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The paper proposes a hypernetwork-based method for stock market prediction through a binary time series problem. Hypernetworks are a random hypergraph structure of higher-order probabilistic relations of data. The problem we tackle concerns the prediction of price movements (up/down) on stock markets. Compared to previous approaches, the proposed method discovers a large population of variable subpatterns, i.e. local and global patterns, using a novel evolutionary hypernetwork. An output is obtained from combining these patterns. In the paper, we describe two methods for assessing the prediction quality of the hypernetwork approach. Applied to the Dow Jones Industrial Average Index and the Korea Composite Stock Price Index data, the experimental results show that the proposed method effectively learns and predicts the time series information. In particular, the hypernetwork approach outperforms other machine learning methods such as support vector machines, naive Bayes, multilayer perceptrons, and k-nearest neighbors.