[论文精读]Hierarchical Graph Convolutional Network Built by Multiscale Atlases for Brain Disorder

⑤Scanning parameters of ADNI: TR = 3 s, TE = 30 ms, flip angle = 80◦ , resolution = 3.3 × 3.3 × 3.3 mm3 , 48 axial slices, and 420 s in duration (140 volumes)

⑥OASIS: 250 samples with 207 HC and 43 AD

⑦Scanning parameters of OASIS: TR = 2.2 s, TE = 27 ms, resolution = 4 × 4 × 4 mm3 , 36 axial slices, and 372 s in duration (169 volumes)

⑧ABIDE: 1011 samples with 512 HC and 499 ASD (excluding time＜300s)

⑨Scanning parameters of ABIDE: TR = 1.5–3 s, TE = 15–33 ms, in-plane resolution 3 × 3–3.438 × 3.438 mm2 , slice thickness = 3–4.5 mm, 28–40 axial slices, and 304–486 s in duration (120–300 volumes)

⑩Dataset table:

⑪Introducing how they process the data

2.3.2. Multiscale Atlases for Brain Parcellation and FCN Construction

①Atlas choosing: 100, 200, 300, 400, 500

2.3.3. Multiscale-Atlases-Based Hierarchical Graph Convolutional Network (MAHGCN)

（1）Graph Convolutional Network

①Laplacian matrix:

$L=I-D^{-\frac{1}{2}}AD^{-\frac{1}{2}}$

②GCN:

$g_\theta*h=V\big(\big(V^Tg_\theta\big)\times\big(V^Th\big)\big)$

where $h\in \mathbb{R}^{R \times ch^{in}}$ is feature matrix, $g_\theta$ denotes graph convolutional kernel, $\theta$ denotes learnable parameter and $V^Th$ represents Fourier transform

③Simplifying this operation to:

$h^{\mathrm{GC}}=\sigma(\tilde{D}^{-\frac{1}{2}}\tilde{A}\tilde{D}^{-\frac{1}{2}}h\theta)$

where $\sigma$ denotes ReLU（其实①②③都没有什么写上去的必要吧，也可以直接写③）

（2）Atlas-Guided Pooling

①Re mapping the matrix by voxel overlapping ratio $\rho$ with threshold Th（体素的重叠通过Schaefer模板算）:

$M_{R\to\wp}(i,j)=\begin{cases}1,&\rho>\text{Th}\\0,&\text{Otherwise}\end{cases}$

这样？

②The computing method of AP:

$(M_{\mathcal{R}\to\wp})^{T}h_{R}^{\mathrm{GC}}=h_{P}^{\mathrm{AP}}$

那这就是(P×R)*(R*chin)=P×chin（但是似乎不能固定留下来几个点，还是得看Th）

③⭐They adopt across scales sum pooling（就是把500*1，400*1，...，100*1的二维张量concatenate起来）

（3）Stacks of GCNs and APs for Hierarchical Architecture

①⭐输入节点特征矩阵是500×500 one hot编码，意思是chin也是500，但是chin按照上面那个AP来说不会变啊。作者也没说是GCN变得，说是AP转换的。啊？？？？

②Overall framework:

2.3.4. Model Explainability Analysis

①⭐To evaluate the importance of each ROI, they introduce gradient-guided class activation map (GradCAM) to calculate Grad-CAM on different scales.

2.4. Experiments

2.4.1. Experimental Settings

（1）Implementation

①Loss: weighted cross entropy loss（为什么是为了解决positive和negative的sample size？？？）. And the weights are set as the inverse of the sample ratio in the training set

②Epoch: 100

③Learning rate: 0.001

④Batch size: 30

⑤Optimizer: Adam

⑥Weight decay: 0.1 for ADNI and 0.01 for others

（2）Validation Scheme and Evaluation Metrics

①Running times: 5

②Training/testing set: 0.8/0.2 randomly

③Metrics: ACC, SEN, SPE, AUC

（3）Statistical Analysis

①Applying one-sided paired t-tests and Wilcoxon signed-rank test to verify the effectiveness of their model

2.4.2. Comparison Methods

①They compare their model with baseline (GCN, ML, RNN), pooling strategies, and multi-scale fusion methods

2.5. Results

2.5.1. Comparison Study

①Comparison table:

②The performance of multi scale model＞single

③⭐“所有的最佳性能都是由基于多尺度地图集的方法获得的，而不是数据驱动的池化方法，这表明基于生物先验的方法比数据驱动的方法在正确捕获多尺度大脑特征方面具有优势。”（这句话挺精炼明了了，我就懒得再paraphrase了）

④⭐Data may influenced by noise and atlases bring hierarchical prior

⑤There is generalizability of their model

2.5.2. Comparison With State-of-the-Art Methods

①Comparison table:

2.5.3. Ablation Study

（1） Effects of the Range of Integrated Scales

①T-test and (∗ ) and Wilcoxon signed-rank test (◦ ) present in (a) HC-versus-eMCI and (b) HC-versus-AD classification on different scales:

②⭐However, there is ceiling in growth of scales

（2）Different Configurations of AP

①Comparison table with different pooling strategies:

（3）Effects of Skip Connections

①Comparison table with skip connection strategies:

（4）Effects of Thresholds for Atlas Mapping Matrix

①⭐They define Th=0, which means they contains all the overlapping

②Performance under different Th:

（5）Effects of Preprocessing Pipeline

①Displayed performances under two different preprocessing pipelines

2.5.4. Explainability Analysis

①Activation value distribution:

2.6. Conclusion

①They proposed a novel multi-scale method

3. 知识补充

3.1. Grad-CAM

论文解读：[论文总结] Grad-CAM - 知乎 (zhihu.com)

4. Reference List

Liu, M. et al. (2023) 'Hierarchical Graph Convolutional Network Built by Multiscale Atlases for Brain Disorder Diagnosis Using Functional Connectivity', IEEE Trans Neural Netw Learn Syst. doi: http://10.1109/TNNLS.2023.3282961

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[论文精读]Hierarchical Graph Convolutional Network Built by Multiscale Atlases for Brain Disorder

计算机-人工智能-脑科学与类脑智能
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