Skin lesions are classified in benign or malignant. Among the malignant, melanoma is a very aggressive cancer and the major cause of deaths. So, early diagnosis of skin cancer is very desired. In the last few years, there is a growing interest in computer aided diagnostic (CAD) using most image and clinical data of the lesion. These sources of information present limitations due to their inability to provide information of the molecular structure of the lesion. NIR spectroscopy may provide an alternative source of information to automated CAD of skin lesions. The most commonly used techniques and classification algorithms used in spectroscopy are Principal Component Analysis (PCA), Partial Least Squares - Discriminant Analysis (PLS-DA), and Support Vector Machines (SVM). Nonetheless, there is a growing interest in applying the modern techniques of machine and deep learning (MDL) to spectroscopy. One of the main limitations to apply MDL to spectroscopy is the lack of public datasets. Since there is no public dataset of NIR spectral data to skin lesions, as far as we know, an effort has been made and a new dataset named NIR-SC-UFES, has been collected, annotated and analyzed generating the gold-standard for classification of NIR spectral data to skin cancer. Next, the machine learning algorithms XGBoost, CatBoost, LightGBM, 1D-convolutional neural network (1D-CNN) were investigated to classify cancer and non-cancer skin lesions. Experimental results indicate the best performance obtained by LightGBM with pre-processing using standard normal variate (SNV), feature extraction providing values of 0.839 for balanced accuracy, 0.851 for recall, 0.852 for precision, and 0.850 for F-score. The obtained results indicate the first steps in CAD of skin lesions aiming the automated triage of patients with skin lesions in vivo using NIR spectral data.
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Intracranial aneurysms are the leading cause of stroke. One of the established treatment approaches is the embolization induced by coil insertion. However, the prediction of treatment and subsequent changed flow characteristics in the aneurysm, is still an open problem. In this work, we present an approach based on patient specific geometry and parameters including a coil representation as inhomogeneous porous medium. The model consists of the volume-averaged Navier-Stokes equations including the non-Newtonian blood rheology. We solve these equations using a problem-adapted lattice Boltzmann method and present a comparison between fully-resolved and volume-averaged simulations. The results indicate the validity of the model. Overall, this workflow allows for patient specific assessment of the flow due to potential treatment.
Coronary artery disease (CAD) remains the leading cause of death globally and invasive coronary angiography (ICA) is considered the gold standard of anatomical imaging evaluation when CAD is suspected. However, risk evaluation based on ICA has several limitations, such as visual assessment of stenosis severity, which has significant interobserver variability. This motivates to development of a lesion classification system that can support specialists in their clinical procedures. Although deep learning classification methods are well-developed in other areas of medical imaging, ICA image classification is still at an early stage. One of the most important reasons is the lack of available and high-quality open-access datasets. In this paper, we reported a new annotated ICA images dataset, CADICA, to provide the research community with a comprehensive and rigorous dataset of coronary angiography consisting of a set of acquired patient videos and associated disease-related metadata. This dataset can be used by clinicians to train their skills in angiographic assessment of CAD severity and by computer scientists to create computer-aided diagnostic systems to help in such assessment. In addition, baseline classification methods are proposed and analyzed, validating the functionality of CADICA and giving the scientific community a starting point to improve CAD detection.
Modeling the behavior of biological tissues and organs often necessitates the knowledge of their shape in the absence of external loads. However, when their geometry is acquired in-vivo through imaging techniques, bodies are typically subject to mechanical deformation due to the presence of external forces, and the load-free configuration needs to be reconstructed. This paper addresses this crucial and frequently overlooked topic, known as the inverse elasticity problem (IEP), by delving into both theoretical and numerical aspects, with a particular focus on cardiac mechanics. In this work, we extend Shield's seminal work to determine the structure of the IEP with arbitrary material inhomogeneities and in the presence of both body and active forces. These aspects are fundamental in computational cardiology, and we show that they may break the variational structure of the inverse problem. In addition, we show that the inverse problem might have no solution even in the presence of constant Neumann boundary conditions and a polyconvex strain energy functional. We then present the results of extensive numerical tests to validate our theoretical framework, and to characterize the computational challenges associated with a direct numerical approximation of the IEP. Specifically, we show that this framework outperforms existing approaches both in terms of robustness and optimality, such as Sellier's iterative procedure, even when the latter is improved with acceleration techniques. A notable discovery is that multigrid preconditioners are, in contrast to standard elasticity, not efficient, where a one-level additive Schwarz and generalized Dryja-Smith-Widlund provide a much more reliable alternative. Finally, we successfully address the IEP for a full-heart geometry, demonstrating that the IEP formulation can compute the stress-free configuration in real-life scenarios.
Non-Hermitian topological phases can produce some remarkable properties, compared with their Hermitian counterpart, such as the breakdown of conventional bulk-boundary correspondence and the non-Hermitian topological edge mode. Here, we introduce several algorithms with multi-layer perceptron (MLP), and convolutional neural network (CNN) in the field of deep learning, to predict the winding of eigenvalues non-Hermitian Hamiltonians. Subsequently, we use the smallest module of the periodic circuit as one unit to construct high-dimensional circuit data features. Further, we use the Dense Convolutional Network (DenseNet), a type of convolutional neural network that utilizes dense connections between layers to design a non-Hermitian topolectrical Chern circuit, as the DenseNet algorithm is more suitable for processing high-dimensional data. Our results demonstrate the effectiveness of the deep learning network in capturing the global topological characteristics of a non-Hermitian system based on training data.
Brain atrophy and white matter hyperintensity (WMH) are critical neuroimaging features for ascertaining brain injury in cerebrovascular disease and multiple sclerosis. Automated segmentation and quantification is desirable but existing methods require high-resolution MRI with good signal-to-noise ratio (SNR). This precludes application to clinical and low-field portable MRI (pMRI) scans, thus hampering large-scale tracking of atrophy and WMH progression, especially in underserved areas where pMRI has huge potential. Here we present a method that segments white matter hyperintensity and 36 brain regions from scans of any resolution and contrast (including pMRI) without retraining. We show results on eight public datasets and on a private dataset with paired high- and low-field scans (3T and 64mT), where we attain strong correlation between the WMH ($\rho$=.85) and hippocampal volumes (r=.89) estimated at both fields. Our method is publicly available as part of FreeSurfer, at: //surfer.nmr.mgh.harvard.edu/fswiki/WMH-SynthSeg.
The incidence of vertebral fragility fracture is increased by the presence of preexisting pathologies such as metastatic disease. Computational tools could support the fracture prediction and consequently the decision of the best medical treatment. Anyway, validation is required to use these tools in clinical practice. To address this necessity, in this study subject-specific homogenized finite element models of single vertebrae were generated from micro CT images for both healthy and metastatic vertebrae and validated against experimental data. More in detail, spine segments were tested under compression and imaged with micro CT. The displacements field could be extracted for each vertebra singularly using the digital volume correlation full-field technique. Homogenized finite element models of each vertebra could hence be built from the micro CT images, applying boundary conditions consistent with the experimental displacements at the endplates. Numerical and experimental displacements and strains fields were eventually compared. In addition, the outcomes of a micro CT based homogenized model were compared to the ones of a clinical-CT based model. Good agreement between experimental and computational displacement fields, both for healthy and metastatic vertebrae, was found. Comparison between micro CT based and clinical-CT based outcomes showed strong correlations. Furthermore, models were able to qualitatively identify the regions which experimentally showed the highest strain concentration. In conclusion, the combination of experimental full-field technique and the in-silico modelling allowed the development of a promising pipeline for validation of fracture risk predictors, although further improvements in both fields are needed to better analyse quantitatively the post-yield behaviour of the vertebra.
Identification of tumor margins is essential for surgical decision-making for glioblastoma patients and provides reliable assistance for neurosurgeons. Despite improvements in deep learning architectures for tumor segmentation over the years, creating a fully autonomous system suitable for clinical floors remains a formidable challenge because the model predictions have not yet reached the desired level of accuracy and generalizability for clinical applications. Generative modeling techniques have seen significant improvements in recent times. Specifically, Generative Adversarial Networks (GANs) and Denoising-diffusion-based models (DDPMs) have been used to generate higher-quality images with fewer artifacts and finer attributes. In this work, we introduce a framework called Re-Diffinet for modeling the discrepancy between the outputs of a segmentation model like U-Net and the ground truth, using DDPMs. By explicitly modeling the discrepancy, the results show an average improvement of 0.55\% in the Dice score and 16.28\% in HD95 from cross-validation over 5-folds, compared to the state-of-the-art U-Net segmentation model.
The integration of large language models (LLMs) into the medical field has gained significant attention due to their promising accuracy in simulated clinical decision-making settings. However, clinical decision-making is more complex than simulations because physicians' decisions are shaped by many factors, including the presence of cognitive bias. However, the degree to which LLMs are susceptible to the same cognitive biases that affect human clinicians remains unexplored. Our hypothesis posits that when LLMs are confronted with clinical questions containing cognitive biases, they will yield significantly less accurate responses compared to the same questions presented without such biases. In this study, we developed BiasMedQA, a novel benchmark for evaluating cognitive biases in LLMs applied to medical tasks. Using BiasMedQA we evaluated six LLMs, namely GPT-4, Mixtral-8x70B, GPT-3.5, PaLM-2, Llama 2 70B-chat, and the medically specialized PMC Llama 13B. We tested these models on 1,273 questions from the US Medical Licensing Exam (USMLE) Steps 1, 2, and 3, modified to replicate common clinically-relevant cognitive biases. Our analysis revealed varying effects for biases on these LLMs, with GPT-4 standing out for its resilience to bias, in contrast to Llama 2 70B-chat and PMC Llama 13B, which were disproportionately affected by cognitive bias. Our findings highlight the critical need for bias mitigation in the development of medical LLMs, pointing towards safer and more reliable applications in healthcare.
Metastases increase the risk of fracture when affecting the femur. Consequently, clinicians need to know if the patients femur can withstand the stress of daily activities. The current tools used in clinics are not sufficiently precise. A new method, the CT-scan-based finite element analysis, gives good predictive results. However, none of the existing models were tested for reproducibility. This is a critical issue to address in order to apply the technique on a large cohort around the world to help evaluate bone metastatic fracture risk in patients. Please see pdf file
Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.
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