Query-Dependent Banding (QDB) for Faster RNA Similarity Searches

When searching sequence databases for RNAs, it is desirable to score both primary sequence and RNA secondary structure similarity. Covariance models (CMs) are probabilistic models well-suited for RNA similarity search applications. However, the computational complexity of CM dynamic programming alignment algorithms has limited their practical application. Here we describe an acceleration method called query-dependent banding (QDB), which uses the probabilistic query CM to precalculate regions of the dynamic programming lattice that have negligible probability, independently of the target database. We have implemented QDB in the freely available Infernal software package. QDB reduces the average case time complexity of CM alignment from LN (2.4) to LN (1.3) for a query RNA of N residues and a target database of L residues, resulting in a 4-fold speedup for typical RNA queries. Combined with other improvements to Infernal, including informative mixture Dirichlet priors on model parameters, benchmarks also show increased sensitivity and specificity resulting from improved parameterization

Better synchronous binarization for machine translation

Binarization of Synchronous Context Free Grammars (SCFG) is essential for achieving polynomial time complexity of decoding for SCFG parsing based machine translation sys-tems. In this paper, we first investigate the excess edge competition issue caused by a left-heavy binary SCFG derived with the method of Zhang et al. (2006). Then we propose a new binarization method to mitigate the problem by exploring other alternative equivalent bi-nary SCFGs. We present an algorithm that ite-ratively improves the resulting binary SCFG, and empirically show that our method can im-prove a string-to-tree statistical machine trans-lations system based on the synchronous bina-rization method in Zhang et al. (2006) on the NIST machine translation evaluation tasks.

Radical Artificial Intelligence: A Postmodern Approach

The dynamic response of end-clamped monolithic beams and sandwich beams has been measured by loading the beams at mid-span using metal foam projectiles. The AISI 304 stainless-steel sandwich beams comprise two identical face sheets and either prismatic Y-frame or corrugated cores. The resistance to shock loading is quantified by the permanent transverse deflection at mid-span of the beams as a function of projectile momentum. The prismatic cores are aligned either longitudinally along the beam length or transversely. It is found that the sandwich beams with a longitudinal core orientation have a higher shock resistance than the monolithic beams of equal mass. In contrast, the performance of the sandwich beams with a transverse core orientation is very similar to that of the monolithic beams. Three-dimensional finite element (FE) simulations are in good agreement with the measured responses. The FE calculations indicate that strain concentrations in the sandwich beams occur at joints within the cores and between the core and face sheets; the level of maximum strain is similar for the Y-frame and corrugated core beams for a given value of projectile momentum. The experimental and FE results taken together reveal that Y-frame and corrugated core sandwich beams of equal mass have similar dynamic performances in terms of rear-face deflection, degree of core compression and level of strain within the beam

Painting Pictures with Words - From Theory to System

A picture paints a thousand words, or so we are told. But how many words does it take to paint a picture? And how can words create pictures in the first place? In this thesis we examine a new theory of linguistic meaning -- where the meaning of words and sentences is determined by the scenes they evoke. We describe how descriptive text is parsed and semantically interpreted and how the semantic interpretation is then depicted as a rendered 3D scene. In doing so, we describe WordsEye, our text-to-scene system, and touch upon many fascinating issues of lexical semantics, knowledge representation, and what we call "graphical semantics." We introduce the notion of vignettes as a way to bridge between function and form, between the semantics of language and the grounded semantics of 3D scenes. And we describe how VigNet, our lexical semantic and graphical knowledge base, mediates the whole process. In the second part of this thesis, we describe four different ways WordsEye has been tested. We first discuss an evaluation of the system in an educational environment where WordsEye was shown to significantly improve literacy skills for sixth grade students versus a control group. We then compare WordsEye with Google Image Search on "realistic" and "imaginative" sentences in order to evaluate its performance on a sentence-by-sentence level and test its potential as a way to augment existing image search tools. Thirdly, we describe what we have learned in testing WordsEye as an online 3D authoring system where it has attracted 20,000 real-world users who have performed almost one million scene depictions. Finally, we describe tests of WordsEye as an elicitation tool for field linguists studying endangered languages. We then sum up by presenting a roadmap for enhancing the capabilities of the system and identifying key opportunities and issues to be addressed