# PUB-SalNet: A Pre-Trained Unsupervised Self-Aware Backpropagation Network for Biomedical Salient Segmentation

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## Abstract

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## 1. Introduction

- We propose the novel PUB-SalNet model for biomedical salient segmentation, which is a completely unsupervised method utilizing weights and knowledge from pre-training and attention-guided refinement during back propagation.
- We aggregate a new biomedical data set called SalSeg-CECT, featuring rich salient objects, different SNR settings, and various resolutions, which also serves for pre-training and fine-tuning for other complex biomedical tasks.
- Extensive experiments show that the proposed PUB-SalNet achieves state-of-the-art performance. The same method can be adapted to process 3D images, demonstrating correctness and generalization ability of our method.

## 2. Related Work

#### 2.1. Pre-Trained Methods in Biomedical Images

#### 2.2. Unsupervised Biomedical Image Segmentation

#### 2.3. Salient Segmentation

## 3. PUB-SalNet

#### 3.1. Pre-Training Method

#### 3.2. U-SalNet Architecture

#### 3.3. Unsupervised Backpropagation

Algorithm 1 Unsupervised Backpropagation Algorithm |

Require: Original biomedical image |

Ensure: Salient segmentation results |

1: $(W,b)=Init\left(\right)$ // Initialize backbone parameters |

2: $({W}^{\prime},{b}^{\prime},nClass)=Init\left(\right)$ // Initialize classifier parameters |

3: ${\left\{{S}_{k}\right\}}_{k=1}^{K}=GetSuperpixels({\left\{{p}_{n}\right\}}_{n=1}^{N})$ |

4: for $iter=1\to I$do |

5: if $nClass>2$ then |

6: ${\left\{{F}_{n}\right\}}_{n=1}^{N}=GetFeatures({\left\{{p}_{n}\right\}}_{n=1}^{N},\{W,b\})$ |

7: ${\left\{G{A}_{n}\right\}}_{n=1}^{N}=GlobalAttention({\left\{{F}_{n}\right\}}_{n=1}^{N})$ |

8: ${\left\{L{A}_{n}\right\}}_{n=1}^{N}=LocalAttention({\left\{{F}_{n}\right\}}_{n=1}^{N})$ |

9: ${\left\{{Y}_{n}\right\}}_{n=1}^{N}={\{{W}^{\prime}(G{A}_{n}\u2a01L{A}_{n})+{b}^{\prime}\}}_{n=1}^{N}$ |

10: ${\left\{{Y}_{n}^{\prime}\right\}}_{n=1}^{N}=BatchNorm({\left\{{Y}_{n}\right\}}_{n=1}^{N})$ |

11: ${\left\{{y}_{n}\right\}}_{n=1}^{N}={\left\{\mathrm{argmax}\phantom{\rule{4pt}{0ex}}{Y}_{n}^{\prime}\right\}}_{n=1}^{N}$ //predict salient labels |

12: for $p=1\to P$ do |

13: ${y}_{\mathrm{max}}=\mathrm{argmax}{\left|{y}_{n}\right|}_{n\in {S}_{p}}$ |

14: ${y}_{n}^{\prime}={y}_{\mathrm{max}}$ for $n\in {S}_{p}$ |

15: end for |

16: $L=CrossEntropyLoss({\{{Y}_{n}^{\prime},{y}_{n}^{\prime}\}}_{n=1}^{N})$ |

17: $\{W,b\},\{{W}^{\prime},{b}^{\prime}\}=Update\left(L\right)$ |

18: end if |

19: end for |

## 4. Experiments

#### 4.1. Datasets Setting

#### 4.2. Implementation Details

#### 4.3. Evaluation Metrics

**Region Similarity F.**To measure the similarity of matching regions from two salient segmentation maps, F is defined as:

**Pixel-wise Accuracy $\epsilon $.**F does not consider true negative saliency predictions. We define the normalized ($[0,1]$) mean absolute error (MAE) between predicted salient segmentation maps and ground truth masks as:

**Enhanced Alignment Measure E.**Proposed by [28], using the enhanced alignment matrix ${\varphi}_{FM}$ to measure the two properties (pixel-level matching and image-level statistics) of a binary map, E is defined as:

**Structural Similarity S.**S proposed by [29] evaluates the structural similarity by considering both regions and objects. Since saliency of potential spacial structures is crucial to biomedical images, we additionally use S to comprehensively evaluate the structural similarity of biomedical images.

#### 4.4. Quantitative Evaluation

#### 4.4.1. Comparison with State-of-the-Art

#### 4.4.2. Ablation Study

**B**stands for backpropagation from [2]’s work, which serves as our baseline because it is a classic unsupervised image segmentation method using deep learning. The experimental results in Table 2 shows that three parts of our PUB-SalNet functions together and are all indispensable. It is even competitive compared to the supervised method.

#### 4.4.3. Parameter Sensitivity Analysis

#### 4.5. Qualitative Evaluation

#### 4.6. Case Study on the ISBI Challenge

## 5. Conclusions

## Author Contributions

## Funding

## Conflicts of Interest

## References

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**Figure 2.**The overview framework of our proposed method. The processing pipeline consists of three main steps: (

**a**) pre-training on the SalSeg-CECT data set; (

**b**) prediction using the U-SalNet model; (

**c**) unsupervised attentional backpropagation iterating on single images. The Enc and Dec stand for the encoder and decoder. The ⨂, ⨂, and ⨂ denote the global attention mechanism, local attention mechanism and convolutional decoding, respectively.

**Figure 3.**The architecture of our U-SalNet model. (

**a**) Global Attention and (

**b**) Local Attention corresponds to ⨂ and ⨂ from Figure 2b, respectively. GA and LA stand for Global Attention and Local Attention. Conv means the convolution operation. ⨁ stands for weighted summation over the feature map.

**Figure 4.**Qualitative visual results of ten unsupervised methods on the simulated biomedical data set with SNR = 0.5 and 1.5. GT stands for ground truth images, PUB is PUB-SalNet, and the other nine methods are referenced in Table 1.

**Figure 5.**Visualization of 3D salient segmentation by PUB-SalNet on a 3D subvolume of size $64\times 64\times 64$ from the CECT test set. The pictures are obtained using UCSF Chimera, which displays the isosurface of the four corresponding 3D images; (

**a**) is the original image with a threshold of 0 (

**b**) is the ground truth of macro-molecular structures (

**c**) is our prediction (

**d**) demonstrates that the predicted salient region greatly overlaps with the ground truth macro-molecular structure.

**Figure 6.**Case study of 2D salient segmentation by PUB-SalNet and the B module on the ISBI Challenge [27].

**Table 1.**Comparison of performance of ten unsupervised methods with four metrics on the simulated biomedical test sets. $\epsilon $ stands for Mean Absolute Error (MAE), F for region similarity, E for the enhanced alignment measure, and S for structural similarity. Lower is better for $\epsilon $, and higher is better for the other three metrics. The results are calculated according to Equations (6)–(8). The best performance of each metric is in

**bold**and the second best is underlined. The improvements of our PUB-SalNet over the best of other methods in relative percentage is shown in the last row.

Data Set | SNR = 0.5 | SNR = 1.5 | |||||||
---|---|---|---|---|---|---|---|---|---|

Metric | $\mathbf{\epsilon}$ | $\mathit{F}$ | $\mathit{E}$ | $\mathit{S}$ | $\mathbf{\epsilon}$ | $\mathit{F}$ | $\mathit{E}$ | $\mathit{S}$ | |

Method | |||||||||

Itti [30] | 0.1277 | 0.4759 | 0.3811 | 0.4445 | 0.1206 | 0.6396 | 0.4639 | 0.4781 | |

LC [31] | 0.1626 | 0.3277 | 0.4466 | 0.4846 | 0.1463 | 0.4615 | 0.4369 | 0.5022 | |

SR [32] | 0.1340 | 0.2535 | 0.3020 | 0.4406 | 0.1316 | 0.3439 | 0.2911 | 0.4423 | |

IG [33] | 0.2843 | 0.1713 | 0.4775 | 0.4262 | 0.2978 | 0.1848 | 0.4739 | 0.4322 | |

SIG [34] | 0.2623 | 0.2647 | 0.4959 | 0.4781 | 0.2310 | 0.3387 | 0.5134 | 0.5177 | |

VA [35] | 0.2843 | 0.1713 | 0.4775 | 0.4262 | 0.2978 | 0.1848 | 0.4739 | 0.4322 | |

SVA [34] | 0.2625 | 0.2647 | 0.4957 | 0.4779 | 0.2305 | 0.3414 | 0.5129 | 0.5186 | |

VBP [36] | 0.1295 | 0.3049 | 0.4033 | 0.4527 | 0.1224 | 0.4588 | 0.4053 | 0.4717 | |

SalGAN [37] | 0.1427 | 0.1984 | 0.3126 | 0.4411 | 0.1585 | 0.2367 | 0.4090 | 0.4629 | |

PUB-SalNet | 0.0914 | 0.6573 | 0.7036 | 0.6494 | 0.0762 | 0.7426 | 0.7522 | 0.7209 | |

Improvement | ↓ 28.43% | ↑ 38.12% | ↑ 41.88% | ↑ 34.01% | ↓ 36.82% | ↑ 16.10% | ↑ 46.51% | ↑ 39.00% |

**Table 2.**Quantitative comparisons between different combination of modules from our PUB-SalNet model.

**B**stands for a single unsupervised backpropagation module;

**U+B**stands for U-SalNet architecture with

**B**;

**P+B**means

**B**based on the pre-training method;

**P+U**means U-SalNet based on the pre-training method, note that this is actually not an unsupervised method;

**P+U+B**is our proposed PUB-SalNet.

Data Set | SNR = 0.5 | SNR = 1.5 | |||||||
---|---|---|---|---|---|---|---|---|---|

Metric | $\mathbf{\epsilon}$ | $\mathit{F}$ | $\mathit{E}$ | $\mathit{S}$ | $\mathbf{\epsilon}$ | $\mathit{F}$ | $\mathit{E}$ | $\mathit{S}$ | |

Method | |||||||||

B | 0.1461 | 0.1628 | 0.3692 | 0.4230 | 0.1433 | 0.1628 | 0.3960 | 0.4223 | |

U+B | 0.2870 | 0.1628 | 0.4834 | 0.3585 | 0.2677 | 0.1628 | 0.5130 | 0.3693 | |

P+B | 0.1063 | 0.5631 | 0.5906 | 0.5661 | 0.0949 | 0.6551 | 0.5947 | 0.5979 | |

P+U | 0.1104 | 0.6214 | 0.6306 | 0.6506 | 0.0973 | 0.7544 | 0.7465 | 0.7617 | |

P+U+B | 0.0914 | 0.6573 | 0.7036 | 0.6494 | 0.0762 | 0.7426 | 0.7522 | 0.7209 |

**Table 3.**The quantitative comparison of parameter sensitivity analysis under four metrics. $\epsilon $, F, E and S are the same as Table 1. For PUB-SalNet-B

**X**,

**X**stands for the initial number of classes to be decreased, as is in Function Init() parameter in Algorithm 1.

Data Set | SNR = 0.5 | SNR = 1.5 | |||||||
---|---|---|---|---|---|---|---|---|---|

Metric | $\mathbf{\epsilon}$ | $\mathit{F}$ | $\mathit{E}$ | $\mathit{S}$ | $\mathbf{\epsilon}$ | $\mathit{F}$ | $\mathit{E}$ | $\mathit{S}$ | |

Method | |||||||||

PUB-SalNet-B20 | 0.0984 | 0.6347 | 0.6964 | 0.6428 | 0.0793 | 0.7239 | 0.7447 | 0.7124 | |

PUB-SalNet-B40 | 0.0961 | 0.6396 | 0.6945 | 0.6443 | 0.0766 | 0.7318 | 0.7320 | 0.7107 | |

PUB-SalNet-B60 | 0.0945 | 0.6437 | 0.6710 | 0.6358 | 0.0774 | 0.7218 | 0.7294 | 0.7032 | |

PUB-SalNet-B80 | 0.0943 | 0.6543 | 0.7221 | 0.6598 | 0.0783 | 0.7327 | 0.7340 | 0.7065 | |

PUB-SalNet-B100 | 0.0914 | 0.6573 | 0.7036 | 0.6494 | 0.0762 | 0.7426 | 0.7522 | 0.7209 |

Data Set | ISBI 2017 Skin | |||
---|---|---|---|---|

Metric | $\mathbf{\epsilon}$ | $\mathit{F}$ | $\mathit{E}$ | |

Method | ||||

B | 0.3136 | 0.3378 | 0.4140 | |

P+U+B | 0.3498 | 0.3378 | 0.4674 |

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## Share and Cite

**MDPI and ACS Style**

Chen, F.; Jiang, Y.; Zeng, X.; Zhang, J.; Gao, X.; Xu, M. PUB-SalNet: A Pre-Trained Unsupervised Self-Aware Backpropagation Network for Biomedical Salient Segmentation. *Algorithms* **2020**, *13*, 126.
https://doi.org/10.3390/a13050126

**AMA Style**

Chen F, Jiang Y, Zeng X, Zhang J, Gao X, Xu M. PUB-SalNet: A Pre-Trained Unsupervised Self-Aware Backpropagation Network for Biomedical Salient Segmentation. *Algorithms*. 2020; 13(5):126.
https://doi.org/10.3390/a13050126

**Chicago/Turabian Style**

Chen, Feiyang, Ying Jiang, Xiangrui Zeng, Jing Zhang, Xin Gao, and Min Xu. 2020. "PUB-SalNet: A Pre-Trained Unsupervised Self-Aware Backpropagation Network for Biomedical Salient Segmentation" *Algorithms* 13, no. 5: 126.
https://doi.org/10.3390/a13050126