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Background Osteoporosis is the most common metabolic bone disease and can cause fragility fractures. Despite this, screening utilization rates for osteoporosis remain low among populations at risk. Automated bone mineral density (BMD) estimation using computed tomography (CT) can help bridge this gap and serve as an alternative screening method to dual-energy X-ray absorptiometry (DXA). Methods The feasibility of an opportunistic and population agnostic screening method for osteoporosis using abdominal CT scans without bone densitometry phantom-based calibration was investigated in this retrospective study. A total of 268 abdominal CT-DXA pairs and 99 abdominal CT studies without DXA scores were obtained from an oncology specialty clinic in the Republic of Korea. The center axial CT slices from the L1, L2, L3, and L4 lumbar vertebrae were annotated with the CT slice level and spine segmentation labels for each subject. Deep learning models were trained to localize the center axial slice from the CT scan of the torso, segment the vertebral bone, and estimate BMD for the top four lumbar vertebrae. Results Automated vertebra-level DXA measurements showed a mean absolute error (MAE) of 0.079, Pearson’s r of 0.852 (P

Abstract Recent successes of foundation models in artificial intelligence have prompted the emergence of large-scale chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, here we present a multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules’ structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model has the capabilities to solve various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

DCE-MRI provides information about vascular permeability and tissue perfusion through the acquisition of pharmacokinetic parameters. However, traditional methods for estimating these pharmacokinetic parameters involve fitting tracer kinetic models, which often suffer from computational complexity and low accuracy due to noisy arterial input function (AIF) measurements. Although some deep learning approaches have been proposed to tackle these challenges, most existing methods rely on supervised learning that requires paired input DCE-MRI and labeled pharmacokinetic parameter maps. This dependency on labeled data introduces significant time and resource constraints and potential noise in the labels, making supervised learning methods often impractical. To address these limitations, we present a novel unpaired deep learning method for estimating pharmacokinetic parameters and the AIF using a physics-driven CycleGAN approach. Our proposed CycleGAN framework is designed based on the underlying physics model, resulting in a simpler architecture with a single generator and discriminator pair. Crucially, our experimental results indicate that our method does not necessitate separate AIF measurements and produces more reliable pharmacokinetic parameters than other techniques.

Abstract Patients with acute coronary syndromes caused by plaque erosion might be managed conservatively without stenting. Currently, the diagnosis of plaque erosion requires an invasive imaging procedure. We sought to develop a deep learning (DL) model that enables an accurate diagnosis of plaque erosion using coronary computed tomography angiography (CTA). A total of 532 CTA scans from 395 patients were used to develop a DL model: 426 CTA scans from 316 patients for training and internal validation, and 106 separate scans from 79 patients for validation. Momentum Distillation-enhanced Composite Transformer Attention (MD-CTA), a novel DL model that can effectively process the entire set of CTA scans to diagnose plaque erosion, was developed. The novel DL model, compared to the convolution neural network, showed significantly improved AUC (0.899 [0.841–0.957] vs. 0.724 [0.622–0.826]), sensitivity (87.1 [70.2–96.4] vs. 71.0 [52.0–85.8]), and specificity (85.3 [75.3–92.4] vs. 68.0 [56.2–78.3]), respectively, for the patient-level prediction. Similar results were obtained at the slice-level prediction AUC (0.897 [0.890–0.904] vs. 0.757 [0.744–0.770]), sensitivity (82.2 [79.8–84.3] vs. 68.9 [66.2–71.6]), and specificity (80.1 [79.1–81.0] vs. 67.3 [66.3–68.4]), respectively. This newly developed DL model enables an accurate CT diagnosis of plaque erosion, which might enable cardiologists to provide tailored therapy without invasive procedures. Clinical Trial Registration: http://www.clinicaltrials.gov , NCT04523194.

Abstract Healed coronary plaques, morphologically characterized by a layered phenotype, are signs of previous plaque destabilization and healing. Recent optical coherence tomography (OCT) studies demonstrated that layered plaque is associated with higher levels of local and systemic inflammation and rapid plaque progression. However, the diagnosis of layered plaque needs expertise in OCT image analysis and is susceptible to inter-observer variability. We developed a deep learning (DL) model for an accurate diagnosis of layered plaque. A Visual Transformer (ViT)-based DL model that integrates information from adjacent frames emulating the cardiologists who review consecutive OCT frames to make a diagnosis was developed and compared with the standard convolutional neural network (CNN) model. A total of 237,021 cross-sectional OCT images from 581 patients collected from 8 sites were used for training and internal validation, and 65,394 images from 292 patients collected from another site were used for external validation. In the five-fold cross-validation, the ViT-based model provided better performance (area under the curve [AUC]: 0.860; 95% confidence interval [CI]: 0.855–0.866) than the standard CNN-based model (AUC: 0.799; 95% CI: 0.792–0.805). The ViT-based model (AUC: 0.845; 95% CI: 0.837–0.853) also surpassed the standard CNN-based model (AUC: 0.791; 95% CI: 0.782–0.800) in the external validation. The ViT-based DL model can accurately diagnose a layered plaque, which could help risk stratification for cardiac events.

Although deep learning-based computer-aided diagnosis systems have recently achieved expert level performance, developing a robust model requires large, high-quality data with annotations. Here, the authors present a framework which can improve the performance of vision transformer simultaneously with self-supervision and self-training.

Volumetric fluorescence microscopy is often limited by anisotropic spatial resolution. Here, the authors present an unsupervised deep-learning approach that enhances axial resolution by learning from high-resolution lateral images, and demonstrate isotropic resolution and restoration of suppressed visual details.

Purpose To develop a denoising convolutional neural network-based image processing technique and investigate its efficacy in diagnosing breast cancer using low-dose mammography imaging. Materials and Methods A total of 6 breast radiologists were included in this prospective study. All radiologists independently evaluated low-dose images for lesion detection and rated them for diagnostic quality using a qualitative scale. After application of the denoising network, the same radiologists evaluated lesion detectability and image quality. For clinical application, a consensus on lesion type and localization on preoperative mammographic examinations of breast cancer patients was reached after discussion. Thereafter, coded low-dose, reconstructed full-dose, and full-dose images were presented and assessed in a random order. Results Lesions on 40% reconstructed full-dose images were better perceived when compared with low-dose images of mastectomy specimens as a reference. In clinical application, as compared to 40% reconstructed images, higher values were given on full-dose images for resolution (p < 0.001); diagnostic quality for calcifications (p < 0.001); and for masses, asymmetry, or architectural distortion (p = 0.037). The 40% reconstructed images showed comparable values to 100% full-dose images for overall quality (p = 0.547), lesion visibility (p = 0.120), and contrast (p = 0.083), without significant differences. Conclusion Effective denoising and image reconstruction processing techniques can enable breast cancer diagnosis with substantial radiation dose reduction.

Ultrasound (US) imaging is a mature technology that has widespread applications especially in the healthcare sector. Despite its widespread use and popularity, it has an inherent disadvantage that ultrasound images are prone to speckle and other kinds of noise. The image quality in the low-cost ultrasound imaging systems is degraded due to the presence of such noise and low resolution of such ultrasound systems. Herein, we propose a method for image enhancement where, the overall quality of the US images is improved by simultaneous enhancement of US image resolution and noise suppression. To avoid over-smoothing and preserving structural/texture information, we devise texture compensation in our proposed method to retain the useful anatomical features. Moreover, we also utilize US image formation physics knowledge to generate augmentation datasets which can improve the training of our proposed method. Our experimental results showcase the performance of the proposed network as well as the effectiveness of the utilization of US physics knowledge to generate augmentation datasets.

Abstract Magnetic resonance imaging (MRI) is an inherently slow imaging modality, since it acquires multi-dimensional k-space data through 1-D free induction decay or echo signals. This often limits the use of MRI, especially for high resolution or dynamic imaging. Accordingly, many investigators has developed various acceleration techniques to allow fast MR imaging. For the last two decades, one of the most important breakthroughs in this direction is the introduction of compressed sensing (CS) that allows accurate reconstruction from sparsely sampled k-space data. The recent FDA approval of compressed sensing products for clinical scans clearly reflect the maturity of this technology. Therefore, this paper reviews the basic idea of CS and how this technology have been evolved for various MR imaging problems.

Abstract This editorial accompanies the launch of BMC Biomedical Engineering, a new open access, peer-reviewed journal within the BMC series, which seeks to publish articles on all aspects of biomedical engineering. As one of the first engineering journals within the BMC series portfolio, it will support and complement existing biomedical communities, but at the same time, it will provide an open access home for engineering research. By publishing original research, methodology, database, software and review articles, BMC Biomedical Engineering will disseminate quality research, with a focus on studies that further the understanding of human disease and that contribute towards the improvement of human health.

Graph neural networks (GNN) rely on graph operations that include neural network training for various graph related tasks. Recently, several attempts have been made to apply the GNNs to functional magnetic resonance image (fMRI) data. Despite recent progresses, a common limitation is its difficulty to explain the classification results in a neuroscientifically explainable way. Here, we develop a framework for analyzing the fMRI data using the Graph Isomorphism Network (GIN), which was recently proposed as a powerful GNN for graph classification. One of the important contributions of this paper is the observation that the GIN is a dual representation of convolutional neural network (CNN) in the graph space where the shift operation is defined using the adjacency matrix. This understanding enables us to exploit CNN-based saliency map techniques for the GNN, which we tailor to the proposed GIN with one-hot encoding, to visualize the important regions of the brain. We validate our proposed framework using large-scale resting-state fMRI (rs-fMRI) data for classifying the sex of the subject based on the graph structure of the brain. The experiment was consistent with our expectation such that the obtained saliency map show high correspondence with previous neuroimaging evidences related to sex differences.

Background: Chest X-ray (CXR) images are commonly used to show the internal structure of the human body without invasive intervention. The quality of CXR is an important factor as it affects the accuracy of a clinical diagnosis. Unfortunately, it is difficult to always get good quality CXR scans due to noises and scatters. Purpose: Recently, wavelet directional CycleGAN (WavCycleGAN) has shown promising results in image restoration tasks by removing noise and artifacts without sacrificing high-frequency components of the input image. Unfortunately, WavCycleGAN directly reconstructs wavelet directional images that require a wavelet transform in both the training and test phases, resulting in additional processing steps and unnatural artifacts originating from the wavelet domain image.In addition,WavCycleGAN can only process artifact-related subbands, so it is difficult to apply WavCycleGAN when different levels of artifacts are present in all subbands. To address this, here we present a novel unsupervised CXR image restoration scheme with similar or even better artifact removal performance than WavCycleGAN in spite of wavelet transform being only applied in the training phase. Methods: We introduce a novel wavelet subband discriminator which can be combined with CycleGAN or switchable CycleGAN, where wavelet transform is applied only in the training phase for discriminators to match the distribution of wavelet subband components. In our framework, the image restoration network can be still applied in the image domain to prevent unnatural artifacts of the wavelet domain image with the help of the image-domain cycle-consistency loss. In addition, using wavelet subband discriminator makes it possible to remove artifacts in all subbands by utilizing frequency-specific wavelet subband discriminators. Results: Through extensive experiments for noise and scatter removal in CXRs, we confirm that our method provides competitive performance compared to existing approaches without additional processing steps in the test phase. Furthermore, we show that our wavelet subband discriminator combined with the switchable CycleGAN can provide the flexibility by generating different levels of artifact removal. Conclusions: The proposed wavelet subband discriminator can be combined with the existing CycleGAN or switchable CycleGAN structures to construct an efficient unsupervised CXR image reconstruction. The advantage of our wavelet subband discriminator-based CXR image restoration is that, unlike traditional WavCycleGAN, it does not require any additional processing steps in the testing phase and does not generate unnatural artifacts originating from the wavelet domain image. We believe that our wavelet subband discriminator can be applied to various CXR image applications. [ABSTRACT FROM AUTHOR]

Ultrasound (US) imaging is a mature technology that has widespread applications especially in the healthcare sector. Despite its widespread use and popularity, it has an inherent disadvantage that ultrasound images are prone to speckle and other kinds of noise. The image quality in the low-cost ultrasound imaging systems is degraded due to the presence of such noise and low resolution of such ultrasound systems. Herein, we propose a method for image enhancement where, the overall quality of the US images is improved by simultaneous enhancement of US image resolution and noise suppression. To avoid over-smoothing and preserving structural/texture information, we devise texture compensation in our proposed method to retain the useful anatomical features. Moreover, we also utilize US image formation physics knowledge to generate augmentation datasets which can improve the training of our proposed method. Our experimental results showcase the performance of the proposed network as well as the effectiveness of the utilization of US physics knowledge to generate augmentation datasets. [ABSTRACT FROM AUTHOR]

Fundamental performance bounds for statistical estimation of parametric surfaces embedded in [R.sup.3], in which the reconstruction of the shape of binary or homogenous objects could be represented by asymptotic global confidence regions that facilitate geometric inference and optimization of the imaging system is derived. Simulation results reveal the tightness of the resulting bound and the efficiency of the three-dimensional global confidence region approach.

To improve the performance of classical generative adversarial networks (GANs), Wasserstein generative adversarial networks (WGANs) were developed as a Kantorovich dual formulation of the optimal transport (OT) problem using Wasserstein-1 distance. However, it was not clear how CycleGANtype generative models can be derived from the OT theory. Here we show that a novel CycleGAN architecture can be derived as a Kantorovich dual OT formulation if a penalized least squares (PLS) cost with deep learning--based inverse path penalty is used as a transportation cost. One of the most important advantages of this formulation is that depending on the knowledge of the forward problem, distinct variations of CycleGAN architecture can be derived: for example, one with two pairs of generators and discriminators, and the other with only a single pair of generator and discriminator. Even for the two generator cases, we show that the structural knowledge of the forward operator can lead to a simpler generator architecture which significantly simplifies the neural network training. The new CycleGAN formulation, which we call the OT-CycleGAN, has been applied for various biomedical imaging problems, such as accelerated magnetic resonance imaging (MRI), super-resolution microscopy, and low-dose X-ray computed tomography (CT). Experimental results confirm the efficacy and flexibility of the theory. [ABSTRACT FROM AUTHOR]

Recently, deep learning approaches with various network architectures have achieved significant performance improvement over existing iterative reconstruction methods in various imaging problems. However, it is still unclear why these deep learning architectures work for specific inverse problems. Moreover, in contrast to the usual evolution of signal processing theory around the classical theories, the link between deep learning and the classical signal processing approaches, such as wavelets, nonlocal processing, and compressed sensing, are not yet well understood. To address these issues, here we show that the long-sought missing link is the convolution framelets for representing a signal by convolving local and nonlocal bases. The convolution framelets were originally developed to generalize the theory of low-rank Hankel matrix approaches for inverse problems, and this paper further extends this idea so as to obtain a deep neural network using multilayer convolution framelets with perfect reconstruction (PR) under rectified linear unit (ReLU) nonlinearity. Our analysis also shows that the popular deep network components such as residual blocks, redundant filter channels, and concatenated ReLU (CReLU) do indeed help to achieve PR, while the pooling and unpooling layers should be augmented with high-pass branches to meet the PR condition. Moreover, by changing the number of filter channels and bias, we can control the shrinkage behaviors of the neural network. This discovery reveals the limitations of many existing deep learning architectures for inverse problems, and leads us to propose a novel theory for a deep convolutional framelet neural network. Using numerical experiments with various inverse problems, we demonstrate that our deep convolutional framelets network shows consistent improvement over existing deep architectures. This discovery suggests that the success of deep learning stems not from a magical black box, but rather from the power of a novel signal representation using a nonlocal basis combined with a data-driven local basis, which is indeed a natural extension of classical signal processing theory. [ABSTRACT FROM AUTHOR]

BACKGROUND: Cone-beam computed tomography (CBCT) is widely used in various medical imaging applications, including dental examinations. Dental CBCT images often suffer from motion artifacts caused by involuntary rigid motion of patients. However, earlier motion compensation studies are not applicable for dental CBCT systems using truncated detectors. OBJECTIVE: This study proposes a novel motion correction algorithm that can be applied for truncated dental CBCT images. METHODS: We propose a two-step method for motion correction. First, we estimate the relative displacement of each pair of opposite projections by finding the motion vector that maximizes the two-dimensional correlation coefficients of the opposite projections. Second, we convert the relative displacement into the absolute coordinate motion that yields the highest image sharpness of the reconstruction image. Using the motion vectors in the absolute coordinate system, motion artifacts are then compensated by modifying the trajectory of the source and detector during the back-projection step of the image reconstruction process. RESULTS: In simulation, the proposed method successfully estimated the true relative displacement. After converting to the absolute coordinate motions, the motion-compensated image was close to the ground-truth image and exhibited a lower mean-square-error than that of the uncompensated image. The results from the real data experiment also confirmed that the proposed method successfully compensated for the motion artifacts. CONCLUSIONS: The experimental results confirmed that the proposed method was applicable to most dental CBCT systems using a truncated detector without any use of an additional motion tracking system nor prior knowledge. [ABSTRACT FROM AUTHOR]

A robust algorithm is proposed to reconstruct the spatial support and the Lamé parameters of multiple inclusions in a homogeneous background elastic material using a few measurements of the displacement field over a finite collection of boundary points. The algorithm does not require any linearization or iterative update of Green's function but still allows very accurate reconstruction. The breakthrough comes from a novel interpretation of Lippmann–Schwinger type integral representation of the displacement field in terms of unknown densities having common sparse support on the location of inclusions. Accordingly, the proposed algorithm consists of a two-step approach. First, the localization problem is recast as a joint sparse recovery problem that renders the densities and the inclusion support simultaneously. Then, a noise robust constrained optimization problem is formulated for the reconstruction of elastic parameters. An efficient algorithm is designed for numerical implementation using the Multiple Sparse Bayesian Learning (M-SBL) for joint sparse recovery problem and the Constrained Split Augmented Lagrangian Shrinkage Algorithm (C-SALSA) for the constrained optimization problem. The efficacy of the proposed framework is manifested through extensive numerical simulations. To the best of our knowledge, this is the first algorithm tailored for parameter reconstruction problems in elastic media using highly under-sampled data in the sense of Nyquist rate. [ABSTRACT FROM AUTHOR]

We present a methodology for the optimization of sampling schemes in diffuse optical tomography (DOT). The proposed method exploits singular value decomposition (SVD) of the sensitivity matrix, or weight matrix, in DOT. Two mathematical metrics are introduced to assess and determine the optimum source–detector measurement configuration in terms of data correlation and image space resolution. The key idea of the work is to weight each data measurement, or rows in the sensitivity matrix, and similarly to weight each unknown image basis, or columns in the sensitivity matrix, according to their contribution to the rank of the sensitivity matrix, respectively. The proposed metrics offer a perspective on the data sampling and provide an efficient way of optimizing the sampling schemes in DOT. We evaluated various acquisition geometries often used in DOT by use of the proposed metrics. By iteratively selecting an optimal sparse set of data measurements, we showed that one can design a DOT scanning protocol that provides essentially the same image quality at a much reduced sampling. [ABSTRACT FROM AUTHOR]

To address the classic interior tomography problem where projections at each view extend only to the shadow of a circular region completely interior to the subject being scanned, previously we showed that the exact recovery of two- and three-dimensional piecewise smooth images is guaranteed using a one-dimensional generalized total variation seminorm penalty which allows a much faster reconstruction. Tofurther accelerate the algorithm up to a level for clinical use, this paper proposes a novel multiscale reconstruction method by exploiting the Bedrosian identity of the Hilbert transform. More specifically, we show that the high frequency parts of the one-dimensional signals can be quickly recovered analytically with the Hilbert transform because of the Bedrosian identity. This implies that computationally expensive iterative reconstruction need only be applied to low resolution images in the downsampled domain, which significantly reduces the computational burden. Moreover, even for incomplete trajectories such as circular cone-beam geometry, we demonstrate that the proposed multiscale interior tomography approach can be combined with a novel spectral blending method in order to mitigate cone-beam artifacts from missing frequency regions. We show the efficacy of the proposed multiscale algorithm using circular fan-beam, helical cone-beam data, and circular conebeam geometry. With a graphics processing unit implementation, we demonstrate that the speed of the algorithm can be significantly accelerated up to the level for clinical use for various acquisition geometries. [ABSTRACT FROM AUTHOR]

Motivated by the interior tomography problem, we propose a method for exact reconstruction of a region of interest of a function from its local Radon transform in any number of dimensions. Our aim is to verify the feasibility of a one-dimensional reconstruction procedure that can provide the foundation for an efficient algorithm. For a broad class of functions, including piecewise polynomials and generalized splines, we prove that an exact reconstruction is possible by minimizing a generalized total variation seminorm along lines. The main difference with previous works is that our approach is inherently one-dimensional and that it imposes less constraints on the class of admissible signals. Within this formulation, we derive unique reconstruction results using properties of the Hilbert transform, and we present numerical examples of the reconstruction. [ABSTRACT FROM AUTHOR]