Background: The deep learning convolution neural network (DL-CNN) benefits evaluating clot burden of acute pulmonary thromboembolism (APE). Our objective was to compare the performance of the deep learning convolution neural network trained by the fine-tuning [DL-CNN (ft)] and the deep learning convolution neural network trained from the scratch [DL-CNN (fs)] in the quantitative assessment of APE. Methods: We included the data of 680 cases for training DL-CNN by DL-CNN (ft) and DL-CNN (fs), then retrospectively included 410 patients (137 patients with APE, 203 males, mean age 60.3 +/- 11.4 years) for testing the models. The distribution and volume of clots were respectively assessed by DL-CNN(ft) and DL-CNN(fs), and sensitivity, specificity, and area under the curve (AUC) were used to evaluate their performances in detecting clots on a per-patient and clot level. Radiologists evaluated the distribution of clots, Qanadli score, and Mastora score and right ventricular metrics, and the correlation of clot volumes with right ventricular metrics were analyzed with Spearman correlation analysis. Results: On a per-patient level, the two DL-CNN models had high sensitivities and moderate specificities (DL-CNN (ft): 100% and 77.29%; DL-CNN (fs): 100% and 75.82%), and their AUCs were comparable (Z=0.30, P=0.38). On a clot level, DL-CNN (ft) and DL-CNN (fs) sensitivities and specificities in detecting central clots were 99.06% and 72.61%, and 100% and 70.63%, respectively. DL-CNN (ft) sensitivities and specificities in detecting peripheral clots were mostly higher than those of DL-CNN (fs), and their AUCs were comparable. Clot volumes measured with the two models were similar (U=85094.500, P=0.741), and significantly correlated with Qanadli scores [DL-CNN(ft) r=0.825, P<0.001, DL-CNN(fs) r=0.827, P<0.001] and Mastora scores [DL-CNN(ft) r=0.859, P<0.001, DL-CNN(fs) r=0.864, P<0.001]. Clot volumes were also correlated with right ventricular metrics. Clot burdens were increased in the low-risk, moderate-risk, and high-risk patients. Binary logistic regression revealed that only the ratio of right ventricular area/left ventricular area (RVa/LVa) was an independent predictor of in-hospital death (odds ratio 6.73; 95% CI, 2.7-18.12, P<0.001). Conclusions: Both DL-CNN (ft) and DL-CNN (fs) have high sensitivities and moderate specificities in detecting clots associated with APE, and their performances are comparable. While clot burdens quantitatively calculated by the two DL-CNN models are correlated with right ventricular function and risk stratification, RVa/LVa is an independent prognostic factor of in-hospital death in patients with APE.