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With increasing amount of data, the threat of malware keeps growing recently. The malicious actions embedded in nonexecutable documents especially (e.g., PDF files) can be more dangerous, because it is difficult to detect and most users are not aware of such type of malicious attacks. In this paper, we design a convolutional neural network to tackle the malware detection on the PDF files. We collect malicious and benign PDF files and manually label the byte sequences within the files. We intensively examine the structure of the input data and illustrate how we design the proposed network based on the characteristics of data. The proposed network is designed to interpret high-level patterns among collectable spatial clues, thereby predicting whether the given byte sequence has malicious actions or not. By experimental results, we demonstrate that the proposed network outperform several representative machine-learning models as well as other networks with different settings.