Xubin Zheng

Xinlei Huang, Zhiqi Ma, Dian Meng et al.

Spatial multi-modal omics technology, highlighted by Nature Methods as an advanced biological technique in 2023, plays a critical role in resolving biological regulatory processes with spatial context. Recently, graph neural networks based on K-nearest neighbor (KNN) graphs have gained prominence in spatial multi-modal omics methods due to their ability to model semantic relations between sequencing spots. However, the fixed KNN graph fails to capture the latent semantic relations hidden by the inevitable data perturbations during the biological sequencing process, resulting in the loss of semantic information. In addition, the common lack of spot annotation and class number priors in practice further hinders the optimization of spatial multi-modal omics models. Here, we propose a novel spatial multi-modal omics resolved framework, termed PRototype-Aware Graph Adaptative Aggregation for Spatial Multi-modal Omics Analysis (PRAGA). PRAGA constructs a dynamic graph to capture latent semantic relations and comprehensively integrate spatial information and feature semantics. The learnable graph structure can also denoise perturbations by learning cross-modal knowledge. Moreover, a dynamic prototype contrastive learning is proposed based on the dynamic adaptability of Bayesian Gaussian Mixture Models to optimize the multi-modal omics representations for unknown biological priors. Quantitative and qualitative experiments on simulated and real datasets with 7 competing methods demonstrate the superior performance of PRAGA. Code is available at https://github.com/Xubin-s-Lab/PRAGA.

Xinlei Huang, Jialiang Tang, Xubin Zheng et al.

Knowledge Distillation (KD) transfers knowledge from a large pre-trained teacher network to a compact and efficient student network, making it suitable for deployment on resource-limited media terminals. However, traditional KD methods require balanced data to ensure robust training, which is often unavailable in practical applications. In such scenarios, a few head categories occupy a substantial proportion of examples. This imbalance biases the trained teacher network towards the head categories, resulting in severe performance degradation on the less represented tail categories for both the teacher and student networks. In this paper, we propose a novel framework called Knowledge Rectification Distillation (KRDistill) to address the imbalanced knowledge inherited in the teacher network through the incorporation of the balanced category priors. Furthermore, we rectify the biased predictions produced by the teacher network, particularly focusing on the tail categories. Consequently, the teacher network can provide balanced and accurate knowledge to train a reliable student network. Intensive experiments conducted on various long-tailed datasets demonstrate that our KRDistill can effectively train reliable student networks in realistic scenarios of data imbalance.

Qingqiang Sun, Chaoqi Chen, Ziyue Qiao et al.

Most graph contrastive learning (GCL) methods heavily rely on cross-view contrast, thus facing several concomitant challenges, such as the complexity of designing effective augmentations, the potential for information loss between views, and increased computational costs. To mitigate reliance on cross-view contrasts, we propose \ttt{SIGNA}, a novel single-view graph contrastive learning framework. Regarding the inconsistency between structural connection and semantic similarity of neighborhoods, we resort to soft neighborhood awareness for GCL. Specifically, we leverage dropout to obtain structurally-related yet randomly-noised embedding pairs for neighbors, which serve as potential positive samples. At each epoch, the role of partial neighbors is switched from positive to negative, leading to probabilistic neighborhood contrastive learning effect. Furthermore, we propose a normalized Jensen-Shannon divergence estimator for a better effect of contrastive learning. Surprisingly, experiments on diverse node-level tasks demonstrate that our simple single-view GCL framework consistently outperforms existing methods by margins of up to 21.74% (PPI). In particular, with soft neighborhood awareness, SIGNA can adopt MLPs instead of complicated GCNs as the encoder to generate representations in transductive learning tasks, thus speeding up its inference process by 109 times to 331 times. The source code is available at https://github.com/sunisfighting/SIGNA.

Dian Meng, Bohao Xing, Xinlei Huang et al.

Single-cell multi-omics (scMulti-omics) refers to the paired multimodal data, such as Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), where the regulation of each cell was measured from different modalities, i.e. genes and proteins. scMulti-omics can reveal heterogeneity inside tumors and understand the distinct genetic properties of diverse cell types, which is crucial to targeted therapy. Currently, deep learning methods based on attention structures in the bioinformatics area face two challenges. The first challenge is the vast number of genes in a single cell. Traditional attention-based modules struggled to effectively leverage all gene information due to their limited capacity for long-context learning and high-complexity computing. The second challenge is that genes in the human genome are ordered and influence each other's expression. Most of the methods ignored this sequential information. The recently introduced Test-Time Training (TTT) layer is a novel sequence modeling approach, particularly suitable for handling long contexts like genomics data because TTT layer is a linear complexity sequence modeling structure and is better suited to data with sequential relationships. In this paper, we propose scFusionTTT, a novel method for Single-Cell multimodal omics Fusion with TTT-based masked autoencoder. Of note, we combine the order information of genes and proteins in the human genome with the TTT layer, fuse multimodal omics, and enhance unimodal omics analysis. Finally, the model employs a three-stage training strategy, which yielded the best performance across most metrics in four multimodal omics datasets and four unimodal omics datasets, demonstrating the superior performance of our model. The dataset and code will be available on https://github.com/DM0815/scFusionTTT.

Chao Hao, Jun Xu, Ji Du et al.

Language-guided segmentation transcends the scope limitations of traditional semantic segmentation, enabling models to segment arbitrary target regions based on natural language instructions. Existing approaches typically adopt a two-stage framework: employing Multimodal Large Language Models (MLLMs) to interpret instructions and generate visual prompts, followed by foundational segmentation models (e.g., SAM) to produce masks. However, due to the limited spatial grounding capabilities of off-the-shelf MLLMs, these methods often rely on extensive training on large-scale datasets to achieve satisfactory accuracy. While recent advances have introduced reasoning mechanisms to improve performance, they predominantly operate within the textual domain, performing chain-of-thought reasoning solely based on abstract text representations without direct visual feedback. In this paper, we propose Seg-Agent, a completely training-free framework that pioneers Explicit Multimodal Chain-of-Reasoning. Unlike prior text-only reasoning, our approach constructs an interactive visual reasoning loop comprising three stages: generation, selection, and refinement. Specifically, we leverage Set-of-Mark (SoM) visual prompting to render candidate regions directly onto the image, allowing the MLLM to ``see'' and iteratively reason about spatial relationships in the visual domain rather than just the textual one. This explicit multimodal interaction enables Seg-Agent to achieve performance comparable to state-of-the-art training-based methods without any parameter updates. Furthermore, to comprehensively evaluate generalization across diverse scenarios, we introduce Various-LangSeg, a novel benchmark covering explicit semantic, generic object, and reasoning-guided segmentation tasks. Extensive experiments demonstrate the effectiveness and robustness of our method.

Xinyu Xie, Yawen Cui, Tao Tan et al.

Multimodal image fusion aims to integrate information from different imaging techniques to produce a comprehensive, detail-rich single image for downstream vision tasks. Existing methods based on local convolutional neural networks (CNNs) struggle to capture global features efficiently, while Transformer-based models are computationally expensive, although they excel at global modeling. Mamba addresses these limitations by leveraging selective structured state space models (S4) to effectively handle long-range dependencies while maintaining linear complexity. In this paper, we propose FusionMamba, a novel dynamic feature enhancement framework that aims to overcome the challenges faced by CNNs and Vision Transformers (ViTs) in computer vision tasks. The framework improves the visual state-space model Mamba by integrating dynamic convolution and channel attention mechanisms, which not only retains its powerful global feature modeling capability, but also greatly reduces redundancy and enhances the expressiveness of local features. In addition, we have developed a new module called the dynamic feature fusion module (DFFM). It combines the dynamic feature enhancement module (DFEM) for texture enhancement and disparity perception with the cross-modal fusion Mamba module (CMFM), which focuses on enhancing the inter-modal correlation while suppressing redundant information. Experiments show that FusionMamba achieves state-of-the-art performance in a variety of multimodal image fusion tasks as well as downstream experiments, demonstrating its broad applicability and superiority.

Yongjun Xiao, Dian Meng, Xinlei Huang et al.

Effectively modeling multimodal spatial omics data is critical for understanding tissue complexity and underlying biological mechanisms. While spatial transcriptomics, proteomics, and epigenomics capture molecular features, they lack pathological morphological context. Integrating these omics with histopathological images is therefore essential for comprehensive disease tissue analysis. However, substantial heterogeneity across omics, imaging, and spatial modalities poses significant challenges. Naive fusion of semantically distinct sources often leads to ambiguous representations. Additionally, the resolution mismatch between high-resolution histology images and lower-resolution sequencing spots complicates spatial alignment. Biological perturbations during sample preparation further distort modality-specific signals, hindering accurate integration. To address these challenges, we propose Graph-guided Representation of Omics and Vision with Expert Regulation for Adaptive Spatial Multi-omics Fusion (GROVER), a novel framework for adaptive integration of spatial multi-omics data. GROVER leverages a Graph Convolutional Network encoder based on Kolmogorov-Arnold Networks to capture the nonlinear dependencies between each modality and its associated spatial structure, thereby producing expressive, modality-specific embeddings. To align these representations, we introduce a spot-feature-pair contrastive learning strategy that explicitly optimizes the correspondence across modalities at each spot. Furthermore, we design a dynamic expert routing mechanism that adaptively selects informative modalities for each spot while suppressing noisy or low-quality inputs. Experiments on real-world spatial omics datasets demonstrate that GROVER outperforms state-of-the-art baselines, providing a robust and reliable solution for multimodal integration.

Yidi Wang, Jiawei Gu, pei Xiaobing et al.

This paper studies a novel problem of out-of-distribution graph models merging, which aims to construct a generalized model from multiple graph models pre-trained on different domains with distribution discrepancy. This problem is challenging because of the difficulty in learning domain-invariant knowledge implicitly in model parameters and consolidating expertise from potentially heterogeneous GNN backbones. In this work, we propose a graph generation strategy that instantiates the mixture distribution of multiple domains. Then, we merge and fine-tune the pre-trained graph models via a MoE module and a masking mechanism for generalized adaptation. Our framework is architecture-agnostic and can operate without any source/target domain data. Both theoretical analysis and experimental results demonstrate the effectiveness of our approach in addressing the model generalization problem.

Lingrui Zhang, Haonan Wu, Nana Jin et al.

Host-response-based diagnostics can improve the accuracy of diagnosing bacterial and viral infections, thereby reducing inappropriate antibiotic prescriptions. However, the existing cohorts with limited sample size and coarse infections types are unable to support the exploration of an accurate and generalizable diagnostic model. Here, we curate the largest infection host-response transcriptome data, including 11,247 samples across 89 blood transcriptome datasets from 13 countries and 21 platforms. We build a diagnostic model for pathogen prediction starting from a pan-infection model as foundation (AUC = 0.97) based on the pan-infection dataset. Then, we utilize knowledge distillation to efficiently transfer the insights from this "teacher" model to four lightweight pathogen "student" models, i.e., staphylococcal infection (AUC = 0.99), streptococcal infection (AUC = 0.94), HIV infection (AUC = 0.93), and RSV infection (AUC = 0.94), as well as a sepsis "student" model (AUC = 0.99). The proposed knowledge distillation framework not only facilitates the diagnosis of pathogens using pan-infection data, but also enables an across-disease study from pan-infection to sepsis. Moreover, the framework enables high-degree lightweight design of diagnostic models, which is expected to be adaptively deployed in clinical settings.