Lei Xing

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.

Qingyue Wei, Lequan Yu, Xianhang Li et al.

Medical imaging has witnessed remarkable progress but usually requires a large amount of high-quality annotated data which is time-consuming and costly to obtain. To alleviate this burden, semi-supervised learning has garnered attention as a potential solution. In this paper, we present Meta-Learning for Bootstrapping Medical Image Segmentation (MLB-Seg), a novel method for tackling the challenge of semi-supervised medical image segmentation. Specifically, our approach first involves training a segmentation model on a small set of clean labeled images to generate initial labels for unlabeled data. To further optimize this bootstrapping process, we introduce a per-pixel weight mapping system that dynamically assigns weights to both the initialized labels and the model's own predictions. These weights are determined using a meta-process that prioritizes pixels with loss gradient directions closer to those of clean data, which is based on a small set of precisely annotated images. To facilitate the meta-learning process, we additionally introduce a consistency-based Pseudo Label Enhancement (PLE) scheme that improves the quality of the model's own predictions by ensembling predictions from various augmented versions of the same input. In order to improve the quality of the weight maps obtained through multiple augmentations of a single input, we introduce a mean teacher into the PLE scheme. This method helps to reduce noise in the weight maps and stabilize its generation process. Our extensive experimental results on public atrial and prostate segmentation datasets demonstrate that our proposed method achieves state-of-the-art results under semi-supervision. Our code is available at https://github.com/aijinrjinr/MLB-Seg.

Jieneng Chen, Jieru Mei, Xianhang Li et al.

Medical image segmentation plays a crucial role in advancing healthcare systems for disease diagnosis and treatment planning. The u-shaped architecture, popularly known as U-Net, has proven highly successful for various medical image segmentation tasks. However, U-Net's convolution-based operations inherently limit its ability to model long-range dependencies effectively. To address these limitations, researchers have turned to Transformers, renowned for their global self-attention mechanisms, as alternative architectures. One popular network is our previous TransUNet, which leverages Transformers' self-attention to complement U-Net's localized information with the global context. In this paper, we extend the 2D TransUNet architecture to a 3D network by building upon the state-of-the-art nnU-Net architecture, and fully exploring Transformers' potential in both the encoder and decoder design. We introduce two key components: 1) A Transformer encoder that tokenizes image patches from a convolution neural network (CNN) feature map, enabling the extraction of global contexts, and 2) A Transformer decoder that adaptively refines candidate regions by utilizing cross-attention between candidate proposals and U-Net features. Our investigations reveal that different medical tasks benefit from distinct architectural designs. The Transformer encoder excels in multi-organ segmentation, where the relationship among organs is crucial. On the other hand, the Transformer decoder proves more beneficial for dealing with small and challenging segmented targets such as tumor segmentation. Extensive experiments showcase the significant potential of integrating a Transformer-based encoder and decoder into the u-shaped medical image segmentation architecture. TransUNet outperforms competitors in various medical applications.

Bingqian Lin, Zicong Chen, Mingjie Li et al.

Medical artificial general intelligence (MAGI) enables one foundation model to solve different medical tasks, which is very practical in the medical domain. It can significantly reduce the requirement of large amounts of task-specific data by sufficiently sharing medical knowledge among different tasks. However, due to the challenges of designing strongly generalizable models with limited and complex medical data, most existing approaches tend to develop task-specific models. To take a step towards MAGI, we propose a new paradigm called Medical-knOwledge-enhanced mulTimOdal pretRaining (MOTOR). In MOTOR, we combine two kinds of basic medical knowledge, i.e., general and specific knowledge, in a complementary manner to boost the general pretraining process. As a result, the foundation model with comprehensive basic knowledge can learn compact representations from pretraining radiographic data for better cross-modal alignment. MOTOR unifies the understanding and generation, which are two kinds of core intelligence of an AI system, into a single medical foundation model, to flexibly handle more diverse medical tasks. To enable a comprehensive evaluation and facilitate further research, we construct a medical multimodal benchmark including a wide range of downstream tasks, such as chest x-ray report generation and medical visual question answering. Extensive experiments on our benchmark show that MOTOR obtains promising results through simple task-oriented adaptation. The visualization shows that the injected knowledge successfully highlights key information in the medical data, demonstrating the excellent interpretability of MOTOR. Our MOTOR successfully mimics the human practice of fulfilling a "medical student" to accelerate the process of becoming a "specialist". We believe that our work makes a significant stride in realizing MAGI.

Yunfei Xie, Ce Zhou, Lang Gao et al.

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities with multigranular annotations for more than 65 diseases. These multigranular annotations encompass both global information, such as modality and organ detection, and local information like ROI analysis, lesion texture, and region-wise correlations. Unlike the existing multimodal datasets, which are limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and textual annotations in the form of image-ROI-description triplets without the need for any paired text descriptions. Specifically, data from over 30 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular textual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. We propose LLaVA-Tri by pretraining LLaVA on MedTrinity-25M, achieving state-of-the-art performance on VQA-RAD, SLAKE, and PathVQA, surpassing representative SOTA multimodal large language models. Furthermore, MedTrinity-25M can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain. We will make our dataset available.

Sheng Liu, Haotian Ye, Lei Xing et al.

Large language models (LLMs) demonstrate emergent in-context learning capabilities, where they adapt to new tasks based on example demonstrations. However, in-context learning has seen limited effectiveness in many settings, is difficult to quantitatively control and takes up context window space. To overcome these limitations, we propose an alternative approach that recasts in-context learning as in-context vectors (ICV). Using ICV has two steps. We first use a forward pass on demonstration examples to create the in-context vector from the latent embedding of the LLM. This vector captures essential information about the intended task. On a new query, instead of adding demonstrations to the prompt, we shift the latent states of the LLM using the ICV. The ICV approach has several benefits: 1) it enables the LLM to more effectively follow the demonstration examples; 2) it's easy to control by adjusting the magnitude of the ICV; 3) it reduces the length of the prompt by removing the in-context demonstrations; 4) ICV is computationally much more efficient than fine-tuning. We demonstrate that ICV achieves better performance compared to standard in-context learning and fine-tuning on diverse tasks including safety, style transfer, role-playing and formatting. Moreover, we show that we can flexibly teach LLM to simultaneously follow different types of instructions by simple vector arithmetics on the corresponding ICVs.

Charles Huang, Varun Vasudevan, Oscar Pastor-Serrano et al.

Objective: Knowledge based planning (KBP) typically involves training an end-to-end deep learning model to predict dose distributions. However, training end-to-end methods may be associated with practical limitations due to the limited size of medical datasets that are often used. To address these limitations, we propose a content based image retrieval (CBIR) method for retrieving dose distributions of previously planned patients based on anatomical similarity. Approach: Our proposed CBIR method trains a representation model that produces latent space embeddings of a patient's anatomical information. The latent space embeddings of new patients are then compared against those of previous patients in a database for image retrieval of dose distributions. All source code for this project is available on github. Main Results: The retrieval performance of various CBIR methods is evaluated on a dataset consisting of both publicly available plans and clinical plans from our institution. This study compares various encoding methods, ranging from simple autoencoders to more recent Siamese networks like SimSiam, and the best performance was observed for the multitask Siamese network. Significance: Applying CBIR to inform subsequent treatment planning potentially addresses many limitations associated with end-to-end KBP. Our current results demonstrate that excellent image retrieval performance can be obtained through slight changes to previously developed Siamese networks. We hope to integrate CBIR into automated planning workflow in future works, potentially through methods like the MetaPlanner framework.

Praveenbalaji Rajendran, Yong Yang, Thomas R. Niedermayr et al.

Radiation therapy (RT) is one of the most effective treatments for cancer, and its success relies on the accurate delineation of targets. However, target delineation is a comprehensive medical decision that currently relies purely on manual processes by human experts. Manual delineation is time-consuming, laborious, and subject to interobserver variations. Although the advancements in artificial intelligence (AI) techniques have significantly enhanced the auto-contouring of normal tissues, accurate delineation of RT target volumes remains a challenge. In this study, we propose a visual language model-based RT target volume auto-delineation network termed Radformer. The Radformer utilizes a hierarichal vision transformer as the backbone and incorporates large language models to extract text-rich features from clinical data. We introduce a visual language attention module (VLAM) for integrating visual and linguistic features for language-aware visual encoding (LAVE). The Radformer has been evaluated on a dataset comprising 2985 patients with head-and-neck cancer who underwent RT. Metrics, including the Dice similarity coefficient (DSC), intersection over union (IOU), and 95th percentile Hausdorff distance (HD95), were used to evaluate the performance of the model quantitatively. Our results demonstrate that the Radformer has superior segmentation performance compared to other state-of-the-art models, validating its potential for adoption in RT practice.

Shuaishuai Guo, Jianheng Guo, KaiFan Ji et al.

With the release of a large amount of astronomical data, an increasing number of close-in hot Jupiters have been discovered. Calculating their evolutionary curves using star-planet interaction models presents a challenge. To expedite the generation of evolutionary curves for these close-in hot Jupiter systems, we utilized tidal interaction models established on MESA to create 15,745 samples of star-planet systems and 7,500 samples of stars. Additionally, we employed a neural network (Multi-Layer Perceptron - MLP) to predict the evolutionary curves of the systems, including stellar effective temperature, radius, stellar rotation period, and planetary orbital period. The median relative errors of the predicted evolutionary curves were found to be 0.15%, 0.43%, 2.61%, and 0.57%, respectively. Furthermore, the speed at which we generate evolutionary curves exceeds that of model-generated curves by more than four orders of magnitude. We also extracted features of planetary migration states and utilized lightGBM to classify the samples into 6 categories for prediction. We found that by combining three types that undergo long-term double synchronization into one label, the classifier effectively recognized these features. Apart from systems experiencing long-term double synchronization, the median relative errors of the predicted evolutionary curves were all below 4%. Our work provides an efficient method to save significant computational resources and time with minimal loss in accuracy. This research also lays the foundation for analyzing the evolutionary characteristics of systems under different migration states, aiding in the understanding of the underlying physical mechanisms of such systems. Finally, to a large extent, our approach could replace the calculations of theoretical models.

Lingting Zhu, Yizheng Chen, Lianli Liu et al.

Multi-modality imaging is widely used in clinical practice and biomedical research to gain a comprehensive understanding of an imaging subject. Currently, multi-modality imaging is accomplished by post hoc fusion of independently reconstructed images under the guidance of mutual information or spatially registered hardware, which limits the accuracy and utility of multi-modality imaging. Here, we investigate a data-driven multi-modality imaging (DMI) strategy for synergetic imaging of CT and MRI. We reveal two distinct types of features in multi-modality imaging, namely intra- and inter-modality features, and present a multi-sensor learning (MSL) framework to utilize the crossover inter-modality features for augmented multi-modality imaging. The MSL imaging approach breaks down the boundaries of traditional imaging modalities and allows for optimal hybridization of CT and MRI, which maximizes the use of sensory data. We showcase the effectiveness of our DMI strategy through synergetic CT-MRI brain imaging. The principle of DMI is quite general and holds enormous potential for various DMI applications across disciplines.

Ziqi Gao, Wendi Yang, Yujia Li et al.

Non-semantic context information is crucial for visual recognition, as the human visual perception system first uses global statistics to process scenes rapidly before identifying specific objects. However, while semantic information is increasingly incorporated into computer vision tasks such as image reconstruction, non-semantic information, such as global spatial structures, is often overlooked. To bridge the gap, we propose a biologically informed non-semantic context descriptor, \textbf{MS-Glance}, along with the Glance Index Measure for comparing two images. A Global Glance vector is formulated by randomly retrieving pixels based on a perception-driven rule from an image to form a vector representing non-semantic global context, while a local Glance vector is a flattened local image window, mimicking a zoom-in observation. The Glance Index is defined as the inner product of two standardized sets of Glance vectors. We evaluate the effectiveness of incorporating Glance supervision in two reconstruction tasks: image fitting with implicit neural representation (INR) and undersampled MRI reconstruction. Extensive experimental results show that MS-Glance outperforms existing image restoration losses across both natural and medical images. The code is available at \url{https://github.com/Z7Gao/MSGlance}.

Yuyin Zhou, Xianhang Li, Fengze Liu et al.

Deep neural networks have shown great success in representation learning. However, when learning with noisy labels (LNL), they can easily overfit and fail to generalize to new data. This paper introduces a simple and effective method, named Learning to Bootstrap (L2B), which enables models to bootstrap themselves using their own predictions without being adversely affected by erroneous pseudo-labels. It achieves this by dynamically adjusting the importance weight between real observed and generated labels, as well as between different samples through meta-learning. Unlike existing instance reweighting methods, the key to our method lies in a new, versatile objective that enables implicit relabeling concurrently, leading to significant improvements without incurring additional costs. L2B offers several benefits over the baseline methods. It yields more robust models that are less susceptible to the impact of noisy labels by guiding the bootstrapping procedure more effectively. It better exploits the valuable information contained in corrupted instances by adapting the weights of both instances and labels. Furthermore, L2B is compatible with existing LNL methods and delivers competitive results spanning natural and medical imaging tasks including classification and segmentation under both synthetic and real-world noise. Extensive experiments demonstrate that our method effectively mitigates the challenges of noisy labels, often necessitating few to no validation samples, and is well generalized to other tasks such as image segmentation. This not only positions it as a robust complement to existing LNL techniques but also underscores its practical applicability. The code and models are available at https://github.com/yuyinzhou/l2b.

Junfei Xiao, Lequan Yu, Zongwei Zhou et al.

Batch normalization (BN) uniformly shifts and scales the activations based on the statistics of a batch of images. However, the intensity distribution of the background pixels often dominates the BN statistics because the background accounts for a large proportion of the entire image. This paper focuses on enhancing BN with the intensity distribution of foreground pixels, the one that really matters for image segmentation. We propose a new normalization strategy, named categorical normalization (CateNorm), to normalize the activations according to categorical statistics. The categorical statistics are obtained by dynamically modulating specific regions in an image that belong to the foreground. CateNorm demonstrates both precise and robust segmentation results across five public datasets obtained from different domains, covering complex and variable data distributions. It is attributable to the ability of CateNorm to capture domain-invariant information from multiple domains (institutions) of medical data. Code is available at https://github.com/lambert-x/CateNorm.

Sheng Liu, Haotian Ye, Lei Xing et al.

Hallucination poses a challenge to the deployment of large vision-language models (LVLMs) in applications. Unlike in large language models (LLMs), hallucination in LVLMs often arises from misalignments between visual inputs and textual outputs. This paper investigates the underlying mechanisms of hallucination, focusing on the unique structure of LVLMs that distinguishes them from large language models (LLMs). We identify that hallucinations often arise from the sensitivity of text decoders to vision inputs, a natural phenomenon when image encoders and text decoders are pre-trained separately. Inspired by this, we introduce Visual and Textual Intervention (VTI), a novel technique designed to reduce hallucinations by steering latent space representations during inference to enhance the stability of vision features. As a task-agnostic test-time intervention, VTI can be easily applied to any problem without additional cost. Extensive experiments demonstrate that it can effectively reduce hallucinations and outperform baseline methods across multiple metrics, highlighting the critical role of vision feature stability in LVLMs.

Sheng Liu, Tianlang Chen, Pan Lu et al.

Test-time compute has emerged as a powerful paradigm for improving the performance of large language models (LLMs), where generating multiple outputs or refining individual chains can significantly boost answer accuracy. However, existing methods like Best-of-N, majority voting, and self-reflection typically apply reasoning in a uniform way across inputs, overlooking the fact that different problems may require different levels of reasoning depth. In this work, we propose Fractional Reasoning, a training-free and model-agnostic framework that enables continuous control over reasoning intensity at inference time, going beyond the limitations of fixed instructional prompts. Our method operates by extracting the latent steering vector associated with deeper reasoning and reapplying it with a tunable scaling factor, allowing the model to tailor its reasoning process to the complexity of each input. This supports two key modes of test-time scaling: (1) improving output quality in breadth-based strategies (e.g., Best-of-N, majority voting), and (2) enhancing the correctness of individual reasoning chains in depth-based strategies (e.g., self-reflection). Experiments on GSM8K, MATH500, and GPQA demonstrate that Fractional Reasoning consistently improves performance across diverse reasoning tasks and models.

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.

Wasif Khan, Lin Gu, Noah Hammarlund et al.

Physical activity is a modifiable lifestyle factor with potential to support cognitive resilience. However, the association of moderate-to-vigorous physical activity (MVPA) intensity, and timing, with cognitive function and region-specific brain structure remain poorly understood. We analyzed data from 45,892 UK Biobank participants aged 60 years and older with valid wrist-worn accelerometer data, cognitive testing, and structural brain MRI. MVPA was measured both continuously (mins per week) and categorically (thresholded using >=150 min/week based on WHO guidelines). Associations with cognitive performance and regional brain volumes were evaluated using multivariable linear models adjusted for demographic, socioeconomic, and health-related covariates. We conducted secondary analyses on MVPA timing and subgroup effects. Higher MVPA was associated with better performance across cognitive domains, including reasoning, memory, executive function, and processing speed. These associations persisted in fully adjusted models and were higher among participants meeting WHO guidelines. Greater MVPA was also associated with subcortical brain regions (caudate, putamen, pallidum, thalamus), as well as regional gray matter volumes involved in emotion, working memory, and perceptual processing. Secondary analyses showed that MVPA at any time of day was associated with cognitive functions and brain volume particularly in the midday-afternoon and evening. Sensitivity analysis shows consistent findings across subgroups, with evidence of dose-response relationships. Higher MVPA is associated with preserved brain structure and enhanced cognitive function in later life. Public health strategies to increase MVPA may support healthy cognitive aging and generate substantial economic benefits, with global gains projected to reach USD 760 billion annually by 2050.

Md Tauhidul Islam, Lei Xing

Advancements in deep learning are revolutionizing science and engineering. The immense success of deep learning is largely due to its ability to extract essential high-dimensional (HD) features from input data and make inference decisions based on this information. However, current deep neural network (DNN) models face several challenges, such as the requirements of extensive amounts of data and computational resources. Here, we introduce a new learning scheme, referred to as deep-and-wide learning (DWL), to systematically capture features not only within individual input data (intra-data features) but also across the data (inter-data features). Furthermore, we propose a dual-interactive-channel network (D-Net) to realize the DWL, which leverages our Bayesian formulation of low-dimensional (LD) inter-data feature extraction and its synergistic interaction with the conventional HD representation of the dataset, for substantially enhanced computational efficiency and inference. The proposed technique has been applied to data across various disciplines for both classification and regression tasks. Our results demonstrate that DWL surpasses state-of-the-art DNNs in accuracy by a substantial margin with limited training data and improves the computational efficiency by order(s) of magnitude. The proposed DWL strategy dramatically alters the data-driven learning techniques, including emerging large foundation models, and sheds significant insights into the evolving field of AI.

Sheng Liu, Oscar Pastor-Serrano, Yizheng Chen et al.

Objective: Radiotherapy treatment planning is a time-consuming and potentially subjective process that requires the iterative adjustment of model parameters to balance multiple conflicting objectives. Recent advancements in frontier Artificial Intelligence (AI) models offer promising avenues for addressing the challenges in planning and clinical decision-making. This study introduces GPT-RadPlan, an automated treatment planning framework that integrates radiation oncology knowledge with the reasoning capabilities of large multi-modal models, such as GPT-4Vision (GPT-4V) from OpenAI. Approach: Via in-context learning, we incorporate clinical requirements and a few (3 in our experiments) approved clinical plans with their optimization settings, enabling GPT-4V to acquire treatment planning domain knowledge. The resulting GPT-RadPlan system is integrated into our in-house inverse treatment planning system through an application programming interface (API). For a given patient, GPT-RadPlan acts as both plan evaluator and planner, first assessing dose distributions and dose-volume histograms (DVHs), and then providing textual feedback on how to improve the plan to match the physician's requirements. In this manner, GPT-RadPlan iteratively refines the plan by adjusting planning parameters, such as weights and dose objectives, based on its suggestions. Main results: The efficacy of the automated planning system is showcased across 17 prostate cancer and 13 head and neck cancer VMAT plans with prescribed doses of 70.2 Gy and 72 Gy, respectively, where we compared GPT-RadPlan results to clinical plans produced by human experts. In all cases, GPT-RadPlan either outperformed or matched the clinical plans, demonstrating superior target coverage and reducing organ-at-risk doses by 5 Gy on average (15 percent for prostate and 10-15 percent for head and neck).

Pierre-Louis Benveniste, Julie Alberge, Lei Xing et al.

Lung cancer is a significant cause of mortality worldwide, emphasizing the importance of early detection for improved survival rates. In this study, we propose a machine learning (ML) tool trained on data from the PLCO Cancer Screening Trial and validated on the NLST to estimate the likelihood of lung cancer occurrence within five years. The study utilized two datasets, the PLCO (n=55,161) and NLST (n=48,595), consisting of comprehensive information on risk factors, clinical measurements, and outcomes related to lung cancer. Data preprocessing involved removing patients who were not current or former smokers and those who had died of causes unrelated to lung cancer. Additionally, a focus was placed on mitigating bias caused by censored data. Feature selection, hyper-parameter optimization, and model calibration were performed using XGBoost, an ensemble learning algorithm that combines gradient boosting and decision trees. The ML model was trained on the pre-processed PLCO dataset and tested on the NLST dataset. The model incorporated features such as age, gender, smoking history, medical diagnoses, and family history of lung cancer. The model was well-calibrated (Brier score=0.044). ROC-AUC was 82% on the PLCO dataset and 70% on the NLST dataset. PR-AUC was 29% and 11% respectively. When compared to the USPSTF guidelines for lung cancer screening, our model provided the same recall with a precision of 13.1% vs. 9.3% on the PLCO dataset and 3.2% vs. 3.1% on the NLST dataset. The developed ML tool provides a freely available web application for estimating the likelihood of developing lung cancer within five years. By utilizing risk factors and clinical data, individuals can assess their risk and make informed decisions regarding lung cancer screening. This research contributes to the efforts in early detection and prevention strategies, aiming to reduce lung cancer-related mortality rates.

Varun Vasudevan, Maxime Bassenne, Md Tauhidul Islam et al.

Prior studies using graph neural networks (GNNs) for image classification have focused on graphs generated from a regular grid of pixels or similar-sized superpixels. In the latter, a single target number of superpixels is defined for an entire dataset irrespective of differences across images and their intrinsic multiscale structure. On the contrary, this study investigates image classification using graphs generated from an image-specific number of multiscale superpixels. We propose WaveMesh, a new wavelet-based superpixeling algorithm, where the number and sizes of superpixels in an image are systematically computed based on its content. WaveMesh superpixel graphs are structurally different from similar-sized superpixel graphs. We use SplineCNN, a state-of-the-art network for image graph classification, to compare WaveMesh and similar-sized superpixels. Using SplineCNN, we perform extensive experiments on three benchmark datasets under three local-pooling settings: 1) no pooling, 2) GraclusPool, and 3) WavePool, a novel spatially heterogeneous pooling scheme tailored to WaveMesh superpixels. Our experiments demonstrate that SplineCNN learns from multiscale WaveMesh superpixels on-par with similar-sized superpixels. In all WaveMesh experiments, GraclusPool performs poorer than no pooling / WavePool, indicating that poor choice of pooling can result in inferior performance while learning from multiscale superpixels.

Yuyin Zhou, Shih-Cheng Huang, Jason Alan Fries et al.

Despite the routine use of electronic health record (EHR) data by radiologists to contextualize clinical history and inform image interpretation, the majority of deep learning architectures for medical imaging are unimodal, i.e., they only learn features from pixel-level information. Recent research revealing how race can be recovered from pixel data alone highlights the potential for serious biases in models which fail to account for demographics and other key patient attributes. Yet the lack of imaging datasets which capture clinical context, inclusive of demographics and longitudinal medical history, has left multimodal medical imaging underexplored. To better assess these challenges, we present RadFusion, a multimodal, benchmark dataset of 1794 patients with corresponding EHR data and high-resolution computed tomography (CT) scans labeled for pulmonary embolism. We evaluate several representative multimodal fusion models and benchmark their fairness properties across protected subgroups, e.g., gender, race/ethnicity, age. Our results suggest that integrating imaging and EHR data can improve classification performance and robustness without introducing large disparities in the true positive rate between population groups.

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.

Qiong Xu, Jeff Wang, Hiroki Shirato et al.

This paper presents a dictionary learning-based method with region-specific image patches to maximize the utility of the powerful sparse data processing technique for CT image reconstruction. Considering heterogeneous distributions of image features and noise in CT, region-specific customization of dictionaries is utilized in iterative reconstruction. Thoracic CT images are partitioned into several regions according to their structural and noise characteristics. Dictionaries specific to each region are then learned from the segmented thoracic CT images and applied to subsequent image reconstruction of the region. Parameters for dictionary learning and sparse representation are determined according to the structural and noise properties of each region. The proposed method results in better performance than the conventional reconstruction based on a single dictionary in recovering structures and suppressing noise in both simulation and human CT imaging. Quantitatively, the simulation study shows maximum improvement of image quality for the whole thorax can achieve 4.88% and 11.1% in terms of the Structure-SIMilarity (SSIM) and Root-Mean-Square Error (RMSE) indices, respectively. For human imaging data, it is found that the structures in the lungs and heart can be better recovered, while simultaneously decreasing noise around the vertebra effectively. The proposed strategy takes into account inherent regional differences inside of the reconstructed object and leads to improved images. The method can be readily extended to CT imaging of other anatomical regions and other applications.

Lequan Yu, Zhicheng Zhang, Xiaomeng Li et al.

Computed tomography (CT) has been widely used for medical diagnosis, assessment, and therapy planning and guidance. In reality, CT images may be affected adversely in the presence of metallic objects, which could lead to severe metal artifacts and influence clinical diagnosis or dose calculation in radiation therapy. In this paper, we propose a generalizable framework for metal artifact reduction (MAR) by simultaneously leveraging the advantages of image domain and sinogram domain-based MAR techniques. We formulate our framework as a sinogram completion problem and train a neural network (SinoNet) to restore the metal-affected projections. To improve the continuity of the completed projections at the boundary of metal trace and thus alleviate new artifacts in the reconstructed CT images, we train another neural network (PriorNet) to generate a good prior image to guide sinogram learning, and further design a novel residual sinogram learning strategy to effectively utilize the prior image information for better sinogram completion. The two networks are jointly trained in an end-to-end fashion with a differentiable forward projection (FP) operation so that the prior image generation and deep sinogram completion procedures can benefit from each other. Finally, the artifact-reduced CT images are reconstructed using the filtered backward projection (FBP) from the completed sinogram. Extensive experiments on simulated and real artifacts data demonstrate that our method produces superior artifact-reduced results while preserving the anatomical structures and outperforms other MAR methods.

Xiaomeng Li, Mengyu Jia, Md Tauhidul Islam et al.

The automatic diagnosis of various retinal diseases from fundus images is important to support clinical decision-making. However, developing such automatic solutions is challenging due to the requirement of a large amount of human-annotated data. Recently, unsupervised/self-supervised feature learning techniques receive a lot of attention, as they do not need massive annotations. Most of the current self-supervised methods are analyzed with single imaging modality and there is no method currently utilize multi-modal images for better results. Considering that the diagnostics of various vitreoretinal diseases can greatly benefit from another imaging modality, e.g., FFA, this paper presents a novel self-supervised feature learning method by effectively exploiting multi-modal data for retinal disease diagnosis. To achieve this, we first synthesize the corresponding FFA modality and then formulate a patient feature-based softmax embedding objective. Our objective learns both modality-invariant features and patient-similarity features. Through this mechanism, the neural network captures the semantically shared information across different modalities and the apparent visual similarity between patients. We evaluate our method on two public benchmark datasets for retinal disease diagnosis. The experimental results demonstrate that our method clearly outperforms other self-supervised feature learning methods and is comparable to the supervised baseline.

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, Yinyu Ye, Sandy Napel et al.

We develop and analyze a projected particle Langevin optimization method to learn the distribution in the Schönberg integral representation of the radial basis functions from training samples. More specifically, we characterize a distributionally robust optimization method with respect to the Wasserstein distance to optimize the distribution in the Schönberg integral representation. To provide theoretical performance guarantees, we analyze the scaling limits of a projected particle online (stochastic) optimization method in the mean-field regime. In particular, we prove that in the scaling limits, the empirical measure of the Langevin particles converges to the law of a reflected Itô diffusion-drift process. Moreover, the drift is also a function of the law of the underlying process. Using Itô lemma for semi-martingales and Grisanov's change of measure for the Wiener processes, we then derive a Mckean-Vlasov type partial differential equation (PDE) with Robin boundary conditions that describes the evolution of the empirical measure of the projected Langevin particles in the mean-field regime. In addition, we establish the existence and uniqueness of the steady-state solutions of the derived PDE in the weak sense. We apply our learning approach to train radial kernels in the kernel locally sensitive hash (LSH) functions, where the training data-set is generated via a $k$-mean clustering method on a small subset of data-base. We subsequently apply our kernel LSH with a trained kernel for image retrieval task on MNIST data-set, and demonstrate the efficacy of our kernel learning approach. We also apply our kernel learning approach in conjunction with the kernel support vector machines (SVMs) for classification of benchmark data-sets.

Charles Huang, Masoud Badiei, Hyunseok Seo et al.

Purpose: Segmentation of organs-at-risk (OARs) is a bottleneck in current radiation oncology pipelines and is often time consuming and labor intensive. In this paper, we propose an atlas-based semi-supervised registration algorithm to generate accurate segmentations of OARs for which there are ground truth contours and rough segmentations of all other OARs in the atlas. To the best of our knowledge, this is the first study to use learning-based registration methods for the segmentation of head and neck patients and demonstrate its utility in clinical applications. Methods: Our algorithm cascades rigid and deformable deformation blocks, and takes on an atlas image (M), set of atlas-space segmentations (S_A), and a patient image (F) as inputs, while outputting patient-space segmentations of all OARs defined on the atlas. We train our model on 475 CT images taken from public archives and Stanford RadOnc Clinic (SROC), validate on 5 CT images from SROC, and test our model on 20 CT images from SROC. Results: Our method outperforms current state of the art learning-based registration algorithms and achieves an overall dice score of 0.789 on our test set. Moreover, our method yields a performance comparable to manual segmentation and supervised segmentation, while solving a much more complex registration problem. Whereas supervised segmentation methods only automate the segmentation process for a select few number of OARs, we demonstrate that our methods can achieve similar performance for OARs of interest, while also providing segmentations for every other OAR on the provided atlas. Conclusions: Our proposed algorithm has significant clinical applications and could help reduce the bottleneck for segmentation of head and neck OARs. Further, our results demonstrate that semi-supervised diffeomorphic registration can be accurately applied to both registration and segmentation problems.

Hyunseok Seo, Charles Huang, Maxime Bassenne et al.

Segmentation of livers and liver tumors is one of the most important steps in radiation therapy of hepatocellular carcinoma. The segmentation task is often done manually, making it tedious, labor intensive, and subject to intra-/inter- operator variations. While various algorithms for delineating organ-at-risks (OARs) and tumor targets have been proposed, automatic segmentation of livers and liver tumors remains intractable due to their low tissue contrast with respect to the surrounding organs and their deformable shape in CT images. The U-Net has gained increasing popularity recently for image analysis tasks and has shown promising results. Conventional U-Net architectures, however, suffer from three major drawbacks. To cope with these problems, we added a residual path with deconvolution and activation operations to the skip connection of the U-Net to avoid duplication of low resolution information of features. In the case of small object inputs, features in the skip connection are not incorporated with features in the residual path. Furthermore, the proposed architecture has additional convolution layers in the skip connection in order to extract high level global features of small object inputs as well as high level features of high resolution edge information of large object inputs. Efficacy of the modified U-Net (mU-Net) was demonstrated using the public dataset of Liver tumor segmentation (LiTS) challenge 2017. The proposed mU-Net outperformed existing state-of-art networks.

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.

Xiaomeng Li, Lequan Yu, Yueming Jin et al.

Rare diseases have extremely low-data regimes, unlike common diseases with large amount of available labeled data. Hence, to train a neural network to classify rare diseases with a few per-class data samples is very challenging, and so far, catches very little attention. In this paper, we present a difficulty-aware meta-learning method to address rare disease classifications and demonstrate its capability to classify dermoscopy images. Our key approach is to first train and construct a meta-learning model from data of common diseases, then adapt the model to perform rare disease classification.To achieve this, we develop the difficulty-aware meta-learning method that dynamically monitors the importance of learning tasks during the meta-optimization stage. To evaluate our method, we use the recent ISIC 2018 skin lesion classification dataset, and show that with only five samples per class, our model can quickly adapt to classify unseen classes by a high AUC of 83.3%. Also, we evaluated several rare disease classification results in the public Dermofit Image Library to demonstrate the potential of our method for real clinical practice.

Masoud Badiei Khuzani, Varun Vasudevan, Hongyi Ren et al.

We study the problem of learning policy of an infinite-horizon, discounted cost, Markov decision process (MDP) with a large number of states. We compute the actions of a policy that is nearly as good as a policy chosen by a suitable oracle from a given mixture policy class characterized by the convex hull of a set of known base policies. To learn the coefficients of the mixture model, we recast the problem as an approximate linear programming (ALP) formulation for MDPs, where the feature vectors correspond to the occupation measures of the base policies defined on the state-action space. We then propose a projection-free stochastic primal-dual method with the Bregman divergence to solve the characterized ALP. Furthermore, we analyze the probably approximately correct (PAC) sample complexity of the proposed stochastic algorithm, namely the number of queries required to achieve near optimal objective value. We also propose a modification of our proposed algorithm with the polytope constraint sampling for the smoothed ALP, where the restriction to lower bounding approximations are relaxed. In addition, we apply the proposed algorithms to a queuing problem, and compare their performance with a penalty function algorithm. The numerical results illustrates that the primal-dual achieves better efficiency and low variance across different trials compared to the penalty function method.

Xiaomeng Li, Lequan Yu, Hao Chen et al.

Deep convolutional neural networks have achieved remarkable progress on a variety of medical image computing tasks. A common problem when applying supervised deep learning methods to medical images is the lack of labeled data, which is very expensive and time-consuming to be collected. In this paper, we present a novel semi-supervised method for medical image segmentation, where the network is optimized by the weighted combination of a common supervised loss for labeled inputs only and a regularization loss for both labeled and unlabeled data. To utilize the unlabeled data, our method encourages the consistent predictions of the network-in-training for the same input under different regularizations. Aiming for the semi-supervised segmentation problem, we enhance the effect of regularization for pixel-level predictions by introducing a transformation, including rotation and flipping, consistent scheme in our self-ensembling model. With the aim of semi-supervised segmentation tasks, we introduce a transformation consistent strategy in our self-ensembling model to enhance the regularization effect for pixel-level predictions. We have extensively validated the proposed semi-supervised method on three typical yet challenging medical image segmentation tasks: (i) skin lesion segmentation from dermoscopy images on International Skin Imaging Collaboration (ISIC) 2017 dataset, (ii) optic disc segmentation from fundus images on Retinal Fundus Glaucoma Challenge (REFUGE) dataset, and (iii) liver segmentation from volumetric CT scans on Liver Tumor Segmentation Challenge (LiTS) dataset. Compared to the state-of-the-arts, our proposed method shows superior segmentation performance on challenging 2D/3D medical images, demonstrating the effectiveness of our semi-supervised method for medical image segmentation.

Masoud Badiei Khuzani, Hongyi Ren, Md Tauhidul Islam et al.

We propose a novel data-driven method to learn a mixture of multiple kernels with random features that is certifiabaly robust against adverserial inputs. Specifically, we consider a distributionally robust optimization of the kernel-target alignment with respect to the distribution of training samples over a distributional ball defined by the Kullback-Leibler (KL) divergence. The distributionally robust optimization problem can be recast as a min-max optimization whose objective function includes a log-sum term. We develop a mini-batch biased stochastic primal-dual proximal method to solve the min-max optimization. To debias the minibatch algorithm, we use the Gumbel perturbation technique to estimate the log-sum term. We establish theoretical guarantees for the performance of the proposed multiple kernel learning method. In particular, we prove the consistency, asymptotic normality, stochastic equicontinuity, and the minimax rate of the empirical estimators. In addition, based on the notion of Rademacher and Gaussian complexities, we establish distributionally robust generalization bounds that are tighter than previous known bounds. More specifically, we leverage matrix concentration inequalities to establish distributionally robust generalization bounds. We validate our kernel learning approach for classification with the kernel SVMs on synthetic dataset generated by sampling multvariate Gaussian distributions with differernt variance structures. We also apply our kernel learning approach to the MNIST data-set and evaluate its robustness to perturbation of input images under different adversarial models. More specifically, we examine the robustness of the proposed kernel model selection technique against FGSM, PGM, C\&W, and DDN adversarial perturbations, and compare its performance with alternative state-of-the-art multiple kernel learning paradigms.

Morteza Mardani, Enhao Gong, Joseph Y. Cheng et al.

Magnetic resonance image (MRI) reconstruction is a severely ill-posed linear inverse task demanding time and resource intensive computations that can substantially trade off {\it accuracy} for {\it speed} in real-time imaging. In addition, state-of-the-art compressed sensing (CS) analytics are not cognizant of the image {\it diagnostic quality}. To cope with these challenges we put forth a novel CS framework that permeates benefits from generative adversarial networks (GAN) to train a (low-dimensional) manifold of diagnostic-quality MR images from historical patients. Leveraging a mixture of least-squares (LS) GANs and pixel-wise $\ell_1$ cost, a deep residual network with skip connections is trained as the generator that learns to remove the {\it aliasing} artifacts by projecting onto the manifold. LSGAN learns the texture details, while $\ell_1$ controls the high-frequency noise. A multilayer convolutional neural network is then jointly trained based on diagnostic quality images to discriminate the projection quality. The test phase performs feed-forward propagation over the generator network that demands a very low computational overhead. Extensive evaluations are performed on a large contrast-enhanced MR dataset of pediatric patients. In particular, images rated based on expert radiologists corroborate that GANCS retrieves high contrast images with detailed texture relative to conventional CS, and pixel-wise schemes. In addition, it offers reconstruction under a few milliseconds, two orders of magnitude faster than state-of-the-art CS-MRI schemes.