OpenRaiser/Intern-Atlas huggingface dataset:
Cross-Stain Contrastive Learning for Paired Immunohistochemistry and Histopathology Slide Representation Learning
Venue: arXiv cs.CV 2025
Year: 2025

Universal, transferable whole-slide image (WSI) representations are central to computational pathology. Incorporating multiple markers (e.g., immunohistochemistry, IHC) alongside H&E enriches H&E-based features with diverse, biologically meaningful information. However, progress is limited by the scarcity of well-aligned multi-stain datasets. Inter-stain misalignment shifts corresponding tissue across slides, hindering consistent patch-level features and degrading slide-level embeddings. To address this, we curated a slide-level aligned, five-stain dataset (H&E, HER2, KI67, ER, PGR) to enable paired H&E-IHC learning and robust cross-stain representation. Leveraging this dataset, we propose Cross-Stain Contrastive Learning (CSCL), a two-stage pretraining framework with a lightweight adapter trained using patch-wise contrastive alignment to improve the compatibility of H&E features with corresponding IHC-derived contextual cues, and slide-level representation learning with Multiple Instance Learning (MIL), which uses a cross-stain attention fusion module to integrate stain-specific patch features and a cross-stain global alignment module to enforce consistency among slide-level embeddings across different stains. Experiments on cancer subtype classification, IHC biomarker status classification, and survival prediction show consistent gains, yielding high-quality, transferable H&E slide-level representations. The code and data are available at https://github.com/lily-zyz/CSCL.
Dynamic Optical Test for Bot Identification (DOT-BI): A simple check to identify bots in surveys and online processes
Venue: arXiv cs.CV 2025
Year: 2025

We propose the Dynamic Optical Test for Bot Identification (DOT-BI): a quick and easy method that uses human perception of motion to differentiate between human respondents and automated systems in surveys and online processes. In DOT-BI, a 'hidden' number is displayed with the same random black-and-white pixel texture as its background. Only the difference in motion and scale between the number and the background makes the number perceptible to humans across frames, while frame-by-frame algorithmic processing yields no meaningful signal. We conducted two preliminary assessments. Firstly, state-of-the-art, video-capable, multimodal models (GPT-5-Thinking and Gemini 2.5 Pro) fail to extract the correct value, even when given explicit instructions about the mechanism. Secondly, in an online survey (n=182), 99.5% (181/182) of participants solved the task, with an average end-to-end completion time of 10.7 seconds; a supervised lab study (n=39) found no negative effects on perceived ease-of-use or completion time relative to a control. We release code to generate tests and 100+ pre-rendered variants to facilitate adoption in surveys and online processes.
Harnessing Hypergraphs in Geometric Deep Learning for 3D RNA Inverse Folding
Venue: arXiv cs.CV 2025
Year: 2025

The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent complexity of this task stems from the intricate relationship between sequence and structure, making it particularly challenging. In this paper, we propose a framework, named HyperRNA, a generative model with an encoder-decoder architecture that leverages hypergraphs to design RNA sequences. Specifically, our HyperRNA model consists of three main components: preprocessing, encoding and decoding. In the preprocessing stage, graph structures are constructed by extracting the atom coordinates of RNA backbone based on 3-bead coarse-grained representation. The encoding stage processes these graphs, capturing higher order dependencies and complex biomolecular interactions using an attention embedding module and a hypergraph-based encoder. Finally, the decoding stage generates the RNA sequence in an autoregressive manner. We conducted quantitative and qualitative experiments on the PDBBind and RNAsolo datasets to evaluate the inverse folding task for RNA sequence generation and RNA-protein complex sequence generation. The experimental results demonstrate that HyperRNA not only outperforms existing RNA design methods but also highlights the potential of leveraging hypergraphs in RNA engineering.
Lightweight Unified Sha-3/Shake Architecture with a Fault-Resilient State
Venue: arXiv cs.AR 2025
Year: 2025

Hash functions have become a key part of standard Post-quantum cryptography (PQC) schemes, especially Sha-3 and Shake, calling arXiv:submit/7045552 [cs.AR] 3 Dec 2025 for lightweight implementation. A fault-resilient design is always desirable to make the whole PQC system reliable. We, therefore, propose a) a unified hash engine supporting Sha-3 and Shake that follows a byte-wise in-place partitioning mechanism of the so-called Keccak state, and b) an according fault detection for Keccak state protection exploiting its cube structure by deploying two-dimensional parity checks. It outperforms the state-of-the-art (SoA) regarding area requirements at competitive register-level fault detection by achieving 100% detection of three and still near 100% of higher numbers of Keccak state faults. Unlike SoA solutions, the proposed unified hash engine covers all standard hash configurations. Moreover, the introduced multidimensional cross-parity check mechanism achieves a 3.7x improvement in area overhead, with an overall 4.5x smaller fault-resilient engine design as demonstrated in ASIC and FPGA implementations. Integrated into a RISC-V environment, the unified hash engine with the integrated fault-resilient mechanism introduced less than 8% area overhead. Our approach thus provides a robust and lightweight fault-detection solution for protecting hash functions deployed in resource-constrained PQC applications.
LAMP: Language-Assisted Motion Planning for Controllable Video Generation
Venue: arXiv cs.CV 2025
Year: 2025

Video generation has achieved remarkable progress in visual fidelity and controllability, enabling conditioning on text, layout, or motion. Among these, motion control - specifying object dynamics and camera trajectories - is essential for composing complex, cinematic scenes, yet existing interfaces remain limited. We introduce LAMP that leverages large language models (LLMs) as motion planners to translate natural language descriptions into explicit 3D trajectories for dynamic objects and (relatively defined) cameras. LAMP defines a motion domain-specific language (DSL), inspired by cinematography conventions. By harnessing program synthesis capabilities of LLMs, LAMP generates structured motion programs from natural language, which are deterministically mapped to 3D trajectories. We construct a large-scale procedural dataset pairing natural text descriptions with corresponding motion programs and 3D trajectories. Experiments demonstrate LAMP's improved performance in motion controllability and alignment with user intent compared to state-of-the-art alternatives establishing the first framework for generating both object and camera motions directly from natural language specifications. Code, models and data are available on our project page.
A Descriptive Model for Modelling Attacker Decision-Making in Cyber-Deception
Venue: arXiv cs.CR 2025
Year: 2025

Cyber-deception is an increasingly important defensive strategy, shaping adversarial decision making through controlled misinformation, uncertainty, and misdirection. Although game-theoretic, Bayesian, Markov decision process, and reinforcement learning models offer insight into deceptive interactions, they typically assume an attacker has already chosen to engage. Such approaches overlook cognitive and perceptual factors that influence an attacker's initial decision to engage or withdraw. This paper presents a descriptive model that incorporates the psychological and strategic elements shaping this decision. The model defines five components, belief (B), scepticism (S), deception fidelity (D), reconnaissance (R), and experience (E), which interact to capture how adversaries interpret deceptive cues and assess whether continued engagement is worthwhile. The framework provides a structured method for analysing engagement decisions in cyber-deception scenarios. A series of experiments has been designed to evaluate this model through Capture the Flag activities incorporating varying levels of deception, supported by behavioural and biometric observations. These experiments have not yet been conducted, and no experimental findings are presented in this paper. These experiments will combine behavioural observations with biometric indicators to produce a multidimensional view of adversarial responses. Findings will improve understanding of the factors influencing engagement decisions and refine the model's relevance to real-world cyber-deception settings. By addressing the gap in existing models that presume engagement, this work supports more cognitively realistic and strategically effective cyber-deception practices.
Colon-X: Advancing Intelligent Colonoscopy from Multimodal Understanding to Clinical Reasoning
Venue: arXiv cs.CV 2025
Year: 2025

In this study, we present Colon-X, an open initiative aimed at advancing multimodal intelligence in colonoscopy. We begin by constructing ColonVQA, the most comprehensive multimodal dataset ever built for colonoscopy, featuring over 1.1M+ visual question answering entries across 76 clinical findings and 18 multimodal tasks. Beyond serving as a community-wide data foundation, we further investigate a critical yet underexplored transition in colonoscopy - evolving from multimodal understanding to clinical reasoning: (a) To capture the current landscape of multimodal understanding behaviors, we systematically assess the generalizability of 22 multimodal large language models and examine their reliability under human-induced perturbations. The results reveal that clinical outputs from leading MLLMs remain far from robust and trustworthy. (b) To narrow this gap, we further explore reasoning-centric intelligence tailored for colonoscopy. Specifically, we curate ColonReason, a clinically grounded reasoning dataset annotated through a multi-expert debating pipeline, and develop ColonR1, the first R1-styled model incorporating task-adaptive rewarding and gradient-stable optimization techniques. Under data-scarce conditions, our ColonR1 achieves 56.61% overall accuracy, outperforming supervised fine-tuning by 25.22%, and sets a new reasoning-enabled baseline for multimodal colonoscopy analysis. All data and model resources are publicly available at https://github.com/ai4colonoscopy/Colon-X.
AR-Med: Automated Relevance Enhancement in Medical Search via LLM-Driven Information Augmentation
Venue: arXiv cs.CL 2025
Year: 2025

Accurate and reliable search on online healthcare platforms is critical for user safety and service efficacy. Traditional methods, however, often fail to comprehend complex and nuanced user queries, limiting their effectiveness. Large language models (LLMs) present a promising solution, offering powerful semantic understanding to bridge this gap. Despite their potential, deploying LLMs in this high-stakes domain is fraught with challenges, including factual hallucinations, specialized knowledge gaps, and high operational costs. To overcome these barriers, we introduce \textbf{AR-Med}, a novel framework for \textbf{A}utomated \textbf{R}elevance assessment for \textbf{Med}ical search that has been successfully deployed at scale on the Online Medical Delivery Platforms. AR-Med grounds LLM reasoning in verified medical knowledge through a retrieval-augmented approach, ensuring high accuracy and reliability. To enable efficient online service, we design a practical knowledge distillation scheme that compresses large teacher models into compact yet powerful student models. We also introduce LocalQSMed, a multi-expert annotated benchmark developed to guide model iteration and ensure strong alignment between offline and online performance. Extensive experiments show AR-Med achieves an offline accuracy of over 93\%, a 24\% absolute improvement over the original online system, and delivers significant gains in online relevance and user satisfaction. Our work presents a practical and scalable blueprint for developing trustworthy, LLM-powered systems in real-world healthcare applications.
Fully Unsupervised Self-debiasing of Text-to-Image Diffusion Models
Venue: arXiv cs.CV 2025
Year: 2025

Text-to-image (T2I) diffusion models have achieved widespread success due to their ability to generate high-resolution, photorealistic images. These models are trained on large-scale datasets, like LAION-5B, often scraped from the internet. However, since this data contains numerous biases, the models inherently learn and reproduce them, resulting in stereotypical outputs. We introduce SelfDebias, a fully unsupervised test-time debiasing method applicable to any diffusion model that uses a UNet as its noise predictor. SelfDebias identifies semantic clusters in an image encoder's embedding space and uses these clusters to guide the diffusion process during inference, minimizing the KL divergence between the output distribution and the uniform distribution. Unlike supervised approaches, SelfDebias does not require human-annotated datasets or external classifiers trained for each generated concept. Instead, it is designed to automatically identify semantic modes. Extensive experiments show that SelfDebias generalizes across prompts and diffusion model architectures, including both conditional and unconditional models. It not only effectively debiases images along key demographic dimensions while maintaining the visual fidelity of the generated images, but also more abstract concepts for which identifying biases is also challenging.
Universally Converging Representations of Matter Across Scientific Foundation Models
Venue: arXiv cs.LG 2025
Year: 2025

Machine learning models of vastly different modalities and architectures are being trained to predict the behavior of molecules, materials, and proteins. However, it remains unclear whether they learn similar internal representations of matter. Understanding their latent structure is essential for building scientific foundation models that generalize reliably beyond their training domains. Although representational convergence has been observed in language and vision, its counterpart in the sciences has not been systematically explored. Here, we show that representations learned by nearly sixty scientific models, spanning string-, graph-, 3D atomistic, and protein-based modalities, are highly aligned across a wide range of chemical systems. Models trained on different datasets have highly similar representations of small molecules, and machine learning interatomic potentials converge in representation space as they improve in performance, suggesting that foundation models learn a common underlying representation of physical reality. We then show two distinct regimes of scientific models: on inputs similar to those seen during training, high-performing models align closely and weak models diverge into local sub-optima in representation space; on vastly different structures from those seen during training, nearly all models collapse onto a low-information representation, indicating that today's models remain limited by training data and inductive bias and do not yet encode truly universal structure. Our findings establish representational alignment as a quantitative benchmark for foundation-level generality in scientific models. More broadly, our work can track the emergence of universal representations of matter as models scale, and for selecting and distilling models whose learned representations transfer best across modalities, domains of matter, and scientific tasks.
Research on Brain Tumor Classification Method Based on Improved ResNet34 Network
Venue: arXiv cs.CV 2025
Year: 2025

Previously, image interpretation in radiology relied heavily on manual methods. However, manual classification of brain tumor medical images is time-consuming and labor-intensive. Even with shallow convolutional neural network models, the accuracy is not ideal. To improve the efficiency and accuracy of brain tumor image classification, this paper proposes a brain tumor classification model based on an improved ResNet34 network. This model uses the ResNet34 residual network as the backbone network and incorporates multi-scale feature extraction. It uses a multi-scale input module as the first layer of the ResNet34 network and an Inception v2 module as the residual downsampling layer. Furthermore, a channel attention mechanism module assigns different weights to different channels of the image from a channel domain perspective, obtaining more important feature information. The results after a five-fold crossover experiment show that the average classification accuracy of the improved network model is approximately 98.8%, which is not only 1% higher than ResNet34, but also only 80% of the number of parameters of the original model. Therefore, the improved network model not only improves accuracy but also reduces clutter, achieving a classification effect with fewer parameters and higher accuracy.
In-Context Representation Hijacking
Venue: arXiv cs.CL 2025
Year: 2025

We introduce $\textbf{Doublespeak}$, a simple in-context representation hijacking attack against large language models (LLMs). The attack works by systematically replacing a harmful keyword (e.g., bomb) with a benign token (e.g., carrot) across multiple in-context examples, provided a prefix to a harmful request. We demonstrate that this substitution leads to the internal representation of the benign token converging toward that of the harmful one, effectively embedding the harmful semantics under a euphemism. As a result, superficially innocuous prompts (e.g., "How to build a carrot?") are internally interpreted as disallowed instructions (e.g., "How to build a bomb?"), thereby bypassing the model's safety alignment. We use interpretability tools to show that this semantic overwrite emerges layer by layer, with benign meanings in early layers converging into harmful semantics in later ones. Doublespeak is optimization-free, broadly transferable across model families, and achieves strong success rates on closed-source and open-source systems, reaching 74% ASR on Llama-3.3-70B-Instruct with a single-sentence context override. Our findings highlight a new attack surface in the latent space of LLMs, revealing that current alignment strategies are insufficient and should instead operate at the representation level.
"MCP Does Not Stand for Misuse Cryptography Protocol": Uncovering Cryptographic Misuse in Model Context Protocol at Scale
Venue: arXiv cs.CR 2025
Year: 2025

The Model Context Protocol (MCP) is rapidly emerging as the middleware for LLM-based applications, offering a standardized interface for tool integration. However, its built-in security mechanisms are minimal: while schemas and declarations prevent malformed requests, MCP provides no guarantees of authenticity or confidentiality, forcing developers to implement cryptography themselves. Such ad hoc practices are historically prone to misuse, and within MCP they threaten sensitive data and services. We present MICRYSCOPE, the first domain-specific framework for detecting cryptographic misuses in MCP implementations. MICRYSCOPE combines three key innovations: a cross-language intermediate representation that normalizes cryptographic APIs across diverse ecosystems, a hybrid dependency analysis that uncovers explicit and implicit function relationships (including insecure runtime compositions orchestrated by LLMs) and a taint-based misuse detector that tracks sensitive data flows and flags violations of established cryptographic rules. Applying MICRYSCOPE to 9,403 MCP servers, we identified 720 with cryptographic logic, of which 19.7% exhibited misuses. These flaws are concentrated in certain markets (e.g., Smithery Registry with 42% insecure servers), languages (Python at 34% misuse rate), and categories (Developer Tools and Data Science & ML accounting for over 50% of all misuses). Case studies reveal real-world consequences, including leaked API keys, insecure DES/ECB tools, and MD5-based authentication bypasses. Our study establishes the first ecosystem-wide view of cryptographic misuse in MCP and provides both tools and insights to strengthen the security foundations of this rapidly growing protocol.
CCN: Decentralized Cross-Chain Channel Networks Supporting Secure and Privacy-Preserving Multi-Hop Interactions
Venue: arXiv cs.CR 2025
Year: 2025

Cross-chain technology enables interoperability among otherwise isolated blockchains, supporting interactions across heterogeneous networks. Similar to how multi-hop communication became fundamental in the evolution of the Internet, the demand for multi-hop cross-chain interactions is gaining increasing attention. However, this growing demand introduces new security and privacy challenges. On the security side, multi-hop interactions depend on the availability of multiple participating nodes. If any node becomes temporarily offline during execution, the protocol may fail to complete correctly, leading to settlement failure or fund loss. On the privacy side, the need for on-chain transparency to validate intermediate states may unintentionally leak linkable information, compromising the unlinkability of user interactions. In this paper, we propose the Cross-Chain Channel Network (CCN), a decentralized network designed to support secure and privacy-preserving multi-hop cross-chain transactions. Through experimental evaluation, we identify two critical types of offline failures, referred to as active and passive offline cases, which have not been adequately addressed by existing solutions. To mitigate these issues, we introduce R-HTLC, a core protocol within CCN. R-HTLC incorporates an hourglass mechanism and a multi-path refund strategy to ensure settlement correctness even when some nodes go offline during execution. Importantly, CCN addresses not only the correctness under offline conditions but also maintains unlinkability in such adversarial settings. To overcome this, CCN leverages zero-knowledge proofs and off-chain coordination, ensuring that interaction relationships remain indistinguishable even when certain nodes are temporarily offline.
Unfolding Challenges in Securing and Regulating Unmanned Air Vehicles
Venue: arXiv cs.CR 2025
Year: 2025

Unmanned Aerial Vehicles (UAVs) or drones are being introduced in a wide range of commercial applications. This has also made them prime targets of attackers who compromise their fundamental security properties, including confidentiality, integrity, and availability. As researchers discover novel threat vectors in UAVs, the government and industry are increasingly concerned about their limited ability to secure and regulate UAVs and their usage. With the aim of unfolding a path for a large-scale commercial UAV network deployment, we conduct a comprehensive state-of-the-art study and examine the prevailing security challenges. Unlike the prior art, we focus on uncovering the research gaps that must be addressed to enforce security policy regulations in civilian off-the-shelf drone systems. To that end, we first examine the known security threats to UAVs based on their impact and effectiveness. We then analyze existing countermeasures to prevent, detect, and respond to these threats in terms of security and performance overhead. We further outline the future research directions for securing UAVs. Finally, we establish the fundamental requirements and highlight critical research challenges in introducing a regulatory entity to achieve a secure and regulated UAV network.