Journal of Southern Medical University ›› 2024, Vol. 44 ›› Issue (9): 1738-1751.doi: 10.12122/j.issn.1673-4254.2024.09.14
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Weiyang FANG1,2(), Hui XIAO1, Shuang WANG2, Xiaoming LIN2(
), Chaomin CHEN1(
)
Received:
2024-06-06
Online:
2024-09-20
Published:
2024-09-30
Contact:
Xiaoming LIN, Chaomin CHEN
E-mail:506486730@qq.com;xiaominglin@gidichina.org;15773839131@163.com
Weiyang FANG, Hui XIAO, Shuang WANG, Xiaoming LIN, Chaomin CHEN. A deep learning model based on magnetic resonance imaging and clinical feature fusion for predicting preoperative cytokeratin 19 status in hepatocellular carcinoma[J]. Journal of Southern Medical University, 2024, 44(9): 1738-1751.
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URL: https://www.j-smu.com/EN/10.12122/j.issn.1673-4254.2024.09.14
Fig.2 Technical framework of the multi-scale and multi-modality feature fusion model. IResnet: The baseline model. MSFF-IResnet: The multi-scale feature fusion model based on IResnet and multi-scale feature fusion methods. MMFF-IResnet: The multi-scale and multi-modality feature fusion model based on MSFF-IResnet and multi-modality data.
Item | CK19- cases | CK19+ cases | Number before augmentation | Number after augmentation |
---|---|---|---|---|
HBP sequence | ||||
Training group | 62 | 30 | 740 | 3000 |
Validation group | 16 | 8 | 190 | 190 |
DWI sequence | ||||
Training group | 62 | 30 | 710 | 3000 |
Validation group | 16 | 8 | 180 | 180 |
Tab.1 Number of MRI samples before and after data augmentation
Item | CK19- cases | CK19+ cases | Number before augmentation | Number after augmentation |
---|---|---|---|---|
HBP sequence | ||||
Training group | 62 | 30 | 740 | 3000 |
Validation group | 16 | 8 | 190 | 190 |
DWI sequence | ||||
Training group | 62 | 30 | 710 | 3000 |
Validation group | 16 | 8 | 180 | 180 |
Fig.3 Comparison of residual blocks. A: Residual blocks of Resnet. B: Residual blocks of IResnet18. Start Block is the first block and End Block the last block in residual blocks.
Input | Operator | Stride | Output |
---|---|---|---|
1×224×224 | Conv2d 7×7 | 2 | 32×112×112 |
32×112×112 | Maxpool2d 2×2 | 32×56×56 | |
32×56×56 | Ires Stage1 (Ires block ×2) | 1 | 32×56×56 |
32×56×56 | Ires Stage2 (Ires block ×2) | 2 | 64×28×28 |
64×28×28 | Ires Stage3 (Ires block ×2) | 2 | 128×14×14 |
128×14×14 | Ires Stage4 (Ires block ×2) | 2 | 256×7×7 |
256×7×7 | GAP 1×1 | 256 | |
256 | FC | 2 |
Tab.2 Network architecture of IResnet18
Input | Operator | Stride | Output |
---|---|---|---|
1×224×224 | Conv2d 7×7 | 2 | 32×112×112 |
32×112×112 | Maxpool2d 2×2 | 32×56×56 | |
32×56×56 | Ires Stage1 (Ires block ×2) | 1 | 32×56×56 |
32×56×56 | Ires Stage2 (Ires block ×2) | 2 | 64×28×28 |
64×28×28 | Ires Stage3 (Ires block ×2) | 2 | 128×14×14 |
128×14×14 | Ires Stage4 (Ires block ×2) | 2 | 256×7×7 |
256×7×7 | GAP 1×1 | 256 | |
256 | FC | 2 |
Fig.4 Multi-scale feature fusion models. A: MSFF-IResnet-a, which concatenates the second Ires Stage's shallow level feature map with the fourth Ires Stage's deep level feature map by channel dimension in IResnet18. B: MSFF-IResnet-b, which concatenates the third Ires Stage's middle level feature map with the fourth Ires Stage's deep level feature map by channel dimension in IResnet18. C: MSFF-IResnet-c, which concatenates the second Ires Stage's shallow level feature map and the third Ires Stage's middle level feature map with the fourth Ires Stage's deep level feature map by channel dimension in IResnet18.
Fig.5 Multi-scale and multi-modality feature fusion models at different stages. A: MMFF-IResnet-a, which fuses two sequences' images by channel dimension in the input stage of MSFF-IResnet. B: MMFF-IResnet-b with fusion of two sequences' feature maps by channel dimension in the feature extraction stage of two independent MSFF-IResnet. C: MMFF-IResnet-c, which concatenates the encoded clinical features by channel dimension in the feature extraction stage of MMFF-IResnet-a.
Machine learning Model | Parameters |
---|---|
KNN | n_neighbors=15, weights=distance |
SVM | kernel=poly, C=2 |
LR | class_weight=balanced, random_state=20 |
DTC | Criterion=entropy, max_depth=6, random_state=20 |
RF | n_estimators=6, criterion=entropy, random_state=20, class_weight=balanced |
Tab.3 Machine learning models and specific parameter settings
Machine learning Model | Parameters |
---|---|
KNN | n_neighbors=15, weights=distance |
SVM | kernel=poly, C=2 |
LR | class_weight=balanced, random_state=20 |
DTC | Criterion=entropy, max_depth=6, random_state=20 |
RF | n_estimators=6, criterion=entropy, random_state=20, class_weight=balanced |
Parameters | Value |
---|---|
Batch size | 128 |
Learning rate | 0.01 |
Weight decay | 1e-4、1e-5 |
Warm up epoch | 5 |
Total epoch | 100 |
Early stopping patience | 10 |
Tab.4 Special parameter settings of the deep learning models
Parameters | Value |
---|---|
Batch size | 128 |
Learning rate | 0.01 |
Weight decay | 1e-4、1e-5 |
Warm up epoch | 5 |
Total epoch | 100 |
Early stopping patience | 10 |
Characteristics | Clinical Data of HCC Patients (n=116) | Qualitative or quantitative analysis | |
---|---|---|---|
CK19- (n=78, 67.2%) | CK19+ (n=38, 32.8%) | P | |
Age (year, Mean±SD) | 57.7±12.4 | 59.4±11.1 | 0.451 |
Gender | 0.485 | ||
Male | 68 (87.2%) | 35 (92.1%) | |
Female | 10 (12.8%) | 3 (7.9%) | |
Hepatitis | 0.815 | ||
Absent | 7 (9.0%) | 3 (7.9%) | |
Present | 71 (91.0%) | 35 (92.1%) | |
AFP (ng/mL) | 0.017* | ||
≤20 | 45 (57.7%) | 11 (28.9%) | |
20<, ≤400 | 25 (32.1%) | 14 (36.8%) | |
>400 | 8 (10.3%) | 13 (34.2%) | |
ALT[U/L, Median (Min, Max)] | 34.0 (9.0, 113.0) | 37.0 (15.0, 129.0) | 0.276 |
AST [U/L, Median (Min, Max)] | 37.0 (15.0, 139.0) | 37.0 (18.0, 205.0) | 0.537 |
GGT [U/L, Median (Min, Max)] | 52.5 (14.0, 1055.0) | 72.0 (13.0, 1013.0) | 0.648 |
LY [109/L, Median (Min, Max)] | 1.54 (0.42, 3.95) | 1.36 (0.42, 2.35) | 0.521 |
NLR [Median (Min, Max)] | 1.78 (0.48, 12.13) | 2.58 (1.14, 8.17) | 0.004* |
ALB [g/L, Median (Min, Max)] | 41.2 (24.9, 74.3) | 41.7 (26.0, 49.9) | 0.239 |
Tbil [μmol/L, Median (Min, Max)] | 14.37 (4.46, 35.12) | 15.29 (5.16, 93.30) | 0.466 |
MVI | 0.099 | ||
Negative | 60 (76.9%) | 23 (60.5%) | |
Positive | 18 (23.1%) | 15 (39.5%) | |
Tumor size[mm, Median (Min, Max)] | 3.50 (1.20, 11.70) | 3.80 (1.58, 14.79) | 0.553 |
Tumor capsule | 0.016* | ||
None | 13 (16.7%) | 0 (0%) | |
Absent | 22 (28.1%) | 21 (55.3%) | |
Present | 43 (55.1%) | 17 (44.7%) | |
Tumor margin | 0.254 | ||
Absent | 10 (12.8%) | 8 (21.1%) | |
Present | 68 (87.2%) | 30 (78.9%) | |
Cystic or necrosis portion or fat deposition | 0.776 | ||
Absent | 49 (63.3%) | 23 (60.5%) | |
Present | 29 (36.7%) | 15 (39.5%) | |
Target sign of DWI | 0.844 | ||
Absent | 47 (60.3%) | 24 (63.2%) | |
Present | 31 (39.7%) | 14 (36.8%) | |
Arterial rim enhancement | 0.097 | ||
Absent | 67 (85.9%) | 27 (71.1%) | |
Present | 11 (14.1%) | 11 (28.9%) | |
Peritumoral eEnhancement | 0.538 | ||
Absent | 57 (73.1%) | 25 (65.8%) | |
Present | 21 (26.9%) | 13 (34.2%) | |
Target sign of HBP | 0.278 | ||
Absent | 45 (57.7%) | 17 (44.7%) | |
Present | 33 (42.3%) | 21 (55.3%) | |
Peritumoral hypo-intensity of HBP | 0.187 | ||
Absent | 60 (76.9%) | 24 (63.2%) | |
Present | 18 (23.1%) | 14 (36.8%) | |
Satellite nodules | 0.155 | ||
Absent | 72 (92.3%) | 38 (100.0%) | |
Present | 6 (7.7%) | 0 (0%) |
Tab.5 Statistical analysis of clinical parameters of HCC patients with CK19 expression
Characteristics | Clinical Data of HCC Patients (n=116) | Qualitative or quantitative analysis | |
---|---|---|---|
CK19- (n=78, 67.2%) | CK19+ (n=38, 32.8%) | P | |
Age (year, Mean±SD) | 57.7±12.4 | 59.4±11.1 | 0.451 |
Gender | 0.485 | ||
Male | 68 (87.2%) | 35 (92.1%) | |
Female | 10 (12.8%) | 3 (7.9%) | |
Hepatitis | 0.815 | ||
Absent | 7 (9.0%) | 3 (7.9%) | |
Present | 71 (91.0%) | 35 (92.1%) | |
AFP (ng/mL) | 0.017* | ||
≤20 | 45 (57.7%) | 11 (28.9%) | |
20<, ≤400 | 25 (32.1%) | 14 (36.8%) | |
>400 | 8 (10.3%) | 13 (34.2%) | |
ALT[U/L, Median (Min, Max)] | 34.0 (9.0, 113.0) | 37.0 (15.0, 129.0) | 0.276 |
AST [U/L, Median (Min, Max)] | 37.0 (15.0, 139.0) | 37.0 (18.0, 205.0) | 0.537 |
GGT [U/L, Median (Min, Max)] | 52.5 (14.0, 1055.0) | 72.0 (13.0, 1013.0) | 0.648 |
LY [109/L, Median (Min, Max)] | 1.54 (0.42, 3.95) | 1.36 (0.42, 2.35) | 0.521 |
NLR [Median (Min, Max)] | 1.78 (0.48, 12.13) | 2.58 (1.14, 8.17) | 0.004* |
ALB [g/L, Median (Min, Max)] | 41.2 (24.9, 74.3) | 41.7 (26.0, 49.9) | 0.239 |
Tbil [μmol/L, Median (Min, Max)] | 14.37 (4.46, 35.12) | 15.29 (5.16, 93.30) | 0.466 |
MVI | 0.099 | ||
Negative | 60 (76.9%) | 23 (60.5%) | |
Positive | 18 (23.1%) | 15 (39.5%) | |
Tumor size[mm, Median (Min, Max)] | 3.50 (1.20, 11.70) | 3.80 (1.58, 14.79) | 0.553 |
Tumor capsule | 0.016* | ||
None | 13 (16.7%) | 0 (0%) | |
Absent | 22 (28.1%) | 21 (55.3%) | |
Present | 43 (55.1%) | 17 (44.7%) | |
Tumor margin | 0.254 | ||
Absent | 10 (12.8%) | 8 (21.1%) | |
Present | 68 (87.2%) | 30 (78.9%) | |
Cystic or necrosis portion or fat deposition | 0.776 | ||
Absent | 49 (63.3%) | 23 (60.5%) | |
Present | 29 (36.7%) | 15 (39.5%) | |
Target sign of DWI | 0.844 | ||
Absent | 47 (60.3%) | 24 (63.2%) | |
Present | 31 (39.7%) | 14 (36.8%) | |
Arterial rim enhancement | 0.097 | ||
Absent | 67 (85.9%) | 27 (71.1%) | |
Present | 11 (14.1%) | 11 (28.9%) | |
Peritumoral eEnhancement | 0.538 | ||
Absent | 57 (73.1%) | 25 (65.8%) | |
Present | 21 (26.9%) | 13 (34.2%) | |
Target sign of HBP | 0.278 | ||
Absent | 45 (57.7%) | 17 (44.7%) | |
Present | 33 (42.3%) | 21 (55.3%) | |
Peritumoral hypo-intensity of HBP | 0.187 | ||
Absent | 60 (76.9%) | 24 (63.2%) | |
Present | 18 (23.1%) | 14 (36.8%) | |
Satellite nodules | 0.155 | ||
Absent | 72 (92.3%) | 38 (100.0%) | |
Present | 6 (7.7%) | 0 (0%) |
Characteristics | Univariate Analysis | Multivariate Analysis | ||||||
---|---|---|---|---|---|---|---|---|
OR | 95% CI | P | OR | 95% CI | P | |||
Lower | Upper | Lower | Upper | |||||
AFP (ng/mL) | ||||||||
≤20 | 0.024 | 0.189 | ||||||
20<, ≤400 | 1 | 1 | ||||||
>400 | 6.000 | 1.650 | 21.824 | 0.007 | 0.121 | |||
NLR | 1.259 | 0.977 | 1.622 | 0.075 | 1.417 | 1.036 | 1.938 | 0.029 |
MVI | 0.493 | |||||||
Negetive | 1 | 1 | ||||||
Positive | 2.274 | 0.848 | 6.102 | 0.103 | ||||
Tumor Capsule | 0.202 | 0.089 | ||||||
None | ||||||||
Absent | 2.422 | 0.918 | 6.387 | 0.074 | 3.250 | 1.136 | 9.301 | 0.028 |
Present | 1 | 1 | ||||||
Arterial rim enhancement | 0.229 | |||||||
Absent | 1 | 1 | ||||||
Present | 2.526 | 0.829 | 7.702 | 0.103 |
Tab.6 Results of univariate and multivariate logistic regression analysis
Characteristics | Univariate Analysis | Multivariate Analysis | ||||||
---|---|---|---|---|---|---|---|---|
OR | 95% CI | P | OR | 95% CI | P | |||
Lower | Upper | Lower | Upper | |||||
AFP (ng/mL) | ||||||||
≤20 | 0.024 | 0.189 | ||||||
20<, ≤400 | 1 | 1 | ||||||
>400 | 6.000 | 1.650 | 21.824 | 0.007 | 0.121 | |||
NLR | 1.259 | 0.977 | 1.622 | 0.075 | 1.417 | 1.036 | 1.938 | 0.029 |
MVI | 0.493 | |||||||
Negetive | 1 | 1 | ||||||
Positive | 2.274 | 0.848 | 6.102 | 0.103 | ||||
Tumor Capsule | 0.202 | 0.089 | ||||||
None | ||||||||
Absent | 2.422 | 0.918 | 6.387 | 0.074 | 3.250 | 1.136 | 9.301 | 0.028 |
Present | 1 | 1 | ||||||
Arterial rim enhancement | 0.229 | |||||||
Absent | 1 | 1 | ||||||
Present | 2.526 | 0.829 | 7.702 | 0.103 |
Model | Accuracy | Precision | Sensitivity | Specificity | AUC |
---|---|---|---|---|---|
KNN | 0.810±0.084 | 0.850±0.200 | 0.567±0.152 | 0.932±0.097 | 0.747±0.084 |
SVM | 0.810±0.084 | 0.810±0.185 | 0.607±0.179 | 0.914±0.091 | 0.759±0.098 |
LR | 0.749±0.111 | 0.628±0.168 | 0.673±0.116 | 0.789±0.123 | 0.731±0.108 |
DTC | 0.798±0.098 | 0.743±0.164 | 0.607±0.179 | 0.895±0.081 | 0.750±0.107 |
RF | 0.762±0.109 | 0.669±0.201 | 0.633±0.099 | 0.824±0.120 | 0.728±0.103 |
Tab.7 Classification performance of the machine learning models
Model | Accuracy | Precision | Sensitivity | Specificity | AUC |
---|---|---|---|---|---|
KNN | 0.810±0.084 | 0.850±0.200 | 0.567±0.152 | 0.932±0.097 | 0.747±0.084 |
SVM | 0.810±0.084 | 0.810±0.185 | 0.607±0.179 | 0.914±0.091 | 0.759±0.098 |
LR | 0.749±0.111 | 0.628±0.168 | 0.673±0.116 | 0.789±0.123 | 0.731±0.108 |
DTC | 0.798±0.098 | 0.743±0.164 | 0.607±0.179 | 0.895±0.081 | 0.750±0.107 |
RF | 0.762±0.109 | 0.669±0.201 | 0.633±0.099 | 0.824±0.120 | 0.728±0.103 |
Item | Accuracy | Precision | Sensitivity | Specificity | AUC |
---|---|---|---|---|---|
HBP sequence | |||||
IResnet | 0.651±0.098 | 0.526±0.141 | 0.700±0.177 | 0.627±0.203 | 0.718±0.080 |
MSFF-IResnet-a | 0.707±0.089 | 0.549±0.086 | 0.846±0.054 | 0.639±0.153 | 0.780±0.068 |
MSFF-IResnet-b | 0.738±0.038 | 0.611±0.078 | 0.620±0.180 | 0.795±0.102 | 0.738±0.077 |
MSFF-IResnet-c | 0.782±0.068 | 0.643±0.079 | 0.673±0.066 | 0.785±0.084 | 0.819±0.083 |
DWI sequence | |||||
IResnet | 0.745±0.056 | 0.606±0.043 | 0.679±0.150 | 0.776±0.060 | 0.752±0.091 |
MSFF-IResnet-a | 0.714±0.067 | 0.551±0.085 | 0.833±0.139 | 0.651±0.107 | 0.764±0.075 |
MSFF-IResnet-b | 0.749±0.059 | 0.605±0.103 | 0.819±0.102 | 0.707±0.117 | 0.781±0.098 |
MSFF-IResnet-c | 0.735±0.111 | 0.578±0.133 | 0.917±0.092 | 0.642±0.136 | 0.796±0.118 |
Tab.8 Classification results of the ablation experiment using multi-scale feature fusion methods
Item | Accuracy | Precision | Sensitivity | Specificity | AUC |
---|---|---|---|---|---|
HBP sequence | |||||
IResnet | 0.651±0.098 | 0.526±0.141 | 0.700±0.177 | 0.627±0.203 | 0.718±0.080 |
MSFF-IResnet-a | 0.707±0.089 | 0.549±0.086 | 0.846±0.054 | 0.639±0.153 | 0.780±0.068 |
MSFF-IResnet-b | 0.738±0.038 | 0.611±0.078 | 0.620±0.180 | 0.795±0.102 | 0.738±0.077 |
MSFF-IResnet-c | 0.782±0.068 | 0.643±0.079 | 0.673±0.066 | 0.785±0.084 | 0.819±0.083 |
DWI sequence | |||||
IResnet | 0.745±0.056 | 0.606±0.043 | 0.679±0.150 | 0.776±0.060 | 0.752±0.091 |
MSFF-IResnet-a | 0.714±0.067 | 0.551±0.085 | 0.833±0.139 | 0.651±0.107 | 0.764±0.075 |
MSFF-IResnet-b | 0.749±0.059 | 0.605±0.103 | 0.819±0.102 | 0.707±0.117 | 0.781±0.098 |
MSFF-IResnet-c | 0.735±0.111 | 0.578±0.133 | 0.917±0.092 | 0.642±0.136 | 0.796±0.118 |
Fig.6 ROC charts of the ablation experiment for multi-scale feature fusion methods. A: ROC of models based on HBP sequence. B: ROC of models based on DWI sequence.
Method | Accuracy | Precision | Sensitivity | Specificity | AUC |
---|---|---|---|---|---|
MSFF-IResnet | 0.782±0.068 | 0.643±0.079 | 0.673±0.066 | 0.785±0.084 | 0.819±0.083 |
MMFF-IResnet-a | 0.796±0.085 | 0.702±0.182 | 0.773±0.118 | 0.804±0.136 | 0.829±0.122 |
MMFF-IResnet-b | 0.790±0.061 | 0.648±0.097 | 0.778±0.173 | 0.787±0.079 | 0.823±0.089 |
MMFF-IResnet-c | 0.806±0.080 | 0.708±0.148 | 0.801±0.128 | 0.812±0.131 | 0.842±0.100 |
Tab.9 Classification results of the ablation experiment using multi-modality feature fusion methods
Method | Accuracy | Precision | Sensitivity | Specificity | AUC |
---|---|---|---|---|---|
MSFF-IResnet | 0.782±0.068 | 0.643±0.079 | 0.673±0.066 | 0.785±0.084 | 0.819±0.083 |
MMFF-IResnet-a | 0.796±0.085 | 0.702±0.182 | 0.773±0.118 | 0.804±0.136 | 0.829±0.122 |
MMFF-IResnet-b | 0.790±0.061 | 0.648±0.097 | 0.778±0.173 | 0.787±0.079 | 0.823±0.089 |
MMFF-IResnet-c | 0.806±0.080 | 0.708±0.148 | 0.801±0.128 | 0.812±0.131 | 0.842±0.100 |
Fig.8 Comparison of positive and negative sample images of HBP sequence (A1-A5) and DWI sequence (B1-B5). A1-A2 and B1-B2: True CK19-positive cases predicted by the baseline model and multi-scale feature fusion models. A3 and B3: CK19-positive cases predicted as negative by the baseline model but corrected to be positive by multi-scale feature fusion models. A4-A5 and B4-B5: true CK19-negative cases predicted by the baseline model and multi-scale feature fusion models. The red arrows in A1, A2, A3, B1, and B3 sequentially represent the imaging features of peritumoral hypo-intensity, HBP target sign, irregular tumor margin, peritumoral hypo-intensity, fat deposition, and lower high signal tumor area.
Research | Method | Year | Cases | Accuracy | Sensitivity | Specificity | AUC |
---|---|---|---|---|---|---|---|
Peng [ | Machine Learning | 2024 | 226 | 0.706 | - | - | 0.706 |
Lu [ | Machine Learning | 2024 | 220 | 0.758 | 0.625 | 0.8 | 0.748 |
Wang [ | Radiomics | 2024 | 137 | - | 0.724 | 0.759 | 0.75 |
Zhang [ | Radiomics | 2023 | 311 | - | 0.769 | 0.818 | 0.795 |
Hu [ | Radiomics | 2023 | 110 | 0.88 | 0.84 | 0.89 | 0.92 |
Ours | Deep Learning | 2024 | 116 | 0.806 | 0.801 | 0.812 | 0.842 |
Tab.10 Comparison with the results of other research
Research | Method | Year | Cases | Accuracy | Sensitivity | Specificity | AUC |
---|---|---|---|---|---|---|---|
Peng [ | Machine Learning | 2024 | 226 | 0.706 | - | - | 0.706 |
Lu [ | Machine Learning | 2024 | 220 | 0.758 | 0.625 | 0.8 | 0.748 |
Wang [ | Radiomics | 2024 | 137 | - | 0.724 | 0.759 | 0.75 |
Zhang [ | Radiomics | 2023 | 311 | - | 0.769 | 0.818 | 0.795 |
Hu [ | Radiomics | 2023 | 110 | 0.88 | 0.84 | 0.89 | 0.92 |
Ours | Deep Learning | 2024 | 116 | 0.806 | 0.801 | 0.812 | 0.842 |
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