Jong Chul Ye

• Ph. D.
• Korea Advanced Institute of Science and Technology

Flow matching is a recent state-of-the-art framework for generative modeling based on ordinary differential equations (ODEs). While closely related to diffusion models, it provides a more general perspective on generative modeling. Although inverse problem solving has been extensively explored using diffusion models, it has not been rigorously exam...

While recent advancements in generative modeling have significantly improved text-image alignment, some residual misalignment between text and image representations still remains. Although many approaches have attempted to address this issue by fine-tuning models using various reward models, etc., we revisit the challenge from the perspective of re...

Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the high variability caused by disease heterogeneity, makes it challenging to integrate snRNA-seq data from multiple...

Minority samples are underrepresented instances located in low-density regions of a data manifold, and are valuable in many generative AI applications, such as data augmentation, creative content generation, etc. Unfortunately, existing diffusion-based minority generators often rely on computationally expensive guidance dedicated for minority gener...

Compressed sensing MRI seeks to accelerate MRI acquisition processes by sampling fewer k-space measurements and then reconstructing the missing data algorithmically. The success of these approaches often relies on strong priors or learned statistical models. While recent diffusion model-based priors have shown great potential, previous methods typi...

Denoising diffusion models have emerged as the go-to generative framework for solving inverse problems in imaging. A critical concern regarding these models is their performance on out-of-distribution tasks, which remains an under-explored challenge. Using a diffusion model on an out-of-distribution dataset, realistic reconstructions can be generat...

Recent medical vision-language models (VLMs) have shown promise in 2D medical image interpretation. However extending them to 3D medical imaging has been challenging due to computational complexities and data scarcity. Although a few recent VLMs specified for 3D medical imaging have emerged, all are limited to learning volumetric representation of...

Diffusion distillation models effectively accelerate reverse sampling by compressing the process into fewer steps. However, these models still exhibit a performance gap compared to their pre-trained diffusion model counterparts, exacerbated by distribution shifts and accumulated errors during multi-step sampling. To address this, we introduce Disti...

While recent foundational video generators produce visually rich output, they still struggle with appearance drift, where objects gradually degrade or change inconsistently across frames, breaking visual coherence. We hypothesize that this is because there is no explicit supervision in terms of spatial tracking at the feature level. We propose Trac...

In this paper, we propose a novel framework for solving high-definition video inverse problems using latent image diffusion models. Building on recent advancements in spatio-temporal optimization for video inverse problems using image diffusion models, our approach leverages latent-space diffusion models to achieve enhanced video quality and resolu...

Diffusion models have achieved impressive results in generative tasks like text-to-image (T2I) and text-to-video (T2V) synthesis. However, achieving accurate text alignment in T2V generation remains challenging due to the complex temporal dependency across frames. Existing reinforcement learning (RL)-based approaches to enhance text alignment often...

As Classifier-Free Guidance (CFG) has proven effective in conditional diffusion model sampling for improved condition alignment, many applications use a negated CFG term to filter out unwanted features from samples. However, simply negating CFG guidance creates an inverted probability distribution, often distorting samples away from the marginal di...

Acute ischemic stroke (AIS) requires time-critical management, with hours of delayed intervention leading to an irreversible disability of the patient. Since diffusion weighted imaging (DWI) using the magnetic resonance image (MRI) plays a crucial role in the detection of AIS, automated prediction of AIS from DWI has been a research topic of clinic...

While text-to-video diffusion models have made significant strides, many still face challenges in generating videos with temporal consistency. Within diffusion frameworks, guidance techniques have proven effective in enhancing output quality during inference; however, applying these methods to video diffusion models introduces additional complexity...

Diffusion models (DMs), which enable both image generation from noise and inversion from data, have inspired powerful unpaired image-to-image (I2I) translation algorithms. However, they often require a larger number of neural function evaluations (NFEs), limiting their practical applicability. In this paper, we tackle this problem with Schrodinger...

Gradient-based methods are a prototypical family of explainability techniques, especially for image-based models. Nonetheless, they have several shortcomings in that they (1) require white-box access to models, (2) are vulnerable to adversarial attacks, and (3) produce attributions that lie off the image manifold, leading to explanations that are n...

Target volume contouring for radiation therapy is considered significantly more challenging than the normal organ segmentation tasks as it necessitates the utilization of both image and text-based clinical information. Inspired by the recent advancement of large language models (LLMs) that can facilitate the integration of the textural information...

Diffusion and flow-matching models achieve remarkable generative performance but at the cost of many sampling steps, this slows inference and limits applicability to time-critical tasks. The ReFlow procedure can accelerate sampling by straightening generation trajectories. However, ReFlow is an iterative procedure, typically requiring training on s...

We investigate the generation of minority samples using pretrained text-to-image (T2I) latent diffusion models. Minority instances, in the context of T2I generation, can be defined as ones living on low-density regions of text-conditional data distributions. They are valuable for various applications of modern T2I generators, such as data augmentat...

Recent progress in large-scale text-to-video (T2V) and image-to-video (I2V) diffusion models has greatly enhanced video generation, especially in terms of keyframe interpolation. However, current image-to-video diffusion models, while powerful in generating videos from a single conditioning frame, need adaptation for two-frame (start & end) conditi...

Despite significant advancements in customizing text-to-image and video generation models, generating images and videos that effectively integrate multiple personalized concepts remains a challenging task. To address this, we present TweedieMix, a novel method for composing customized diffusion models during the inference phase. By analyzing the pr...

Text-to-image (T2I) diffusion models have revolutionized visual content creation, but extending these capabilities to text-to-video (T2V) generation remains a challenge, particularly in preserving temporal consistency. Existing methods that aim to improve consistency often cause trade-offs such as reduced imaging quality and impractical computation...

Autoregressive models (ARMs) and diffusion models (DMs) represent two leading paradigms in generative modeling, each excelling in distinct areas: ARMs in global context modeling and long-sequence generation, and DMs in generating high-quality local contexts, especially for continuous data such as images and short videos. However, ARMs often suffer...

Diffusion models have become increasingly popular for generative modeling due to their ability to generate high-quality samples. This has unlocked exciting new possibilities for solving inverse problems, especially in image restoration and reconstruction, by treating diffusion models as unsupervised priors. This survey provides a comprehensive over...

Clinical experts employ diverse philosophies and strategies in patient care, influenced by regional patient populations. However, existing medical artificial intelligence (AI) models are often trained on data distributions that disproportionately reflect highly prevalent patterns, reinforcing biases and overlooking the diverse expertise of clinicia...

We propose FD3, a fundus image enhancement method based on direct diffusion bridges, which can cope with a wide range of complex degradations, including haze, blur, noise, and shadow. We first propose a synthetic forward model through a human feedback loop with board-certified ophthalmologists for maximal quality improvement of low-quality in-vivo...

Recently, diffusion model-based inverse problem solvers (DIS) have emerged as state-of-the-art approaches for addressing inverse problems, including image super-resolution, deblurring, inpainting, etc. However, their application to video inverse problems arising from spatio-temporal degradation remains largely unexplored due to the challenges in tr...

We propose FD3, a fundus image enhancement method based on direct diffusion bridges, which can cope with a wide range of complex degradations, including haze, blur, noise, and shadow. We first propose a synthetic forward model through a human feedback loop with board-certified ophthalmologists for maximal quality improvement of low-quality in-vivo...

We propose a variational inference approach to sample from the posterior distribution for solving inverse problems. From a pre-trained diffusion model, our approach trains a conditional flow model to minimize the divergence between the proposal variational distribution and the posterior distribution implicitly defined through the diffusion model. O...

In this work, we propose to study the global geometrical properties of generative models. We introduce a new Riemannian metric to assess the similarity between any two data points. Importantly , our metric is agnostic to the parametriza-tion of the generative model and requires only the evaluation of its data likelihood. Moreover, the metric leads...

We present a novel approach for generating minority samples that live on low-density regions of a data manifold. Our framework is built upon diffusion models, leveraging the principle of guided sampling that incorporates an arbitrary energy-based guidance during inference time. The key defining feature of our sampler lies in its \emph{self-containe...

Recent inverse problem solvers that leverage generative diffusion priors have garnered significant attention due to their exceptional quality. However, adaptation of the prior is necessary when there exists a discrepancy between the training and testing distributions. In this work, we propose deep diffusion image prior (DDIP), which generalizes the...

In this work, we propose to study the global geometrical properties of generative models. We introduce a new Riemannian metric to assess the similarity between any two data points. Importantly, our metric is agnostic to the parametrization of the generative model and requires only the evaluation of its data likelihood. Moreover, the metric leads to...

Despite promising advancements in deep learning in medical domains, challenges still remain owing to data scarcity, compounded by privacy concerns and data ownership disputes. Recent explorations of distributed-learning paradigms, particularly federated learning, have aimed to mitigate these challenges. However, these approaches are often encumbere...

Classifier-free guidance (CFG) is a fundamental tool in modern diffusion models for text-guided generation. Although effective, CFG has notable drawbacks. For instance, DDIM with CFG lacks invertibility, complicating image editing; furthermore, high guidance scales, essential for high-quality outputs, frequently result in issues like mode collapse....

With the emergence of diffusion models as the frontline of generative models, many researchers have proposed molecule generation techniques using conditional diffusion models. However, due to the fundamental nature of a molecule, which carries highly entangled correlations within a small number of atoms and bonds, it becomes difficult for a model t...

While text-to-image models have achieved impressive capabilities in image generation and editing, their application across various modalities often necessitates training separate models. Inspired by existing method of single image editing with self attention injection and video editing with shared attention, we propose a novel unified editing frame...

Research efforts to understand neural signals have been ongoing for many years, with visual decoding from fMRI signals attracting considerable attention. Particularly, the advent of image diffusion models has advanced the reconstruction of images from fMRI data significantly. However, existing approaches often introduce inter- and intra- subject va...

Background: Osteoporosis is the most common metabolic bone disease and can cause fragility fractures. Despite this, screening utilization rates for osteoporosis remain low among populations at risk. Automated bone mineral density (BMD) estimation using computed tomography (CT) can help bridge this gap and serve as an alternative screening method t...

Recently, patch-wise contrastive learning is drawing attention for the image translation by exploring the semantic correspondence between the input image and the output image. To further explore the patch-wise topology for high-level semantic understanding, here we exploit the graph neural network to capture the topology-aware features. Specificall...

Recent successes of foundation models in artificial intelligence have prompted the emergence of large-scale chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited...

DCE-MRI provides information about vascular permeability and tissue perfusion through the acquisition of pharmacokinetic parameters. However, traditional methods for estimating these pharmacokinetic parameters involve fitting tracer kinetic models, which often suffer from computational complexity and low accuracy due to noisy arterial input functio...

Purpose: We present a dehazing algorithm using dark channel prior (DCP) and bright channel prior (BCP) to enhance the quality of retinal images obtained through conventional fundus photography.Methods: A retrospective analysis was conducted on retinal images from patients who visited Gangnam Sacred Heart Hospital between January 2000 and September...

Patients with acute coronary syndromes caused by plaque erosion might be managed conservatively without stenting. Currently, the diagnosis of plaque erosion requires an invasive imaging procedure. We sought to develop a deep learning (DL) model that enables an accurate diagnosis of plaque erosion using coronary computed tomography angiography (CTA)...

Automatic Speech Recognition (ASR) is a technology that converts spoken words into text, facilitating interaction between humans and machines. One of the most common applications of ASR is Speech-To-Text (STT) technology, which simplifies user workflows by transcribing spoken words into text. In the medical field, STT has the potential to significa...

Discover the power of deep neural networks for image reconstruction with this state-of-the-art review of modern theories and applications. The background theory of deep learning is introduced step-by-step, and by incorporating modeling fundamentals this book explains how to implement deep learning in a variety of modalities, including X-ray, CT, MR...

Discover the power of deep neural networks for image reconstruction with this state-of-the-art review of modern theories and applications. The background theory of deep learning is introduced step-by-step, and by incorporating modeling fundamentals this book explains how to implement deep learning in a variety of modalities, including X-ray, CT, MR...

Discover the power of deep neural networks for image reconstruction with this state-of-the-art review of modern theories and applications. The background theory of deep learning is introduced step-by-step, and by incorporating modeling fundamentals this book explains how to implement deep learning in a variety of modalities, including X-ray, CT, MR...

Discover the power of deep neural networks for image reconstruction with this state-of-the-art review of modern theories and applications. The background theory of deep learning is introduced step-by-step, and by incorporating modeling fundamentals this book explains how to implement deep learning in a variety of modalities, including X-ray, CT, MR...

Discover the power of deep neural networks for image reconstruction with this state-of-the-art review of modern theories and applications. The background theory of deep learning is introduced step-by-step, and by incorporating modeling fundamentals this book explains how to implement deep learning in a variety of modalities, including X-ray, CT, MR...

Discover the power of deep neural networks for image reconstruction with this state-of-the-art review of modern theories and applications. The background theory of deep learning is introduced step-by-step, and by incorporating modeling fundamentals this book explains how to implement deep learning in a variety of modalities, including X-ray, CT, MR...

Denoising diffusion models have emerged as the go-to framework for solving inverse problems in imaging. A critical concern regarding these models is their performance on out-of-distribution (OOD) tasks, which remains an under-explored challenge. Realistic reconstructions inconsistent with the measured data can be generated, hallucinating image feat...

Objective: To assess whether computed tomography (CT) conversion across different scan parameters and manufacturers using a routable generative adversarial network (RouteGAN) can improve the accuracy and variability in quantifying interstitial lung disease (ILD) using a deep learning-based automated software. Materials and methods: This study in...

Blood vessel segmentation in medical imaging is one of the essential steps for vascular disease diagnosis and interventional planning in a broad spectrum of clinical scenarios in image-based medicine and interventional medicine. Unfortunately, manual annotation of the vessel masks is challenging and resource-intensive due to subtle branches and com...

Recent advances in generative AI have brought incredible breakthroughs in several areas, including medical imaging. These generative models have tremendous potential not only to help safely share medical data via synthetic datasets but also to perform an array of diverse applications, such as anomaly detection, image-to-image translation, denoising...

Twenty-five years ago, the field of computational imaging arguably did not exist, at least not as a standalone arena of research activity and technical development. Of course, the idea of using computation to form images had been around for several decades, largely thanks to the development of medical imaging—such as magnetic resonance imaging (MRI...

There are many recent research efforts to fine-tune a pre-trained generator with a few target images to generate images of a novel domain. Unfortunately, these methods often suffer from overfitting or under-fitting when fine-tuned with a single target image. To address this, here we present a novel single-shot GAN adaptation method through unified...

Despite the remarkable performance of text-to-image diffusion models in image generation tasks, recent studies have raised the issue that generated images sometimes cannot capture the intended semantic contents of the text prompts, which phenomenon is often called semantic misalignment. To address this, here we present a novel energy-based model (E...

DCE-MRI provides information about vascular permeability and tissue perfusion through the acquisition of pharmacokinetic parameters. However, traditional methods for estimating these pharmacokinetic parameters involve fitting tracer kinetic models, which often suffer from computational complexity and low accuracy due to noisy arterial input functio...

Diffusion models have shown significant progress in image translation tasks recently. However, due to their stochastic nature, there's often a trade-off between style transformation and content preservation. Current strategies aim to disentangle style and content, preserving the source image's structure while successfully transitioning from a sourc...

Objective: Detection of pneumoperitoneum using abdominal radiography, particularly in the supine position, is often challenging. This study aimed to develop and externally validate a deep learning model for the detection of pneumoperitoneum using supine and erect abdominal radiography. Materials and methods: A model that can utilize "pneumoperit...

Diffusion model-based inverse problem solvers have shown impressive performance, but are limited in speed, mostly as they require reverse diffusion sampling starting from noise. Several recent works have tried to alleviate this problem by building a diffusion process, directly bridging the clean and the corrupted for specific inverse problems. In t...

This paper explores the use of score-based diffusion models for Bayesian image reconstruction. Diffusion models are an efficient tool for generative modeling. Diffusion models can also be used for solving image reconstruction problems. We present a simple and flexible algorithm for training a diffusion model and using it for maximum a posteriori re...

This paper investigates the relationship between the universal approximation property of deep neural networks and topological characteristics of datasets. Our primary contribution is to introduce data topology-dependent upper bounds on the network width. Specifically, we first show that a three-layer neural network, applying a ReLU activation funct...

Diffusion models are a powerful class of generative models which simulate stochastic differential equations (SDEs) to generate data from noise. Although diffusion models have achieved remarkable progress in recent years, they have limitations in the unpaired image-to-image translation tasks due to the Gaussian prior assumption. Schr\"odinger Bridge...

Building on the recent remarkable development of large language models (LLMs), active attempts are being made to extend the utility of LLMs to multimodal tasks. There have been previous efforts to link language and visual information, and attempts to add visual capabilities to LLMs are ongoing as well. However, existing attempts use LLMs only as im...

Gastric endoscopic screening is an effective way to decide appropriate gastric cancer treatment at an early stage, reducing gastric cancer-associated mortality rate. Although artificial intelligence has brought a great promise to assist pathologist to screen digitalized endoscopic biopsies, existing artificial intelligence systems are limited to be...

Diffusion models have shown great promise in text-guided image style transfer, but there is a trade-off between style transformation and content preservation due to their stochastic nature. Existing methods require computationally expensive fine-tuning of diffusion models or additional neural network. To address this, here we propose a zero-shot co...

Diffusion models have shown exceptional performance in solving inverse problems. However, one major limitation is the slow inference time. While faster diffusion samplers have been developed for unconditional sampling, there has been limited research on conditional sampling in the context of inverse problems. In this study, we propose a novel and e...

Thanks to the tremendous interest from the research community, the focus of the March issue of the IEEE Signal Processing Magazine is on the second volume of the special issue on physics-driven machine learning for computational imaging, which brings together nine articles of the 19 accepted papers from the original 47 submissions.

Automatic Speech Recognition (ASR) is a technology that converts spoken words into text, facilitating interaction between humans and machines. One of the most common applications of ASR is Speech-To-Text (STT) technology, which simplifies user workflows by transcribing spoken words into text. In the medical field, STT has the potential to significa...

Healed coronary plaques, morphologically characterized by a layered phenotype, are signs of previous plaque destabilization and healing. Recent optical coherence tomography (OCT) studies demonstrated that layered plaque is associated with higher levels of local and systemic inflammation and rapid plaque progression. However, the diagnosis of layere...