Background Hepatocellular carcinoma (HCC) is the fourth most common cause of cancer death worldwide, and the prognosis remains dismal. In this study, two pivotal factors, microvascular invasion (MVI) and vessels encapsulating tumor clusters (VETC) were preoperatively predicted simultaneously to assess prognosis. Methods A total of 133 HCC patients who underwent surgical resection and preoperative gadolinium ethoxybenzyl-diethylenetriaminepentaacetic acid (Gd-EOB-DTPA)-enhanced magnetic resonance imaging (MRI) were included. The statuses of MVI and VETC were obtained from the pathological report and CD34 immunohistochemistry, respectively. A three-dimensional convolutional neural network (3D CNN) for single-task learning aimed at MVI prediction and for multitask learning aimed at simultaneous prediction of MVI and VETC was established by using multiphase Gd-EOB-DTPA-enhanced MRI. Results The 3D CNN for single-task learning achieved an area under receiver operating characteristics curve (AUC) of 0.896 (95% CI: 0.797–0.994). Multitask learning with simultaneous extraction of MVI and VETC features improved the performance of MVI prediction, with an AUC value of 0.917 (95% CI: 0.825–1.000), and achieved an AUC value of 0.860 (95% CI: 0.728–0.993) for the VETC prediction. The multitask learning framework could stratify high- and low-risk groups regarding overall survival (p < 0.0001) and recurrence-free survival (p < 0.0001), revealing that patients with MVI+/VETC+ were associated with poor prognosis. Conclusions A deep learning framework based on 3D CNN for multitask learning to predict MVI and VETC simultaneously could improve the performance of MVI prediction while assessing the VETC status. This combined prediction can stratify prognosis and enable individualized prognostication in HCC patients before curative resection.

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