基于3D ResNet50改进模型的TOF-MRA脑动脉瘤分类方法
A Classification Method for Cerebral Aneurysms in TOF-MRA Based on Improved 3D ResNet50 Model
通讯作者: #Tel: 18679050077, E-mail:359918717@qq.com;*Tel: 15850168495, E-mail:daiyk@sibet.ac.cn.
收稿日期: 2024-06-17 网络出版日期: 2024-08-26
基金资助: |
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Corresponding authors: #Tel: 18679050077, E-mail:359918717@qq.com;*Tel: 15850168495, E-mail:daiyk@sibet.ac.cn.
Received: 2024-06-17 Online: 2024-08-26
脑动脉瘤的不规则形态,尤其是子瘤的存在,是动脉瘤破裂风险的关键因素.临床上对子瘤的评估主要是通过时间飞跃法磁共振血管造影(Time of Flight-Magnetic Resonance Angiography,TOF-MRA)进行图像重建及基于医生视觉和经验的判断,这限制了诊断的效率和准确性.本文提出了一种基于3D ResNet50改进的并行多尺度注意力融合网络(Parallel Multiscale Attention Fusion Networks,PMAF-Net)的子瘤自动分类方法,PMAF-Net采用多尺度卷积并加权融合通道和空间注意力权重以提高特征提取能力.实验所用TOF-MRA数据291例,其中训练集128例,验证集32例,测试集131例.与其他分类网络比较,PMAF-Net在测试集上表现最好,准确率为83.97%,召回率为84.48%,精确率为80.33%,F1分数为0.823 5,受试者工作特征曲线(ROC)也显示出模型最佳的分类性能(AUC为0.900 8).实验结果表明该网络能更准确地识别出子瘤型动脉瘤,有望对动脉瘤破裂风险评估和量化提供支持.
关键词:
The irregular morphology of cerebral aneurysms, especially the presence of a daughter sac, is a crucial risk factor for aneurysm rupture. Clinical assessment of daughter sac relies mainly on image reconstruction by time of flight-magnetic resonance angiography (TOF-MRA) and judgment based on physicians' vision and experience, which limits the efficiency and accuracy of diagnosis. In this paper, we propose an improved parallel multiscale fusion attention network (PMAF-Net) based on 3D ResNet50 for classification. PMAF-Net uses multi-scale convolution and weighted fusion channel and spatial attention weights to enhance the feature extraction capability. The experiment used 291 cases of TOF-MRA data, including 128 cases in the training set, 32 cases in the validation set, and 131 cases in the test set. Compared with other classification networks, PMAF-Net performs best on the test set, with the accuracy of 83.97%, recall of 84.48%, precision of 80.33%, and F1-score of 0.823 5, and the receiver operating characteristic curve (ROC) also reflects the model's optimal classification performance (AUC of 0.900 8). The results show that the network can identify daughter sac type aneurysms more accurately, which is expected to support the assessment and quantification of the risk of aneurysm rupture.
Keywords:
本文引用格式
薛培阳, 耿辰, 李郁欣, 鲍奕仿, 鲁宇澄, 戴亚康.
XUE Peiyang, GENG Chen, LI Yuxin, BAO Yifang, LU Yucheng, DAI Yakang.
引言
脑动脉瘤是一种常见的高风险脑血管疾病,是因血管壁结构改变而引起的血管壁病理性膨出或扩张[1].根据Forbes等[2]在国际未破裂颅内动脉瘤研究(International Study of Unruptured Intracranial Aneurysms,ISUIA)提出的分类方案,动脉瘤的形态可以分为四种类型(如图1所示):I型,具有均匀边缘的单一囊状结构;II型,表面呈波纹状的单一囊状结构;III型,从主囊中突出的一个或多个次级囊,其体积不超过总囊体积的25%;IV型,从动脉瘤的主颈部或主囊体上突起的一个囊状结构,占主囊体积的25%或以上.此外,日本未破裂脑动脉瘤研究(UCAS)委员会将子瘤定义为二维或三维图像上动脉瘤壁的不规则突出[3],这一标准也与ISUIA的III型、IV型分类一致,可认为这两种类型的动脉瘤即为子瘤型动脉瘤.脑动脉瘤在一般人群中大约有3.2%的致病率[4],其每年的破裂率约为0.95%~1.4%[5],一旦破裂将会引起蛛网膜下腔出血,导致脑梗死、脑出血等高致死率现象发生[6,7].而子瘤型动脉瘤年破裂率为28.3%[8],明显高于无子瘤的动脉瘤.Backes等[9]提出的早期蛛网膜下腔出血、动脉瘤位置、年龄大于60岁、人口、动脉瘤大小和形状(ELAPSS)评分也将动脉瘤的不规则形态视为其破裂风险的关键因素.因此提高对子瘤型动脉瘤的认识、及时准确地识别子瘤对临床诊断具有重要意义.
图1
图1
动脉瘤形态分类示意图(上)和三维重建效果图(下).I、II型为正常动脉瘤,III、IV型为子瘤型动脉瘤
Fig. 1
Overview of aneurysm morphology classification (top) and 3D reconstruction (bottom). Types I and II represent normal aneurysms, while types III and IV represent subsidiary aneurysms
目前,时间飞跃法磁共振血管造影(TOF-MRA)因无创伤、无需造影剂并且无X射线辐射,被广泛用于诊断脑动脉疾病和描绘动脉解剖结[10,11].在临床实践中,子瘤的诊断通常需要先对图像进行三维重建处理,随后医生对这些图像进行评估.Salimi等[12]在三维血管造影创建的患者图像中识别并标记了子瘤,并借助表面曲率图突出了以病灶曲率变化为特征的子瘤结构.他们在270个动脉瘤中识别出了83%的子瘤,然而其中有17%的子瘤难以识别,观察者之间的差异性大且诊断时间长、准确性较低.近年来,基于深度学习的方法已经证实在医学图像分析中的有效性[13,14].但在脑动脉瘤领域,现有的研究主要集中在动脉瘤的检测识别、分割以及动脉瘤的直径分类方面.在脑动脉瘤识别和直径分类方面,如Ueda等[15]利用脑动脉的曲率特征提取包括瘤体、血管分叉等在内的数百种动脉异常表现作为候选目标[16],再以ResNet18分类网络对其是否为动脉瘤进行分类.Zhao等[17]提出了一种简单有效的综合残差注意网络(CRANet),利用其结构对直径小于3 mm、3~7 mm和大于7 mm的动脉瘤进行分类,平均准确率达到了92.55%.Hu等[18]提出一种脑动脉瘤循环分类网络,他们先将CNN和RNN结合并利用多视图最大强度投影图像之间的空间信息进行特征融合,然后通过特征分类器来预测是否为动脉瘤,在测试集上达到了85.1%的准确率.在脑动脉瘤检测、分割方面,如Chen等[19]提出了一种基于变体3D U-Net和双分支通道注意力的检测网络DCAU-Net,使用DCA模块自适应调整通道特征响应,提高特征提取能力,最终在43例测试集上达到90.69%的敏感度.Zhang等[10]提出一种双分支连通网络并采用先定位后分割的两步训练策略进行动脉树区域分割,最终在10例测试集上分割出动脉树的6个主要区域,平均Dice系数为74.72%.
1 实验部分
1.1 实验方法
本文提出了一种基于深度学习的TOF-MRA脑动脉瘤子瘤自动分类方法,该方法的主要实验流程如图2所示,首先对原始TOF-MRA图像进行归一化处理,接着根据动脉瘤标注坐标相应地在原图上裁剪出感兴趣区域(Region of Interest,ROI),然后对所有处理后的数据进行划分得到训练集、验证集和测试集,然后使用扩增后的训练集训练PMAF-Net并在验证集上评估模型的分类结果,最后将得到的最佳模型在测试集上完成性能评估.
图2
1.2 基于3D ResNet50改进的并行多尺度注意力融合网络(PMAF-Net)
图3
图3
PMAF-Net架构图,上方为网络整体结构,下方A为MDC模块,B、C为CSA模块.残差块底部的数字代表每次下采样后特征图的尺寸和通道数(如323×64表示特征图大小为32×32×32,输出通道数为64)
Fig. 3
PMAF-Net architecture diagram. The top part shows the overall network structure, while the bottom part displays the MDC module (A) and the CSA modules (B and C). The numbers at the bottom of the residual blocks indicate the size and number of channels of the feature map after each downsampling (e.g., 323×64 indicates a feature map size of 32×32×32 with 64 output channels)
由于子瘤型动脉瘤附着子瘤,随着网络层数的加深,单尺度分类网络[20]在下采样过程中往往会造成细小子瘤特征的丢失,而普通卷积使用固定尺寸的卷积核,限制了其捕获全局上下文不同特征信息的能力,从而导致图像部分重要的信息随之丢失,给网络能够表征动脉瘤及子瘤区域的特征信息造成干扰.此外对提取的浅层多尺度特征进一步细化对深层抽象图像特征的融合至关重要.因此,本文通过在残差瓶颈结构中引入PMAF模块,以有效提取并细化全局上下文的多尺度特征.图3下方展示了PMAF残差块的具体细节,其中多尺度MDC模块改进了原来的单一卷积层[23],它包含了卷积核大小为1×1×1、3×3×3和5×5×5的卷积层,并且每个卷积后接一个批量归一化层(BN)和一个ReLU激活函数,以不同大小的卷积核来匹配不同对象的尺寸.这种多尺度滤波适应尺度变化,优化跨不同大小对象的特征提取能力.CSA模块是基于Woo等[24]提出的卷积块注意力模型(CBAM),包含通道和空间注意力机制.根据本文的任务,我们将其扩展到三维结构并融合了多尺度MDC,从而能够更好地细化多尺度特征.其中通道注意力模块对上层输出的特征图进行加权,以获得更为重要的通道特征,空间注意力模块则通过空间降维生成注意力图,增强对特征图上特定区域的注意力.首先,输入特征图依次进入多尺度的卷积核中进行卷积操作,输出的各通道特征图拼接后通过引入一个额外的1×1×1卷积使输出特征图与输入的形状一样,从而使它们可以相加.接着这些特征图被送入至通道注意力模块中,经过全局平均池化(GAP)和全局最大池化(GMP)共享多层感知机(Multilayer Perceptron,MLP)权重后得到不同特征,相加后使用Sigmoid激活函数得到通道权重,将其与多尺度特征图相乘得到输出.然后将修正后的输出特征图作为空间注意力模块的输入,通过GAP和GMP拼接操作后进行1×1×1卷积,将通道数降为1,再经过Sigmoid函数生成空间注意力权重.最后将通道加权的多尺度特征图与空间注意力权重相乘进行特征细化,得到PMAF模块最终的输出.
1.3 模型评估
本研究使用以下指标来评估模型的分类性能:准确率(Accuracy)、召回率(Recall)、精确率(Precision)及F1分数(F1_Score).计算公式如(1~4)式所示.同时基于混淆矩阵计算出各种性能指标,从而评估模型在不同类别上的表现.其中True Positive (TP) 表示模型将实际为正类别(有子瘤)的样本正确预测为正类别,False Negative(FN)表示模型将实际为正类别的样本错误预测为负类别(无子瘤),False Positive(FP)表示模型将实际为负类别的样本错误预测为正类别,True Negative(TN)表示模型将实际为负类别的样本正确预测为负类别.
准确率是指所有预测正确的样本数占总样本数的比例:
召回率也称敏感度,是指预测正确的正类别数占所有实际为正类别数的比例:
精确率是指预测正确的正类别数占所有预测为正类别的比例:
F1分数是精确率和召回率的调和平均数,是评价分类器性能的综合指标,F1分数介于0和1之间,越接近1说明模型的性能越好:
1.4 训练环境与参数设置
本研究的实验基于一块16 GB显存的NVIDIA GeForce RTX 3080 Ti GPU进行,主要软件环境为CUDA10.0、Python3.11.5和PyTorch2.1.0.相关参数设置为:输入图像大小为64×64×64;批处理大小为10;优化器为随机梯度下降(SGD);初始学习率为0.001,每迭代10个周期,学习率衰减为上一周期的0.5.训练过程采用早停法,交叉熵作为模型训练的损失函数.
2 结果与讨论
2.1 实验数据集
本研究的实验数据来源于复旦大学附属华山医院,收集自2016年3月至2019年12月在华山医院诊疗的颅内囊状未破裂动脉瘤患者的3D TOF-MRA影像资料.所有TOF-MRA图像均在常规临床工作中获得,同时本回顾性研究已获得合作医院机构伦理委员会的批准(IRB No. KY2019-009).数据排除标准:(1)已经治疗的动脉瘤,(2)已破裂的动脉瘤,(3)夹层和梭形动脉瘤,(4)MRA成像质量不佳或未进行MRA检查.排除上述标准后最后入组291例数据,其中训练集160例,测试集131例,网络训练过程中按8 : 2的比例划分为训练集128例,验证集32例.患者的年龄、性别、动脉瘤大小和子瘤的数量等信息如表1所示.三组数据集的所有入组的数据由两位十年以上经验的影像科医师进行标注和核对,将双方评定一致的结果确定为子瘤的金标准.实验数据采集设备为3.0T GE Discovery MR750、3.0T SIEMENS Verio和3.0T Philips Ingenia,表2展示了本研究数据在采集时所使用的相关参数.
表1 数据分组信息表
Table 1
组别 | 训练集 | 验证集 | 测试集 |
---|---|---|---|
患者数量 | 128 | 32 | 131 |
男性/女性 | 56/72 | 12/20 | 71/60 |
年龄(岁) | 56±12 | 58±9 | 62±14 |
正常动脉瘤/子瘤型动脉瘤 | 78/50 | 19/13 | 76/55 |
动脉瘤大小(mm) | 6.75±5.23 | 6.04±4.21 | 6.92±6.27 |
小型动脉瘤(<5mm)/子瘤 | 46/10 | 11/4 | 47/9 |
中型动脉瘤(5≤最大径<15mm)/子瘤 | 74/37 | 19/8 | 81/46 |
大型动脉瘤(15≤最大径<25mm)/子瘤 | 8/3 | 2/1 | 3/0 |
表2 数据采集参数表
Table 2
采集设备 | 重复时间 | 回波时间 | 图像分辨率 | 层厚 | 翻转角 | 采集矩阵 | 扫描时间 |
---|---|---|---|---|---|---|---|
GE 3.0T | 25 ms | 5.7 ms | 1024×1024×240 | 1.2 mm | 20˚ | 320×256 | 3min22s |
SIEMENS 3.0T | 21 ms | 3.6 ms | 512×512×128 | 0.9 mm | 18˚ | 256×197 | 2min53s |
Philips 3.0T | 18 ms | 3.5 ms | 512×512×128 | 1.0 mm | 20˚ | 308×203 | 2min22s |
2.2 数据预处理
本研究的数据预处理分为TOF-MRA归一化处理、ROI裁剪和数据扩增三个步骤.
(1)TOF-MRA归一化.由于不同的仪器采集数据,患者图像的灰度分布范围存在差异,因此将 3D TOF-MRA影像的灰度范围映射到0~1 024之间并重采样至各向同性.
(2)ROI裁剪.由于动脉瘤目标区域在整个脑动脉区域占比极小,直接用MRA图像参与训练会有周围大量冗余信息的干扰,故我们基于动脉瘤标注坐标在原图上裁剪出ROI包围盒,并重采样至64×64×64大小.
(3)数据扩增.为了防止网络训练过程因数据量较少而出现过拟合现象,我们按照图2扩增的方法将训练集扩增至8倍.具体地讲,先使用伽马变换将原始训练集扩增为原来的2倍;然后使用仿射变换将原始训练集和伽马变换后数据扩增至4倍;最后使用弹性形变将现有的全部数据扩增至8倍.
2.3 基于PMAF-Net的脑动脉瘤子瘤自动分类结果
本研究使用131例TOF-MRA作为外部测试集对训练好的模型进行评估.根据模型在测试集上的预测结果,我们绘制了对应的混淆矩阵,其可视化结果见图4.混淆矩阵中从左上到右下表示每个类别模型预测正确的个数,主对角线上的数值越大,说明模型对该类别的分类准确率就越高.具体表现为正常动脉瘤这一类中有83.56%(61/73)预测正确,子瘤型动脉瘤中有84.48%(49/58)预测正确.基于混淆矩阵,我们计算出模型用于子瘤型脑动脉瘤分类在准确率、召回率和精确率上的指标分别为83.97%、84.48%和80.33%,综合评价指标F1分数的值为0.823 5.此外,为了验证模型对子瘤型动脉瘤和正常动脉瘤的分类性能,我们还计算了它们各自的指标.表3结果显示,子瘤型动脉瘤和正常动脉瘤的精确率和召回率均在80%以上,综合指标F1分数值分别为0.823 5和0.853 1.实验结果表明PMAF-Net针对不同类型的动脉瘤均有较好的分类能力,具有一定的鲁棒性,能够区分子瘤型动脉瘤和正常动脉瘤.
图4
图4
模型在测试集上预测结果的混淆矩阵
Fig. 4
Confusion matrix of the model's prediction results on the test set
表3 模型在不同类型动脉瘤上的分类性能
Table 3
类别 Category | 精确率 Precision | 召回率 Recall | F1分数 F1_Score |
---|---|---|---|
子瘤型动脉瘤(有子瘤) | 80.33% | 84.48% | 0.8235 |
正常动脉瘤(无子瘤) | 87.14% | 83.56% | 0.8531 |
平均 | 83.74% | 84.02% | 0.8383 |
2.4 基于脑动脉瘤最大径的分组统计分析
考虑到脑动脉瘤形态尺寸的不同可能会对模型性能产生不同的影响,因此我们基于《颅内动脉瘤影像学判读专家共识》[25]中对动脉瘤最大径的划分标准,统计了131例测试集中小型动脉瘤(最大径<5 mm)、中型动脉瘤(5 mm£最大径<15 mm)和大型动脉瘤(15 mm£最大径<25 mm)的分布情况(见图5).表4列出了PMAF-Net在每个分组下的分类性能.从分类性能指标来看,模型对小型动脉瘤的分类准确率为80.85%,比中、大型分别低了4.34%和19.15%;对小型动脉瘤中子瘤型动脉瘤的识别精确率为50%,相比较而言,模型对中大型动脉瘤中子瘤型动脉瘤的识别精确率较高,分别为88.64%、100%.同时,中大型动脉瘤中子瘤型动脉瘤的召回率(敏感度)分别为84.78%和100%,高于小型动脉瘤,这表明模型对其比较敏感,代表着更少的误判和漏分.虽然大型动脉瘤仅有三例,但是模型不仅识别出了全部的正常动脉瘤,而且还准确识别出了全部的子瘤.从综合指标F1分数来看,模型对中大型动脉瘤(F1分数分别为0.866 7和1.000 0)的分类表现更加稳定.
图5
图5
脑动脉瘤最大径分布统计.小型动脉瘤(<5 mm)、中型动脉瘤([5, 15) mm)和大型动脉瘤([15, 25) mm)
Fig. 5
Statistical distribution of cerebral aneurysm maximum diameters. Small aneurysms (<5 mm), medium aneurysms ([5, 15) mm) and large aneurysms ([15, 25) mm)
表4 PMAF-Net在脑动脉瘤最大径不同分组上的分类性能
Table 4
亚组分析 Subgroup analysis | 准确率 Accuracy | 召回率 Recall | 精确率 Precision | F1分数 F1_Score |
---|---|---|---|---|
总体性能 | 83.97% | 84.48% | 80.33% | 0.8235 |
按最大径划分 | ||||
小型动脉瘤(47) | 80.85% | 77.78% | 50.00% | 0.6087 |
中型动脉瘤(81) | 85.19% | 84.78% | 88.64% | 0.8667 |
大型动脉瘤(3) | 100.00% | 100.00% | 100.00% | 1.0000 |
2.5 不同网络模型的性能对比
在相同的实验数据和训练环境下,本研究对比了PMAF-Net与其他5种网络模型的分类性能.图6为对比不同网络的受试者工作特征(Receiver Operating Characteristic Curve,ROC)曲线,通过将模型在不同阈值下的真正率(True Positive Rate,TPR)和假正率(False Positive Rate,FPR)进行对比,来直观地展示其各自的分类性能.图6中的AUC(Area Under the Curve)值为曲线下的面积,数值介于0~1之间,越接近1,模型的分类效果越好、泛化能力越强.其中PMAF-Net的AUC值最大,为0.900 8,分类性能最好.DenseNet的AUC值最小,为0.742 8,分类性能最差.所有模型在外测集上的定量分类指标的结果如表5所示,从中可以看出PMAF-Net不仅在整体准确率上表现最好(83.97%),与ResNet18(74.81%)、ResNet50(72.52%)、DenseNet(67.94%)、MobileNet(77.86%)、EfficientNet(72.52%)相比分别提高了9.16%、11.45%、16.03%、6.11%、11.45%,而且在精确率和召回率上也是最高,分别为80.33%和84.48%.实验结果表明,PMAF-Net的分类错误率最低并且对子瘤最为敏感,能够很好地区分子瘤型动脉瘤和正常动脉瘤,说明我们所提出的模型在子瘤分类任务中的有效性.通过对比其他网络模型,综合各项指标结果和ROC曲线表现,表明PMAF-Net的分类性能最好.
图6
图6
PMAF-Net与其他网络模型的ROC曲线.黑色对角线表示一个完全随机的分类器表现,其余分别为ResNet18(红色)、ResNet50(绿色)、DenseNet(蓝色)、MobileNet(橙色)、EfficientNet(紫色)和PMAF-Net(棕色)的ROC曲线
Fig. 6
ROC curves of PMAF-Net compared with other network models. The black diagonal line represents the performance of a completely randomized classifier, and the rest are the ROC curves for ResNet18 (red), ResNet50 (green), DenseNet (blue), MobileNet (orange), EfficientNet (purple), and PMAF-Net (brown), respectively
表5 本文方法与现有方法在测试集上的分类性能比较
Table 5
2.6 讨论
本文提出了一种用于自动分类TOF-MRA影像中脑动脉瘤形态的深度学习模型.为了解决网络深层抽象图像特征的丢失问题和单一卷积核局限的特征提取能力,我们搭建了PMAF-Net分类网络,其中MDC模块集成了多尺度特征信息和建立全局依赖,CSA模块则通过学习特征图中的通道和空间注意力权重,加权融合不同尺度的特征,从而进一步提高网络的特征表达能力.同时为了保证网络训练过程有充足的数据,实验使用伽马变换、仿射变换和弹性形变方法扩增训练集,模型训练后在外部测试集上进行测试和评估.
测试集的结果表明,PMAF-Net识别出了大部分子瘤型动脉瘤,整体准确率为83.97%,召回率为84.48%,精确率为80.33%.此外,为了全面评估模型性能,我们基于脑动脉瘤最大径进行了分组统计分析.实验结果发现,模型对中大型动脉瘤比较敏感,然而模型对小型动脉瘤的召回率为77.78%,其中对子瘤的识别准确率仅为50%,这表明模型对小型动脉瘤尤其是子瘤还不够敏感,错误地将动脉瘤的表面不规整识别为局部突起的子瘤特征.因此在后续的工作中可以尝试通过提取动脉瘤的边界纹理信息来引导网络学习,促使网络关注那些小尺寸动脉瘤区域的形态特征信息.为进一步比较PMAF-Net的性能,我们与五种主流的分类网络进行了对比,由图6和表5的结果可见,PMAF-Net比ResNet18、ResNet50、DenseNet、MobileNet和EfficientNet的准确率和AUC值分别提高了9.16%和0.0753,11.45%和0.1174,16.03%和0.1580,6.11%和0.0732,11.45%和0.1294.这表明对比其他模型,PMAF-Net表现更好,有着更强的特征提取能力.
本研究还存在一定的局限性,首先,实验所使用的是单模态的TOF-MRA数据,虽然包含了不同类型的动脉瘤,但这仍然是一项单中心研究,模型的泛化能力还需进一步验证.其次,动脉瘤数量之间有一定的差异,未来可以收集更多部位的数据或按不同类型动脉瘤进行数据增强手段来保证其分布的均衡性.此外,针对小型动脉瘤中子瘤的识别,其准确率、召回率等仍有提升空间,下一步可能需要结合动脉瘤的边界纹理等先验知识进一步优化模型.
3 结论
针对3D TOF-MRA影像中脑动脉瘤子瘤的识别问题,本文提出了一种基于深度学习的脑动脉瘤子瘤分类网络PMAF-Net,通过在残差瓶颈块中引入PMAF模块,该模块采用多尺度卷积并加权融合通道和空间注意力权重,有效提升了网络的分类性能.实验结果表明,相较于其他经典分类网络,PMAF-Net在准确率、召回率、精确率、AUC值和F1分数等指标上均取得了更优的结果,可以为临床进一步筛查子瘤型动脉瘤提供支持.
利益冲突
无
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