Xiaobo Sun

Wenlin Li, Yucheng Xu, Xiaoqing Zheng et al.

Sparse and noisy images (SNIs), like those in spatial gene expression data, pose significant challenges for effective representation learning and clustering, which are essential for thorough data analysis and interpretation. In response to these challenges, we propose Dual Advancement of Representation Learning and Clustering (DARLC), an innovative framework that leverages contrastive learning to enhance the representations derived from masked image modeling. Simultaneously, DARLC integrates cluster assignments in a cohesive, end-to-end approach. This integrated clustering strategy addresses the "class collision problem" inherent in contrastive learning, thus improving the quality of the resulting representations. To generate more plausible positive views for contrastive learning, we employ a graph attention network-based technique that produces denoised images as augmented data. As such, our framework offers a comprehensive approach that improves the learning of representations by enhancing their local perceptibility, distinctiveness, and the understanding of relational semantics. Furthermore, we utilize a Student's t mixture model to achieve more robust and adaptable clustering of SNIs. Extensive experiments, conducted across 12 different types of datasets consisting of SNIs, demonstrate that DARLC surpasses the state-of-the-art methods in both image clustering and generating image representations that accurately capture gene interactions. Code is available at https://github.com/zipging/DARLC.

Kaichen Xu, Yueyang Ding, Suyang Hou et al.

Fined-grained anomalous cell detection from affected tissues is critical for clinical diagnosis and pathological research. Single-cell sequencing data provide unprecedented opportunities for this task. However, current anomaly detection methods struggle to handle domain shifts prevalent in multi-sample and multi-domain single-cell sequencing data, leading to suboptimal performance. Moreover, these methods fall short of distinguishing anomalous cells into pathologically distinct subtypes. In response, we propose ACSleuth, a novel, reconstruction deviation-guided generative framework that integrates the detection, domain adaptation, and fine-grained annotating of anomalous cells into a methodologically cohesive workflow. Notably, we present the first theoretical analysis of using reconstruction deviations output by generative models for anomaly detection in lieu of domain shifts. This analysis informs us to develop a novel and superior maximum mean discrepancy-based anomaly scorer in ACSleuth. Extensive benchmarks over various single-cell data and other types of tabular data demonstrate ACSleuth's superiority over the state-of-the-art methods in identifying and subtyping anomalies in multi-sample and multi-domain contexts. Our code is available at https://github.com/Catchxu/ACsleuth.

Yihang Du, Jiaying Hu, Suyang Hou et al.

Spatial labeling assigns labels to specific spatial locations to characterize their spatial properties and relationships, with broad applications in scientific research and practice. Measuring the similarity between two spatial labelings is essential for understanding their differences and the contributing factors, such as changes in location properties or labeling methods. An adequate and unbiased measurement of spatial labeling similarity should consider the number of matched labels (label agreement), the topology of spatial label distribution, and the heterogeneous impacts of mismatched labels. However, existing methods often fail to account for all these aspects. To address this gap, we propose a methodological framework to guide the development of methods that meet these requirements. Given two spatial labelings, the framework transforms them into graphs based on location organization, labels, and attributes (e.g., location significance). The distributions of their graph attributes are then extracted, enabling an efficient computation of distributional discrepancy to reflect the dissimilarity level between the two labelings. We further provide a concrete implementation of this framework, termed Spatial Labeling Analogy Metric (SLAM), along with an analysis of its theoretical foundation, for evaluating spatial labeling results in spatial transcriptomics (ST) \textit{as per} their similarity with ground truth labeling. Through a series of carefully designed experimental cases involving both simulated and real ST data, we demonstrate that SLAM provides a comprehensive and accurate reflection of labeling quality compared to other well-established evaluation metrics. Our code is available at https://github.com/YihDu/SLAM.

Kaichen Xu, Yihang Du, Mianpeng Liu et al.

Positional encoding is essential for supplementing transformer with positional information of tokens. Existing positional encoding methods demand predefined token/feature order, rendering them unsuitable for real-world data with non-sequential yet causally-related features. To address this limitation, we propose CAPE, a novel method that identifies underlying causal structure over non-sequential features as a weighted directed acyclic graph (DAG) using generalized structural equation modeling. The DAG is then embedded in hyperbolic space where its geometric structure is well-preserved using a hyperboloid model-based approach that effectively captures two important causal graph properties (causal strength & causal specificity). This step yields causality-aware positional encodings for the features, which are converted into their rotary form for integrating with transformer's self-attention mechanism. Theoretical analysis reveals that CAPE-generated rotary positional encodings possess three valuable properties for enhanced self-attention, including causal distance-induced attenuation, causal generality-induced attenuation, and robustness to positional disturbances. We evaluate CAPE over both synthetic and real-word datasets, empirically demonstrating its theoretical properties and effectiveness in enhancing transformer for data with non-sequential features. Our code is available at https://github.com/Catchxu/CAPE.

Kaichen Xu, Qilong Wu, Yan Lu et al.

The detection of anomalous tissue regions (ATRs) within affected tissues is crucial in clinical diagnosis and pathological studies. Conventional automated ATR detection methods, primarily based on histology images alone, falter in cases where ATRs and normal tissues have subtle visual differences. The recent spatial transcriptomics (ST) technology profiles gene expressions across tissue regions, offering a molecular perspective for detecting ATRs. However, there is a dearth of ATR detection methods that effectively harness complementary information from both histology images and ST. To address this gap, we propose MEATRD, a novel ATR detection method that integrates histology image and ST data. MEATRD is trained to reconstruct image patches and gene expression profiles of normal tissue spots (inliers) from their multimodal embeddings, followed by learning a one-class classification AD model based on latent multimodal reconstruction errors. This strategy harmonizes the strengths of reconstruction-based and one-class classification approaches. At the heart of MEATRD is an innovative masked graph dual-attention transformer (MGDAT) network, which not only facilitates cross-modality and cross-node information sharing but also addresses the model over-generalization issue commonly seen in reconstruction-based AD methods. Additionally, we demonstrate that modality-specific, task-relevant information is collated and condensed in multimodal bottleneck encoding generated in MGDAT, marking the first theoretical analysis of the informational properties of multimodal bottleneck encoding. Extensive evaluations across eight real ST datasets reveal MEATRD's superior performance in ATR detection, surpassing various state-of-the-art AD methods. Remarkably, MEATRD also proves adept at discerning ATRs that only show slight visual deviations from normal tissues.