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Abstract Human chromosomes carry genetic information about our life. Chromosome classification is crucial for karyotype analysis. Existing chromosome classification methods do not take into account reasoning, such as: analyzing the relationship between variables, modeling uncertainty, and performing causal reasoning. In this paper, we introduce a knowledge engine for reasoning-based human chromosome classification that stores knowledge of chromosomes via a novel representation structure, the Chromosome Part Description （CPD）, and reasons over CPDs by utilizing the probability tree model （PTM） for classification. Each CPD keeps information on a particular feature of chromosomes, while the PTM provides causal reasoning capability taking CPDs as nodes and dependencies between CPDs and types as edges. Experimental results show that the proposed knowledge engines performance increases when providing more CPDs and achieves 100% classification accuracy with more than three CPDs.
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