Ikbeom Jang

Matthias Eisenmann, Annika Reinke, Vivienn Weru et al. · utoronto

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Matthias Eisenmann, Annika Reinke, Vivienn Weru et al.

International benchmarking competitions have become fundamental for the comparative performance assessment of image analysis methods. However, little attention has been given to investigating what can be learnt from these competitions. Do they really generate scientific progress? What are common and successful participation strategies? What makes a solution superior to a competing method? To address this gap in the literature, we performed a multi-center study with all 80 competitions that were conducted in the scope of IEEE ISBI 2021 and MICCAI 2021. Statistical analyses performed based on comprehensive descriptions of the submitted algorithms linked to their rank as well as the underlying participation strategies revealed common characteristics of winning solutions. These typically include the use of multi-task learning (63%) and/or multi-stage pipelines (61%), and a focus on augmentation (100%), image preprocessing (97%), data curation (79%), and postprocessing (66%). The "typical" lead of a winning team is a computer scientist with a doctoral degree, five years of experience in biomedical image analysis, and four years of experience in deep learning. Two core general development strategies stood out for highly-ranked teams: the reflection of the metrics in the method design and the focus on analyzing and handling failure cases. According to the organizers, 43% of the winning algorithms exceeded the state of the art but only 11% completely solved the respective domain problem. The insights of our study could help researchers (1) improve algorithm development strategies when approaching new problems, and (2) focus on open research questions revealed by this work.

Juneyong Lee, Geonwoo Baek, Ikbeom Jang

Alzheimer's disease (AD) progresses heterogeneously across individuals, motivating subject-specific synthesis of follow-up magnetic resonance imaging (MRI) to support progression assessment. While Diffusion Transformers (DiT), an emerging transformer-based diffusion model, offer a scalable backbone for image synthesis, longitudinal AD MRI generation with clinically interpretable control over follow-up time and participant metadata remains underexplored. We present ADP-DiT, an interval-aware, clinically text-conditioned diffusion transformer for longitudinal AD MRI synthesis. ADP-DiT encodes follow-up interval together with multi-domain demographic, diagnostic (CN/MCI/AD), and neuropsychological information as a natural-language prompt, enabling time-specific control beyond coarse diagnostic stages. To inject this conditioning effectively, we use dual text encoders-OpenCLIP for vision-language alignment and T5 for richer clinical-language understanding. Their embeddings are fused into DiT through cross-attention for fine-grained guidance and adaptive layer normalization for global modulation. We further enhance anatomical fidelity by applying rotary positional embeddings to image tokens and performing diffusion in a pre-trained SDXL-VAE latent space to enable efficient high-resolution reconstruction. On 3,321 longitudinal 3T T1-weighted scans from 712 participants (259,038 image slices), ADP-DiT achieves SSIM 0.8739 and PSNR 29.32 dB, improving over a DiT baseline by +0.1087 SSIM and +6.08 dB PSNR while capturing progression-related changes such as ventricular enlargement and shrinking hippocampus. These results suggest that integrating comprehensive, subject-specific clinical conditions with architectures can improve longitudinal AD MRI synthesis.

Jiwon Kim, Ikbeom Jang

Medical imaging archives are growing rapidly in both size and resolution, making efficient compression increasingly important for storage and data transfer. Most existing codecs compress full images/volumes(including non-diagnostic background) or apply differential ROI coding that still preserves background bits. We propose MedROI, a codec-agnostic, plug-and-play ROI-centric framework that discards background voxels prior to compression. MedROI extracts a tight tissue bounding box via lightweight intensity-based thresholding and stores a fixed 54byte meta data record to enable spatial restoration during decompression. The cropped ROI is then compressed using any existing 2D or 3D codec without architectural modifications or retraining. We evaluate MedROI on 200 T1-weighted brain MRI volumes from ADNI using 6 codec configurations spanning conventional codecs (JPEG2000 2D/3D, HEIF) and neural compressors (LIC_TCM, TCM+AuxT, BCM-Net, SirenMRI). MedROI yields statistically significant improvements in compression ratio and encoding/decoding time for most configurations (two-sided t-test with multiple-comparison correction), while maintaining comparable reconstruction quality when measured within the ROI; HEIF is the primary exception in compression-ratio gains. For example, on JPEG20002D (lv3), MedROI improves CR from 20.35 to 27.37 while reducing average compression time from 1.701s to 1.380s. Code is available at https://github.com/labhai/MedROI.

Chris Hyunchul Jo, Jiwoong Yang, Byunghwan Jeon et al.

Research question: We test whether a plane shoulder radiograph can be used together with deep learning methods to identify patients with rotator cuff tears as opposed to using an MRI in standard of care. Findings: By integrating convolutional block attention modules into a deep neural network, our model demonstrates high accuracy in detecting patients with rotator cuff tears, achieving an average AUC of 0.889 and an accuracy of 0.831. Meaning: This study validates the efficacy of our deep learning model to accurately detect rotation cuff tears from radiographs, offering a viable pre-assessment or alternative to more expensive imaging techniques such as MRI.

Junho Moon, Haejun Chung, Ikbeom Jang

Facial wrinkle detection plays a crucial role in cosmetic dermatology. Precise manual segmentation of facial wrinkles is challenging and time-consuming, with inherent subjectivity leading to inconsistent results among graders. To address this issue, we propose two solutions. First, we build and release the first public facial wrinkle dataset, 'FFHQ-Wrinkle', an extension of the NVIDIA FFHQ dataset. It includes 1,000 images with human labels and 50,000 images with automatically generated weak labels. This dataset could serve as a foundation for the research community to develop advanced wrinkle detection algorithms. Second, we introduce a simple training strategy utilizing texture maps, applicable to various segmentation models, to detect wrinkles across the face. Our two-stage training strategy first pretrain models on a large dataset with weak labels (N=50k), or masked texture maps generated through computer vision techniques, without human intervention. We then finetune the models using human-labeled data (N=1k), which consists of manually labeled wrinkle masks. The network takes as input a combination of RGB and masked texture map of the image, comprising four channels, in finetuning. We effectively combine labels from multiple annotators to minimize subjectivity in manual labeling. Our strategies demonstrate improved segmentation performance in facial wrinkle segmentation both quantitatively and visually compared to existing pretraining methods. The dataset is available at https://github.com/labhai/ffhq-wrinkle-dataset.

Junho Moon, Haejun Chung, Ikbeom Jang

Accurate segmentation of thin, tortuous anatomical structures, such as retinal vessels, cerebral vasculature, and facial wrinkles, remains challenging due to low contrast, frequent discontinuities, and severe class imbalance. Although recent convolutional and Transformer-based models have improved performance, they often yield fragmented predictions and fail to recover fine branches. We propose CSWinUNETR, a general-purpose backbone for 2D and 3D thin-structure segmentation. It employs cross-shaped stripe self-attention to model long-range principal-axis context and incorporates cyclic shifts to enhance information exchange across stripes. To better preserve fine-grained details, we further introduce a detail-enhanced multi-scale self-attention module that aggregates contextual features from multi-resolution representations. In addition, we propose sparse-control dynamic snake convolution, which reconstructs reliable dense curvilinear kernels from sparsely predicted control points to better follow tortuous geometry. Extensive experiments on four benchmarks across ophthalmology, neurovascular imaging, and dermatology demonstrate that CSWinUNETR consistently outperforms state-of-the-art methods without task-specific post-processing or topology-aware losses. The code is available at https://github.com/labhai/CSWinUNETR.

Jiwoong Yang, Haejun Chung, Ikbeom Jang

Multi-view imaging, such as mammography and chest radiography, is a standard component of clinical practice. However, medical images are often unregistered and contain view-specific artifacts or irrelevant background cues that can obscure diagnostically relevant findings. Many existing methods directly fuse per-view representations, allowing such irrelevant content to contaminate the fused embedding and reducing robustness under varying view configurations. We propose OTCHA, a confidence-aware latent hub token alignment module based on optimal transport (OT) that refines patch tokens before fusion for multi-view classification. OTCHA introduces a set of learnable latent hub tokens shared across views. For each view, we compute an OT plan between patch tokens and hub tokens that jointly considers feature similarity and geometry, and augment the OT formulation with token-conditional dustbins to enable partial matching and discard irrelevant tokens. The resulting transport plan provides token-wise matching confidence, which gates hub-mediated message passing and weights a novel optimal-transport-based representation alignment loss to stabilize refinement. Experiments on three multi-view medical image datasets demonstrate consistent improvements over competing baselines across diverse anatomies and view configurations. Our code is available at https://github.com/labhai/OTCHA.

Daehwan Kim, Haejun Chung, Ikbeom Jang

Medical tabular data are ubiquitous in clinical research, but deep learning for tables remains underexplored because reliable labels often require costly expert adjudication, even though structured clinical variables are routinely available in tabular form. Self-supervised learning can leverage these unlabeled tables, and recent binning-based pretexts offer a promising inductive bias, but existing objectives fix a single global quantile discretization and apply feature-agnostic supervision. We propose Adaptive Binning, a training-adaptive discretization pretext for tabular SSL that couples discretization to learning through a feature-wise coarse-to-fine curriculum. Motivated by the spectral bias of neural networks and the principles of curriculum learning, our method progressively refines discretization per feature upon plateau detection and selects representation-aware splits to jointly improve value-space concentration and representation-space coherence. A heterogeneity-aware objective unifies categorical reconstruction with ordinal supervision for numerical features, and experiments on public medical tabular datasets under unified evaluation protocols show consistent gains for linear probing and fine-tuning without dataset-specific discretization tuning. We further introduce a medical tabular SSL benchmark with standardized protocols to support reproducible progress in this underexplored domain. Our code is available at https://github.com/labhai/Adaptive-Binning.

Yujin Park, Haejun Chung, Ikbeom Jang

Image quality in modern imaging systems emerges from the coupled effects of the sensor, optics, and computational reconstruction. Ultra-thin metalenses offer a path toward substantial miniaturization of optical modules, but practical designs often exhibit pronounced chromatic and field-dependent aberrations that necessitate computational reconstruction. In current metalens pipelines, reconstruction models are commonly trained and selected using distortion-based fidelity objectives, such as PSNR, yet these proxies can be weakly correlated with human preference and downstream utility, reflecting the well-known perception--distortion trade-off. We introduce MetaRanker, a human-in-the-loop active ranking framework that formalizes metalens image quality in terms of semantic interpretability, defined as the degree to which humans can reliably recognize objects and structures in the presence of optical artifacts. MetaRanker combines a probabilistic preference model with uncertainty-aware query selection, and leverages vision--language models to provide lightweight semantic priors. Importantly, these priors are used only to guide the sampling of informative comparisons; human judgments remain the primary supervision signal throughout. Across real-world and synthetic metalens datasets with distinct degradation profiles, MetaRanker produces rankings that align most closely with human assessments, while reducing the number of pairwise annotations required by approximately 80% relative to exhaustive pairwise evaluation. Finally, we show that standard image quality assessment metrics exhibit limited alignment with human interpretability in the metalens domain, positioning MetaRanker as a practical step toward perceptually grounded metalens evaluation and co-design.

Geonwoo Baek, Ikbeom Jang

Confirming Alzheimer's disease (AD) typically relies on positron emission tomography (PET), which remains costly and invasive, motivating the use of structural MRI-based prescreening. Deep learning on non-Euclidean manifolds, particularly brain cortical surfaces, faces significant challenges due to the data's spherical topology. Recent surface models have enabled learning from cortical surface data; however, imposing face-based uniform patches often causes duplicate vertices at patch boundaries. In general, many surface-based models are limited in their awareness of the region of interest (ROI), which can result in non-cortical regions, such as the medial wall, being included. We propose a cortical surface tokenization that performs ROI-preserving, vertex-based, variable-sized patch partitioning. We refer to these cortical surface patches as cortical supervertices (CSVs). Building on this representation, we design the CSV Vision Transformer (CSV-ViT), a variable-size patch-tolerant Vision Transformer that uses padding and a mask-aware patch embedding. We used T1-weighted MRI and evaluated our framework by classifying AD-related status into three categories: AD diagnosis, amyloid positivity, and tau positivity. Across the experiments, CSV-ViT achieved higher classification performance than recent surface-based models. The results suggest that the proposed CSV-ViT may support MRI-based prediction of AD-related status prior to PET or CSF confirmation.

Ik Jun Moon, Junho Moon, Ikbeom Jang

1. Research question: With the growing interest in skin diseases and skin aesthetics, the ability to predict facial wrinkles is becoming increasingly important. This study aims to evaluate whether a computational model, convolutional neural networks (CNN), can be trained for automated facial wrinkle segmentation. 2. Findings: Our study presents an effective technique for integrating data from multiple annotators and illustrates that transfer learning can enhance performance, resulting in dependable segmentation of facial wrinkles. 3. Meaning: This approach automates intricate and time-consuming tasks of wrinkle analysis with a deep learning framework. It could be used to facilitate skin treatments and diagnostics.

Geonwoo Baek, David H. Salat, Ikbeom Jang

Alzheimer's disease (AD) confirmation often relies on positron emission tomography (PET) or cerebrospinal fluid (CSF) analysis, which are costly and invasive. Consequently, structural MRI biomarkers such as cortical thickness (CT) are widely used for non-invasive AD screening. Multiscale structural mapping (MSSM) was recently proposed to integrate gray-white matter contrasts (GWCs) with CT from a single T1-weighted MRI (T1w) scan. Building on this framework, we propose MSSM+, together with surface supervertex mapping (SSVM) and a Supervertex Vision Transformer (SV-ViT). 3D T1w images from individuals with AD and cognitively normal (CN) controls were analyzed. MSSM+ extends MSSM by incorporating sulcal depth and cortical curvature at the vertex level. SSVM partitions the cortical surface into supervertices (surface patches) that effectively represent inter- and intra-regional spatial relationships. SV-ViT is a Vision Transformer architecture operating on these supervertices, enabling anatomically informed learning from surface mesh representations. Compared with MSSM, MSSM+ identified more spatially extensive and statistically significant group differences between AD and CN. In AD vs. CN classification, MSSM+ achieved a 3%p higher area under the precision-recall curve than MSSM. Vendor-specific analyses further demonstrated reduced signal variability and consistently improved classification performance across MR manufacturers relative to CT, GWCs, and MSSM. These findings suggest that MSSM+ combined with SV-ViT is a promising MRI-based imaging marker for AD detection prior to CSF/PET confirmation.

Yujin Park, Haejun Chung, Ikbeom Jang

Pairwise comparison is often favored over absolute rating or ordinal classification in subjective or difficult annotation tasks due to its improved reliability. However, exhaustive comparisons require a massive number of annotations (O(n^2)). Recent work has greatly reduced the annotation burden (O(n log n)) by actively sampling pairwise comparisons using a sorting algorithm. We further improve annotation efficiency by (1) roughly pre-ordering items using the Contrastive Language-Image Pre-training (CLIP) model hierarchically without training, and (2) replacing easy, obvious human comparisons with automated comparisons. The proposed EZ-Sort first produces a CLIP-based zero-shot pre-ordering, then initializes bucket-aware Elo scores, and finally runs an uncertainty-guided human-in-the-loop MergeSort. Validation was conducted using various datasets: face-age estimation (FGNET), historical image chronology (DHCI), and retinal image quality assessment (EyePACS). It showed that EZ-Sort reduced human annotation cost by 90.5% compared to exhaustive pairwise comparisons and by 19.8% compared to prior work (when n = 100), while improving or maintaining inter-rater reliability. These results demonstrate that combining CLIP-based priors with uncertainty-aware sampling yields an efficient and scalable solution for pairwise ranking.

Jiwoong Yang, Haejun Chung, Ikbeom Jang

Multi-view learning often faces challenges in effectively leveraging images captured from different angles and locations. This challenge is particularly pronounced when addressing inconsistencies and uncertainties between views. In this paper, we propose a novel Multi-View Uncertainty-Weighted Mutual Distillation (MV-UWMD) method. Our method enhances prediction consistency by performing hierarchical mutual distillation across all possible view combinations, including single-view, partial multi-view, and full multi-view predictions. This introduces an uncertainty-based weighting mechanism through mutual distillation, allowing effective exploitation of unique information from each view while mitigating the impact of uncertain predictions. We extend a CNN-Transformer hybrid architecture to facilitate robust feature learning and integration across multiple view combinations. We conducted extensive experiments using a large, unstructured dataset captured from diverse, non-fixed viewpoints. The results demonstrate that MV-UWMD improves prediction accuracy and consistency compared to existing multi-view learning approaches.

Daehwan Kim, Haejun Chung, Ikbeom Jang

Recent studies have shown that deep neural networks are not well-calibrated and often produce over-confident predictions. The miscalibration issue primarily stems from using cross-entropy in classifications, which aims to align predicted softmax probabilities with one-hot labels. In ordinal regression tasks, this problem is compounded by an additional challenge: the expectation that softmax probabilities should exhibit unimodal distribution is not met with cross-entropy. The ordinal regression literature has focused on learning orders and overlooked calibration. To address both issues, we propose a novel loss function that introduces ordinal-aware calibration, ensuring that prediction confidence adheres to ordinal relationships between classes. It incorporates soft ordinal encoding and ordinal-aware regularization to enforce both calibration and unimodality. Extensive experiments across four popular ordinal regression benchmarks demonstrate that our approach achieves state-of-the-art calibration without compromising classification accuracy.

Junho Moon, Symac Kim, Haejun Chung et al.

There is a demand for medical image synthesis or translation to generate synthetic images of missing modalities from available data. This need stems from challenges such as restricted access to high-cost imaging devices, government regulations, or failure to follow up with patients or study participants. In medical imaging, preserving high-level semantic features is often more critical than achieving pixel-level accuracy. Perceptual loss functions are widely employed to train medical image synthesis or translation models, as they quantify differences in high-level image features using a pre-trained feature extraction network. While 3D and 2.5D perceptual losses are used in 3D medical image synthesis, they face challenges, such as the lack of pre-trained 3D models or difficulties in balancing loss reduction across different planes. In this work, we focus on synthesizing 3D tau PET images from 3D T1-weighted MR images. We propose a cyclic 2.5D perceptual loss that sequentially computes the 2D average perceptual loss for each of the axial, coronal, and sagittal planes over epochs, with the cycle duration gradually decreasing. Additionally, we process tau PET images using by-manufacturer standardization to enhance the preservation of high-SUVR regions indicative of tau pathology and mitigate SUVR variability caused by inter-manufacturer differences. We combine the proposed loss with SSIM and MSE losses and demonstrate its effectiveness in improving both quantitative and qualitative performance across various generative models, including U-Net, UNETR, SwinUNETR, CycleGAN, and Pix2Pix.

Ikbeom Jang, Garrison Danley, Ken Chang et al.

Ranking by pairwise comparisons has shown improved reliability over ordinal classification. However, as the annotations of pairwise comparisons scale quadratically, this becomes less practical when the dataset is large. We propose a method for reducing the number of pairwise comparisons required to rank by a quantitative metric, demonstrating the effectiveness of the approach in ranking medical images by image quality in this proof of concept study. Using the medical image annotation software that we developed, we actively subsample pairwise comparisons using a sorting algorithm with a human rater in the loop. We find that this method substantially reduces the number of comparisons required for a full ordinal ranking without compromising inter-rater reliability when compared to pairwise comparisons without sorting.

Yukai Zou, Ikbeom Jang

A desire to achieve large medical imaging datasets keeps increasing as machine learning algorithms, parallel computing, and hardware technology evolve. Accordingly, there is a growing demand in pooling data from multiple clinical and academic institutes to enable large-scale clinical or translational research studies. Magnetic resonance imaging (MRI) is a frequently used, non-invasive imaging modality. However, constructing a big MRI data repository has multiple challenges related to privacy, data size, DICOM format, logistics, and non-standardized images. Not only building the data repository is difficult, but using data pooled from the repository is also challenging, due to heterogeneity in image acquisition, reconstruction, and processing pipelines across MRI vendors and imaging sites. This position paper describes challenges in constructing a large MRI data repository and using data downloaded from such data repositories in various aspects. To help address the challenges, the paper proposes introducing a quality assessment pipeline, with considerations and general design principles.