arXiv:2605.24489v1 Announce Type: new Abstract: Enzyme-reaction retrieval is a fundamental problem in computational biology, underpinning enzyme characterization, reaction mechanism elucidation, and the rational design of metabolic pathways and biocatalysts. As a bidirectional task, it entails both enzyme-to-reaction and reaction-to-enzyme mapping. However, existing approaches suffer from poor generalization across tasks and distributions, with performance highly sensitive to dataset splits and substantial asymmetry between retrieval directions. To address these challenges, we present TIGER, a Text-Informed Generalized Enzyme-Reaction Retrieval framework that leverages protein-to-text generation models to distill textual semantic knowledge from enzyme sequences, providing a generalized representation that bridges enzymes and biochemical reactions. To ensure the quality and reliability of textual semantics, we design a Dynamic Gating Network that adaptively fuses text-derived knowledge with sequence features, enabling more consistent and informative enzyme representations, while a Structure-Shared Feature Projector aligns enzyme and reaction representations within a unified latent space. Extensive experiments demonstrate that, under bidirectional retrieval supervision, TIGER significantly outperforms state-of-the-art baselines across diverse distributions and exhibits strong robustness and transferability across tasks.

arXiv:2605.26089v1 Announce Type: cross Abstract: We present Channel-wise Vector Quantization (CVQ), a novel image tokenization paradigm that replaces patch-wise tokens with channel-wise tokens. Unlike conventional vector quantization, which assigns a discrete token to each patch feature vector, CVQ quantizes each channel of the feature map. This formulation represents an image as discrete levels of visual details, rather than as a grid of spatial patches. Based on CVQ, we introduce a new visual autoregressive framework with "next-channel prediction". Instead of rendering images patch by patch in raster order, our Channel-wise Autoregressive (CAR) model predicts image channels sequentially, producing progressively enriched visual details. Specifically, it first sketches global structure and then refines fine-grained attributes, akin to a human artist's workflow. Empirically, we show that: (1) CVQ achieves 100% codebook utilization with a 16K+ codebook size without any bells and whistles, and substantially improves reconstruction quality over conventional VQ; and (2) CAR attains a DPG score of 86.7 and a GenEval score of 0.79, demonstrating strong effectiveness for text-to-image generation.

arXiv:2602.23916v2 Announce Type: replace-cross Abstract: The advent of large-scale self-supervised learning (SSL) has produced a vast zoo of medical foundation models. However, selecting optimal medical foundation models for specific segmentation tasks remains a computational bottleneck. Existing Transferability Estimation (TE) metrics, primarily designed for classification, rely on global statistical assumptions and fail to capture the topological complexity essential for dense prediction. We propose a novel Topology-Driven Transferability Estimation framework that evaluates manifold tractability rather than statistical overlap. Our approach introduces three components: (1) Global Representation Topology Divergence (GRTD), utilizing Minimum Spanning Trees to quantify feature-label structural isomorphism; (2) Local Boundary-Aware Topological Consistency (LBTC), which assesses manifold separability specifically at critical anatomical boundaries; and (3) Task-Adaptive Fusion, which dynamically integrates global and local metrics based on the semantic cardinality of the target task. Validated on the large-scale OpenMind benchmark across diverse anatomical targets and SSL foundation models, our approach significantly outperforms state-of-the-art baselines by around 31% relative improvement in the weighted Kendall metric, providing a robust, training-free proxy for efficient model selection without the cost of fine-tuning. The code will be made publicly available upon acceptance.