Spoken dialogue systems (SDS) typically require a predefined semantic ontology to train a spoken language understanding (SLU) module. In addition to the annotation cost, a key challenge for designing such an ontology is to define a coherent slot set while considering their complex relations. This paper introduces a novel matrix factorization (MF) approach to learn latent feature vectors for utterances and semantic elements without the need of corpus annotations. Specifically, our model learns the semantic slots for a domain-specific SDS in an unsupervised fashion, and carries out semantic parsing using latent MF techniques. To further consider the global semantic structure, such as inter-word and inter-slot relations, we augment the latent MF-based model with a knowledge graph propagation model based on a slot-based semantic graph and a word-based lexical graph. Our experiments show that the proposed MF approaches produce better SLU models that are able to predict semantic slots and word patterns taking into account their relations and domain-specificity in a joint manner.