Query-Driven Sampling for Collective Entity Resolution

Probabilistic databases play a preeminent role in the processing and management of uncertain data. Recently, many database research efforts have integrated probabilistic models into databases to support tasks such as information extraction and labeling. Many of these efforts are based on batch oriented inference which inhibits a realtime workflow. One important task is entity resolution (ER). ER is the process of determining records (mentions) in a database that correspond to the same real-world entity. Traditional pairwise ER methods can lead to inconsistencies and low accuracy due to localized decisions. Leading ER systems solve this problem by collectively resolving all records using a probabilistic graphical model and Markov chain Monte Carlo (MCMC) inference. However, for large datasets this is an extremely expensive process. One key observation is that, such exhaustive ER process incurs a huge up-front cost, which is wasteful in practice because most users are interested in only a small subset of entities. In this paper, we advocate pay-as-you-go entity resolution by developing a number of query-driven collective ER techniques. We introduce two classes of SQL queries that involve ER operators --- selection-driven ER and join-driven ER. We implement novel variations of the MCMC Metropolis Hastings algorithm to generate biased samples and selectivity-based scheduling algorithms to support the two classes of ER queries. Finally, we show that query-driven ER algorithms can converge and return results within minutes over a database populated with the extraction from a newswire dataset containing 71 million mentions

Strong Solutions of Stochastic Generalized Porous Media Equations: Existence, Uniqueness and Ergodicity

Explicit conditions are presented for the existence, uniqueness and ergodicity of the strong solution to a class of generalized stochastic porous media equations. Our estimate of the convergence rate is sharp according to the known optimal decay for the solution of the classical (deterministic) porous medium equation.Comment: 15 pages; BiBoS-Preprint No. 04-09-157; to appear in Commun. PD

Limits of the equivalence of time and ensemble averages in shear flows

In equilibrium systems, time and ensemble averages of physical quantities are equivalent due to ergodic exploration of phase space. In driven systems, it is unknown if a similar equivalence of time and ensemble averages exists. We explore effective limits of such convergence in a sheared bubble raft using averages of the bubble velocities. In independent experiments, averaging over time leads to well converged velocity profiles. However, the time-averages from independent experiments result in distinct velocity averages. Ensemble averages are approximated by randomly selecting bubble velocities from independent experiments. Increasingly better approximations of ensemble averages converge toward a unique velocity profile. Therefore, the experiments establish that in practical realizations of non-equilibrium systems, temporal averaging and ensemble averaging can yield convergent (stationary) but distinct distributions.Comment: accepted to PRL - final figure revision

Rex1p Deficiency Leads to Accumulation of Precursor Initiator tRNA\u3csup\u3eMet\u3c/sup\u3e and Polyadenylation of Substrate RNAs in \u3cem\u3eSaccharomyces cerevisiae\u3c/em\u3e

A synthetic genetic array was used to identify lethal and slow-growth phenotypes produced when a mutation in TRM6, which encodes a tRNA modification enzyme subunit, was combined with the deletion of any non-essential gene in Saccharomyces cerevisiae. We found that deletion of the REX1 gene resulted in a slow-growth phenotype in the trm6-504 strain. Previously, REX1 was shown to be involved in processing the 3′ ends of 5S rRNA and the dimeric tRNAArg-tRNAAsp. In this study, we have discovered a requirement for Rex1p in processing the 3′ end of tRNAiMet precursors and show that precursor tRNAiMet accumulates in a trm6-504 rex1Δ strain. Loss of Rex1p results in polyadenylation of its substrates, including tRNAiMet, suggesting that defects in 3′ end processing can activate the nuclear surveillance pathway. Finally, purified Rex1p displays Mg2+-dependent ribonuclease activity in vitro, and the enzyme is inactivated by mutation of two highly conserved amino acids