Probabilistic Constraint Logic Programming

This paper addresses two central problems for probabilistic processing models: parameter estimation from incomplete data and efficient retrieval of most probable analyses. These questions have been answered satisfactorily only for probabilistic regular and context-free models. We address these problems for a more expressive probabilistic constraint logic programming model. We present a log-linear probability model for probabilistic constraint logic programming. On top of this model we define an algorithm to estimate the parameters and to select the properties of log-linear models from incomplete data. This algorithm is an extension of the improved iterative scaling algorithm of Della-Pietra, Della-Pietra, and Lafferty (1995). Our algorithm applies to log-linear models in general and is accompanied with suitable approximation methods when applied to large data spaces. Furthermore, we present an approach for searching for most probable analyses of the probabilistic constraint logic programming model. This method can be applied to the ambiguity resolution problem in natural language processing applications.Comment: 35 pages, uses sfbart.cl

A Tutorial on the Expectation-Maximization Algorithm Including Maximum-Likelihood Estimation and EM Training of Probabilistic Context-Free Grammars

The paper gives a brief review of the expectation-maximization algorithm (Dempster 1977) in the comprehensible framework of discrete mathematics. In Section 2, two prominent estimation methods, the relative-frequency estimation and the maximum-likelihood estimation are presented. Section 3 is dedicated to the expectation-maximization algorithm and a simpler variant, the generalized expectation-maximization algorithm. In Section 4, two loaded dice are rolled. A more interesting example is presented in Section 5: The estimation of probabilistic context-free grammars.Comment: Presented at the 15th European Summer School in Logic, Language and Information (ESSLLI 2003). Example 5 extended (and partially corrected

Data-Oriented Language Processing. An Overview

During the last few years, a new approach to language processing has started to emerge, which has become known under various labels such as "data-oriented parsing", "corpus-based interpretation", and "tree-bank grammar" (cf. van den Berg et al. 1994; Bod 1992-96; Bod et al. 1996a/b; Bonnema 1996; Charniak 1996a/b; Goodman 1996; Kaplan 1996; Rajman 1995a/b; Scha 1990-92; Sekine & Grishman 1995; Sima'an et al. 1994; Sima'an 1995-96; Tugwell 1995). This approach, which we will call "data-oriented processing" or "DOP", embodies the assumption that human language perception and production works with representations of concrete past language experiences, rather than with abstract linguistic rules. The models that instantiate this approach therefore maintain large corpora of linguistic representations of previously occurring utterances. When processing a new input utterance, analyses of this utterance are constructed by combining fragments from the corpus; the occurrence-frequencies of the fragments are used to estimate which analysis is the most probable one. In this paper we give an in-depth discussion of a data-oriented processing model which employs a corpus of labelled phrase-structure trees. Then we review some other models that instantiate the DOP approach. Many of these models also employ labelled phrase-structure trees, but use different criteria for extracting fragments from the corpus or employ different disambiguation strategies (Bod 1996b; Charniak 1996a/b; Goodman 1996; Rajman 1995a/b; Sekine & Grishman 1995; Sima'an 1995-96); other models use richer formalisms for their corpus annotations (van den Berg et al. 1994; Bod et al., 1996a/b; Bonnema 1996; Kaplan 1996; Tugwell 1995).Comment: 34 pages, Postscrip

XRate: a fast prototyping, training and annotation tool for phylo-grammars

BACKGROUND: Recent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists. RESULTS: We have developed an open source software tool, xrate, for working with reversible, irreversible or parametric substitution models combined with stochastic context-free grammars. xrate efficiently estimates maximum-likelihood parameters and phylogenetic trees using a novel "phylo-EM" algorithm that we describe. The grammar is specified in an external configuration file, allowing users to design new grammars, estimate rate parameters from training data and annotate multiple sequence alignments without the need to recompile code from source. We have used xrate to measure codon substitution rates and predict protein and RNA secondary structures. CONCLUSION: Our results demonstrate that xrate estimates biologically meaningful rates and makes predictions whose accuracy is comparable to that of more specialized tools

Toric grammars: a new statistical approach to natural language modeling

We propose a new statistical model for computational linguistics. Rather than trying to estimate directly the probability distribution of a random sentence of the language, we define a Markov chain on finite sets of sentences with many finite recurrent communicating classes and define our language model as the invariant probability measures of the chain on each recurrent communicating class. This Markov chain, that we call a communication model, recombines at each step randomly the set of sentences forming its current state, using some grammar rules. When the grammar rules are fixed and known in advance instead of being estimated on the fly, we can prove supplementary mathematical properties. In particular, we can prove in this case that all states are recurrent states, so that the chain defines a partition of its state space into finite recurrent communicating classes. We show that our approach is a decisive departure from Markov models at the sentence level and discuss its relationships with Context Free Grammars. Although the toric grammars we use are closely related to Context Free Grammars, the way we generate the language from the grammar is qualitatively different. Our communication model has two purposes. On the one hand, it is used to define indirectly the probability distribution of a random sentence of the language. On the other hand it can serve as a (crude) model of language transmission from one speaker to another speaker through the communication of a (large) set of sentences

Parameter Learning of Logic Programs for Symbolic-Statistical Modeling

We propose a logical/mathematical framework for statistical parameter learning of parameterized logic programs, i.e. definite clause programs containing probabilistic facts with a parameterized distribution. It extends the traditional least Herbrand model semantics in logic programming to distribution semantics, possible world semantics with a probability distribution which is unconditionally applicable to arbitrary logic programs including ones for HMMs, PCFGs and Bayesian networks. We also propose a new EM algorithm, the graphical EM algorithm, that runs for a class of parameterized logic programs representing sequential decision processes where each decision is exclusive and independent. It runs on a new data structure called support graphs describing the logical relationship between observations and their explanations, and learns parameters by computing inside and outside probability generalized for logic programs. The complexity analysis shows that when combined with OLDT search for all explanations for observations, the graphical EM algorithm, despite its generality, has the same time complexity as existing EM algorithms, i.e. the Baum-Welch algorithm for HMMs, the Inside-Outside algorithm for PCFGs, and the one for singly connected Bayesian networks that have been developed independently in each research field. Learning experiments with PCFGs using two corpora of moderate size indicate that the graphical EM algorithm can significantly outperform the Inside-Outside algorithm

Parsing Inside-Out

The inside-outside probabilities are typically used for reestimating Probabilistic Context Free Grammars (PCFGs), just as the forward-backward probabilities are typically used for reestimating HMMs. I show several novel uses, including improving parser accuracy by matching parsing algorithms to evaluation criteria; speeding up DOP parsing by 500 times; and 30 times faster PCFG thresholding at a given accuracy level. I also give an elegant, state-of-the-art grammar formalism, which can be used to compute inside-outside probabilities; and a parser description formalism, which makes it easy to derive inside-outside formulas and many others.Comment: Ph.D. Thesis, 257 pages, 40 postscript figure

CONTRAfold: RNA secondary structure prediction without physics-based models

doi:10.1093/bioinformatics/btl24