Identifying promising research as early as possible is vital to determine which research deserves investment. Additionally, developing a technology for automatically predicting future research trends is necessary because of increasing digital publications and research fragmentation. In previous studies, many researchers have performed the prediction of scientific indices using specially designed features for each index. However, this does not capture real research trends. It is necessary to develop a more integrated method to capture actual research trends from various directions. Recent deep learning technology integrates different individual models and makes it easier to construct more general-purpose models. The purpose of this paper is to show the possibility of integrating multiple prediction models for scientific indices by network-based representation learning. This paper will conduct predictive analysis of multiple future scientific impacts by embedding a heterogeneous network and showing that a network embedding method is a promising tool for capturing and expressing scientific trends. Experimental results show that the multiple heterogeneous network embedding improved 1.6 points than a single citation network embedding. Experimental results show better results than baseline for the number of indices, including the author h-index, the journal impact factor (JIF), and the Nature Index after three years from publication. These results suggest that distributed representations of a heterogeneous network for scientific papers are the basis for the automatic prediction of scientific trends.