We propose Dirichlet-Bernoulli Alignment (DBA), a generative model for corpora in which each pattern (e.g., a document) contains a set of instances (e.g., paragraphs in the document) and belongs to multiple classes. By casting predefined classes as latent Dirichlet variables (i.e., instance level labels), and modeling the multi-label of each pattern as Bernoulli variables conditioned on the weighted empirical average of topic assignments, DBA automatically aligns the latent topics discovered from data to human-defined classes. DBA is useful for both pattern classification and instance disambiguation, which are tested on text classification and named entity disambiguation for web search queries respectively.