Huajun Zhou

Fengtao Zhou, Yingxue Xu, Zhengyu Zhang et al.

Comprehensive molecular profiling is essential for modern precision oncology but remains hindered by prohibitive costs, specimen exhaustion, and protracted turnaround times. While pathology foundation models (PFMs) have demonstrated potential for inferring molecular phenotypes from routine hematoxylin and eosin (H&E) whole-slide images (WSIs), current architectures primarily rely on vision-centric self-supervised learning or vision-language alignment, lacking the spatially resolved molecular supervision required to connect subtle morphological features with underlying genomic alterations. Spatial transcriptomics (ST) emerges as a transformative technology that enables transcriptomic quantification within intact tissue sections, thereby preserving the precise spatial link between histology and molecular profiles. In this study, we present a Spatial Transcriptomics-guided Alignment framework for Molecular Profiling (STAMP), which endows PFMs with intrinsic molecular awareness. To support this paradigm, we curated HumanST-1k, a human ST dataset spanning diverse anatomical organs and sequencing platforms. This atlas yields 1.8 million pairs of H&E patches and corresponding transcriptomic profiles, providing a corpus that links histological structures with their molecular states. To mitigate the technical noise inherent to raw transcriptomics, STAMP applies a pathway-informed alignment strategy that aggregates transcriptomic data into biologically functional pathways, which are subsequently integrated into PFMs via parameter-efficient fine-tuning. This alignment enriches the representation space of PFMs and unlocks their capacity to resolve sub-visual molecular signatures. The clinical utility of these augmented representations was validated through a multi-tier evaluation framework.

Huajun Zhou, Bo Qiao, Lingxiao Yang et al.

Deep Learning-based Unsupervised Salient Object Detection (USOD) mainly relies on the noisy saliency pseudo labels that have been generated from traditional handcraft methods or pre-trained networks. To cope with the noisy labels problem, a class of methods focus on only easy samples with reliable labels but ignore valuable knowledge in hard samples. In this paper, we propose a novel USOD method to mine rich and accurate saliency knowledge from both easy and hard samples. First, we propose a Confidence-aware Saliency Distilling (CSD) strategy that scores samples conditioned on samples' confidences, which guides the model to distill saliency knowledge from easy samples to hard samples progressively. Second, we propose a Boundary-aware Texture Matching (BTM) strategy to refine the boundaries of noisy labels by matching the textures around the predicted boundary. Extensive experiments on RGB, RGB-D, RGB-T, and video SOD benchmarks prove that our method achieves state-of-the-art USOD performance.

Yingxue Xu, Yihui Wang, Fengtao Zhou et al.

Remarkable strides in computational pathology have been made in the task-agnostic foundation model that advances the performance of a wide array of downstream clinical tasks. Despite the promising performance, there are still several challenges. First, prior works have resorted to either vision-only or image-caption data, disregarding pathology reports with more clinically authentic information from pathologists and gene expression profiles which respectively offer distinct knowledge for versatile clinical applications. Second, the current progress in pathology FMs predominantly concentrates on the patch level, where the restricted context of patch-level pretraining fails to capture whole-slide patterns. Even recent slide-level FMs still struggle to provide whole-slide context for patch representation. In this study, for the first time, we develop a pathology foundation model incorporating three levels of modalities: pathology slides, pathology reports, and gene expression data, which resulted in 26,169 slide-level modality pairs from 10,275 patients across 32 cancer types, amounting to over 116 million pathological patch images. To leverage these data for CPath, we propose a novel whole-slide pretraining paradigm that injects the multimodal whole-slide context into the patch representation, called Multimodal Self-TAught PRetraining (mSTAR). The proposed paradigm revolutionizes the pretraining workflow for CPath, enabling the pathology FM to acquire the whole-slide context. To the best of our knowledge, this is the first attempt to incorporate three modalities at the whole-slide context for enhancing pathology FMs. To systematically evaluate the capabilities of mSTAR, we built the largest spectrum of oncological benchmark, spanning 7 categories of oncological applications in 15 types of 97 practical oncological tasks.

Jiahao Zhu, Huajun Zhou, Zixuan Chen et al.

3D deep models consuming point clouds have achieved sound application effects in computer vision. However, recent studies have shown they are vulnerable to 3D adversarial point clouds. In this paper, we regard these malicious point clouds as 3D steganography examples and present a new perspective, 3D steganalysis, to counter such examples. Specifically, we propose 3D-VFD, a victim-free detector against 3D adversarial point clouds. Its core idea is to capture the discrepancies between residual geometric feature distributions of benign point clouds and adversarial point clouds and map these point clouds to a lower dimensional space where we can efficiently distinguish them. Unlike existing detection techniques against 3D adversarial point clouds, 3D-VFD does not rely on the victim 3D deep model's outputs for discrimination. Extensive experiments demonstrate that 3D-VFD achieves state-of-the-art detection and can effectively detect 3D adversarial attacks based on point adding and point perturbation while keeping fast detection speed.

Yingxue Xu, Zhengyu Zhang, Xiuming Zhang et al.

Pathology foundation models have shown strong retrospective performance, but whether such systems can support clinically relevant use remains unclear. This challenge is particularly important in breast cancer, where pathological assessment serves as the gold standard for diagnosis and guides treatment planning, surgical decision-making and risk stratification across pre-, intra- and post-operative stages. Here we present \textbf{BRAVE}, a breast-adaptive pathology foundation model developed and evaluated using a total resource of 101,638 breast whole-slide images from 32 sources across Asia, Europe and North America. We assessed BRAVE across 34 tasks in 82 cohorts spanning pre-operative biopsy, intra-operative frozen section and post-operative resection, using an evidence chain comprising retrospective benchmarking, clinically challenging scenarios, workflow-oriented clinical impact simulations, prospective observational validation with the thresholds locked in the retrospective cohorts and crossover pathologist-AI interaction studies. Across these settings, BRAVE supported practical roles in the clinical workflow, including safe exclusion of low-risk cases from routine review, AI-assisted second-review rescue of initially missed positives and prioritization of cases for further assessment. In prospective validation across three centres, BRAVE excluded 76.9% of negative biopsy cases (NPV 0.953) and 70.1% of negative frozen-section cases (NPV 0.973), and triaged 78.8% of post-operative subtyping cases as high-confidence clear-cut cases (NPV 1.000). In reader studies, AI assistance improved balanced accuracy from 88.5% to 95.1% (OR 3.14, P<0.001), with better efficiency, confidence and inter-rater agreement. BRAVE-derived scores also independently predicted disease-free survival (adjusted HR 4.79, P<0.001) and overall survival (adjusted HR 8.14, P<0.001).

Huajun Zhou, Fengtao Zhou, Hao Chen

Recently, we have witnessed impressive achievements in cancer survival analysis by integrating multimodal data, e.g., pathology images and genomic profiles. However, the heterogeneity and high dimensionality of these modalities pose significant challenges for extracting discriminative representations while maintaining good generalization. In this paper, we propose a Cohort-individual Cooperative Learning (CCL) framework to advance cancer survival analysis by collaborating knowledge decomposition and cohort guidance. Specifically, first, we propose a Multimodal Knowledge Decomposition (MKD) module to explicitly decompose multimodal knowledge into four distinct components: redundancy, synergy and uniqueness of the two modalities. Such a comprehensive decomposition can enlighten the models to perceive easily overlooked yet important information, facilitating an effective multimodal fusion. Second, we propose a Cohort Guidance Modeling (CGM) to mitigate the risk of overfitting task-irrelevant information. It can promote a more comprehensive and robust understanding of the underlying multimodal data, while avoiding the pitfalls of overfitting and enhancing the generalization ability of the model. By cooperating the knowledge decomposition and cohort guidance methods, we develop a robust multimodal survival analysis model with enhanced discrimination and generalization abilities. Extensive experimental results on five cancer datasets demonstrate the effectiveness of our model in integrating multimodal data for survival analysis.

Lei Xie, Qingrun Zeng, Huajun Zhou et al.

Diffusion MRI tractography is an important tool for identifying and analyzing the intracranial course of cranial nerves (CNs). However, the complex environment of the skull base leads to ambiguous spatial correspondence between diffusion directions and fiber geometry, and existing diffusion tractography methods of CNs identification are prone to producing erroneous trajectories and missing true positive connections. To overcome the above challenge, we propose a novel CNs identification framework with anatomy-guided fiber trajectory distribution, which incorporates anatomical shape prior knowledge during the process of CNs tracing to build diffusion tensor vector fields. We introduce higher-order streamline differential equations for continuous flow field representations to directly characterize the fiber trajectory distribution of CNs from the tract-based level. The experimental results on the vivo HCP dataset and the clinical MDM dataset demonstrate that the proposed method reduces false-positive fiber production compared to competing methods and produces reconstructed CNs (i.e. CN II, CN III, CN V, and CN VII/VIII) that are judged to better correspond to the known anatomy.

Huajun Zhou, Fengtao Zhou, Jiabo Ma et al.

Multimodal data provides heterogeneous information for a holistic understanding of the tumor microenvironment. However, existing AI models often struggle to harness the rich information within multimodal data and extract poorly generalizable representations. Here we present MICE (Multimodal data Integration via Collaborative Experts), a multimodal foundation model that effectively integrates pathology images, clinical reports, and genomics data for precise pan-cancer prognosis prediction. Instead of conventional multi-expert modules, MICE employs multiple functionally diverse experts to comprehensively capture both cross-cancer and cancer-specific insights. Leveraging data from 11,799 patients across 30 cancer types, we enhanced MICE's generalizability by coupling contrastive and supervised learning. MICE outperformed both unimodal and state-of-the-art multi-expert-based multimodal models, demonstrating substantial improvements in C-index ranging from 3.8% to 11.2% on internal cohorts and 5.8% to 8.8% on independent cohorts, respectively. Moreover, it exhibited remarkable data efficiency across diverse clinical scenarios. With its enhanced generalizability and data efficiency, MICE establishes an effective and scalable foundation for pan-cancer prognosis prediction, holding strong potential to personalize tailored therapies and improve treatment outcomes.

Cheng Jin, Fengtao Zhou, Yunfang Yu et al.

Precision oncology requires accurate molecular insights, yet obtaining these directly from genomics is costly and time-consuming for broad clinical use. Predicting complex molecular features and patient prognosis directly from routine whole-slide images (WSI) remains a major challenge for current deep learning methods. Here we introduce PathLUPI, which uses transcriptomic privileged information during training to extract genome-anchored histological embeddings, enabling effective molecular prediction using only WSIs at inference. Through extensive evaluation across 49 molecular oncology tasks using 11,257 cases among 20 cohorts, PathLUPI demonstrated superior performance compared to conventional methods trained solely on WSIs. Crucially, it achieves AUC $\geq$ 0.80 in 14 of the biomarker prediction and molecular subtyping tasks and C-index $\geq$ 0.70 in survival cohorts of 5 major cancer types. Moreover, PathLUPI embeddings reveal distinct cellular morphological signatures associated with specific genotypes and related biological pathways within WSIs. By effectively encoding molecular context to refine WSI representations, PathLUPI overcomes a key limitation of existing models and offers a novel strategy to bridge molecular insights with routine pathology workflows for wider clinical application.

Lei Xie, Huajun Zhou, Junxiong Huang et al.

The segmentation of cranial nerves (CNs) tract provides a valuable quantitative tool for the analysis of the morphology and trajectory of individual CNs. Multimodal CNs tract segmentation networks, e.g., CNTSeg, which combine structural Magnetic Resonance Imaging (MRI) and diffusion MRI, have achieved promising segmentation performance. However, it is laborious or even infeasible to collect complete multimodal data in clinical practice due to limitations in equipment, user privacy, and working conditions. In this work, we propose a novel arbitrary-modal fusion network for volumetric CNs tract segmentation, called CNTSeg-v2, which trains one model to handle different combinations of available modalities. Instead of directly combining all the modalities, we select T1-weighted (T1w) images as the primary modality due to its simplicity in data acquisition and contribution most to the results, which supervises the information selection of other auxiliary modalities. Our model encompasses an Arbitrary-Modal Collaboration Module (ACM) designed to effectively extract informative features from other auxiliary modalities, guided by the supervision of T1w images. Meanwhile, we construct a Deep Distance-guided Multi-stage (DDM) decoder to correct small errors and discontinuities through signed distance maps to improve segmentation accuracy. We evaluate our CNTSeg-v2 on the Human Connectome Project (HCP) dataset and the clinical Multi-shell Diffusion MRI (MDM) dataset. Extensive experimental results show that our CNTSeg-v2 achieves state-of-the-art segmentation performance, outperforming all competing methods.

Huajun Zhou, Fengtao Zhou, Chenyu Zhao et al.

The essence of precision oncology lies in its commitment to tailor targeted treatments and care measures to each patient based on the individual characteristics of the tumor. The inherent heterogeneity of tumors necessitates gathering information from diverse data sources to provide valuable insights from various perspectives, fostering a holistic comprehension of the tumor. Over the past decade, multimodal data integration technology for precision oncology has made significant strides, showcasing remarkable progress in understanding the intricate details within heterogeneous data modalities. These strides have exhibited tremendous potential for improving clinical decision-making and model interpretation, contributing to the advancement of cancer care and treatment. Given the rapid progress that has been achieved, we provide a comprehensive overview of about 300 papers detailing cutting-edge multimodal data integration techniques in precision oncology. In addition, we conclude the primary clinical applications that have reaped significant benefits, including early assessment, diagnosis, prognosis, and biomarker discovery. Finally, derived from the findings of this survey, we present an in-depth analysis that explores the pivotal challenges and reveals essential pathways for future research in the field of multimodal data integration for precision oncology.

Huajun Zhou, Yang Lin, Lingxiao Yang et al.

In recent years, deep network-based methods have continuously refreshed state-of-the-art performance on Salient Object Detection (SOD) task. However, the performance discrepancy caused by different implementation details may conceal the real progress in this task. Making an impartial comparison is required for future researches. To meet this need, we construct a general SALient Object Detection (SALOD) benchmark to conduct a comprehensive comparison among several representative SOD methods. Specifically, we re-implement 14 representative SOD methods by using consistent settings for training. Moreover, two additional protocols are set up in our benchmark to investigate the robustness of existing methods in some limited conditions. In the first protocol, we enlarge the difference between objectness distributions of train and test sets to evaluate the robustness of these SOD methods. In the second protocol, we build multiple train subsets with different scales to validate whether these methods can extract discriminative features from only a few samples. In the above experiments, we find that existing loss functions usually specialized in some metrics but reported inferior results on the others. Therefore, we propose a novel Edge-Aware (EA) loss that promotes deep networks to learn more discriminative features by integrating both pixel- and image-level supervision signals. Experiments prove that our EA loss reports more robust performances compared to existing losses.

Huajun Zhou, Peijia Chen, Lingxiao Yang et al.

Existing deep learning-based Unsupervised Salient Object Detection (USOD) methods rely on supervised pre-trained deep models. Moreover, they generate pseudo labels based on hand-crafted features, which lack high-level semantic information. In order to overcome these shortcomings, we propose a new two-stage Activation-to-Saliency (A2S) framework that effectively excavates high-quality saliency cues to train a robust saliency detector. It is worth noting that our method does not require any manual annotation, even in the pre-training phase. In the first stage, we transform an unsupervisedly pre-trained network to aggregate multi-level features to a single activation map, where an Adaptive Decision Boundary (ADB) is proposed to assist the training of the transformed network. Moreover, a new loss function is proposed to facilitate the generation of high-quality pseudo labels. In the second stage, a self-rectification learning paradigm strategy is developed to train a saliency detector and refine the pseudo labels online. In addition, we construct a lightweight saliency detector using two Residual Attention Modules (RAMs) to largely reduce the risk of overfitting. Extensive experiments on several SOD benchmarks prove that our framework reports significant performance compared with existing USOD methods. Moreover, training our framework on 3,000 images consumes about 1 hour, which is over 30$\times$ faster than previous state-of-the-art methods.

Peijia Chen, Jianhuang Lai, Guangcong Wang et al.

Video salient object detection (VSOD) aims to locate and segment the most attractive object by exploiting both spatial cues and temporal cues hidden in video sequences. However, spatial and temporal cues are often unreliable in real-world scenarios, such as low-contrast foreground, fast motion, and multiple moving objects. To address these problems, we propose a new framework to adaptively capture available information from spatial and temporal cues, which contains Confidence-guided Adaptive Gate (CAG) modules and Dual Differential Enhancement (DDE) modules. For both RGB features and optical flow features, CAG estimates confidence scores supervised by the IoU between predictions and the ground truths to re-calibrate the information with a gate mechanism. DDE captures the differential feature representation to enrich the spatial and temporal information and generate the fused features. Experimental results on four widely used datasets demonstrate the effectiveness of the proposed method against thirteen state-of-the-art methods.

Zixuan Chen, Huajun Zhou, Xiaohua Xie et al.

We present a learning model that makes full use of boundary information for salient object segmentation. Specifically, we come up with a novel loss function, i.e., Contour Loss, which leverages object contours to guide models to perceive salient object boundaries. Such a boundary-aware network can learn boundary-wise distinctions between salient objects and background, hence effectively facilitating the saliency detection. Yet the Contour Loss emphasizes on the local saliency. We further propose the hierarchical global attention module (HGAM), which forces the model hierarchically attend to global contexts, thus captures the global visual saliency. Comprehensive experiments on six benchmark datasets show that our method achieves superior performance over state-of-the-art ones. Moreover, our model has a real-time speed of 26 fps on a TITAN X GPU.