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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.