粗粒(CG)分子模拟已成为研究全原子模拟无法访问的时间和长度尺度上分子过程的标准工具。参数化CG力场以匹配全原子模拟,主要依赖于力匹配或相对熵最小化,这些熵最小化分别需要来自具有全原子或CG分辨率的昂贵模拟中的许多样本。在这里,我们提出了流量匹配,这是一种针对CG力场的新训练方法,它通过利用正常流量(一种生成的深度学习方法)来结合两种方法的优势。流量匹配首先训练标准化流程以表示CG概率密度,这等同于最小化相对熵而无需迭代CG模拟。随后,该流量根据学习分布生成样品和力,以通过力匹配来训练所需的CG能量模型。即使不需要全部原子模拟的力,流程匹配就数据效率的数量级优于经典力匹配,并产生CG模型,可以捕获小蛋白质的折叠和展开过渡。
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归一化流量是用于在物理系统中建模概率分布的有希望的工具。虽然最先进的流动精确地近似分布和能量,但物理中的应用还需要平滑能量来计算力量和高阶导数。此外,这种密度通常在非琐碎拓扑上定义。最近的一个例子是用于产生肽和小蛋白质的3D结构的Boltzmann发电机。这些生成模型利用内部坐标(Dihedrals,角度和粘合)的空间,这是过度矫戈尔和紧凑的间隔的产物。在这项工作中,我们介绍了一类在紧凑型间隔和高血症上工作的平滑混合转换。混合物转化采用根除方法在实践中反转它们,这已经防止了双向流动训练。为此,我们示出了通过逆函数定理从前向评估计算这种反转的参数梯度和力。我们展示了如此平滑流动的两个优点:它们允许通过力匹配匹配模拟数据,并且可以用作分子动力学模拟的电位。
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晶格Boltzmann方法(LBM)是一种用于计算流体力学及超越的有效仿真技术。它基于笛卡尔网格上的简单流和碰撞算法,这与现代机器学习架构很容易兼容。虽然变得越来越明显,深度学习可以为古典仿真技术提供决定性刺激,但最近的研究没有解决机器学习和LBM之间可能的连接。在这里,我们引入了生菜,基于Pytorch的LBM代码,具有三倍的目标。生菜使GPU加速计算具有最小源代码,便于LBM模型的快速原型设计,并且可以将LBM模拟与Pytorch的深度学习和自动分化设施集成在一起。作为与LBM组合机器学习的概念证明,开发了一种神经碰撞模型,在双周期性剪切层上训练,然后转移到不同的流动,衰减湍流。我们还举例说明了Pytorch自动差异化框架在流量控制和优化中的增加的好处。为此,保持强制各向同性湍流的光谱,而无需进一步约束速度场。源代码可从https://github.com/lettucecfd/lettuce自由使用。
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Coronary Computed Tomography Angiography (CCTA) provides information on the presence, extent, and severity of obstructive coronary artery disease. Large-scale clinical studies analyzing CCTA-derived metrics typically require ground-truth validation in the form of high-fidelity 3D intravascular imaging. However, manual rigid alignment of intravascular images to corresponding CCTA images is both time consuming and user-dependent. Moreover, intravascular modalities suffer from several non-rigid motion-induced distortions arising from distortions in the imaging catheter path. To address these issues, we here present a semi-automatic segmentation-based framework for both rigid and non-rigid matching of intravascular images to CCTA images. We formulate the problem in terms of finding the optimal \emph{virtual catheter path} that samples the CCTA data to recapitulate the coronary artery morphology found in the intravascular image. We validate our co-registration framework on a cohort of $n=40$ patients using bifurcation landmarks as ground truth for longitudinal and rotational registration. Our results indicate that our non-rigid registration significantly outperforms other co-registration approaches for luminal bifurcation alignment in both longitudinal (mean mismatch: 3.3 frames) and rotational directions (mean mismatch: 28.6 degrees). By providing a differentiable framework for automatic multi-modal intravascular data fusion, our developed co-registration modules significantly reduces the manual effort required to conduct large-scale multi-modal clinical studies while also providing a solid foundation for the development of machine learning-based co-registration approaches.
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The release of ChatGPT, a language model capable of generating text that appears human-like and authentic, has gained significant attention beyond the research community. We expect that the convincing performance of ChatGPT incentivizes users to apply it to a variety of downstream tasks, including prompting the model to simplify their own medical reports. To investigate this phenomenon, we conducted an exploratory case study. In a questionnaire, we asked 15 radiologists to assess the quality of radiology reports simplified by ChatGPT. Most radiologists agreed that the simplified reports were factually correct, complete, and not potentially harmful to the patient. Nevertheless, instances of incorrect statements, missed key medical findings, and potentially harmful passages were reported. While further studies are needed, the initial insights of this study indicate a great potential in using large language models like ChatGPT to improve patient-centered care in radiology and other medical domains.
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Artificial Intelligence (AI) has become commonplace to solve routine everyday tasks. Because of the exponential growth in medical imaging data volume and complexity, the workload on radiologists is steadily increasing. We project that the gap between the number of imaging exams and the number of expert radiologist readers required to cover this increase will continue to expand, consequently introducing a demand for AI-based tools that improve the efficiency with which radiologists can comfortably interpret these exams. AI has been shown to improve efficiency in medical-image generation, processing, and interpretation, and a variety of such AI models have been developed across research labs worldwide. However, very few of these, if any, find their way into routine clinical use, a discrepancy that reflects the divide between AI research and successful AI translation. To address the barrier to clinical deployment, we have formed MONAI Consortium, an open-source community which is building standards for AI deployment in healthcare institutions, and developing tools and infrastructure to facilitate their implementation. This report represents several years of weekly discussions and hands-on problem solving experience by groups of industry experts and clinicians in the MONAI Consortium. We identify barriers between AI-model development in research labs and subsequent clinical deployment and propose solutions. Our report provides guidance on processes which take an imaging AI model from development to clinical implementation in a healthcare institution. We discuss various AI integration points in a clinical Radiology workflow. We also present a taxonomy of Radiology AI use-cases. Through this report, we intend to educate the stakeholders in healthcare and AI (AI researchers, radiologists, imaging informaticists, and regulators) about cross-disciplinary challenges and possible solutions.
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The future of population-based breast cancer screening is likely personalized strategies based on clinically relevant risk models. Mammography-based risk models should remain robust to domain shifts caused by different populations and mammographic devices. Modern risk models do not ensure adaptation across vendor-domains and are often conflated to unintentionally rely on both precursors of cancer and systemic/global mammographic information associated with short- and long-term risk, respectively, which might limit performance. We developed a robust, cross-vendor model for long-term risk assessment. An augmentation-based domain adaption technique, based on flavorization of mammographic views, ensured generalization to an unseen vendor-domain. We trained on samples without diagnosed/potential malignant findings to learn systemic/global breast tissue features, called mammographic texture, indicative of future breast cancer. However, training so may cause erratic convergence. By excluding noise-inducing samples and designing a case-control dataset, a robust ensemble texture model was trained. This model was validated in two independent datasets. In 66,607 Danish women with flavorized Siemens views, the AUC was 0.71 and 0.65 for prediction of interval cancers within two years (ICs) and from two years after screening (LTCs), respectively. In a combination with established risk factors, the model's AUC increased to 0.68 for LTCs. In 25,706 Dutch women with Hologic-processed views, the AUCs were not different from the AUCs in Danish women with flavorized views. The results suggested that the model robustly estimated long-term risk while adapting to an unseen processed vendor-domain. The model identified 8.1% of Danish women accounting for 20.9% of ICs and 14.2% of LTCs.
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Quaternion valued neural networks experienced rising popularity and interest from researchers in the last years, whereby the derivatives with respect to quaternions needed for optimization are calculated as the sum of the partial derivatives with respect to the real and imaginary parts. However, we can show that product- and chain-rule does not hold with this approach. We solve this by employing the GHRCalculus and derive quaternion backpropagation based on this. Furthermore, we experimentally prove the functionality of the derived quaternion backpropagation.
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In this work, a method for obtaining pixel-wise error bounds in Bayesian regularization of inverse imaging problems is introduced. The proposed method employs estimates of the posterior variance together with techniques from conformal prediction in order to obtain coverage guarantees for the error bounds, without making any assumption on the underlying data distribution. It is generally applicable to Bayesian regularization approaches, independent, e.g., of the concrete choice of the prior. Furthermore, the coverage guarantees can also be obtained in case only approximate sampling from the posterior is possible. With this in particular, the proposed framework is able to incorporate any learned prior in a black-box manner. Guaranteed coverage without assumptions on the underlying distributions is only achievable since the magnitude of the error bounds is, in general, unknown in advance. Nevertheless, experiments with multiple regularization approaches presented in the paper confirm that in practice, the obtained error bounds are rather tight. For realizing the numerical experiments, also a novel primal-dual Langevin algorithm for sampling from non-smooth distributions is introduced in this work.
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Multi-class ensemble classification remains a popular focus of investigation within the research community. The popularization of cloud services has sped up their adoption due to the ease of deploying large-scale machine-learning models. It has also drawn the attention of the industrial sector because of its ability to identify common problems in production. However, there are challenges to conform an ensemble classifier, namely a proper selection and effective training of the pool of classifiers, the definition of a proper architecture for multi-class classification, and uncertainty quantification of the ensemble classifier. The robustness and effectiveness of the ensemble classifier lie in the selection of the pool of classifiers, as well as in the learning process. Hence, the selection and the training procedure of the pool of classifiers play a crucial role. An (ensemble) classifier learns to detect the classes that were used during the supervised training. However, when injecting data with unknown conditions, the trained classifier will intend to predict the classes learned during the training. To this end, the uncertainty of the individual and ensemble classifier could be used to assess the learning capability. We present a novel approach for novel detection using ensemble classification and evidence theory. A pool selection strategy is presented to build a solid ensemble classifier. We present an architecture for multi-class ensemble classification and an approach to quantify the uncertainty of the individual classifiers and the ensemble classifier. We use uncertainty for the anomaly detection approach. Finally, we use the benchmark Tennessee Eastman to perform experiments to test the ensemble classifier's prediction and anomaly detection capabilities.
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