Liyue Shen

Rui Yan, Liangqiong Qu, Qingyue Wei et al.

The collection and curation of large-scale medical datasets from multiple institutions is essential for training accurate deep learning models, but privacy concerns often hinder data sharing. Federated learning (FL) is a promising solution that enables privacy-preserving collaborative learning among different institutions, but it generally suffers from performance deterioration due to heterogeneous data distributions and a lack of quality labeled data. In this paper, we present a robust and label-efficient self-supervised FL framework for medical image analysis. Our method introduces a novel Transformer-based self-supervised pre-training paradigm that pre-trains models directly on decentralized target task datasets using masked image modeling, to facilitate more robust representation learning on heterogeneous data and effective knowledge transfer to downstream models. Extensive empirical results on simulated and real-world medical imaging non-IID federated datasets show that masked image modeling with Transformers significantly improves the robustness of models against various degrees of data heterogeneity. Notably, under severe data heterogeneity, our method, without relying on any additional pre-training data, achieves an improvement of 5.06%, 1.53% and 4.58% in test accuracy on retinal, dermatology and chest X-ray classification compared to the supervised baseline with ImageNet pre-training. In addition, we show that our federated self-supervised pre-training methods yield models that generalize better to out-of-distribution data and perform more effectively when fine-tuning with limited labeled data, compared to existing FL algorithms. The code is available at https://github.com/rui-yan/SSL-FL.

Bowen Song, Soo Min Kwon, Zecheng Zhang et al.

Diffusion models have recently emerged as powerful generative priors for solving inverse problems. However, training diffusion models in the pixel space are both data-intensive and computationally demanding, which restricts their applicability as priors for high-dimensional real-world data such as medical images. Latent diffusion models, which operate in a much lower-dimensional space, offer a solution to these challenges. However, incorporating latent diffusion models to solve inverse problems remains a challenging problem due to the nonlinearity of the encoder and decoder. To address these issues, we propose \textit{ReSample}, an algorithm that can solve general inverse problems with pre-trained latent diffusion models. Our algorithm incorporates data consistency by solving an optimization problem during the reverse sampling process, a concept that we term as hard data consistency. Upon solving this optimization problem, we propose a novel resampling scheme to map the measurement-consistent sample back onto the noisy data manifold and theoretically demonstrate its benefits. Lastly, we apply our algorithm to solve a wide range of linear and nonlinear inverse problems in both natural and medical images, demonstrating that our approach outperforms existing state-of-the-art approaches, including those based on pixel-space diffusion models.

Jiankun Zhao, Bowen Song, Liyue Shen

Diffusion models have been demonstrated as strong priors for solving general inverse problems. Most existing Diffusion model-based Inverse Problem Solvers (DIS) employ a plug-and-play approach to guide the sampling trajectory with either projections or gradients. Though effective, these methods generally necessitate hundreds of sampling steps, posing a dilemma between inference time and reconstruction quality. In this work, we try to push the boundary of inference steps to 1-2 NFEs while still maintaining high reconstruction quality. To achieve this, we propose to leverage a pretrained distillation of diffusion model, namely consistency model, as the data prior. The key to achieving few-step guidance is to enforce two types of constraints during the sampling process of the consistency model: soft measurement constraint with ControlNet and hard measurement constraint via optimization. Supporting both single-step reconstruction and multistep refinement, the proposed framework further provides a way to trade image quality with additional computational cost. Within comparable NFEs, our method achieves new state-of-the-art in diffusion-based inverse problem solving, showcasing the significant potential of employing prior-based inverse problem solvers for real-world applications. Code is available at: https://github.com/BioMed-AI-Lab-U-Michgan/cosign.

Haijie Yuan, Chaoyan Huang, Srijita Bandopadhyay et al.

3D volumetric reconstruction from incomplete or noisy measurements is a fundamental problem in medical imaging and computational tomography. Deep image prior (DIP)-based methods have recently shown strong capability for solving inverse problems without requiring large training datasets. However, directly extending DIP to 3D reconstruction by fully 3D networks can incur high computational cost, while slice-by-slice 2D DIP approaches may lead to inter-slice inconsistencies due to the lack of explicit regularization along the third direction. In this paper, we propose a novel volumetric reconstruction framework, Fractional-gradient Autoencoding Sequential Tomography DIP (FAST-DIP), which integrates input-adaptive sequential deep image prior modeling of slices with fractional sparsity regularization to capture inter-slice dependencies. Specifically, we introduce a fractionall1/l2-based sparsity prior on the gradients along the slice (z) direction to explicitly enforce inter-slice structural consistency. We further provide theoretical analysis of the proposed alternating minimization algorithm under the majorization-minimization (MM) framework, establishing monotonic descent of the objective function and convergence to a critical point under the Kurdyka-Lojasiewicz (KL) property. Experimental results for 3D X-ray computed tomography (CT) reconstruction demonstrate that the proposed method improved reconstruction quality and structural consistency compared with existing DIP-based approaches.

James Song, Yifan Wang, Chuan Zhou et al.

Early diagnosis of lung cancer is challenging due to biological uncertainty and the limited understanding of the biological mechanisms driving nodule progression. To address this, we propose Nodule-Aligned Multimodal (Latent) Diffusion (NAMD), a novel framework that predicts lung nodule progression by generating 1-year follow-up nodule computed tomography images with baseline scans and the patient's and nodule's Electronic Health Record (EHR). NAMD introduces a nodule-aligned latent space, where distances between latents directly correspond to changes in nodule attributes, and utilizes an LLM-driven control mechanism to condition the diffusion backbone on patient data. On the National Lung Screening Trial (NLST) dataset, our method synthesizes follow-up nodule images that achieve an AUROC of 0.805 and an AUPRC of 0.346 for lung nodule malignancy prediction, significantly outperforming both baseline scans and state-of-the-art synthesis methods, while closely approaching the performance of real follow-up scans (AUROC: 0.819, AUPRC: 0.393). These results demonstrate that NAMD captures clinically relevant features of lung nodule progression, facilitating earlier and more accurate diagnosis.

Zitao Shuai, Chenwei Wu, Zhengxu Tang et al.

Diffusion Transformers (DiTs) have achieved remarkable success in diverse and high-quality text-to-image(T2I) generation. However, how text and image latents individually and jointly contribute to the semantics of generated images, remain largely unexplored. Through our investigation of DiT's latent space, we have uncovered key findings that unlock the potential for zero-shot fine-grained semantic editing: (1) Both the text and image spaces in DiTs are inherently decomposable. (2) These spaces collectively form a disentangled semantic representation space, enabling precise and fine-grained semantic control. (3) Effective image editing requires the combined use of both text and image latent spaces. Leveraging these insights, we propose a simple and effective Extract-Manipulate-Sample (EMS) framework for zero-shot fine-grained image editing. Our approach first utilizes a multi-modal Large Language Model to convert input images and editing targets into text descriptions. We then linearly manipulate text embeddings based on the desired editing degree and employ constrained score distillation sampling to manipulate image embeddings. We quantify the disentanglement degree of the latent space of diffusion models by proposing a new metric. To evaluate fine-grained editing performance, we introduce a comprehensive benchmark incorporating both human annotations, manual evaluation, and automatic metrics. We have conducted extensive experimental results and in-depth analysis to thoroughly uncover the semantic disentanglement properties of the diffusion transformer, as well as the effectiveness of our proposed method. Our annotated benchmark dataset is publicly available at https://anonymous.com/anonymous/EMS-Benchmark, facilitating reproducible research in this domain.

Jason Hu, Bowen Song, Jeffrey A. Fessler et al.

Diffusion models have achieved excellent success in solving inverse problems due to their ability to learn strong image priors, but existing approaches require a large training dataset of images that should come from the same distribution as the test dataset. When the training and test distributions are mismatched, artifacts and hallucinations can occur in reconstructed images due to the incorrect priors. In this work, we systematically study out of distribution (OOD) problems where a known training distribution is first provided. We first study the setting where only a single measurement obtained from the unknown test distribution is available. Next we study the setting where a very small sample of data belonging to the test distribution is available, and our goal is still to reconstruct an image from a measurement that came from the test distribution. In both settings, we use a patch-based diffusion prior that learns the image distribution solely from patches. Furthermore, in the first setting, we include a self-supervised loss that helps the network output maintain consistency with the measurement. Extensive experiments show that in both settings, the patch-based method can obtain high quality image reconstructions that can outperform whole-image models and can compete with methods that have access to large in-distribution training datasets. Furthermore, we show how whole-image models are prone to memorization and overfitting, leading to artifacts in the reconstructions, while a patch-based model can resolve these issues.

Liang Qiu, Liyue Shen, Lianli Liu et al.

During and after a course of therapy, imaging is routinely used to monitor the disease progression and assess the treatment responses. Despite of its significance, reliably capturing and predicting the spatial-temporal anatomic changes from a sequence of patient-specific image series presents a considerable challenge. Thus, the development of a computational framework becomes highly desirable for a multitude of practical applications. In this context, we propose a strategy of Spatial-Temporal Neural Representation learning with Prior embedding (ST-NeRP) for patient-specific imaging study. Our strategy involves leveraging an Implicit Neural Representation (INR) network to encode the image at the reference time point into a prior embedding. Subsequently, a spatial-temporally continuous deformation function is learned through another INR network. This network is trained using the whole patient-specific image sequence, enabling the prediction of deformation fields at various target time points. The efficacy of the ST-NeRP model is demonstrated through its application to diverse sequential image series, including 4D CT and longitudinal CT datasets within thoracic and abdominal imaging. The proposed ST-NeRP model exhibits substantial potential in enabling the monitoring of anatomical changes within a patient throughout the therapeutic journey.

Bowen Song, Zecheng Zhang, Zhaoxu Luo et al.

Diffusion models have emerged as powerful tools for generative tasks, producing high-quality outputs across diverse domains. However, how the generated data responds to the initial noise perturbation in diffusion models remains under-explored, which hinders understanding the controllability of the sampling process. In this work, we first observe an interesting phenomenon: the relationship between the change of generation outputs and the scale of initial noise perturbation is highly linear through the diffusion ODE sampling. Then we provide both theoretical and empirical study to justify this linearity property of this input-output (noise-generation data) relationship. Inspired by these new insights, we propose a novel Controllable and Constrained Sampling method (CCS) together with a new controller algorithm for diffusion models to sample with desired statistical properties while preserving good sample quality. We perform extensive experiments to compare our proposed sampling approach with other methods on both sampling controllability and sampled data quality. Results show that our CCS method achieves more precisely controlled sampling while maintaining superior sample quality and diversity.

Zitao Shuai, Chenwei Wu, Zhengxu Tang et al.

Diffusion Transformers (DiTs) have recently achieved remarkable success in text-guided image generation. In image editing, DiTs project text and image inputs to a joint latent space, from which they decode and synthesize new images. However, it remains largely unexplored how multimodal information collectively forms this joint space and how they guide the semantics of the synthesized images. In this paper, we investigate the latent space of DiT models and uncover two key properties: First, DiT's latent space is inherently semantically disentangled, where different semantic attributes can be controlled by specific editing directions. Second, consistent semantic editing requires utilizing the entire joint latent space, as neither encoded image nor text alone contains enough semantic information. We show that these editing directions can be obtained directly from text prompts, enabling precise semantic control without additional training or mask annotations. Based on these insights, we propose a simple yet effective Encode-Identify-Manipulate (EIM) framework for zero-shot fine-grained image editing. Specifically, we first encode both the given source image and the text prompt that describes the image, to obtain the joint latent embedding. Then, using our proposed Hessian Score Distillation Sampling (HSDS) method, we identify editing directions that control specific target attributes while preserving other image features. These directions are guided by text prompts and used to manipulate the latent embeddings. Moreover, we propose a new metric to quantify the disentanglement degree of the latent space of diffusion models. Extensive experiment results on our new curated benchmark dataset and analysis demonstrate DiT's disentanglement properties and effectiveness of the EIM framework.

Bowen Song, Jason Hu, Zhaoxu Luo et al.

Diffusion models face significant challenges when employed for large-scale medical image reconstruction in real practice such as 3D Computed Tomography (CT). Due to the demanding memory, time, and data requirements, it is difficult to train a diffusion model directly on the entire volume of high-dimensional data to obtain an efficient 3D diffusion prior. Existing works utilizing diffusion priors on single 2D image slice with hand-crafted cross-slice regularization would sacrifice the z-axis consistency, which results in severe artifacts along the z-axis. In this work, we propose a novel framework that enables learning the 3D image prior through position-aware 3D-patch diffusion score blending for reconstructing large-scale 3D medical images. To the best of our knowledge, we are the first to utilize a 3D-patch diffusion prior for 3D medical image reconstruction. Extensive experiments on sparse view and limited angle CT reconstruction show that our DiffusionBlend method significantly outperforms previous methods and achieves state-of-the-art performance on real-world CT reconstruction problems with high-dimensional 3D image (i.e., $256 \times 256 \times 500$). Our algorithm also comes with better or comparable computational efficiency than previous state-of-the-art methods.

Jason Hu, Bowen Song, Xiaojian Xu et al.

Diffusion models can learn strong image priors from underlying data distribution and use them to solve inverse problems, but the training process is computationally expensive and requires lots of data. Such bottlenecks prevent most existing works from being feasible for high-dimensional and high-resolution data such as 3D images. This paper proposes a method to learn an efficient data prior for the entire image by training diffusion models only on patches of images. Specifically, we propose a patch-based position-aware diffusion inverse solver, called PaDIS, where we obtain the score function of the whole image through scores of patches and their positional encoding and utilize this as the prior for solving inverse problems. First of all, we show that this diffusion model achieves an improved memory efficiency and data efficiency while still maintaining the capability to generate entire images via positional encoding. Additionally, the proposed PaDIS model is highly flexible and can be plugged in with different diffusion inverse solvers (DIS). We demonstrate that the proposed PaDIS approach enables solving various inverse problems in both natural and medical image domains, including CT reconstruction, deblurring, and superresolution, given only patch-based priors. Notably, PaDIS outperforms previous DIS methods trained on entire image priors in the case of limited training data, demonstrating the data efficiency of our proposed approach by learning patch-based prior.

Zongyu Li, Jason Hu, Xiaojian Xu et al.

Phase retrieval (PR) is a crucial problem in many imaging applications. This study focuses on resolving the holographic phase retrieval problem in situations where the measurements are affected by a combination of Poisson and Gaussian noise, which commonly occurs in optical imaging systems. To address this problem, we propose a new algorithm called "AWFS" that uses the accelerated Wirtinger flow (AWF) with a score function as generative prior. Specifically, we formulate the PR problem as an optimization problem that incorporates both data fidelity and regularization terms. We calculate the gradient of the log-likelihood function for PR and determine its corresponding Lipschitz constant. Additionally, we introduce a generative prior in our regularization framework by using score matching to capture information about the gradient of image prior distributions. We provide theoretical analysis that establishes a critical-point convergence guarantee for the proposed algorithm. The results of our simulation experiments on three different datasets show the following: 1) By using the PG likelihood model, the proposed algorithm improves reconstruction compared to algorithms based solely on Gaussian or Poisson likelihood. 2) The proposed score-based image prior method, performs better than the method based on denoising diffusion probabilistic model (DDPM), as well as plug-and-play alternating direction method of multipliers (PnP-ADMM) and regularization by denoising (RED).

Fabian Falck, Yuyin Zhou, Emma Rocheteau et al.

A collection of the accepted abstracts for the Machine Learning for Health (ML4H) symposium 2021. This index is not complete, as some accepted abstracts chose to opt-out of inclusion.

Yang Song, Liyue Shen, Lei Xing et al.

Reconstructing medical images from partial measurements is an important inverse problem in Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). Existing solutions based on machine learning typically train a model to directly map measurements to medical images, leveraging a training dataset of paired images and measurements. These measurements are typically synthesized from images using a fixed physical model of the measurement process, which hinders the generalization capability of models to unknown measurement processes. To address this issue, we propose a fully unsupervised technique for inverse problem solving, leveraging the recently introduced score-based generative models. Specifically, we first train a score-based generative model on medical images to capture their prior distribution. Given measurements and a physical model of the measurement process at test time, we introduce a sampling method to reconstruct an image consistent with both the prior and the observed measurements. Our method does not assume a fixed measurement process during training, and can thus be flexibly adapted to different measurement processes at test time. Empirically, we observe comparable or better performance to supervised learning techniques in several medical imaging tasks in CT and MRI, while demonstrating significantly better generalization to unknown measurement processes.

Liyue Shen, John Pauly, Lei Xing

Image reconstruction is an inverse problem that solves for a computational image based on sampled sensor measurement. Sparsely sampled image reconstruction poses addition challenges due to limited measurements. In this work, we propose an implicit Neural Representation learning methodology with Prior embedding (NeRP) to reconstruct a computational image from sparsely sampled measurements. The method differs fundamentally from previous deep learning-based image reconstruction approaches in that NeRP exploits the internal information in an image prior, and the physics of the sparsely sampled measurements to produce a representation of the unknown subject. No large-scale data is required to train the NeRP except for a prior image and sparsely sampled measurements. In addition, we demonstrate that NeRP is a general methodology that generalizes to different imaging modalities such as CT and MRI. We also show that NeRP can robustly capture the subtle yet significant image changes required for assessing tumor progression.

Liyue Shen, Wei Zhao, Dante Capaldi et al.

Deep learning affords enormous opportunities to augment the armamentarium of biomedical imaging, albeit its design and implementation have potential flaws. Fundamentally, most deep learning models are driven entirely by data without consideration of any prior knowledge, which dramatically increases the complexity of neural networks and limits the application scope and model generalizability. Here we establish a geometry-informed deep learning framework for ultra-sparse 3D tomographic image reconstruction. We introduce a novel mechanism for integrating geometric priors of the imaging system. We demonstrate that the seamless inclusion of known priors is essential to enhance the performance of 3D volumetric computed tomography imaging with ultra-sparse sampling. The study opens new avenues for data-driven biomedical imaging and promises to provide substantially improved imaging tools for various clinical imaging and image-guided interventions.

Liyue Shen, Wentao Zhu, Xiaosong Wang et al.

Multi-domain data are widely leveraged in vision applications taking advantage of complementary information from different modalities, e.g., brain tumor segmentation from multi-parametric magnetic resonance imaging (MRI). However, due to possible data corruption and different imaging protocols, the availability of images for each domain could vary amongst multiple data sources in practice, which makes it challenging to build a universal model with a varied set of input data. To tackle this problem, we propose a general approach to complete the random missing domain(s) data in real applications. Specifically, we develop a novel multi-domain image completion method that utilizes a generative adversarial network (GAN) with a representational disentanglement scheme to extract shared skeleton encoding and separate flesh encoding across multiple domains. We further illustrate that the learned representation in multi-domain image completion could be leveraged for high-level tasks, e.g., segmentation, by introducing a unified framework consisting of image completion and segmentation with a shared content encoder. The experiments demonstrate consistent performance improvement on three datasets for brain tumor segmentation, prostate segmentation, and facial expression image completion respectively.

Masoud Badiei Khuzani, Liyue Shen, Shahin Shahrampour et al.

We propose a novel supervised learning method to optimize the kernel in the maximum mean discrepancy generative adversarial networks (MMD GANs), and the kernel support vector machines (SVMs). Specifically, we characterize a distributionally robust optimization problem to compute a good distribution for the random feature model of Rahimi and Recht. Due to the fact that the distributional optimization is infinite dimensional, we consider a Monte-Carlo sample average approximation (SAA) to obtain a more tractable finite dimensional optimization problem. We subsequently leverage a particle stochastic gradient descent (SGD) method to solve the derived finite dimensional optimization problem. Based on a mean-field analysis, we then prove that the empirical distribution of the interactive particles system at each iteration of the SGD follows the path of the gradient descent flow on the Wasserstein manifold. We also establish the non-asymptotic consistency of the finite sample estimator. We evaluate our kernel learning method for the hypothesis testing problem by evaluating the kernel MMD statistics, and show that our learning method indeed attains better power of the test for larger threshold values compared to an untrained kernel. Moreover, our empirical evaluation on benchmark data-sets shows the advantage of our kernel learning approach compared to alternative kernel learning methods.

Liyue Shen, Katie Shpanskaya, Edward Lee et al.

Fetal brain imaging is a cornerstone of prenatal screening and early diagnosis of congenital anomalies. Knowledge of fetal gestational age is the key to the accurate assessment of brain development. This study develops an attention-based deep learning model to predict gestational age of the fetal brain. The proposed model is an end-to-end framework that combines key insights from multi-view MRI including axial, coronal, and sagittal views. The model also uses age-activated weakly-supervised attention maps to enable rotation-invariant localization of the fetal brain among background noise. We evaluate our methods on the collected fetal brain MRI cohort with a large age distribution from 125 to 273 days. Our extensive experiments show age prediction performance with R2 = 0.94 using multi-view MRI and attention.

Serena Yeung, Vignesh Ramanathan, Olga Russakovsky et al.

Understanding the simultaneously very diverse and intricately fine-grained set of possible human actions is a critical open problem in computer vision. Manually labeling training videos is feasible for some action classes but doesn't scale to the full long-tailed distribution of actions. A promising way to address this is to leverage noisy data from web queries to learn new actions, using semi-supervised or "webly-supervised" approaches. However, these methods typically do not learn domain-specific knowledge, or rely on iterative hand-tuned data labeling policies. In this work, we instead propose a reinforcement learning-based formulation for selecting the right examples for training a classifier from noisy web search results. Our method uses Q-learning to learn a data labeling policy on a small labeled training dataset, and then uses this to automatically label noisy web data for new visual concepts. Experiments on the challenging Sports-1M action recognition benchmark as well as on additional fine-grained and newly emerging action classes demonstrate that our method is able to learn good labeling policies for noisy data and use this to learn accurate visual concept classifiers.

Liang Zheng, Liyue Shen, Lu Tian et al.

For long time, person re-identification and image search are two separately studied tasks. However, for person re-identification, the effectiveness of local features and the "query-search" mode make it well posed for image search techniques. In the light of recent advances in image search, this paper proposes to treat person re-identification as an image search problem. Specifically, this paper claims two major contributions. 1) By designing an unsupervised Bag-of-Words representation, we are devoted to bridging the gap between the two tasks by integrating techniques from image search in person re-identification. We show that our system sets up an effective yet efficient baseline that is amenable to further supervised/unsupervised improvements. 2) We contribute a new high quality dataset which uses DPM detector and includes a number of distractor images. Our dataset reaches closer to realistic settings, and new perspectives are provided. Compared with approaches that rely on feature-feature match, our method is faster by over two orders of magnitude. Moreover, on three datasets, we report competitive results compared with the state-of-the-art methods.