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Breast cancer is the most common malignant tumor among women and the second cause of cancer-related death. Early diagnosis in clinical practice is crucial for timely treatment and prognosis. Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has revealed great usability in the preoperative diagnosis and assessing therapy effects thanks to its capability to reflect the morphology and dynamic characteristics of breast lesions. However, most existing computer-assisted diagnosis algorithms only consider conventional radiomic features when classifying benign and malignant lesions in DCE-MRI. In this study, we propose to fully leverage the dynamic characteristics from the kinetic curves as well as the radiomic features to boost the classification accuracy of benign and malignant breast lesions. The proposed method is a fully automated solution by directly analyzing the 3D features from the DCE-MRI. The proposed method is evaluated on an in-house dataset including 200 DCE-MRI scans with 298 breast tumors (172 benign and 126 malignant tumors), achieving favorable classification accuracy with an area under curve (AUC) of 0.94. By simultaneously considering the dynamic and radiomic features, it is beneficial to effectively distinguish between benign and malignant breast lesions.

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Parkinson's disease ranks as the second most prevalent neurodegenerative disorder globally. This research aims to develop a system leveraging Mixed Reality capabilities for tracking and assessing eye movements. In this paper, we present a medical scenario and outline the development of an application designed to capture eye-tracking signals through Mixed Reality technology for the evaluation of neurodegenerative diseases. Additionally, we introduce a pipeline for extracting clinically relevant features from eye-gaze analysis, describing the capabilities of the proposed system from a medical perspective. The study involved a cohort of healthy control individuals and patients suffering from Parkinson's disease, showcasing the feasibility and potential of the proposed technology for non-intrusive monitoring of eye movement patterns for the diagnosis of neurodegenerative diseases. Clinical relevance - Developing a non-invasive biomarker for Parkinson's disease is urgently needed to accurately detect the disease's onset. This would allow for the timely introduction of neuroprotective treatment at the earliest stage and enable the continuous monitoring of intervention outcomes. The ability to detect subtle changes in eye movements allows for early diagnosis, offering a critical window for intervention before more pronounced symptoms emerge. Eye tracking provides objective and quantifiable biomarkers, ensuring reliable assessments of disease progression and cognitive function. The eye gaze analysis using Mixed Reality glasses is wireless, facilitating convenient assessments in both home and hospital settings. The approach offers the advantage of utilizing hardware that requires no additional specialized attachments, enabling examinations through personal eyewear.

Breast cancer is a significant health concern affecting millions of women worldwide. Accurate survival risk stratification plays a crucial role in guiding personalised treatment decisions and improving patient outcomes. Here we present BioFusionNet, a deep learning framework that fuses image-derived features with genetic and clinical data to obtain a holistic profile and achieve survival risk stratification of ER+ breast cancer patients. We employ multiple self-supervised feature extractors (DINO and MoCoV3) pretrained on histopathological patches to capture detailed image features. These features are then fused by a variational autoencoder and fed to a self-attention network generating patient-level features. A co-dual-cross-attention mechanism combines the histopathological features with genetic data, enabling the model to capture the interplay between them. Additionally, clinical data is incorporated using a feed-forward network, further enhancing predictive performance and achieving comprehensive multimodal feature integration. Furthermore, we introduce a weighted Cox loss function, specifically designed to handle imbalanced survival data, which is a common challenge. Our model achieves a mean concordance index of 0.77 and a time-dependent area under the curve of 0.84, outperforming state-of-the-art methods. It predicts risk (high versus low) with prognostic significance for overall survival in univariate analysis (HR=2.99, 95% CI: 1.88--4.78, p<0.005), and maintains independent significance in multivariate analysis incorporating standard clinicopathological variables (HR=2.91, 95\% CI: 1.80--4.68, p<0.005).

Addressing the global challenge of breast cancer, this research explores the fusion of generative AI, focusing on ChatGPT 3.5 turbo model, and the intricacies of breast cancer risk assessment. The research aims to evaluate ChatGPT's reasoning capabilities, emphasizing its potential to process rules and provide explanations for screening recommendations. The study seeks to bridge the technology gap between intelligent machines and clinicians by demonstrating ChatGPT's unique proficiency in natural language reasoning. The methodology employs a supervised prompt-engineering approach to enforce detailed explanations for ChatGPT's recommendations. Synthetic use cases, generated algorithmically, serve as the testing ground for the encoded rules, evaluating the model's processing prowess. Findings highlight ChatGPT's promising capacity in processing rules comparable to Expert System Shells, with a focus on natural language reasoning. The research introduces the concept of reinforcement explainability, showcasing its potential in elucidating outcomes and facilitating user-friendly interfaces for breast cancer risk assessment.

Gun violence is a major source of injury and death in the United States. However, relatively little is known about the effects of firearm injuries on survivors and their family members and how these effects vary across subpopulations. To study these questions and, more generally, to address a gap in the causal inference literature, we present a framework for the study of effect modification or heterogeneous treatment effects in difference-in-differences designs. We implement a new matching technique, which combines profile matching and risk set matching, to (i) preserve the time alignment of covariates, exposure, and outcomes, avoiding pitfalls of other common approaches for difference-in-differences, and (ii) explicitly control biases due to imbalances in observed covariates in subgroups discovered from the data. Our case study shows significant and persistent effects of nonfatal firearm injuries on several health outcomes for those injured and on the mental health of their family members. Sensitivity analyses reveal that these results are moderately robust to unmeasured confounding bias. Finally, while the effects for those injured vary largely by the severity of the injury and its documented intent, for families, effects are strongest for those whose relative's injury is documented as resulting from an assault, self-harm, or law enforcement intervention.

Transthoracic Echocardiography (TTE) is a fundamental, non-invasive diagnostic tool in cardiovascular medicine, enabling detailed visualization of cardiac structures crucial for diagnosing various heart conditions. Despite its widespread use, TTE ultrasound imaging faces inherent limitations, notably the trade-off between field of view (FoV) and resolution. This paper introduces a novel application of conditional Generative Adversarial Networks (cGANs), specifically designed to extend the FoV in TTE ultrasound imaging while maintaining high resolution. Our proposed cGAN architecture, termed echoGAN, demonstrates the capability to generate realistic anatomical structures through outpainting, effectively broadening the viewable area in medical imaging. This advancement has the potential to enhance both automatic and manual ultrasound navigation, offering a more comprehensive view that could significantly reduce the learning curve associated with ultrasound imaging and aid in more accurate diagnoses. The results confirm that echoGAN reliably reproduce detailed cardiac features, thereby promising a significant step forward in the field of non-invasive cardiac naviagation and diagnostics.

In various biomedical studies, the focus of analysis centers on the magnitudes of data, particularly when algebraic signs are irrelevant or lost. To analyze the magnitude outcomes in repeated measures studies, using models with random effects is essential. This is because random effects can account for individual heterogeneity, enhancing parameter estimation precision. However, there are currently no established regression methods that incorporate random effects and are specifically designed for magnitude outcomes. This article bridges this gap by introducing Bayesian regression modeling approaches for analyzing magnitude data, with a key focus on the incorporation of random effects. Additionally, the proposed method is extended to address multiple causes of informative dropout, commonly encountered in repeated measures studies. To tackle the missing data challenge arising from dropout, a joint modeling strategy is developed, building upon the previously introduced regression techniques. Two numerical simulation studies are conducted to assess the validity of our method. The chosen simulation scenarios aim to resemble the conditions of our motivating study. The results demonstrate that the proposed method for magnitude data exhibits good performance in terms of both estimation accuracy and precision, and the joint models effectively mitigate bias due to missing data. Finally, we apply proposed models to analyze the magnitude data from the motivating study, investigating if sex impacts the magnitude change in diaphragm thickness over time for ICU patients.

Inspired by the human cognitive system, attention is a mechanism that imitates the human cognitive awareness about specific information, amplifying critical details to focus more on the essential aspects of data. Deep learning has employed attention to boost performance for many applications. Interestingly, the same attention design can suit processing different data modalities and can easily be incorporated into large networks. Furthermore, multiple complementary attention mechanisms can be incorporated in one network. Hence, attention techniques have become extremely attractive. However, the literature lacks a comprehensive survey specific to attention techniques to guide researchers in employing attention in their deep models. Note that, besides being demanding in terms of training data and computational resources, transformers only cover a single category in self-attention out of the many categories available. We fill this gap and provide an in-depth survey of 50 attention techniques categorizing them by their most prominent features. We initiate our discussion by introducing the fundamental concepts behind the success of attention mechanism. Next, we furnish some essentials such as the strengths and limitations of each attention category, describe their fundamental building blocks, basic formulations with primary usage, and applications specifically for computer vision. We also discuss the challenges and open questions related to attention mechanism in general. Finally, we recommend possible future research directions for deep attention.

Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.

Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translational research. In recent years, deep neural networks have achieved significant success in named entity recognition and many other Natural Language Processing (NLP) tasks. Most of these algorithms are trained end to end, and can automatically learn features from large scale labeled datasets. However, these data-driven methods typically lack the capability of processing rare or unseen entities. Previous statistical methods and feature engineering practice have demonstrated that human knowledge can provide valuable information for handling rare and unseen cases. In this paper, we address the problem by incorporating dictionaries into deep neural networks for the Chinese CNER task. Two different architectures that extend the Bi-directional Long Short-Term Memory (Bi-LSTM) neural network and five different feature representation schemes are proposed to handle the task. Computational results on the CCKS-2017 Task 2 benchmark dataset show that the proposed method achieves the highly competitive performance compared with the state-of-the-art deep learning methods.

Many natural language processing tasks solely rely on sparse dependencies between a few tokens in a sentence. Soft attention mechanisms show promising performance in modeling local/global dependencies by soft probabilities between every two tokens, but they are not effective and efficient when applied to long sentences. By contrast, hard attention mechanisms directly select a subset of tokens but are difficult and inefficient to train due to their combinatorial nature. In this paper, we integrate both soft and hard attention into one context fusion model, "reinforced self-attention (ReSA)", for the mutual benefit of each other. In ReSA, a hard attention trims a sequence for a soft self-attention to process, while the soft attention feeds reward signals back to facilitate the training of the hard one. For this purpose, we develop a novel hard attention called "reinforced sequence sampling (RSS)", selecting tokens in parallel and trained via policy gradient. Using two RSS modules, ReSA efficiently extracts the sparse dependencies between each pair of selected tokens. We finally propose an RNN/CNN-free sentence-encoding model, "reinforced self-attention network (ReSAN)", solely based on ReSA. It achieves state-of-the-art performance on both Stanford Natural Language Inference (SNLI) and Sentences Involving Compositional Knowledge (SICK) datasets.

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