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Unlike homopolymers, biopolymers are composed of specific sequences of different types of monomers. In proteins and RNA molecules, one-dimensional sequence information encodes a three-dimensional fold, leading to a corresponding molecular function. Such folded structures are not treated adequately through traditional methods of polymer statistical mechanics. A promising new way to solve problems of the statistical mechanics of biomolecules comes from computational linguistics, the field that uses computers to parse and understand the sentences in natural languages. Here, we give two examples. First, we show that a dynamic programming method of computational linguistics gives a fast way to search protein models for native structures. Interestingly, the computational search process closely resembles the physical folding process. Second, linguistics-based dynamic programming methods are also useful for computing partition functions and densities of states for some foldable biopolymers e helix-bundle proteins are reviewed here. In these ways, computational linguistics is helping to solve problems of the searching and counting of biopolymer conformations.

The ability to associate images with natural language sentences that describe what is depicted in them is a hallmark of image understanding, and a prerequisite for applications such as sentence-based image search. In analogy to image search, we propose to frame sentence-based image annotation as the task of ranking a given pool of captions. We introduce a new benchmark collection for sentence-based image description and search, consisting of 8,000 images that are each paired with five different captions which provide clear descriptions of the salient entities and events. We introduce a number of systems that perform quite well on this task, even though they are only based on features that can be obtained with minimal supervision. Our results clearly indicate the importance of training on multiple captions per image, and of capturing syntactic (word order-based) and semantic features of these captions. We also perform an in-depth comparison of human and automatic evaluation metrics for this task, and propose strategies for collecting human judgments cheaply and on a very large scale, allowing us to augment our collection with additional relevance judgments of which captions describe which image. Our analysis shows that metrics that consider the ranked list of results for each query image or sentence are significantly more robust than metrics that are based on a single response per query. Moreover, our study suggests that the evaluation of ranking-based image description systems may be fully automated. [ABSTRACT FROM AUTHOR]

This article presents an algorithm for translating the Penn Treebank into a corpus of Combinatory Categorial Grammar (CCG) derivations augmented with local and long-range word--word dependencies. The resulting corpus,CCGbank, includes 99.4% of the sentences in the Penn Treebank. It is available from the Linguistic Data Consortium,and has been used to train wide-coverage statistical parsers that obtain state-of-the-art rates of dependency recovery. In order to obtain linguistically adequate CCG analyses, and to eliminate noise and inconsistencies in the original annotation, an extensive analysis of the constructions and annotations in the Penn Treebank was called for, and a substantial number of changes to the Treebank were necessary. We discuss the implications of our findings for the extraction of other linguistically expressive grammars from the Treebank, and for the design of future treebanks. [ABSTRACT FROM AUTHOR]

An important puzzle in structural biology is the question of how proteins are able to fold so quickly into their unique native structures. There is much evidence that protein folding is hierarchic. In that case, folding routes are not linear, but have a tree structure. Trees are commonly used to represent the grammatical structure of natural language sentences, and chart parsing algorithms efficiently search the space of all possible trees for a given input string. Here we show that one such method, the CKY algorithm, can be useful both for providing novel insight into the physical protein folding process, and for computational protein structure prediction. As proof of concept, we apply this algorithm to the HP lattice model of proteins. Our algorithm identifies all direct folding route trees to the native state and allows us to construct a simple model of the folding process. Despite its simplicity, our model provides an account for the fact that folding rates depend only on the topology of the native state but not on sequence composition. Proteins 2007. © 2006 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]