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Aug 6

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.

Autoregressive Images Watermarking through Lexical Biasing: An Approach Resistant to Regeneration Attack

Autoregressive (AR) image generation models have gained increasing attention for their breakthroughs in synthesis quality, highlighting the need for robust watermarking to prevent misuse. However, existing in-generation watermarking techniques are primarily designed for diffusion models, where watermarks are embedded within diffusion latent states. This design poses significant challenges for direct adaptation to AR models, which generate images sequentially through token prediction. Moreover, diffusion-based regeneration attacks can effectively erase such watermarks by perturbing diffusion latent states. To address these challenges, we propose Lexical Bias Watermarking (LBW), a novel framework designed for AR models that resists regeneration attacks. LBW embeds watermarks directly into token maps by biasing token selection toward a predefined green list during generation. This approach ensures seamless integration with existing AR models and extends naturally to post-hoc watermarking. To increase the security against white-box attacks, instead of using a single green list, the green list for each image is randomly sampled from a pool of green lists. Watermark detection is performed via quantization and statistical analysis of the token distribution. Extensive experiments demonstrate that LBW achieves superior watermark robustness, particularly in resisting regeneration attacks.

CRISP: Clustering Multi-Vector Representations for Denoising and Pruning

Multi-vector models, such as ColBERT, are a significant advancement in neural information retrieval (IR), delivering state-of-the-art performance by representing queries and documents by multiple contextualized token-level embeddings. However, this increased representation size introduces considerable storage and computational overheads which have hindered widespread adoption in practice. A common approach to mitigate this overhead is to cluster the model's frozen vectors, but this strategy's effectiveness is fundamentally limited by the intrinsic clusterability of these embeddings. In this work, we introduce CRISP (Clustered Representations with Intrinsic Structure Pruning), a novel multi-vector training method which learns inherently clusterable representations directly within the end-to-end training process. By integrating clustering into the training phase rather than imposing it post-hoc, CRISP significantly outperforms post-hoc clustering at all representation sizes, as well as other token pruning methods. On the BEIR retrieval benchmarks, CRISP achieves a significant rate of ~3x reduction in the number of vectors while outperforming the original unpruned model. This indicates that learned clustering effectively denoises the model by filtering irrelevant information, thereby generating more robust multi-vector representations. With more aggressive clustering, CRISP achieves an 11x reduction in the number of vectors with only a 3.6% quality loss.

HD-Painter: High-Resolution and Prompt-Faithful Text-Guided Image Inpainting with Diffusion Models

Recent progress in text-guided image inpainting, based on the unprecedented success of text-to-image diffusion models, has led to exceptionally realistic and visually plausible results. However, there is still significant potential for improvement in current text-to-image inpainting models, particularly in better aligning the inpainted area with user prompts and performing high-resolution inpainting. Therefore, in this paper we introduce HD-Painter, a completely training-free approach that accurately follows to prompts and coherently scales to high-resolution image inpainting. To this end, we design the Prompt-Aware Introverted Attention (PAIntA) layer enhancing self-attention scores by prompt information and resulting in better text alignment generations. To further improve the prompt coherence we introduce the Reweighting Attention Score Guidance (RASG) mechanism seamlessly integrating a post-hoc sampling strategy into general form of DDIM to prevent out-of-distribution latent shifts. Moreover, HD-Painter allows extension to larger scales by introducing a specialized super-resolution technique customized for inpainting, enabling the completion of missing regions in images of up to 2K resolution. Our experiments demonstrate that HD-Painter surpasses existing state-of-the-art approaches qualitatively and quantitatively, achieving an impressive generation accuracy improvement of 61.4% vs 51.9%. We will make the codes publicly available at: https://github.com/Picsart-AI-Research/HD-Painter

A survey of agent interoperability protocols: Model Context Protocol (MCP), Agent Communication Protocol (ACP), Agent-to-Agent Protocol (A2A), and Agent Network Protocol (ANP)

Large language model powered autonomous agents demand robust, standardized protocols to integrate tools, share contextual data, and coordinate tasks across heterogeneous systems. Ad-hoc integrations are difficult to scale, secure, and generalize across domains. This survey examines four emerging agent communication protocols: Model Context Protocol (MCP), Agent Communication Protocol (ACP), Agent-to-Agent Protocol (A2A), and Agent Network Protocol (ANP), each addressing interoperability in deployment contexts. MCP provides a JSON-RPC client-server interface for secure tool invocation and typed data exchange. ACP defines a general-purpose communication protocol over RESTful HTTP, supporting MIME-typed multipart messages and synchronous and asynchronous interactions. Its lightweight and runtime-independent design enables scalable agent invocation, while features like session management, message routing, and integration with role-based and decentralized identifiers (DIDs). A2A enables peer-to-peer task delegation using capability-based Agent Cards, supporting secure and scalable collaboration across enterprise agent workflows. ANP supports open network agent discovery and secure collaboration using W3C decentralized identifiers DIDs and JSON-LD graphs. The protocols are compared across multiple dimensions, including interaction modes, discovery mechanisms, communication patterns, and security models. Based on the comparative analysis, a phased adoption roadmap is proposed: beginning with MCP for tool access, followed by ACP for structured, multimodal messaging session-aware interaction and both online and offline agent discovery across scalable, HTTP-based deployments A2A for collaborative task execution, and extending to ANP for decentralized agent marketplaces. This work provides a comprehensive foundation for designing secure, interoperable, and scalable ecosystems of LLM-powered agents.

Categorical semiotics: Foundations for Knowledge Integration

The integration of knowledge extracted from diverse models, whether described by domain experts or generated by machine learning algorithms, has historically been challenged by the absence of a suitable framework for specifying and integrating structures, learning processes, data transformations, and data models or rules. In this work, we extend algebraic specification methods to address these challenges within such a framework. In our work, we tackle the challenging task of developing a comprehensive framework for defining and analyzing deep learning architectures. We believe that previous efforts have fallen short by failing to establish a clear connection between the constraints a model must adhere to and its actual implementation. Our methodology employs graphical structures that resemble Ehresmann's sketches, interpreted within a universe of fuzzy sets. This approach offers a unified theory that elegantly encompasses both deterministic and non-deterministic neural network designs. Furthermore, we highlight how this theory naturally incorporates fundamental concepts from computer science and automata theory. Our extended algebraic specification framework, grounded in graphical structures akin to Ehresmann's sketches, offers a promising solution for integrating knowledge across disparate models and domains. By bridging the gap between domain-specific expertise and machine-generated insights, we pave the way for more comprehensive, collaborative, and effective approaches to knowledge integration and modeling.