Ziquan Wei

Ziquan Wei, Shenghua Cheng, Jing Cai et al.

Cervical glandular cell (GC) detection is a key step in computer-aided diagnosis for cervical adenocarcinomas screening. It is challenging to accurately recognize GCs in cervical smears in which squamous cells are the major. Widely existing Out-Of-Distribution (OOD) data in the entire smear leads decreasing reliability of machine learning system for GC detection. Although, the State-Of-The-Art (SOTA) deep learning model can outperform pathologists in preselected regions of interest, the mass False Positive (FP) prediction with high probability is still unsolved when facing such gigapixel whole slide image. This paper proposed a novel PolarNet based on the morphological prior knowledge of GC trying to solve the FP problem via a self-attention mechanism in eight-neighbor. It estimates the polar orientation of nucleus of GC. As a plugin module, PolarNet can guide the deep feature and predicted confidence of general object detection models. In experiments, we discovered that general models based on four different frameworks can reject FP in small image set and increase the mean of average precision (mAP) by $\text{0.007}\sim\text{0.015}$ in average, where the highest exceeds the recent cervical cell detection model 0.037. By plugging PolarNet, the deployed C++ program improved by 8.8\% on accuracy of top-20 GC detection from external WSIs, while sacrificing 14.4 s of computational time. Code is available in https://github.com/Chrisa142857/PolarNet-GCdet

Tingting Dan, Jiaqi Ding, Ziquan Wei et al.

Graph neural networks (GNNs) are widely used in domains like social networks and biological systems. However, the locality assumption of GNNs, which limits information exchange to neighboring nodes, hampers their ability to capture long-range dependencies and global patterns in graphs. To address this, we propose a new inductive bias based on variational analysis, drawing inspiration from the Brachistochrone problem. Our framework establishes a mapping between discrete GNN models and continuous diffusion functionals. This enables the design of application-specific objective functions in the continuous domain and the construction of discrete deep models with mathematical guarantees. To tackle over-smoothing in GNNs, we analyze the existing layer-by-layer graph embedding models and identify that they are equivalent to l2-norm integral functionals of graph gradients, which cause over-smoothing. Similar to edge-preserving filters in image denoising, we introduce total variation (TV) to align the graph diffusion pattern with global community topologies. Additionally, we devise a selective mechanism to address the trade-off between model depth and over-smoothing, which can be easily integrated into existing GNNs. Furthermore, we propose a novel generative adversarial network (GAN) that predicts spreading flows in graphs through a neural transport equation. To mitigate vanishing flows, we customize the objective function to minimize transportation within each community while maximizing inter-community flows. Our GNN models achieve state-of-the-art (SOTA) performance on popular graph learning benchmarks such as Cora, Citeseer, and Pubmed.

Ziquan Wei, Tingting Dan, Jiaqi Ding et al.

Although modern imaging technologies allow us to study connectivity between two distinct brain regions in-vivo, an in-depth understanding of how anatomical structure supports brain function and how spontaneous functional fluctuations emerge remarkable cognition is still elusive. Meanwhile, tremendous efforts have been made in the realm of machine learning to establish the nonlinear mapping between neuroimaging data and phenotypic traits. However, the absence of neuroscience insight in the current approaches poses significant challenges in understanding cognitive behavior from transient neural activities. To address this challenge, we put the spotlight on the coupling mechanism of structural connectivity (SC) and functional connectivity (FC) by formulating such network neuroscience question into an expressive graph representation learning problem for high-order topology. Specifically, we introduce the concept of topological detour to characterize how a ubiquitous instance of FC (direct link) is supported by neural pathways (detour) physically wired by SC, which forms a cyclic loop interacted by brain structure and function. In the cliché of machine learning, the multi-hop detour pathway underlying SC-FC coupling allows us to devise a novel multi-head self-attention mechanism within Transformer to capture multi-modal feature representation from paired graphs of SC and FC. Taken together, we propose a biological-inspired deep model, coined as NeuroPath, to find putative connectomic feature representations from the unprecedented amount of neuroimages, which can be plugged into various downstream applications such as task recognition and disease diagnosis. We have evaluated NeuroPath on large-scale public datasets including HCP and UK Biobank under supervised and zero-shot learning, where the state-of-the-art performance by our NeuroPath indicates great potential in network neuroscience.

Jiaqi Ding, Tingting Dan, Ziquan Wei et al.

An unprecedented amount of existing functional Magnetic Resonance Imaging (fMRI) data provides a new opportunity to understand the relationship between functional fluctuation and human cognition/behavior using a data-driven approach. To that end, tremendous efforts have been made in machine learning to predict cognitive states from evolving volumetric images of blood-oxygen-level-dependent (BOLD) signals. Due to the complex nature of brain function, however, the evaluation on learning performance and discoveries are not often consistent across current state-of-the-arts (SOTA). By capitalizing on large-scale existing neuroimaging data (34,887 data samples from six public databases), we seek to establish a well-founded empirical guideline for designing deep models for functional neuroimages by linking the methodology underpinning with knowledge from the neuroscience domain. Specifically, we put the spotlight on (1) What is the current SOTA performance in cognitive task recognition and disease diagnosis using fMRI? (2) What are the limitations of current deep models? and (3) What is the general guideline for selecting the suitable machine learning backbone for new neuroimaging applications? We have conducted a comprehensive evaluation and statistical analysis, in various settings, to answer the above outstanding questions.

Ziquan Wei, Tingting Dan, Guorong Wu

Despite the central role of sensor-derived measurements such as imaging traits and plasma biomarkers in biomedical research and clinical practice, existing generative models for disease prediction largely depend on event-level representations from hospital and registry data. Given the multi-factorial nature of human disease, the absence of explicit modeling of social determinants of health (SDoH), even in the limited form of ICD-coded proxies (chapters Z and V--Y in ICD-10), limits the capacity for personalized disease modeling and clinical decision support. To address this limitation, we propose a generative model with ICD-coded proxies of SDoH for \textit{in silico} modeling of disease reasoning, a conditioned latent diffusion framework that establishes the connection between multi-organ sensor data with tokenized healthcare events. Specifically, we introduce a novel geometric diffusion model to characterize the temporal evolution of complex data representation such as brain networks (region-to-region connectivity encoded in a graph), in parallel with diffusion models for tabular data from other organ systems. Together, we integrate the generative model with digitalized SDoH proxies (coined \modelname{}) for simulated intervention and reasoning of future disease trajectories. We conduct extensive experiments on the UK Biobank (UKB) dataset, which contains organ-specific imaging traits, including brain (44,834), heart (23,987), liver (28,722), and kidney (32,155), along with nearly 500k medical history sequences (age range: 25$\sim$89 years). Our \modelname{} achieves significant improvements over state-of-the-art human disease autoregressive models and imaging trait generative baselines.

Su Zhang, Yi Ding, Ziquan Wei et al.

We propose an audio-visual spatial-temporal deep neural network with: (1) a visual block containing a pretrained 2D-CNN followed by a temporal convolutional network (TCN); (2) an aural block containing several parallel TCNs; and (3) a leader-follower attentive fusion block combining the audio-visual information. The TCN with large history coverage enables our model to exploit spatial-temporal information within a much larger window length (i.e., 300) than that from the baseline and state-of-the-art methods (i.e., 36 or 48). The fusion block emphasizes the visual modality while exploits the noisy aural modality using the inter-modality attention mechanism. To make full use of the data and alleviate over-fitting, cross-validation is carried out on the training and validation set. The concordance correlation coefficient (CCC) centering is used to merge the results from each fold. On the test (validation) set of the Aff-Wild2 database, the achieved CCC is 0.463 (0.469) for valence and 0.492 (0.649) for arousal, which significantly outperforms the baseline method with the corresponding CCC of 0.200 (0.210) and 0.190 (0.230) for valence and arousal, respectively. The code is available at https://github.com/sucv/ABAW2.

Ziquan Wei, Shenghua Cheng, Junbo Hu et al.

Digital gigapixel whole slide image (WSI) is widely used in clinical diagnosis, and automated WSI analysis is key for computer-aided diagnosis. Currently, analyzing the integrated descriptor of probabilities or feature maps from massive local patches encoded by ResNet classifier is the main manner for WSI-level prediction. Feature representations of the sparse and tiny lesion cells in cervical slides, however, are still challenging, while the unused location representations are available to supply the semantics classification. This study designs a novel and efficient framework with a new module InCNet constructed lightweight model YOLCO (You Only Look Cytology Once). It directly extracts feature inside the single cell (cluster) instead of the traditional way that from image tile with a fixed size. The InCNet (Inline Connection Network) enriches the multi-scale connectivity without efficiency loss. The proposal allows the input size enlarged to megapixel that can stitch the WSI by the average repeats decreased from $10^3\sim10^4$ to $10^1\sim10^2$ for collecting features and predictions at two scales. Based on Transformer for classifying the integrated multi-scale multi-task WSI features, the experimental results appear $0.872$ AUC score better than the best conventional model on our dataset ($n$=2,019) from four scanners. The code is available at https://github.com/Chrisa142857/You-Only-Look-Cytopathology-Once , where the deployment version has the speed $\sim$70 s/WSI.

Ziquan Wei, Tingting Dan, Guorong Wu

A reliable foundation model of functional neuroimages is critical to promote clinical applications where the performance of current AI models is significantly impeded by a limited sample size. To that end, tremendous efforts have been made to pretraining large models on extensive unlabeled fMRI data using scalable self-supervised learning. Since self-supervision is not necessarily aligned with the brain-to-outcome relationship, most foundation models are suboptimal to the downstream task, such as predicting disease outcomes. By capitalizing on rich environmental variables and demographic data along with an unprecedented amount of functional neuroimages, we form the brain modeling as a multitask learning and present a scalable model architecture for (i) multitask pretraining by tokenizing multiple brain-environment interactions (BEI) and (ii) semi-supervised finetuning by assigning pseudo-labels of pretrained BEI. We have evaluated our foundation model on a variety of applications, including sex prediction, human behavior recognition, and disease early diagnosis of Autism, Parkinson's disease, Alzheimer's disease, and {Schizophrenia}, where promising results indicate the great potential to facilitate current neuroimaging applications in clinical routines.

Ziquan Wei, Tingting Dan, Guorong Wu

Graph learning is crucial in the fields of bioinformatics, social networks, and chemicals. Although high-order graphlets, such as cycles, are critical to achieving an informative graph representation for node classification, edge prediction, and graph recognition, modeling high-order topological characteristics poses significant computational challenges, restricting its widespread applications in machine learning. To address this limitation, we introduce the concept of \textit{message detouring} to hierarchically characterize cycle representation throughout the entire graph, which capitalizes on the contrast between the shortest and longest pathways within a range of local topologies associated with each graph node. The topological feature representations derived from our message detouring landscape demonstrate comparable expressive power to high-order \textit{Weisfeiler-Lehman} (WL) tests but much less computational demands. In addition to the integration with graph kernel and message passing neural networks, we present a novel message detouring neural network, which uses Transformer backbone to integrate cycle representations across nodes and edges. Aside from theoretical results, experimental results on expressiveness, graph classification, and node classification show message detouring can significantly outperform current counterpart approaches on various benchmark datasets.