ICML 2005 Conference Review Session

Integer Linear Programming Inference for Conditional Random Fields
by Dan Roth and Wen-tau Yih

Pradeep Ravikumar

Inference in Conditional Random Fields and Hidden Markov Models is done using the Viterbi algorithm, an efficient dynamic programming algorithm. In many cases, general (non-local and non-sequential) constraints may exist over the output sequence, but cannot be incorporated and exploited in a natural way by this inference procedure. This paper proposes a novel inference procedure based on integer linear programming (ILP) and extends CRF models to naturally and efficiently support general constraint structures. For sequential constraints, this procedure reduces to simple linear programming as the inference process. Experimental evidence is supplied in the context of an important NLP problem, semantic role labeling.

Predicting Protein Folds with Structural Repeats Using a Chain Graph Model
by Yan Liu, Eric Xing, Jaime Carbonell

Yan Liu

Protein fold recognition is a key step towards inferring the tertiary structures from amino-acid sequences. Complex folds such as those consisting of interacting structural repeats are prevalent in proteins involved in a wide spectrum of biological functions. In this paper, we propose a chain graph model built on a causally connected series of segmentation conditional random fields (SCRFs) to address these issues. Specifically, the SCRF model captures long-range interactions within recurring structural units and the Bayesian network backbone decomposes cross-repeat interactions into locally computable modules consisting of repeat-specific SCRFs and a model for sequence motifs. We applied this model to predict beta-helices and leucine-rich repeats, and found it significantly outperforms extant methods in predictive accuracy and/or computational efficiency.

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Pradeep Ravikumar
Last modified: Thu Sep 22 13:55:44 EDT 2005