Mun Yong Yi

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

Jiwon Jeong, Donghee Han, Sungrae Hong et al.

Recent work has shown that large language models (LLMs) can enhance recommender systems by integrating collaborative filtering (CF) signals through hybrid prompting. However, most existing CF-LLM frameworks collapse explicit ratings into implicit or positive-only feedback, discarding the ordinal structure that conveys fine-grained preference strength. As a result, these models struggle to exploit graded semantics and nuanced preference distinctions. We propose Ordinal Semantic Anchoring (OSA), a hybrid CF-LLM framework that explicitly incorporates preference strength by modeling interaction-level user feedback. OSA represents ordinal preference levels as numeric textual tokens and uses their token embeddings as semantic anchors to align user-item interaction representations in the LLM latent space. Through strength-aware alignment across ordinal levels, OSA preserves preference semantics when integrating collaborative signals with LLMs. Experiments on multiple real-world datasets demonstrate that OSA consistently outperforms existing baselines, particularly in pairwise preference evaluation, highlighting its effectiveness in modeling fine-grained user preferences over prior CF-LLM methods.

Sungrae Hong, Jiwon Jeong, Jisu Shin et al.

Multiple Instance Learning (MIL) has emerged as a promising paradigm for Whole Slide Image (WSI) diagnosis, offering effective learning with limited annotations. However, existing MIL frameworks overlook diagnostic priorities and fail to differentiate the severity of misclassifications in multiclass, leaving clinically critical errors unaddressed. We propose a mistake-severity-aware training strategy that organizes diagnostic classes into a hierarchical structure, with each level optimized using a severity-weighted cross-entropy loss that penalizes high-severity misclassifications more strongly. Additionally, hierarchical consistency is enforced through probabilistic alignment, a semantic feature remix applied to the instance bag to robustly train class priority and accommodate clinical cases involving multiple symptoms. An asymmetric Mikel's Wheel-based metric is also introduced to quantify the severity of errors specific to medical fields. Experiments on challenging public and real-world in-house datasets demonstrate that our approach significantly mitigates critical errors in MIL diagnosis compared to existing methods. We present additional experimental results on natural domain data to demonstrate the generalizability of our proposed method beyond medical contexts.

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

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/.

Daeyoung Roh, Donghee Han, Daehee Kim et al.

Hypergraphs provide a superior modeling framework for representing complex multidimensional relationships in the context of real-world interactions that often occur in groups, overcoming the limitations of traditional homogeneous graphs. However, there have been few studies on hypergraphbased contrastive learning, and existing graph-based contrastive learning methods have not been able to fully exploit the highorder correlation information in hypergraphs. Here, we propose a Hypergraph Fine-grained contrastive learning (HyFi) method designed to exploit the complex high-dimensional information inherent in hypergraphs. While avoiding traditional graph augmentation methods that corrupt the hypergraph topology, the proposed method provides a simple and efficient learning augmentation function by adding noise to node features. Furthermore, we expands beyond the traditional dichotomous relationship between positive and negative samples in contrastive learning by introducing a new relationship of weak positives. It demonstrates the importance of fine-graining positive samples in contrastive learning. Therefore, HyFi is able to produce highquality embeddings, and outperforms both supervised and unsupervised baselines in average rank on node classification across 10 datasets. Our approach effectively exploits high-dimensional hypergraph information, shows significant improvement over existing graph-based contrastive learning methods, and is efficient in terms of training speed and GPU memory cost. The source code is available at https://github.com/Noverse0/HyFi.git.

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}.

Seongyeub Chu, Jongwoo Kim, Mun Yong Yi

MOOC recommendation systems have received increasing attention to help learners navigate and select preferred learning content. Traditional methods such as collaborative filtering and content-based filtering suffer from data sparsity and over-specialization. To alleviate these limitations, graph-based approaches have been proposed; however, they still rely heavily on manually predefined metapaths, which often capture only superficial structural relationships and impose substantial burdens on domain experts as well as significant engineering costs. To overcome these limitations, we propose AMR (Aspect-aware MOOC Recommendation), a novel framework that models path-specific multiple aspects by embedding the semantic content of nodes within each metapath. AMR automatically discovers metapaths through bi-directional walks, derives aspect-aware path representations using a bi-LSTM-based encoder, and incorporates these representations as edge features in the learner-learner and KC-KC subgraphs to achieve fine-grained semantically informed KC recommendations. Extensive experiments on the large-scale MOOCCube and PEEK datasets show that AMR consistently outperforms state-of-the-art graph neural network baselines across key metrics such as HR@K and nDCG@K. Further analysis confirms that AMR effectively captures rich path-specific aspect information, allowing more accurate recommendations than those methods that rely solely on predefined metapaths. The code will be available upon accepted.

Sungrae Hong, Jiwon Jeong, Soeun Cheon et al.

Multiple Instance Learning (MIL) is a standard paradigm for Whole-Slide Image (WSI) analysis and has achieved strong results in computational pathology. However, most MIL pipelines assume a single "gold" label per slide, which conflicts with clinical practice where substantial inter-pathologist variability is common. Existing multi-annotator learning and label-refinement methods typically estimate global annotator reliability or rely on single-instance assumptions, making them poorly suited to MIL and to localized diagnostic contexts where experts disagree. We propose RaLMPH (Reliability-aware Learning for Multi-Pathologist Harmonization), a MIL-based label reconciliation framework for WSIs annotated by multiple pathologists. RaLMPH introduces a reliability field that jointly models (i) local neighborhood structure in WSI feature space and (ii) expert uncertainty (entropy), enabling per-sample identification of trustworthy reference neighborhoods. Leveraging this field, RaLMPH performs sample-wise local annotator ranking to select reliable opinions per slide and applies an adaptive gating mechanism to fuse labels conditioned on local reliability. Experiments on a clinical WSI dataset with labels from six pathologists, as well as controlled simulated benchmarks, show that RaLMPH consistently outperforms existing approaches. Further analyses clarify how our reliability-aware mechanism improves label reconciliation and downstream MIL performance.

Sungrae Hong, Kyungeun Kim, Juhyeon Kim et al.

Multiple Instance Learning (MIL) is increasingly being used as a support tool within clinical settings for pathological diagnosis decisions, achieving high performance and removing the annotation burden. However, existing approaches for clinical MIL tasks have not adequately addressed the priority issues that exist in relation to pathological symptoms and diagnostic classes, causing MIL models to ignore priority among classes. To overcome this clinical limitation of MIL, we propose a new method that addresses priority issues using two hierarchies: vertical inter-hierarchy and horizontal intra-hierarchy. The proposed method aligns MIL predictions across each hierarchical level and employs an implicit feature re-usability during training to facilitate clinically more serious classes within the same level. Experiments with real-world patient data show that the proposed method effectively reduces misdiagnosis and prioritizes more important symptoms in multiclass scenarios. Further analysis verifies the efficacy of the proposed components and qualitatively confirms the MIL predictions against challenging cases with multiple symptoms.

Donghee Han, Daehee Kim, Minjun Lee et al.

The rise of online learning has led to the development of various knowledge tracing (KT) methods. However, existing methods have overlooked the problem of increasing computational cost when utilizing large graphs and long learning sequences. To address this issue, we introduce Dual Graph Attention-based Knowledge Tracing (DGAKT), a graph neural network model designed to leverage high-order information from subgraphs representing student-exercise-KC relationships. DGAKT incorporates a subgraph-based approach to enhance computational efficiency. By processing only relevant subgraphs for each target interaction, DGAKT significantly reduces memory and computational requirements compared to full global graph models. Extensive experimental results demonstrate that DGAKT not only outperforms existing KT models but also sets a new standard in resource efficiency, addressing a critical need that has been largely overlooked by prior KT approaches.

Sungrae Hong, Sol Lee, Mun Yong Yi

Medical AI diagnosis including histopathology segmentation has derived benefits from the recent development of deep learning technology. However, deep learning itself requires a large amount of training data and the medical image segmentation masking, in particular, requires an extremely high cost due to the shortage of medical specialists. To mitigate this issue, we propose a new data augmentation method built upon the conventional Copy and Paste (CP) augmentation technique, called CP-Dilatation, and apply it to histopathology image segmentation. To the well-known traditional CP technique, the proposed method adds a dilation operation that can preserve the boundary context information of the malignancy, which is important in histopathological image diagnosis, as the boundary between the malignancy and its margin is mostly unclear and a significant context exists in the margin. In our experiments using histopathology benchmark datasets, the proposed method was found superior to the other state-of-the-art baselines chosen for comparison.

Donghee Han, Hwanjun Song, Mun Yong Yi

Recent studies have explored integrating large language models (LLMs) into recommendation systems but face several challenges, including training-induced bias and bottlenecks from serialized architecture. To effectively address these issues, we propose a Query-toRecommendation, a parallel recommendation framework that decouples LLMs from candidate pre-selection and instead enables direct retrieval over the entire item pool. Our framework connects LLMs and recommendation models in a parallel manner, allowing each component to independently utilize its strengths without interfering with the other. In this framework, LLMs are utilized to generate feature-enriched item descriptions and personalized user queries, allowing for capturing diverse preferences and enabling rich semantic matching in a zero-shot manner. To effectively combine the complementary strengths of LLM and collaborative signals, we introduce an adaptive reranking strategy. Extensive experiments demonstrate an improvement in performance up to 57%, while also improving the novelty and diversity of recommendations.

Gautam Singh, Saemi Jang, Mun Y. Yi

Ontologies in different natural languages often differ in quality in terms of richness of schema or richness of internal links. This difference is markedly visible when comparing a rich English language ontology with a non-English language counterpart. Discovering alignment between them is a useful endeavor as it serves as a starting point in bridging the disparity. In particular, our work is motivated by the absence of inter-language links for predicates in the localised versions of DBpedia. In this paper, we propose and demonstrate an ad-hoc system to find possible owl:equivalentProperty links between predicates in ontologies of different natural languages. We seek to achieve this mapping by using pre-existing inter-language links of the resources connected by the given predicate. Thus, our methodology stresses on semantic similarity rather than lexical. Moreover, through an evaluation, we show that our system is capable of outperforming a baseline system that is similar to the one used in recent OAEI campaigns.