Joohyeok Kim

Taejin Jeong, Joohyeok Kim, Jinyeong Kim et al.

Spatial Transcriptomics (ST) provides spatially-resolved gene expression, offering crucial insights into tissue architecture and complex diseases. However, its prohibitive cost limits widespread adoption, leading to significant attention on inferring spatial gene expression from readily available whole slide images. While graph neural networks have been proposed to model interactions between tissue regions, their reliance on pre-defined sparse graphs prevents them from considering potentially interacting spot pairs, resulting in a structural limitation in capturing complex biological relationships. To address this, we propose FEAST (Fully connected Expressive Attention for Spatial Transcriptomics), an attention-based framework that models the tissue as a fully connected graph, enabling the consideration of all pairwise interactions. To better reflect biological interactions, we introduce negative-aware attention, which models both excitatory and inhibitory interactions, capturing essential negative relationships that standard attention often overlooks. Furthermore, to mitigate the information loss from truncated or ignored context in standard spot image extraction, we introduce an off-grid sampling strategy that gathers additional images from intermediate regions, allowing the model to capture a richer morphological context. Experiments on public ST datasets show that FEAST surpasses state-of-the-art methods in gene expression prediction while providing biologically plausible attention maps that clarify positive and negative interactions. Our code is available at https://github.com/starforTJ/ FEAST.

Joohyeok Kim, Joonhyeon Song, Seohwan Yun et al.

The Foundation model for image segmentation, Segment Anything (SAM), has been actively researched in various fields since its proposal. Various researches have been proposed to adapt SAM to specific domains, with one notable approach involving the addition and training of lightweight adapter modules. While adapter-based fine-tuning approaches have reported parameter efficiency and significant performance improvements, they face a often overlooked issue: the excessive consumption of GPU memory relative to the number of trainable parameters. Addressing this issue, this paper proposes a memory-efficient parallel convolutional adapter architecture. This architecture connects in parallel with SAM's image encoder, eliminating the need to store activations and gradients of the image encoder during model training. Our proposed architecture demonstrated competitive experimental results while using less than half the GPU memory compared to SAM Adapter, indicating its value as an alternative to simple decoder fine-tuning when hardware limitations preclude adapter-based learning. Our code implementation is available at our github.

Joonhyeon Song, Seohwan Yun, Seongho Yoon et al.

This work proposes a novel approach beyond supervised learning for effective pathological image analysis, addressing the challenge of limited robust labeled data. Pathological diagnosis of diseases like cancer has conventionally relied on the evaluation of morphological features by physicians and pathologists. However, recent advancements in compute-aided diagnosis (CAD) systems are gaining significant attention as diagnostic support tools. Although the advancement of deep learning has improved CAD significantly, segmentation models typically require large pixel-level annotated dataset, and such labeling is expensive. Existing studies not based on supervised approaches still struggle with limited generalization, and no practical approach has emerged yet. To address this issue, we present a weakly supervised semantic segmentation (WSSS) model by combining class activation map and Segment Anything Model (SAM)-based pseudo-labeling. For effective pretraining, we adopt the SAM-a foundation model that is pretrained on large datasets and operates in zero-shot configurations using only coarse prompts. The proposed approach transfer enhanced Attention Dropout Layer's knowledge to SAM, thereby generating pseudo-labels. To demonstrate the superiority of the proposed method, experimental studies are conducted on histopathological breast cancer datasets. The proposed method outperformed other WSSS methods across three datasets, demonstrating its efficiency by achieving this with only 12GB of GPU memory during training. Our code is available at : https://github.com/QI-NemoSong/EP-SAM

Taejin Jeong, Joohyeok Kim, Jaehoon Joo et al.

Glaucoma is a major cause of irreversible blindness, with significant diagnostic subjectivity. This inherent uncertainty, combined with the overconfidence of models optimized solely for accuracy can lead to fatal issues such as overdiagnosis or missing critical diseases. To ensure clinical trust, model calibration is essential for reliable predictions, yet study in this field remains limited. Existing calibration study have overlooked glaucoma's systemic associations and high diagnostic subjectivity. To overcome these limitations, we propose V-ViT (Voting-based ViT), a framework that enhances calibration by integrating a patient's binocular information and metadata. Furthermore, to mitigate diagnostic subjectivity, V-ViT utilizes an iterative dropout-based Voting System to maximize calibration performance. The proposed framework achieved state-of-the-art performance across all metrics, including the primary calibration metrics. Our results demonstrate that V-ViT effectively resolves the issue of overconfidence in predictions in glaucoma diagnosis, providing highly reliable predictions for clinical use. Our source code is available at https://github.com/starforTJ/V-ViT.

Jinyeong Kim, Junhyeok Kim, Yumin Shim et al.

How do vision transformers (ViTs) represent and process the world? This paper addresses this long-standing question through the first systematic analysis of 6.6K features across all layers, extracted via sparse autoencoders, and by introducing the residual replacement model, which replaces ViT computations with interpretable features in the residual stream. Our analysis reveals not only a feature evolution from low-level patterns to high-level semantics, but also how ViTs encode curves and spatial positions through specialized feature types. The residual replacement model scalably produces a faithful yet parsimonious circuit for human-scale interpretability by significantly simplifying the original computations. As a result, this framework enables intuitive understanding of ViT mechanisms. Finally, we demonstrate the utility of our framework in debiasing spurious correlations.