arXiv subjects

Linhao Qu

Publications and source records attributed to Linhao Qu.

At least 19 recordsLinked to original sources

arXiv2026

Fusing Pixels and Genes: Spatially-Aware Learning in Computational Pathology

Recent years have witnessed remarkable progress in multimodal learning within computational pathology. Existing models primarily rely on vision and language modalities; however, language alone lacks molecular specificity and offers limited pathological supervision, leading to representational bottlenecks. In this paper, we propose STAMP, a Spatial Transcriptomics-Augmented Multimodal Pathology representation learning framework that integrates spatially-resolved gene expression profiles to enable molecule-guided joint embedding of pathology images and transcriptomic data. Our study shows that self-supervised, gene-guided training provides a robust and task-agnostic signal for learning pathology image representations. Incorporating spatial context and multi-scale information further enhances model performance and generalizability. To support this, we constructed SpaVis-6M, the largest Visium-based spatial transcriptomics dataset to date, and trained a spatially-aware gene encoder on this resource. Leveraging hierarchical multi-scale contrastive alignment and cross-scale patch localization mechanisms, STAMP effectively aligns spatial transcriptomics with pathology images, capturing spatial structure and molecular variation. We validate STAMP across six datasets and four downstream tasks, where it consistently achieves strong performance. These results highlight the value and necessity of integrating spatially resolved molecular supervision for advancing multimodal learning in computational pathology. The code is included in the supplementary materials. The pretrained weights and SpaVis-6M are available at: https://github.com/Hanminghao/STAMP.

cs.CV↗

arXiv2026

HUR-MACL: High-Uncertainty Region-Guided Multi-Architecture Collaborative Learning for Head and Neck Multi-Organ Segmentation

Accurate segmentation of organs at risk in the head and neck is essential for radiation therapy, yet deep learning models often fail on small, complexly shaped organs. While hybrid architectures that combine different models show promise, they typically just concatenate features without exploiting the unique strengths of each component. This results in functional overlap and limited segmentation accuracy. To address these issues, we propose a high uncertainty region-guided multi-architecture collaborative learning (HUR-MACL) model for multi-organ segmentation in the head and neck. This model adaptively identifies high uncertainty regions using a convolutional neural network, and for these regions, Vision Mamba as well as Deformable CNN are utilized to jointly improve their segmentation accuracy. Additionally, a heterogeneous feature distillation loss was proposed to promote collaborative learning between the two architectures in high uncertainty regions to further enhance performance. Our method achieves SOTA results on two public datasets and one private dataset.

cs.CV↗

arXiv2025

ME-Mamba: Multi-Expert Mamba with Efficient Knowledge Capture and Fusion for Multimodal Survival Analysis

Survival analysis using whole-slide images (WSIs) is crucial in cancer research. Despite significant successes, pathology images typically only provide slide-level labels, which hinders the learning of discriminative representations from gigapixel WSIs. With the rapid advancement of high-throughput sequencing technologies, multimodal survival analysis integrating pathology images and genomics data has emerged as a promising approach. We propose a Multi-Expert Mamba (ME-Mamba) system that captures discriminative pathological and genomic features while enabling efficient integration of both modalities. This approach achieves complementary information fusion without losing critical information from individual modalities, thereby facilitating accurate cancer survival analysis. Specifically, we first introduce a Pathology Expert and a Genomics Expert to process unimodal data separately. Both experts are designed with Mamba architectures that incorporate conventional scanning and attention-based scanning mechanisms, allowing them to extract discriminative features from long instance sequences containing substantial redundant or irrelevant information. Second, we design a Synergistic Expert responsible for modality fusion. It explicitly learns token-level local correspondences between the two modalities via Optimal Transport, and implicitly enhances distribution consistency through a global cross-modal fusion loss based on Maximum Mean Discrepancy. The fused feature representations are then passed to a mamba backbone for further integration. Through the collaboration of the Pathology Expert, Genomics Expert, and Synergistic Expert, our method achieves stable and accurate survival analysis with relatively low computational complexity. Extensive experimental results on five datasets in The Cancer Genome Atlas (TCGA) demonstrate our state-of-the-art performance.

cs.CV↗

arXiv2025

SemaMIL: Semantic-Aware Multiple Instance Learning with Retrieval-Guided State Space Modeling for Whole Slide Images

Multiple instance learning (MIL) has become the leading approach for extracting discriminative features from whole slide images (WSIs) in computational pathology. Attention-based MIL methods can identify key patches but tend to overlook contextual relationships. Transformer models are able to model interactions but require quadratic computational cost and are prone to overfitting. State space models (SSMs) offer linear complexity, yet shuffling patch order disrupts histological meaning and reduces interpretability. In this work, we introduce SemaMIL, which integrates Semantic Reordering (SR), an adaptive method that clusters and arranges semantically similar patches in sequence through a reversible permutation, with a Semantic-guided Retrieval State Space Module (SRSM) that chooses a representative subset of queries to adjust state space parameters for improved global modeling. Evaluation on four WSI subtype datasets shows that, compared to strong baselines, SemaMIL achieves state-of-the-art accuracy with fewer FLOPs and parameters.

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arXiv2025

Enhancing Zero-Shot Brain Tumor Subtype Classification via Fine-Grained Patch-Text Alignment

The fine-grained classification of brain tumor subtypes from histopathological whole slide images is highly challenging due to subtle morphological variations and the scarcity of annotated data. Although vision-language models have enabled promising zero-shot classification, their ability to capture fine-grained pathological features remains limited, resulting in suboptimal subtype discrimination. To address these challenges, we propose the Fine-Grained Patch Alignment Network (FG-PAN), a novel zero-shot framework tailored for digital pathology. FG-PAN consists of two key modules: (1) a local feature refinement module that enhances patch-level visual features by modeling spatial relationships among representative patches, and (2) a fine-grained text description generation module that leverages large language models to produce pathology-aware, class-specific semantic prototypes. By aligning refined visual features with LLM-generated fine-grained descriptions, FG-PAN effectively increases class separability in both visual and semantic spaces. Extensive experiments on multiple public pathology datasets, including EBRAINS and TCGA, demonstrate that FG-PAN achieves state-of-the-art performance and robust generalization in zero-shot brain tumor subtype classification.

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arXiv2025

Weakly Semi-supervised Whole Slide Image Classification by Two-level Cross Consistency Supervision

Computer-aided Whole Slide Image (WSI) classification has the potential to enhance the accuracy and efficiency of clinical pathological diagnosis. It is commonly formulated as a Multiple Instance Learning (MIL) problem, where each WSI is treated as a bag and the small patches extracted from the WSI are considered instances within that bag. However, obtaining labels for a large number of bags is a costly and time-consuming process, particularly when utilizing existing WSIs for new classification tasks. This limitation renders most existing WSI classification methods ineffective. To address this issue, we propose a novel WSI classification problem setting, more aligned with clinical practice, termed Weakly Semi-supervised Whole slide image Classification (WSWC). In WSWC, a small number of bags are labeled, while a significant number of bags remain unlabeled. The MIL nature of the WSWC problem, coupled with the absence of patch labels, distinguishes it from typical semi-supervised image classification problems, making existing algorithms for natural images unsuitable for directly solving the WSWC problem. In this paper, we present a concise and efficient framework, named CroCo, to tackle the WSWC problem through two-level Cross Consistency supervision. CroCo comprises two heterogeneous classifier branches capable of performing both instance classification and bag classification. The fundamental idea is to establish cross-consistency supervision at both the bag-level and instance-level between the two branches during training. Extensive experiments conducted on four datasets demonstrate that CroCo achieves superior bag classification and instance classification performance compared to other comparative methods when limited WSIs with bag labels are available. To the best of our knowledge, this paper presents for the first time the WSWC problem and gives a successful resolution.

cs.CV↗

arXiv2024

Towards Unified Molecule-Enhanced Pathology Image Representation Learning via Integrating Spatial Transcriptomics

Recent advancements in multimodal pre-training models have significantly advanced computational pathology. However, current approaches predominantly rely on visual-language models, which may impose limitations from a molecular perspective and lead to performance bottlenecks. Here, we introduce a Unified Molecule-enhanced Pathology Image REpresentationn Learning framework (UMPIRE). UMPIRE aims to leverage complementary information from gene expression profiles to guide the multimodal pre-training, enhancing the molecular awareness of pathology image representation learning. We demonstrate that this molecular perspective provides a robust, task-agnostic training signal for learning pathology image embeddings. Due to the scarcity of paired data, approximately 4 million entries of spatial transcriptomics gene expression were collected to train the gene encoder. By leveraging powerful pre-trained encoders, UMPIRE aligns the encoders across over 697K pathology image-gene expression pairs. The performance of UMPIRE is demonstrated across various molecular-related downstream tasks, including gene expression prediction, spot classification, and mutation state prediction in whole slide images. Our findings highlight the effectiveness of multimodal data integration and open new avenues for exploring computational pathology enhanced by molecular perspectives. The code and pre-trained weights are available at https://github.com/Hanminghao/UMPIRE.

cs.CV↗

arXiv2024

Local Implicit Wavelet Transformer for Arbitrary-Scale Super-Resolution

Implicit neural representations have recently demonstrated promising potential in arbitrary-scale Super-Resolution (SR) of images. Most existing methods predict the pixel in the SR image based on the queried coordinate and ensemble nearby features, overlooking the importance of incorporating high-frequency prior information in images, which results in limited performance in reconstructing high-frequency texture details in images. To address this issue, we propose the Local Implicit Wavelet Transformer (LIWT) to enhance the restoration of high-frequency texture details. Specifically, we decompose the features extracted by an encoder into four sub-bands containing different frequency information using Discrete Wavelet Transform (DWT). We then introduce the Wavelet Enhanced Residual Module (WERM) to transform these four sub-bands into high-frequency priors, followed by utilizing the Wavelet Mutual Projected Fusion (WMPF) and the Wavelet-aware Implicit Attention (WIA) to fully exploit the high-frequency prior information for recovering high-frequency details in images. We conducted extensive experiments on benchmark datasets to validate the effectiveness of LIWT. Both qualitative and quantitative results demonstrate that LIWT achieves promising performance in arbitrary-scale SR tasks, outperforming other state-of-the-art methods. The code is available at https://github.com/dmhdmhdmh/LIWT.

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arXiv2024

FANCL: Feature-Guided Attention Network with Curriculum Learning for Brain Metastases Segmentation

Accurate segmentation of brain metastases (BMs) in MR image is crucial for the diagnosis and follow-up of patients. Methods based on deep convolutional neural networks (CNNs) have achieved high segmentation performance. However, due to the loss of critical feature information caused by convolutional and pooling operations, CNNs still face great challenges in small BMs segmentation. Besides, BMs are irregular and easily confused with healthy tissues, which makes it difficult for the model to effectively learn tumor structure during training. To address these issues, this paper proposes a novel model called feature-guided attention network with curriculum learning (FANCL). Based on CNNs, FANCL utilizes the input image and its feature to establish the intrinsic connections between metastases of different sizes, which can effectively compensate for the loss of high-level feature from small tumors with the information of large tumors. Furthermore, FANCL applies the voxel-level curriculum learning strategy to help the model gradually learn the structure and details of BMs. And baseline models of varying depths are employed as curriculum-mining networks for organizing the curriculum progression. The evaluation results on the BraTS-METS 2023 dataset indicate that FANCL significantly improves the segmentation performance, confirming the effectiveness of our method.

eess.IV↗

arXiv2024

FAST: A Dual-tier Few-Shot Learning Paradigm for Whole Slide Image Classification

The expensive fine-grained annotation and data scarcity have become the primary obstacles for the widespread adoption of deep learning-based Whole Slide Images (WSI) classification algorithms in clinical practice. Unlike few-shot learning methods in natural images that can leverage the labels of each image, existing few-shot WSI classification methods only utilize a small number of fine-grained labels or weakly supervised slide labels for training in order to avoid expensive fine-grained annotation. They lack sufficient mining of available WSIs, severely limiting WSI classification performance. To address the above issues, we propose a novel and efficient dual-tier few-shot learning paradigm for WSI classification, named FAST. FAST consists of a dual-level annotation strategy and a dual-branch classification framework. Firstly, to avoid expensive fine-grained annotation, we collect a very small number of WSIs at the slide level, and annotate an extremely small number of patches. Then, to fully mining the available WSIs, we use all the patches and available patch labels to build a cache branch, which utilizes the labeled patches to learn the labels of unlabeled patches and through knowledge retrieval for patch classification. In addition to the cache branch, we also construct a prior branch that includes learnable prompt vectors, using the text encoder of visual-language models for patch classification. Finally, we integrate the results from both branches to achieve WSI classification. Extensive experiments on binary and multi-class datasets demonstrate that our proposed method significantly surpasses existing few-shot classification methods and approaches the accuracy of fully supervised methods with only 0.22$\%$ annotation costs. All codes and models will be publicly available on https://github.com/fukexue/FAST.

cs.CV↗

arXiv2024

MSCPT: Few-shot Whole Slide Image Classification with Multi-scale and Context-focused Prompt Tuning

Multiple instance learning (MIL) has become a standard paradigm for the weakly supervised classification of whole slide images (WSIs). However, this paradigm relies on using a large number of labeled WSIs for training. The lack of training data and the presence of rare diseases pose significant challenges for these methods. Prompt tuning combined with pre-trained Vision-Language models (VLMs) is an effective solution to the Few-shot Weakly Supervised WSI Classification (FSWC) task. Nevertheless, applying prompt tuning methods designed for natural images to WSIs presents three significant challenges: 1) These methods fail to fully leverage the prior knowledge from the VLM's text modality; 2) They overlook the essential multi-scale and contextual information in WSIs, leading to suboptimal results; and 3) They lack exploration of instance aggregation methods. To address these problems, we propose a Multi-Scale and Context-focused Prompt Tuning (MSCPT) method for FSWC task. Specifically, MSCPT employs the frozen large language model to generate pathological visual language prior knowledge at multiple scales, guiding hierarchical prompt tuning. Additionally, we design a graph prompt tuning module to learn essential contextual information within WSI, and finally, a non-parametric cross-guided instance aggregation module has been introduced to derive the WSI-level features. Extensive experiments, visualizations, and interpretability analyses were conducted on five datasets and three downstream tasks using three VLMs, demonstrating the strong performance of our MSCPT. All codes have been made publicly accessible at https://github.com/Hanminghao/MSCPT.

cs.CV↗

arXiv2024

Advancing H&E-to-IHC Stain Translation in Breast Cancer: A Multi-Magnification and Attention-Based Approach

Breast cancer presents a significant healthcare challenge globally, demanding precise diagnostics and effective treatment strategies, where histopathological examination of Hematoxylin and Eosin (H&E) stained tissue sections plays a central role. Despite its importance, evaluating specific biomarkers like Human Epidermal Growth Factor Receptor 2 (HER2) for personalized treatment remains constrained by the resource-intensive nature of Immunohistochemistry (IHC). Recent strides in deep learning, particularly in image-to-image translation, offer promise in synthesizing IHC-HER2 slides from H\&E stained slides. However, existing methodologies encounter challenges, including managing multiple magnifications in pathology images and insufficient focus on crucial information during translation. To address these issues, we propose a novel model integrating attention mechanisms and multi-magnification information processing. Our model employs a multi-magnification processing strategy to extract and utilize information from various magnifications within pathology images, facilitating robust image translation. Additionally, an attention module within the generative network prioritizes critical information for image distribution translation while minimizing less pertinent details. Rigorous testing on a publicly available breast cancer dataset demonstrates superior performance compared to existing methods, establishing our model as a state-of-the-art solution in advancing pathology image translation from H&E to IHC staining.

eess.IV↗

arXiv2024

Multi-modal Data Binding for Survival Analysis Modeling with Incomplete Data and Annotations

Survival analysis stands as a pivotal process in cancer treatment research, crucial for predicting patient survival rates accurately. Recent advancements in data collection techniques have paved the way for enhancing survival predictions by integrating information from multiple modalities. However, real-world scenarios often present challenges with incomplete data, particularly when dealing with censored survival labels. Prior works have addressed missing modalities but have overlooked incomplete labels, which can introduce bias and limit model efficacy. To bridge this gap, we introduce a novel framework that simultaneously handles incomplete data across modalities and censored survival labels. Our approach employs advanced foundation models to encode individual modalities and align them into a universal representation space for seamless fusion. By generating pseudo labels and incorporating uncertainty, we significantly enhance predictive accuracy. The proposed method demonstrates outstanding prediction accuracy in two survival analysis tasks on both employed datasets. This innovative approach overcomes limitations associated with disparate modalities and improves the feasibility of comprehensive survival analysis using multiple large foundation models.

cs.LG↗

arXiv2024

Deep Mutual Learning among Partially Labeled Datasets for Multi-Organ Segmentation

The task of labeling multiple organs for segmentation is a complex and time-consuming process, resulting in a scarcity of comprehensively labeled multi-organ datasets while the emergence of numerous partially labeled datasets. Current methods are inadequate in effectively utilizing the supervised information available from these datasets, thereby impeding the progress in improving the segmentation accuracy. This paper proposes a two-stage multi-organ segmentation method based on mutual learning, aiming to improve multi-organ segmentation performance by complementing information among partially labeled datasets. In the first stage, each partial-organ segmentation model utilizes the non-overlapping organ labels from different datasets and the distinct organ features extracted by different models, introducing additional mutual difference learning to generate higher quality pseudo labels for unlabeled organs. In the second stage, each full-organ segmentation model is supervised by fully labeled datasets with pseudo labels and leverages true labels from other datasets, while dynamically sharing accurate features across different models, introducing additional mutual similarity learning to enhance multi-organ segmentation performance. Extensive experiments were conducted on nine datasets that included the head and neck, chest, abdomen, and pelvis. The results indicate that our method has achieved SOTA performance in segmentation tasks that rely on partial labels, and the ablation studies have thoroughly confirmed the efficacy of the mutual learning mechanism.

cs.CV↗

arXiv2024

Pathology-knowledge Enhanced Multi-instance Prompt Learning for Few-shot Whole Slide Image Classification

Current multi-instance learning algorithms for pathology image analysis often require a substantial number of Whole Slide Images for effective training but exhibit suboptimal performance in scenarios with limited learning data. In clinical settings, restricted access to pathology slides is inevitable due to patient privacy concerns and the prevalence of rare or emerging diseases. The emergence of the Few-shot Weakly Supervised WSI Classification accommodates the significant challenge of the limited slide data and sparse slide-level labels for diagnosis. Prompt learning based on the pre-trained models (\eg, CLIP) appears to be a promising scheme for this setting; however, current research in this area is limited, and existing algorithms often focus solely on patch-level prompts or confine themselves to language prompts. This paper proposes a multi-instance prompt learning framework enhanced with pathology knowledge, \ie, integrating visual and textual prior knowledge into prompts at both patch and slide levels. The training process employs a combination of static and learnable prompts, effectively guiding the activation of pre-trained models and further facilitating the diagnosis of key pathology patterns. Lightweight Messenger (self-attention) and Summary (attention-pooling) layers are introduced to model relationships between patches and slides within the same patient data. Additionally, alignment-wise contrastive losses ensure the feature-level alignment between visual and textual learnable prompts for both patches and slides. Our method demonstrates superior performance in three challenging clinical tasks, significantly outperforming comparative few-shot methods.

cs.CV↗

arXiv2024

Asynchronous Multimodal Video Sequence Fusion via Learning Modality-Exclusive and -Agnostic Representations

Understanding human intentions (e.g., emotions) from videos has received considerable attention recently. Video streams generally constitute a blend of temporal data stemming from distinct modalities, including natural language, facial expressions, and auditory clues. Despite the impressive advancements of previous works via attention-based paradigms, the inherent temporal asynchrony and modality heterogeneity challenges remain in multimodal sequence fusion, causing adverse performance bottlenecks. To tackle these issues, we propose a Multimodal fusion approach for learning modality-Exclusive and modality-Agnostic representations (MEA) to refine multimodal features and leverage the complementarity across distinct modalities. On the one hand, MEA introduces a predictive self-attention module to capture reliable context dynamics within modalities and reinforce unique features over the modality-exclusive spaces. On the other hand, a hierarchical cross-modal attention module is designed to explore valuable element correlations among modalities over the modality-agnostic space. Meanwhile, a double-discriminator strategy is presented to ensure the production of distinct representations in an adversarial manner. Eventually, we propose a decoupled graph fusion mechanism to enhance knowledge exchange across heterogeneous modalities and learn robust multimodal representations for downstream tasks. Numerous experiments are implemented on three multimodal datasets with asynchronous sequences. Systematic analyses show the necessity of our approach.

cs.CV↗

arXiv2024

Separate and Conquer: Decoupling Co-occurrence via Decomposition and Representation for Weakly Supervised Semantic Segmentation

Weakly supervised semantic segmentation (WSSS) with image-level labels aims to achieve segmentation tasks without dense annotations. However, attributed to the frequent coupling of co-occurring objects and the limited supervision from image-level labels, the challenging co-occurrence problem is widely present and leads to false activation of objects in WSSS. In this work, we devise a 'Separate and Conquer' scheme SeCo to tackle this issue from dimensions of image space and feature space. In the image space, we propose to 'separate' the co-occurring objects with image decomposition by subdividing images into patches. Importantly, we assign each patch a category tag from Class Activation Maps (CAMs), which spatially helps remove the co-context bias and guide the subsequent representation. In the feature space, we propose to 'conquer' the false activation by enhancing semantic representation with multi-granularity knowledge contrast. To this end, a dual-teacher-single-student architecture is designed and tag-guided contrast is conducted, which guarantee the correctness of knowledge and further facilitate the discrepancy among co-contexts. We streamline the multi-staged WSSS pipeline end-to-end and tackle this issue without external supervision. Extensive experiments are conducted, validating the efficiency of our method and the superiority over previous single-staged and even multi-staged competitors on PASCAL VOC and MS COCO. Code is available at https://github.com/zwyang6/SeCo.git.

cs.CV↗

arXiv2024

An efficient dual-branch framework via implicit self-texture enhancement for arbitrary-scale histopathology image super-resolution

High-quality whole-slide scanning is expensive, complex, and time-consuming, thus limiting the acquisition and utilization of high-resolution histopathology images in daily clinical work. Deep learning-based single-image super-resolution (SISR) techniques provide an effective way to solve this problem. However, the existing SISR models applied in histopathology images can only work in fixed integer scaling factors, decreasing their applicability. Though methods based on implicit neural representation (INR) have shown promising results in arbitrary-scale super-resolution (SR) of natural images, applying them directly to histopathology images is inadequate because they have unique fine-grained image textures different from natural images. Thus, we propose an Implicit Self-Texture Enhancement-based dual-branch framework (ISTE) for arbitrary-scale SR of histopathology images to address this challenge. The proposed ISTE contains a feature aggregation branch and a texture learning branch. We employ the feature aggregation branch to enhance the learning of the local details for SR images while utilizing the texture learning branch to enhance the learning of high-frequency texture details. Then, we design a two-stage texture enhancement strategy to fuse the features from the two branches to obtain the SR images. Experiments on publicly available datasets, including TMA, HistoSR, and the TCGA lung cancer datasets, demonstrate that ISTE outperforms existing fixed-scale and arbitrary-scale SR algorithms across various scaling factors. Additionally, extensive experiments have shown that the histopathology images reconstructed by the proposed ISTE are applicable to downstream pathology image analysis tasks.

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