular relationships. We present SemanticST, a biologically informed, graph-based deep learning framework that models diverse cellular contexts through multi-semantic graph construction. SemanticST builds multiple context-specific graphs capturing spatial proximity, gene expression similarity, and tissue domain structure, and learns disentangled embeddings for each. These are fused using an attention-inspired strategy to yield a unified, biologically meaningful representation. A community-aware min-cut loss improves robustness over contrastive learning, particularly in sparse ST data. SemanticST supports mini-batch training, making it the first graph neural network scalable to large-scale datasets such as Xenium (500,000 cells). Benchmarking across four platforms (Visium, Slide-seq, Stereo-seq, Xenium) and multiple human and mouse tissues shows consistent 20 percentage gains in ARI, NMI, and trajectory fidelity over DeepST, GraphST, and IRIS. In re-analysis of breast cancer Xenium data, SemanticST revealed rare and clinically significant niches, including triple receptor-positive clusters, spatially distinct DCIS-to-IDC transition zones, and FOXC2 tumour-associated myoepithelial cells, suggesting non-canonical EMT programs with stem-like features. SemanticST thus provides a scalable, interpretable, and biologically grounded framework for spatial transcriptomics analysis, enabling robust discovery across tissue types and diseases, and paving the way for spatially resolved tissue atlases and next-generation precision medicine.

Training Superior Sparse Autoencoders for Instruct Models

As large language models (LLMs) grow in scale and capability, understanding their internal mechanisms becomes increasingly critical. Sparse autoencoders (SAEs) have emerged as a key tool in mechanistic interpretability, enabling the extraction of human-interpretable features from LLMs. However, existing SAE training methods are primarily designed for base models, resulting in reduced reconstruction quality and interpretability when applied to instruct models. To bridge this gap, we propose $\underline{\textbf{F}}$inetuning-$\underline{\textbf{a}}$ligned $\underline{\textbf{S}}$equential $\underline{\textbf{T}}$raining ($\textit{FAST}$), a novel training method specifically tailored for instruct models. $\textit{FAST}$ aligns the training process with the data distribution and activation patterns characteristic of instruct models, resulting in substantial improvements in both reconstruction and feature interpretability. On Qwen2.5-7B-Instruct, $\textit{FAST}$ achieves a mean squared error of 0.6468 in token reconstruction, significantly outperforming baseline methods with errors of 5.1985 and 1.5096. In feature interpretability, $\textit{FAST}$ yields a higher proportion of high-quality features, for Llama3.2-3B-Instruct, $21.1\%$ scored in the top range, compared to $7.0\%$ and $10.2\%$ for $\textit{BT(P)}$ and $\textit{BT(F)}$. Surprisingly, we discover that intervening on the activations of special tokens via the SAEs leads to improvements in output quality, suggesting new opportunities for fine-grained control of model behavior. Code, data, and 240 trained SAEs are available at https://github.com/Geaming2002/FAST.

CLaSp: In-Context Layer Skip for Self-Speculative Decoding

Speculative decoding (SD) is a promising method for accelerating the decoding process of Large Language Models (LLMs). The efficiency of SD primarily hinges on the consistency between the draft model and the verify model. However, existing drafting approaches typically require additional modules to be trained, which can be challenging to implement and ensure compatibility across various LLMs. In this paper, we propose CLaSp, an in-context layer-skipping strategy for self-speculative decoding. Unlike prior methods, CLaSp does not require additional drafting modules or extra training. Instead, it employs a plug-and-play mechanism by skipping intermediate layers of the verify model to construct a compressed draft model. Specifically, we develop a dynamic programming algorithm that optimizes the layer-skipping process by leveraging the complete hidden states from the last verification stage as an objective. This enables CLaSp to dynamically adjust its layer-skipping strategy after each verification stage, without relying on pre-optimized sets of skipped layers. Experimental results across diverse downstream tasks demonstrate that CLaSp achieves a speedup of 1.3x ~ 1.7x on LLaMA3 series models without altering the original distribution of the generated text.

ChARM: Character-based Act-adaptive Reward Modeling for Advanced Role-Playing Language Agents

Role-Playing Language Agents (RPLAs) aim to simulate characters for realistic and engaging human-computer interactions. However, traditional reward models often struggle with scalability and adapting to subjective conversational preferences. We propose ChARM, a Character-based Act-adaptive Reward Model, addressing these challenges through two innovations: (1) an act-adaptive margin that significantly enhances learning efficiency and generalizability, and (2) a self-evolution mechanism leveraging large-scale unlabeled data to improve training coverage. Additionally, we introduce RoleplayPref, the first large-scale preference dataset specifically for RPLAs, featuring 1,108 characters, 13 subcategories, and 16,888 bilingual dialogues, alongside RoleplayEval, a dedicated evaluation benchmark. Experimental results show a 13% improvement over the conventional Bradley-Terry model in preference rankings. Furthermore, applying ChARM-generated rewards to preference learning techniques (e.g., direct preference optimization) achieves state-of-the-art results on CharacterEval and RoleplayEval. Code and dataset are available at https://github.com/calubkk/ChARM.

EVADE: Multimodal Benchmark for Evasive Content Detection in E-Commerce Applications

E-commerce platforms increasingly rely on Large Language Models (LLMs) and Vision-Language Models (VLMs) to detect illicit or misleading product content. However, these models remain vulnerable to evasive content: inputs (text or images) that superficially comply with platform policies while covertly conveying prohibited claims. Unlike traditional adversarial attacks that induce overt failures, evasive content exploits ambiguity and context, making it far harder to detect. Existing robustness benchmarks provide little guidance for this demanding, real-world challenge. We introduce EVADE, the first expert-curated, Chinese, multimodal benchmark specifically designed to evaluate foundation models on evasive content detection in e-commerce. The dataset contains 2,833 annotated text samples and 13,961 images spanning six demanding product categories, including body shaping, height growth, and health supplements. Two complementary tasks assess distinct capabilities: Single-Violation, which probes fine-grained reasoning under short prompts, and All-in-One, which tests long-context reasoning by merging overlapping policy rules into unified instructions. Notably, the All-in-One setting significantly narrows the performance gap between partial and full-match accuracy, suggesting that clearer rule definitions improve alignment between human and model judgment. We benchmark 26 mainstream LLMs and VLMs and observe substantial performance gaps: even state-of-the-art models frequently misclassify evasive samples. By releasing EVADE and strong baselines, we provide the first rigorous standard for evaluating evasive-content detection, expose fundamental limitations in current multimodal reasoning, and lay the groundwork for safer and more transparent content moderation systems in e-commerce. The dataset is publicly available at https://huggingface.co/datasets/koenshen/EVADE-Bench.

Enhancing Monte Carlo Dropout Performance for Uncertainty Quantification

Knowing the uncertainty associated with the output of a deep neural network is of paramount importance in making trustworthy decisions, particularly in high-stakes fields like medical diagnosis and autonomous systems. Monte Carlo Dropout (MCD) is a widely used method for uncertainty quantification, as it can be easily integrated into various deep architectures. However, conventional MCD often struggles with providing well-calibrated uncertainty estimates. To address this, we introduce innovative frameworks that enhances MCD by integrating different search solutions namely Grey Wolf Optimizer (GWO), Bayesian Optimization (BO), and Particle Swarm Optimization (PSO) as well as an uncertainty-aware loss function, thereby improving the reliability of uncertainty quantification. We conduct comprehensive experiments using different backbones, namely DenseNet121, ResNet50, and VGG16, on various datasets, including Cats vs. Dogs, Myocarditis, Wisconsin, and a synthetic dataset (Circles). Our proposed algorithm outperforms the MCD baseline by 2-3% on average in terms of both conventional accuracy and uncertainty accuracy while achieving significantly better calibration. These results highlight the potential of our approach to enhance the trustworthiness of deep learning models in safety-critical applications.

Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

IPBench: Benchmarking the Knowledge of Large Language Models in Intellectual Property

Intellectual Property (IP) is a unique domain that integrates technical and legal knowledge, making it inherently complex and knowledge-intensive. As large language models (LLMs) continue to advance, they show great potential for processing IP tasks, enabling more efficient analysis, understanding, and generation of IP-related content. However, existing datasets and benchmarks either focus narrowly on patents or cover limited aspects of the IP field, lacking alignment with real-world scenarios. To bridge this gap, we introduce the first comprehensive IP task taxonomy and a large, diverse bilingual benchmark, IPBench, covering 8 IP mechanisms and 20 tasks. This benchmark is designed to evaluate LLMs in real-world intellectual property applications, encompassing both understanding and generation. We benchmark 16 LLMs, ranging from general-purpose to domain-specific models, and find that even the best-performing model achieves only 75.8% accuracy, revealing substantial room for improvement. Notably, open-source IP and law-oriented models lag behind closed-source general-purpose models. We publicly release all data and code of IPBench and will continue to update it with additional IP-related tasks to better reflect real-world challenges in the intellectual property domain.

xJailbreak: Representation Space Guided Reinforcement Learning for Interpretable LLM Jailbreaking

Safety alignment mechanism are essential for preventing large language models (LLMs) from generating harmful information or unethical content. However, cleverly crafted prompts can bypass these safety measures without accessing the model's internal parameters, a phenomenon known as black-box jailbreak. Existing heuristic black-box attack methods, such as genetic algorithms, suffer from limited effectiveness due to their inherent randomness, while recent reinforcement learning (RL) based methods often lack robust and informative reward signals. To address these challenges, we propose a novel black-box jailbreak method leveraging RL, which optimizes prompt generation by analyzing the embedding proximity between benign and malicious prompts. This approach ensures that the rewritten prompts closely align with the intent of the original prompts while enhancing the attack's effectiveness. Furthermore, we introduce a comprehensive jailbreak evaluation framework incorporating keywords, intent matching, and answer validation to provide a more rigorous and holistic assessment of jailbreak success. Experimental results show the superiority of our approach, achieving state-of-the-art (SOTA) performance on several prominent open and closed-source LLMs, including Qwen2.5-7B-Instruct, Llama3.1-8B-Instruct, and GPT-4o-0806. Our method sets a new benchmark in jailbreak attack effectiveness, highlighting potential vulnerabilities in LLMs. The codebase for this work is available at https://github.com/Aegis1863/xJailbreak.

OpenOmni: Large Language Models Pivot Zero-shot Omnimodal Alignment across Language with Real-time Self-Aware Emotional Speech Synthesis

Recent advancements in omnimodal learning have been achieved in understanding and generation across images, text, and speech, though mainly within proprietary models. Limited omnimodal datasets and the inherent challenges associated with real-time emotional speech generation have hindered open-source progress. To address these issues, we propose openomni, a two-stage training method combining omnimodal alignment and speech generation to develop a state-of-the-art omnimodal large language model. In the alignment phase, a pre-trained speech model is further trained on text-image tasks to generalize from vision to speech in a (near) zero-shot manner, outperforming models trained on tri-modal datasets. In the speech generation phase, a lightweight decoder facilitates real-time emotional speech through training on speech tasks and preference learning. Experiments demonstrate that openomni consistently improves across omnimodal, vision-language, and speech-language evaluations, enabling natural, emotion-rich dialogues and real-time emotional speech generation.