Computer Science Department
School of Computer Science, Carnegie Mellon University


Kernel Conditional Random Fields:
Representation, Clique Selection, and Semi-Supervised Learning

John Lafferty, Yan Liu, Xiaojin Zhu

February 2004

Keywords: Sequence analysis, graphical models, conditional models, kernels, semi-supervised learning, protein secondary structure

Kernel conditional random fields are introduced as a framework for discriminative modeling of graph-structured data. A representer theorem for conditional graphical models is given which shows how kernel conditional random fields arise from risk minimization procedures defined using Mercer kernels on labeled graphs. A procedure for greedily selecting cliques in the dual representation is then proposed, which allows sparse representations. By incorporating kernels and implicit feature spaces into conditional graphical models, the framework enables semi-supervised learning algorithms for structured data through the use of graph kernels. The clique selection and semi-supervised methods are demonstrated in synthetic data experiments, and are also applied to the problem of protein secondary structure prediction.

15 pages

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