arXiv subjects

Joseph J. Y. Sung

Publications and source records attributed to Joseph J. Y. Sung.

7 recordsLinked to original sources

arXiv2026

Exploiting Low-Dimensional Manifold of Features for Few-Shot Whole Slide Image Classification

Few-shot Whole Slide Image (WSI) classification is severely hampered by overfitting. We argue that this is not merely a data-scarcity issue but a fundamentally geometric problem. Grounded in the manifold hypothesis, our analysis shows that features from pathology foundation models exhibit a low-dimensional manifold geometry that is easily perturbed by downstream models. This insight reveals a key potential issue in downstream multiple instance learning models: linear layers are geometry-agnostic and, as we show empirically, can distort the manifold geometry of the features. To address this, we propose the Manifold Residual (MR) block, a plug-and-play module that is explicitly geometry-aware. The MR block reframes the linear layer as residual learning and decouples it into two pathways: (1) a fixed, random matrix serving as a geometric anchor that approximately preserves topology while also acting as a spectral shaper to sharpen the feature spectrum; and (2) a trainable, low-rank residual pathway that acts as a residual learner for task-specific adaptation, with its structural bottleneck explicitly mirroring the low effective rank of the features. This decoupling imposes a structured inductive bias and reduces learning to a simpler residual fitting task. Through extensive experiments, we demonstrate that our approach achieves state-of-the-art results with significantly fewer parameters, offering a new paradigm for few-shot WSI classification. Code is available in https://github.com/BearCleverProud/MR-Block.

cs.CV↗

arXiv2026

ConSurv: Multimodal Continual Learning for Survival Analysis

Survival prediction of cancers is crucial for clinical practice, as it informs mortality risks and influences treatment plans. However, a static model trained on a single dataset fails to adapt to the dynamically evolving clinical environment and continuous data streams, limiting its practical utility. While continual learning (CL) offers a solution to learn dynamically from new datasets, existing CL methods primarily focus on unimodal inputs and suffer from severe catastrophic forgetting in survival prediction. In real-world scenarios, multimodal inputs often provide comprehensive and complementary information, such as whole slide images and genomics; and neglecting inter-modal correlations negatively impacts the performance. To address the two challenges of catastrophic forgetting and complex inter-modal interactions between gigapixel whole slide images and genomics, we propose ConSurv, the first multimodal continual learning (MMCL) method for survival analysis. ConSurv incorporates two key components: Multi-staged Mixture of Experts (MS-MoE) and Feature Constrained Replay (FCR). MS-MoE captures both task-shared and task-specific knowledge at different learning stages of the network, including two modality encoders and the modality fusion component, learning inter-modal relationships. FCR further enhances learned knowledge and mitigates forgetting by restricting feature deviation of previous data at different levels, including encoder-level features of two modalities and the fusion-level representations. Additionally, we introduce a new benchmark integrating four datasets, Multimodal Survival Analysis Incremental Learning (MSAIL), for comprehensive evaluation in the CL setting. Extensive experiments demonstrate that ConSurv outperforms competing methods across multiple metrics.

cs.LG↗

arXiv2025

multivariateGPT: a decoder-only transformer for multivariate categorical and numeric data

Real-world processes often generate data that are a mix of categorical and numeric values that are recorded at irregular and informative intervals. Discrete token-based approaches are limited in numeric representation capacity while methods like neural ordinary differential equations are not well suited for categorical data or informative sampling and require augmentation to handle certain classes of trajectories. Here, we present multivariateGPT, a single architecture for modeling sequences of mixed categorical (including tokenized text) and numeric data. This is accomplished with an autoregressive sequence decomposition, embedding scheme, and loss function that extend the next token prediction task to likelihood estimation of the joint distribution of next token class and value. We demonstrate how this approach can efficiently learn to generalize patterns in simple physical systems and model complex time series including electrocardiograms and multivariate electronic health record data. This work extends the utility of transformer based models to additional classes of data.

cs.LG↗

arXiv2025

A Survey of Pathology Foundation Model: Progress and Future Directions

Computational pathology, which involves analyzing whole slide images for automated cancer diagnosis, relies on multiple instance learning, where performance depends heavily on the feature extractor and aggregator. Recent Pathology Foundation Models (PFMs), pretrained on large-scale histopathology data, have significantly enhanced both the extractor and aggregator, but they lack a systematic analysis framework. In this survey, we present a hierarchical taxonomy organizing PFMs through a top-down philosophy applicable to foundation model analysis in any domain: model scope, model pretraining, and model design. Additionally, we systematically categorize PFM evaluation tasks into slide-level, patch-level, multimodal, and biological tasks, providing comprehensive benchmarking criteria. Our analysis identifies critical challenges in both PFM development (pathology-specific methodology, end-to-end pretraining, data-model scalability) and utilization (effective adaptation, model maintenance), paving the way for future directions in this promising field. Resources referenced in this survey are available at https://github.com/BearCleverProud/AwesomeWSI.

cs.CV↗

arXiv2024

TAKT: Target-Aware Knowledge Transfer for Whole Slide Image Classification

Transferring knowledge from a source domain to a target domain can be crucial for whole slide image classification, since the number of samples in a dataset is often limited due to high annotation costs. However, domain shift and task discrepancy between datasets can hinder effective knowledge transfer. In this paper, we propose a Target-Aware Knowledge Transfer framework, employing a teacher-student paradigm. Our framework enables the teacher model to learn common knowledge from the source and target domains by actively incorporating unlabelled target images into the training of the teacher model. The teacher bag features are subsequently adapted to supervise the training of the student model on the target domain. Despite incorporating the target features during training, the teacher model tends to overlook them under the inherent domain shift and task discrepancy. To alleviate this, we introduce a target-aware feature alignment module to establish a transferable latent relationship between the source and target features by solving the optimal transport problem. Experimental results show that models employing knowledge transfer outperform those trained from scratch, and our method achieves state-of-the-art performance among other knowledge transfer methods on various datasets, including TCGA-RCC, TCGA-NSCLC, and Camelyon16.

cs.CV↗

arXiv2024

MoME: Mixture of Multimodal Experts for Cancer Survival Prediction

Survival analysis, as a challenging task, requires integrating Whole Slide Images (WSIs) and genomic data for comprehensive decision-making. There are two main challenges in this task: significant heterogeneity and complex inter- and intra-modal interactions between the two modalities. Previous approaches utilize co-attention methods, which fuse features from both modalities only once after separate encoding. However, these approaches are insufficient for modeling the complex task due to the heterogeneous nature between the modalities. To address these issues, we propose a Biased Progressive Encoding (BPE) paradigm, performing encoding and fusion simultaneously. This paradigm uses one modality as a reference when encoding the other. It enables deep fusion of the modalities through multiple alternating iterations, progressively reducing the cross-modal disparities and facilitating complementary interactions. Besides modality heterogeneity, survival analysis involves various biomarkers from WSIs, genomics, and their combinations. The critical biomarkers may exist in different modalities under individual variations, necessitating flexible adaptation of the models to specific scenarios. Therefore, we further propose a Mixture of Multimodal Experts (MoME) layer to dynamically selects tailored experts in each stage of the BPE paradigm. Experts incorporate reference information from another modality to varying degrees, enabling a balanced or biased focus on different modalities during the encoding process. Extensive experimental results demonstrate the superior performance of our method on various datasets, including TCGA-BLCA, TCGA-UCEC and TCGA-LUAD. Codes are available at https://github.com/BearCleverProud/MoME.

eess.IV↗

arXiv2023

Diagnose Like a Pathologist: Transformer-Enabled Hierarchical Attention-Guided Multiple Instance Learning for Whole Slide Image Classification

Multiple Instance Learning (MIL) and transformers are increasingly popular in histopathology Whole Slide Image (WSI) classification. However, unlike human pathologists who selectively observe specific regions of histopathology tissues under different magnifications, most methods do not incorporate multiple resolutions of the WSIs, hierarchically and attentively, thereby leading to a loss of focus on the WSIs and information from other resolutions. To resolve this issue, we propose a Hierarchical Attention-Guided Multiple Instance Learning framework to fully exploit the WSIs. This framework can dynamically and attentively discover the discriminative regions across multiple resolutions of the WSIs. Within this framework, an Integrated Attention Transformer is proposed to further enhance the performance of the transformer and obtain a more holistic WSI (bag) representation. This transformer consists of multiple Integrated Attention Modules, which is the combination of a transformer layer and an aggregation module that produces a bag representation based on every instance representation in that bag. The experimental results show that our method achieved state-of-the-art performances on multiple datasets, including Camelyon16, TCGA-RCC, TCGA-NSCLC, and an in-house IMGC dataset. The code is available at https://github.com/BearCleverProud/HAG-MIL.

cs.CV↗