Yalin Wang

Yujian Xiong, Mohammad Farazi, Yanxi Chen et al.

Representation learning on large-scale unstructured volumetric and surface meshes poses significant challenges in neuroimaging, especially when models must incorporate diverse vertex-level morphometric descriptors, such as cortical thickness, curvature, sulcal depth, and myelin content, which carry subtle disease-related signals. Current approaches either ignore these clinically informative features or support only a single mesh topology, restricting their use across imaging pipelines. We introduce a hierarchical transformer framework designed for heterogeneous mesh analysis that operates on spatially adaptive tree partitions constructed from simplicial complexes of arbitrary order. This design accommodates both volumetric and surface discretizations within a single architecture, enabling efficient multi-scale attention without topology-specific modifications. A feature projection module maps variable-length per-vertex clinical descriptors into the spatial hierarchy, separating geometric structure from feature dimensionality and allowing seamless integration of different neuroimaging feature sets. Self-supervised pretraining via masked reconstruction of both coordinates and morphometric channels on large unlabeled cohorts yields a transferable encoder backbone applicable to diverse downstream tasks and mesh modalities. We validate our approach on Alzheimer's disease classification and amyloid burden prediction using volumetric brain meshes from ADNI, as well as focal cortical dysplasia detection on cortical surface meshes from the MELD dataset, achieving state-of-the-art results across all benchmarks.

Xiwen Chen, Peijie Qiu, Wenhui Zhu et al.

Deep neural networks, including transformers and convolutional neural networks, have significantly improved multivariate time series classification (MTSC). However, these methods often rely on supervised learning, which does not fully account for the sparsity and locality of patterns in time series data (e.g., diseases-related anomalous points in ECG). To address this challenge, we formally reformulate MTSC as a weakly supervised problem, introducing a novel multiple-instance learning (MIL) framework for better localization of patterns of interest and modeling time dependencies within time series. Our novel approach, TimeMIL, formulates the temporal correlation and ordering within a time-aware MIL pooling, leveraging a tokenized transformer with a specialized learnable wavelet positional token. The proposed method surpassed 26 recent state-of-the-art methods, underscoring the effectiveness of the weakly supervised TimeMIL in MTSC. The code will be available at https://github.com/xiwenc1/TimeMIL.

Xuanzhao Dong, Wenhui Zhu, Xiwen Chen et al.

Over the past decade, generative models have demonstrated success in enhancing fundus images. However, the evaluation of these models remains a challenge. A benchmark for fundus image enhancement is needed for three main reasons:(1) Conventional denoising metrics such as PSNR and SSIM fail to capture clinically relevant features, such as lesion preservation and vessel morphology consistency, limiting their applicability in real-world settings; (2) There is a lack of unified evaluation protocols that address both paired and unpaired enhancement methods, particularly those guided by clinical expertise; and (3) An evaluation framework should provide actionable insights to guide future advancements in clinically aligned enhancement models. To address these gaps, we introduce EyeBench-V2, a benchmark designed to bridge the gap between enhancement model performance and clinical utility. Our work offers three key contributions:(1) Multi-dimensional clinical-alignment through downstream evaluations: Beyond standard enhancement metrics, we assess performance across clinically meaningful tasks including vessel segmentation, diabetic retinopathy (DR) grading, generalization to unseen noise patterns, and lesion segmentation. (2) Expert-guided evaluation design: We curate a novel dataset enabling fair comparisons between paired and unpaired enhancement methods, accompanied by a structured manual assessment protocol by medical experts, which evaluates clinically critical aspects such as lesion structure alterations, background color shifts, and the introduction of artificial structures. (3) Actionable insights: Our benchmark provides a rigorous, task-oriented analysis of existing generative models, equipping clinical researchers with the evidence needed to make informed decisions, while also identifying limitations in current methods to inform the design of next-generation enhancement models.

Xiwen Chen, Wenhui Zhu, Peijie Qiu et al.

Analyzing time series data is crucial to a wide spectrum of applications, including economics, online marketplaces, and human healthcare. In particular, time series classification plays an indispensable role in segmenting different phases in stock markets, predicting customer behavior, and classifying worker actions and engagement levels. These aspects contribute significantly to the advancement of automated decision-making and system optimization in real-world applications. However, there is a large consensus that time series data often suffers from domain shifts between training and test sets, which dramatically degrades the classification performance. Despite the success of (reversible) instance normalization in handling the domain shifts for time series regression tasks, its performance in classification is unsatisfactory. In this paper, we propose \textit{FIC-TSC}, a training framework for time series classification that leverages Fisher information as the constraint. We theoretically and empirically show this is an efficient and effective solution to guide the model converge toward flatter minima, which enhances its generalizability to distribution shifts. We rigorously evaluate our method on 30 UEA multivariate and 85 UCR univariate datasets. Our empirical results demonstrate the superiority of the proposed method over 14 recent state-of-the-art methods.

Xin Li, Wenhui Zhu, Peijie Qiu et al.

In the field of medical imaging, the advent of deep learning, especially the application of convolutional neural networks (CNNs) has revolutionized the analysis and interpretation of medical images. Nevertheless, deep learning methods usually rely on large amounts of labeled data. In medical imaging research, the acquisition of high-quality labels is both expensive and difficult. The introduction of Vision Transformers (ViT) and self-supervised learning provides a pre-training strategy that utilizes abundant unlabeled data, effectively alleviating the label acquisition challenge while broadening the breadth of data utilization. However, ViT's high computational density and substantial demand for computing power, coupled with the lack of localization characteristics of its operations on image patches, limit its efficiency and applicability in many application scenarios. In this study, we employ nn-MobileNet, a lightweight CNN framework, to implement a BERT-style self-supervised learning approach. We pre-train the network on the unlabeled retinal fundus images from the UK Biobank to improve downstream application performance. We validate the results of the pre-trained model on Alzheimer's disease (AD), Parkinson's disease (PD), and various retinal diseases identification. The results show that our approach can significantly improve performance in the downstream tasks. In summary, this study combines the benefits of CNNs with the capabilities of advanced self-supervised learning in handling large-scale unlabeled data, demonstrating the potential of CNNs in the presence of label scarcity.

Yujian Xiong, Xuanzhao Dong, Sebastian Waz et al.

Ultra-high-field (7 Tesla) BOLD fMRI offers exceptional detail in both spatial and temporal domains, along with robust signal-to-noise characteristics, making it a powerful modality for studying visual information processing in the brain. However, due to the limited accessibility of 7T scanners, the majority of neuroimaging studies are still conducted using 3T systems, which inherently suffer from reduced fidelity in both resolution and SNR. To mitigate this limitation, we introduce a new computational approach designed to enhance the quality of 3T BOLD fMRI acquisitions. Specifically, we project both 3T and 7T datasets, sourced from different individuals and experimental setups, into a shared low-dimensional representation space. Within this space, we employ a lightweight, unsupervised Schrödinger Bridge framework to infer a high-SNR, high-resolution counterpart of the 3T data, without relying on paired supervision. This methodology is evaluated across multiple fMRI retinotopy datasets, including synthetically generated samples, and demonstrates a marked improvement in the reliability and fit of population receptive field (pRF) models applied to the enhanced 3T outputs. Our findings suggest that it is feasible to computationally approximate 7T-level quality from standard 3T acquisitions.