CopilotCAD: Empowering Radiologists with Report Completion Models and Quantitative Evidence from Medical Image Foundation Models

Computer-aided diagnosis systems hold great promise to aid radiologists and clinicians in radiological clinical practice and enhance diagnostic accuracy and efficiency. However, the conventional systems primarily focus on delivering diagnostic results through text report generation or medical image classification, positioning them as standalone decision-makers rather than helpers and ignoring radiologists' expertise. This study introduces an innovative paradigm to create an assistive co-pilot system for empowering radiologists by leveraging Large Language Models (LLMs) and medical image analysis tools. Specifically, we develop a collaborative framework to integrate LLMs and quantitative medical image analysis results generated by foundation models with radiologists in the loop, achieving efficient and safe generation of radiology reports and effective utilization of computational power of AI and the expertise of medical professionals. This approach empowers radiologists to generate more precise and detailed diagnostic reports, enhancing patient outcomes while reducing the burnout of clinicians. Our methodology underscores the potential of AI as a supportive tool in medical diagnostics, promoting a harmonious integration of technology and human expertise to advance the field of radiology.

Versatile Medical Image Segmentation Learned from Multi-Source Datasets via Model Self-Disambiguation

A versatile medical image segmentation model applicable to imaging data collected with diverse equipment and protocols can facilitate model deployment and maintenance. However, building such a model typically requires a large, diverse, and fully annotated dataset, which is rarely available due to the labor-intensive and costly data curation. In this study, we develop a cost-efficient method by harnessing readily available data with partially or even sparsely annotated segmentation labels. We devise strategies for model self-disambiguation, prior knowledge incorporation, and imbalance mitigation to address challenges associated with inconsistently labeled data from various sources, including label ambiguity and imbalances across modalities, datasets, and segmentation labels. Experimental results on a multi-modal dataset compiled from eight different sources for abdominal organ segmentation have demonstrated our method's effectiveness and superior performance over alternative state-of-the-art methods, highlighting its potential for optimizing the use of existing annotated data and reducing the annotation efforts for new data to further enhance model capability.

Medical Image Segmentation with Domain Adaptation: A Survey

Deep learning (DL) has shown remarkable success in various medical imaging data analysis applications. However, it remains challenging for DL models to achieve good generalization, especially when the training and testing datasets are collected at sites with different scanners, due to domain shift caused by differences in data distributions. Domain adaptation has emerged as an effective means to address this challenge by mitigating domain gaps in medical imaging applications. In this review, we specifically focus on domain adaptation approaches for DL-based medical image segmentation. We first present the motivation and background knowledge underlying domain adaptations, then provide a comprehensive review of domain adaptation applications in medical image segmentations, and finally discuss the challenges, limitations, and future research trends in the field to promote the methodology development of domain adaptation in the context of medical image segmentation. Our goal was to provide researchers with up-to-date references on the applications of domain adaptation in medical image segmentation studies.

HNAS-reg: hierarchical neural architecture search for deformable medical image registration

Convolutional neural networks (CNNs) have been widely used to build deep learning models for medical image registration, but manually designed network architectures are not necessarily optimal. This paper presents a hierarchical NAS framework (HNAS-Reg), consisting of both convolutional operation search and network topology search, to identify the optimal network architecture for deformable medical image registration. To mitigate the computational overhead and memory constraints, a partial channel strategy is utilized without losing optimization quality. Experiments on three datasets, consisting of 636 T1-weighted magnetic resonance images (MRIs), have demonstrated that the proposal method can build a deep learning model with improved image registration accuracy and reduced model size, compared with state-of-the-art image registration approaches, including one representative traditional approach and two unsupervised learning-based approaches.

SurfNN: Joint Reconstruction of Multiple Cortical Surfaces from Magnetic Resonance Images

To achieve fast, robust, and accurate reconstruction of the human cortical surfaces from 3D magnetic resonance images (MRIs), we develop a novel deep learning-based framework, referred to as SurfNN, to reconstruct simultaneously both inner (between white matter and gray matter) and outer (pial) surfaces from MRIs. Different from existing deep learning-based cortical surface reconstruction methods that either reconstruct the cortical surfaces separately or neglect the interdependence between the inner and outer surfaces, SurfNN reconstructs both the inner and outer cortical surfaces jointly by training a single network to predict a midthickness surface that lies at the center of the inner and outer cortical surfaces. The input of SurfNN consists of a 3D MRI and an initialization of the midthickness surface that is represented both implicitly as a 3D distance map and explicitly as a triangular mesh with spherical topology, and its output includes both the inner and outer cortical surfaces, as well as the midthickness surface. The method has been evaluated on a large-scale MRI dataset and demonstrated competitive cortical surface reconstruction performance.

Deep Clustering Survival Machines with Interpretable Expert Distributions

Conventional survival analysis methods are typically ineffective to characterize heterogeneity in the population while such information can be used to assist predictive modeling. In this study, we propose a hybrid survival analysis method, referred to as deep clustering survival machines, that combines the discriminative and generative mechanisms. Similar to the mixture models, we assume that the timing information of survival data is generatively described by a mixture of certain numbers of parametric distributions, i.e., expert distributions. We learn weights of the expert distributions for individual instances according to their features discriminatively such that each instance's survival information can be characterized by a weighted combination of the learned constant expert distributions. This method also facilitates interpretable subgrouping/clustering of all instances according to their associated expert distributions. Extensive experiments on both real and synthetic datasets have demonstrated that the method is capable of obtaining promising clustering results and competitive time-to-event predicting performance.

Learning Apparent Diffusion Coefficient Maps from Undersampled Radial k-Space Diffusion-Weighted MRI in Mice using a Deep CNN-Transformer Model in Conjunction with a Monoexponential Model

Purpose: To accelerate radially sampled diffusion weighted spin-echo (Rad-DW-SE) acquisition method for generating high quality of apparent diffusion coefficient (ADC) maps. Methods: A deep learning method was developed to generate accurate ADC map reconstruction from undersampled DWI data acquired with the Rad-DW-SE method. The deep learning method integrates convolutional neural networks (CNNs) with vison transformers to generate high quality ADC maps from undersampled DWI data, regularized by a monoexponential ADC model fitting term. A model was trained on DWI data of 147 mice and evaluated on DWI data of 36 mice, with undersampling rates of 4x and 8x. Results: Ablation studies and experimental results have demonstrated that the proposed deep learning model can generate high quality ADC maps from undersampled DWI data, better than alternative deep learning methods under comparison, with their performance quantified on different levels of images, tumors, kidneys, and muscles. Conclusions: The deep learning method with integrated CNNs and transformers provides an effective means to accurately compute ADC maps from undersampled DWI data acquired with the Rad-DW-SE method.

Multidimensional representations in late-life depression: convergence in neuroimaging, cognition, clinical symptomatology and genetics

Late-life depression (LLD) is characterized by considerable heterogeneity in clinical manifestation. Unraveling such heterogeneity would aid in elucidating etiological mechanisms and pave the road to precision and individualized medicine. We sought to delineate, cross-sectionally and longitudinally, disease-related heterogeneity in LLD linked to neuroanatomy, cognitive functioning, clinical symptomatology, and genetic profiles. Multimodal data from a multicentre sample (N=996) were analyzed. A semi-supervised clustering method (HYDRA) was applied to regional grey matter (GM) brain volumes to derive dimensional representations. Two dimensions were identified, which accounted for the LLD-related heterogeneity in voxel-wise GM maps, white matter (WM) fractional anisotropy (FA), neurocognitive functioning, clinical phenotype, and genetics. Dimension one (Dim1) demonstrated relatively preserved brain anatomy without WM disruptions relative to healthy controls. In contrast, dimension two (Dim2) showed widespread brain atrophy and WM integrity disruptions, along with cognitive impairment and higher depression severity. Moreover, one de novo independent genetic variant (rs13120336) was significantly associated with Dim 1 but not with Dim 2. Notably, the two dimensions demonstrated significant SNP-based heritability of 18-27% within the general population (N=12,518 in UKBB). Lastly, in a subset of individuals having longitudinal measurements, Dim2 demonstrated a more rapid longitudinal decrease in GM and brain age, and was more likely to progress to Alzheimers disease, compared to Dim1 (N=1,413 participants and 7,225 scans from ADNI, BLSA, and BIOCARD datasets).

Disentangling Alzheimer's disease neurodegeneration from typical brain aging using machine learning

Neuroimaging biomarkers that distinguish between typical brain aging and Alzheimer's disease (AD) are valuable for determining how much each contributes to cognitive decline. Machine learning models can derive multi-variate brain change patterns related to the two processes, including the SPARE-AD (Spatial Patterns of Atrophy for Recognition of Alzheimer's Disease) and SPARE-BA (of Brain Aging) investigated herein. However, substantial overlap between brain regions affected in the two processes confounds measuring them independently. We present a methodology toward disentangling the two. T1-weighted MRI images of 4,054 participants (48-95 years) with AD, mild cognitive impairment (MCI), or cognitively normal (CN) diagnoses from the iSTAGING (Imaging-based coordinate SysTem for AGIng and NeurodeGenerative diseases) consortium were analyzed. First, a subset of AD patients and CN adults were selected based purely on clinical diagnoses to train SPARE-BA1 (regression of age using CN individuals) and SPARE-AD1 (classification of CN versus AD). Second, analogous groups were selected based on clinical and molecular markers to train SPARE-BA2 and SPARE-AD2: amyloid-positive (A+) AD continuum group (consisting of A+AD, A+MCI, and A+ and tau-positive CN individuals) and amyloid-negative (A-) CN group. Finally, the combined group of the AD continuum and A-/CN individuals was used to train SPARE-BA3, with the intention to estimate brain age regardless of AD-related brain changes. Disentangled SPARE models derived brain patterns that were more specific to the two types of the brain changes. Correlation between the SPARE-BA and SPARE-AD was significantly reduced. Correlation of disentangled SPARE-AD was non-inferior to the molecular measurements and to the number of APOE4 alleles, but was less to AD-related psychometric test scores, suggesting contribution of advanced brain aging to these scores.

Unsupervised deep learning for individualized brain functional network identification

A novel unsupervised deep learning method is developed to identify individual-specific large scale brain functional networks (FNs) from resting-state fMRI (rsfMRI) in an end-to-end learning fashion. Our method leverages deep Encoder-Decoder networks and conventional brain decomposition models to identify individual-specific FNs in an unsupervised learning framework and facilitate fast inference for new individuals with one forward pass of the deep network. Particularly, convolutional neural networks (CNNs) with an Encoder-Decoder architecture are adopted to identify individual-specific FNs from rsfMRI data by optimizing their data fitting and sparsity regularization terms that are commonly used in brain decomposition models. Moreover, a time-invariant representation learning module is designed to learn features invariant to temporal orders of time points of rsfMRI data. The proposed method has been validated based on a large rsfMRI dataset and experimental results have demonstrated that our method could obtain individual-specific FNs which are consistent with well-established FNs and are informative for predicting brain age, indicating that the individual-specific FNs identified truly captured the underlying variability of individualized functional neuroanatomy.