Jee Seok Yoon

Jee Seok Yoon, Chenghao Zhang, Heung-Il Suk et al.

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

Jee Seok Yoon, Kwanseok Oh, Yooseung Shin et al.

Medical image analysis (MedIA) has become an essential tool in medicine and healthcare, aiding in disease diagnosis, prognosis, and treatment planning, and recent successes in deep learning (DL) have made significant contributions to its advances. However, deploying DL models for MedIA in real-world situations remains challenging due to their failure to generalize across the distributional gap between training and testing samples - a problem known as domain shift. Researchers have dedicated their efforts to developing various DL methods to adapt and perform robustly on unknown and out-of-distribution (OOD) data distributions. This article comprehensively reviews domain generalization (DG) studies specifically tailored for MedIA. We provide a holistic view of how DG techniques interact within the broader MedIA system, going beyond methodologies to consider the operational implications on the entire MedIA workflow. Specifically, we categorize DG methods into data-level, feature-level, model-level, and analysis-level methods. We show how those methods can be used in various stages of the MedIA workflow with DL equipped from data acquisition to model prediction and analysis. Furthermore, we critically analyze the strengths and weaknesses of various methods, unveiling future research opportunities.

Ahmad Wisnu Mulyadi, Wonsik Jung, Kwanseok Oh et al.

Diagnosing Alzheimer's disease (AD) involves a deliberate diagnostic process owing to its innate traits of irreversibility with subtle and gradual progression. These characteristics make AD biomarker identification from structural brain imaging (e.g., structural MRI) scans quite challenging. Furthermore, there is a high possibility of getting entangled with normal aging. We propose a novel deep-learning approach through eXplainable AD Likelihood Map Estimation (XADLiME) for AD progression modeling over 3D sMRIs using clinically-guided prototype learning. Specifically, we establish a set of topologically-aware prototypes onto the clusters of latent clinical features, uncovering an AD spectrum manifold. We then measure the similarities between latent clinical features and well-established prototypes, estimating a "pseudo" likelihood map. By considering this pseudo map as an enriched reference, we employ an estimating network to estimate the AD likelihood map over a 3D sMRI scan. Additionally, we promote the explainability of such a likelihood map by revealing a comprehensible overview from two perspectives: clinical and morphological. During the inference, this estimated likelihood map served as a substitute over unseen sMRI scans for effectively conducting the downstream task while providing thorough explainable states.

Sangmin Jo, Jee Seok Yoon, Wootaek Jeong et al.

Deep learning-based automatic sleep staging has significantly advanced in performance and plays a crucial role in the diagnosis of sleep disorders. However, those models often struggle to generalize on unseen subjects due to variability in physiological signals, resulting in degraded performance in out-of-distribution scenarios. To address this issue, domain generalization approaches have recently been studied to ensure generalized performance on unseen domains during training. Among those techniques, contrastive learning has proven its validity in learning domain-invariant features by aligning samples of the same class across different domains. Despite its potential, many existing methods are insufficient to extract adequately domain-invariant representations, as they do not explicitly address domain characteristics embedded within the unshared information across samples. In this paper, we posit that mitigating such domain-relevant attributes-referred to as excess domain-relevant information-is key to bridging the domain gap. However, the direct strategy to mitigate the domain-relevant attributes often overfits features at the high-level information, limiting their ability to leverage the diverse temporal and spectral information encoded in the multiple feature levels. To address these limitations, we propose a novel MEASURE (Multi-scalE minimAl SUfficient Representation lEarning) framework, which effectively reduces domain-relevant information while preserving essential temporal and spectral features for sleep stage classification. In our exhaustive experiments on publicly available sleep staging benchmark datasets, SleepEDF-20 and MASS, our proposed method consistently outperformed state-of-the-art methods. Our code is available at : https://github.com/ku-milab/Measure

Kwanseok Oh, Jee Seok Yoon, Heung-Il Suk

Existing studies on disease diagnostic models focus either on diagnostic model learning for performance improvement or on the visual explanation of a trained diagnostic model. We propose a novel learn-explain-reinforce (LEAR) framework that unifies diagnostic model learning, visual explanation generation (explanation unit), and trained diagnostic model reinforcement (reinforcement unit) guided by the visual explanation. For the visual explanation, we generate a counterfactual map that transforms an input sample to be identified as an intended target label. For example, a counterfactual map can localize hypothetical abnormalities within a normal brain image that may cause it to be diagnosed with Alzheimer's disease (AD). We believe that the generated counterfactual maps represent data-driven and model-induced knowledge about a target task, i.e., AD diagnosis using structural MRI, which can be a vital source of information to reinforce the generalization of the trained diagnostic model. To this end, we devise an attention-based feature refinement module with the guidance of the counterfactual maps. The explanation and reinforcement units are reciprocal and can be operated iteratively. Our proposed approach was validated via qualitative and quantitative analysis on the ADNI dataset. Its comprehensibility and fidelity were demonstrated through ablation studies and comparisons with existing methods.

Kwanseok Oh, Jee Seok Yoon, Heung-Il Suk

There exists an apparent negative correlation between performance and interpretability of deep learning models. In an effort to reduce this negative correlation, we propose a Born Identity Network (BIN), which is a post-hoc approach for producing multi-way counterfactual maps. A counterfactual map transforms an input sample to be conditioned and classified as a target label, which is similar to how humans process knowledge through counterfactual thinking. For example, a counterfactual map can localize hypothetical abnormalities from a normal brain image that may cause it to be diagnosed with a disease. Specifically, our proposed BIN consists of two core components: Counterfactual Map Generator and Target Attribution Network. The Counterfactual Map Generator is a variation of conditional GAN which can synthesize a counterfactual map conditioned on an arbitrary target label. The Target Attribution Network provides adequate assistance for generating synthesized maps by conditioning a target label into the Counterfactual Map Generator. We have validated our proposed BIN in qualitative and quantitative analysis on MNIST, 3D Shapes, and ADNI datasets, and showed the comprehensibility and fidelity of our method from various ablation studies.

Eunjin Jeon, Wonjun Ko, Jee Seok Yoon et al.

In recent years, deep learning-based feature representation methods have shown a promising impact in electroencephalography (EEG)-based brain-computer interface (BCI). Nonetheless, owing to high intra- and inter-subject variabilities, many studies on decoding EEG were designed in a subject-specific manner by using calibration samples, with no concern of its practical use, hampered by time-consuming steps and a large data requirement. To this end, recent studies adopted a transfer learning strategy, especially domain adaptation techniques. Among those, to our knowledge, an adversarial learning has shown its potential in BCIs. In the meantime, it is known that adversarial learning-based domain adaptation methods are prone to negative transfer that disrupts learning generalized feature representations, applicable to diverse domains, e.g., subjects or sessions in BCIs. In this paper, we propose a novel framework that learns class-relevant and subject-invariant feature representations in an information-theoretic manner, without using adversarial learning. To be specific, we devise two operational components in a deep network that explicitly estimate mutual information between feature representations; (1) to decompose features in an intermediate layer into class-relevant and class-irrelevant ones, (2) to enrich class-discriminative feature representation. On two large EEG datasets, we validated the effectiveness of our proposed framework by comparing with several comparative methods in performance. Further, we conducted rigorous analyses by performing an ablation study in regard to the components in our network, explaining our model's decision on input EEG signals via layer-wise relevance propagation, and visualizing the distribution of learned features via t-SNE.

Jee Seok Yoon, Myung-Cheol Roh, Heung-Il Suk

In this article, we focus on decomposing latent representations in generative adversarial networks or learned feature representations in deep autoencoders into semantically controllable factors in a semisupervised manner, without modifying the original trained models. Particularly, we propose factors' decomposer-entangler network (FDEN) that learns to decompose a latent representation into mutually independent factors. Given a latent representation, the proposed framework draws a set of interpretable factors, each aligned to independent factors of variations by minimizing their total correlation in an information-theoretic means. As a plug-in method, we have applied our proposed FDEN to the existing networks of adversarially learned inference and pioneer network and performed computer vision tasks of image-to-image translation in semantic ways, e.g., changing styles, while keeping the identity of a subject, and object classification in a few-shot learning scheme. We have also validated the effectiveness of the proposed method with various ablation studies in the qualitative, quantitative, and statistical examination.