Bryan Wong

Bryan Wong, Sungrae Hong, Mun Yong Yi

Multiple instance learning (MIL) has become a preferred method for gigapixel whole slide image (WSI) classification without requiring patch-level annotations. Current MIL research primarily relies on embedding-based approaches, which extract patch features using a pre-trained feature extractor and aggregate them for slide-level prediction. Despite the critical role of feature extraction, there is limited guidance on selecting optimal feature extractors to maximize WSI performance. This study addresses this gap by systematically evaluating MIL feature extractors across three dimensions: pre-training dataset, backbone model, and pre-training method. Extensive experiments were conducted on two public WSI datasets (TCGA-NSCLC and Camelyon16) using four state-of-the-art (SOTA) MIL models. Our findings reveal that: 1) selecting a robust self-supervised learning (SSL) method has a greater impact on performance than relying solely on an in-domain pre-training dataset; 2) prioritizing Transformer-based backbones with deeper architectures over CNN-based models; and 3) using larger, more diverse pre-training datasets significantly enhances classification outcomes. We hope that these insights can provide practical guidance for optimizing WSI classification and explain the reasons behind the performance advantages of the current SOTA pathology foundation models. Furthermore, this work may inform the development of more effective pathology foundation models. Our code is publicly available at https://github.com/bryanwong17/MIL-Feature-Extractor-Selection

Jongwoo Kim, Seongyeub Chu, Hyeongmin Park et al.

Recent advancements in graph neural networks (GNNs) and heterogeneous GNNs (HGNNs) have advanced node embeddings and relationship learning for various tasks. However, existing methods often rely on domain-specific predefined meta-paths, which are coarse-grained and focus solely on aspects like node type, limiting their ability to capture complex interactions. We introduce MF2Vec, a model that uses multi-faceted (fine-grained) paths instead of predefined meta-paths. MF2Vec extracts paths via random walks and generates multi-faceted vectors, ignoring predefined schemas. This method learns diverse aspects of nodes and their relationships, constructs a homogeneous network, and creates node embeddings for classification, link prediction, and clustering. Extensive experiments show that MF2Vec outperforms existing methods, offering a more flexible and comprehensive framework for analyzing complex networks. The code is available at https://anonymous.4open.science/r/MF2Vec-6ABC.

Bryan Wong, Mun Yong Yi

Multiple instance learning (MIL) has emerged as a powerful framework for weakly supervised whole slide image (WSI) classification, enabling slide-level predictions without requiring detailed patch-level annotations. Despite its success, a critical limitation of current MIL methods lies in the underutilization of pre-training for the MIL aggregator. Most existing approaches initialize the aggregator randomly and train it from scratch, making performance highly sensitive to the quantity of labeled WSIs and ignoring the abundance of unlabeled WSIs commonly available in clinical settings. To address this, we propose PreMix, a novel framework that leverages a non-contrastive pre-training method, Barlow Twins, augmented with the Slide Mixing approach to generate additional positive pairs and enhance feature learning, particularly under limited labeled WSI conditions. Fine-tuning with Mixup and Manifold Mixup further enhances robustness by effectively handling the diverse sizes of gigapixel WSIs. Experimental results demonstrate that integrating PreMix as a plug-in module into HIPT yields an average F1 improvement of 4.7% over the baseline HIPT across various WSI training sizes and datasets. These findings underscore its potential to advance WSI classification with limited labeled data and its applicability to real-world histopathology practices. The code is available at https://github.com/bryanwong17/PreMix

Jongwoo Kim, Bryan Wong, Huazhu Fu et al.

Cancer diagnosis has greatly benefited from the integration of whole-slide images (WSIs) with multiple instance learning (MIL), enabling high-resolution analysis of tissue morphology. Graph-based MIL (GNN-MIL) approaches have emerged as powerful solutions for capturing contextual information in WSIs, thereby improving diagnostic accuracy. However, WSIs require significant computational and infrastructural resources, limiting accessibility in resource-constrained settings. Conventional light microscopes offer a cost-effective alternative, but applying GNN-MIL to such data is challenging due to extensive redundant images and missing spatial coordinates, which hinder contextual learning. To address these issues, we introduce MicroMIL, the first weakly-supervised MIL framework specifically designed for images acquired from conventional light microscopes. MicroMIL leverages a representative image extractor (RIE) that employs deep cluster embedding (DCE) and hard Gumbel-Softmax to dynamically reduce redundancy and select representative images. These images serve as graph nodes, with edges computed via cosine similarity, eliminating the need for spatial coordinates while preserving contextual information. Extensive experiments on a real-world colon cancer dataset and the BreakHis dataset demonstrate that MicroMIL achieves state-of-the-art performance, improving both diagnostic accuracy and robustness to redundancy. The code is available at https://github.com/kimjongwoo-cell/MicroMIL

SeongYeub Chu, JongWoo Kim, Bryan Wong et al.

Existing automated essay scoring (AES) has solely relied on essay text without using explanatory rationales for the scores, thereby forgoing an opportunity to capture the specific aspects evaluated by rubric indicators in a fine-grained manner. This paper introduces Rationale-based Multiple Trait Scoring (RMTS), a novel approach for multi-trait essay scoring that integrates prompt-engineering-based large language models (LLMs) with a fine-tuning-based essay scoring model using a smaller large language model (S-LLM). RMTS uses an LLM-based trait-wise rationale generation system where a separate LLM agent generates trait-specific rationales based on rubric guidelines, which the scoring model uses to accurately predict multi-trait scores. Extensive experiments on benchmark datasets, including ASAP, ASAP++, and Feedback Prize, show that RMTS significantly outperforms state-of-the-art models and vanilla S-LLMs in trait-specific scoring. By assisting quantitative assessment with fine-grained qualitative rationales, RMTS enhances the trait-wise reliability, providing partial explanations about essays. The code is available at https://github.com/BBeeChu/RMTS.git.

Bryan Wong, Jong Woo Kim, Huazhu Fu et al.

Vision-language models (VLMs) have recently been integrated into multiple instance learning (MIL) frameworks to address the challenge of few-shot, weakly supervised classification of whole slide images (WSIs). A key trend involves leveraging multi-scale information to better represent hierarchical tissue structures. However, existing methods often face two key limitations: (1) insufficient modeling of interactions within the same modalities across scales (e.g., 5x and 20x) and (2) inadequate alignment between visual and textual modalities on the same scale. To address these gaps, we propose HiVE-MIL, a hierarchical vision-language framework that constructs a unified graph consisting of (1) parent-child links between coarse (5x) and fine (20x) visual/textual nodes to capture hierarchical relationships, and (2) heterogeneous intra-scale edges linking visual and textual nodes on the same scale. To further enhance semantic consistency, HiVE-MIL incorporates a two-stage, text-guided dynamic filtering mechanism that removes weakly correlated patch-text pairs, and introduces a hierarchical contrastive loss to align textual semantics across scales. Extensive experiments on TCGA breast, lung, and kidney cancer datasets demonstrate that HiVE-MIL consistently outperforms both traditional MIL and recent VLM-based MIL approaches, achieving gains of up to 4.1% in macro F1 under 16-shot settings. Our results demonstrate the value of jointly modeling hierarchical structure and multimodal alignment for efficient and scalable learning from limited pathology data. The code is available at https://github.com/bryanwong17/HiVE-MIL.

Willmer Rafell Quinones Robles, Sakonporn Noree, Young Sin Ko et al.

Deep learning has shown strong potential in cancer classification from whole-slide images (WSIs), but the need for extensive expert annotations often limits its success. Annotation-free approaches, such as multiple instance learning (MIL) and self-supervised learning (SSL), have emerged as promising alternatives to traditional annotation-based methods. However, conventional SSL methods typically rely on synthetic data augmentations, which may fail to capture the spatial structure critical to histopathology. In this work, we propose a spatial context-driven positive pair sampling strategy that enhances SSL by leveraging the morphological coherence of spatially adjacent patches within WSIs. Our method is modular and compatible with established joint embedding SSL frameworks, including Barlow Twins, BYOL, VICReg, and DINOv2. We evaluate its effectiveness on both slide-level classification using MIL and patch-level linear probing. Experiments across four datasets demonstrate consistent performance improvements, with accuracy gains of 5\% to 10\% compared to standard augmentation-based sampling. These findings highlight the value of spatial context in improving representation learning for computational pathology and provide a biologically meaningful enhancement for pretraining models in annotation-limited settings. The code is available at https://anonymous.4open.science/r/contextual-pairs-E72F/.

JongWoo Kim, SeongYeub Chu, Bryan Wong et al.

Large Language Models (LLMs) have recently emerged as promising tools for knowledge tracing (KT) due to their strong reasoning and generalization abilities. While recent LLM-based KT methods have proposed new prompt formats, they struggle to represent the full interaction histories of example learners within a single prompt during in-context learning (ICL), resulting in limited scalability and high computational cost under token constraints. In this work, we present \textit{LLM-based Option-weighted Knowledge Tracing (LOKT)}, a simple yet effective framework that encodes the interaction histories of example learners in context as \textit{textual categorical option weights (TCOW)}. TCOW are semantic labels (e.g., ``inadequate'') assigned to the options selected by learners when answering questions, enhancing the interpretability of LLMs. Experiments on multiple-choice datasets show that LOKT outperforms existing non-LLM and LLM-based KT models in both cold-start and warm-start settings. Moreover, LOKT enables scalable and cost-efficient inference, achieving strong performance even under strict token constraints. Our code is available at \href{https://anonymous.4open.science/r/LOKT_model-3233}{https://anonymous.4open.science/r/LOKT\_model-3233}.

Sungrae Hong, Hyeongmin Park, Youngsin Ko et al.

As the frontline data for cancer diagnosis, microscopic pathology images are fundamental for providing patients with rapid and accurate treatment. However, despite their practical value, the deep learning community has largely overlooked their usage. This paper proposes a novel approach to classifying microscopy images as time series data, addressing the unique challenges posed by their manual acquisition and weakly labeled nature. The proposed method fits image sequences of varying lengths to a fixed-length target by leveraging Dynamic Time-series Warping (DTW). Attention-based pooling is employed to predict the class of the case simultaneously. We demonstrate the effectiveness of our approach by comparing performance with various baselines and showcasing the benefits of using various inference strategies in achieving stable and reliable results. Ablation studies further validate the contribution of each component. Our approach contributes to medical image analysis by not only embracing microscopic images but also lifting them to a trustworthy level of performance.