Goal of this master's thesis was in cooperation with the company Avast to design a system, which can extract knowledge from a database of graphs. Graphs, used for data mining, describe behaviour of computer systems and they are anonymously inserted into the company's database from systems of the company's products users. Each graph in the database can be assigned with one of two labels: clean or malware (malicious) graph. The task of the proposed self-learning system is to find clusters of graphs in the graph database, in which the classes of graphs do not mix. Graph clusters with only one class of graphs can be interpreted as different types of clean or malware graphs and they are a useful source of further analysis on the graphs. To evaluate the quality of the clusters, a custom metric, named as monochromaticity, was designed. The metric evaluates the quality of the clusters based on how much clean and malware graphs are mixed in the clusters. The best results of the metric were obtained when vector representations of graphs were created by a deep learning model (variational  graph autoencoder with two relation graph convolution operators) and the parameterless method MeanShift was used for clustering over vectors.