Abstract not found

Hidden Markov models (HMMs) have been successfully applied to the tasks of transmembrane protein topology prediction and signal peptide prediction. In this paper we expand upon this work by making use of the more powerful class of dynamic Bayesian networks (DBNs). Our model, Philius, is inspired by a previously published HMM, Phobius, and combines a signal peptide submodel with a transmembrane submodel. We introduce a two-stage DBN decoder that combines the power of posterior decoding with the grammar constraints of Viterbi-style decoding. Philius also provides protein type, segment, and topology confidence metrics to aid in the interpretation of the predictions. We report a relative improvement of 13 % over Phobius in full-topology prediction accuracy on transmembrane proteins, and a sensitivity and specificity of 0.96 in detecting signal peptides. We also show that our confidence metrics correlate well with the observed precision. In addition, we have made predictions on all 6.3 million proteins in the Yeast Resource Center (YRC) database. This large-scale study provides an overall picture of the relative numbers of proteins that include a signal-peptide and/or one or more transmembrane segments as well as a valuable resource for the scientific community. All DBNs are implemented using the Graphical Models Toolkit. Source code for the models described here is available at

We present an algorithm for computing n-gram probabilities from stochastic context-free grammars, a procedure that can alleviate some of the standard problems associated with n-grams (estimation from sparse data, lack of linguistic structure, among others). The method operates via the computation of substring expectations, which in turn is accomplished by solving systems of linear equations derived from the grammar. The procedure is fully implemented and has proved viable and useful in practice.

Chinese word segmentation is a difficult, important and widely-studied sequence modeling problem. This paper demonstrates the ability of linear-chain conditional random fields (CRFs) to perform robust and accurate Chinese word segmentation by providing a principled framework that easily supports the integration of domain knowledge in the form of multiple lexicons of characters and words. We also present a probabilistic new word detection method, which further improves performance. Our system is evaluated on four datasets used in a recent comprehensive Chinese word segmentation competition. State-of-the-art performance is obtained. 1

A common obstacle preventing the rapid deployment of supervised machine learning algorithms is the lack of labeled training data. This is particularly expensive to obtain for structured prediction tasks, where each training instance may have multiple, interacting labels, all of which must be correctly annotated for the instance to be of use to the learner. Traditional active learning addresses this problem by optimizing the order in which the examples are labeled to increase learning efficiency. However, this approach does not consider the difficulty of labeling each example, which can vary widely in structured prediction tasks. For example, the labeling predicted by a partially trained system may be easier to correct for some instances than for others. We propose a new active learning paradigm which reduces not only how many instances the annotator must label, but also how difficult each instance is to annotate. The system also leverages information from partially correct predictions to efficiently solicit annotations from the user. We validate this active learning framework in an interactive information extraction system, reducing the total number of annotation actions by 22%.

This thesis examines how artificial neural networks can benefit a large vocabulary, speaker independent, continuous speech recognition system. Currently, most speech recognition systems are based on hidden Markov models (HMMs), a statistical framework that supports both acoustic and temporal modeling. Despite their state-of-the-art performance, HMMs make a number of suboptimal modeling assumptions that limit their potential effectiveness. Neural networks avoid many of these assumptions, while they can also learn complex functions, generalize effectively, tolerate noise, and support parallelism. While neural networks can readily be applied to acoustic modeling, it is not yet clear how they can be used for temporal modeling. Therefore, we explore a class of systems called NN-HMM hybrids, in which neural networks perform acoustic modeling, and HMMs perform temporal modeling. We argue that a NN-HMM hybrid has several theoretical advantages over a pure HMM system, including better acoustic ...

A text-based and spoken language processing framework based on the Constraint Dependency Grammar (CDG) developed by Maruyama [24, 25] is discussed. The scope of CDG is expanded to allow for the analysis of sentences containing lexically ambiguous words, to allow feature analysis in constraints, and to efficiently process multiple sentence candidates that are likely to arise in spoken language processing. The benefits of the CDG parsing approach are summarized. Additionally, the development of CDG grammars using our grammar tools and parser is discussed.

Segment-based speech recognition systems must explicitly hypothesize segment start and end times. The purpose of a segmentation algorithm is to hypothesize those times and to compose a graph of segments from them. During recognition, this graph is an input to a search that finds the optimal sequence of sound units through the graph. The goal of this thesis is to create a high-quality, real-time phonetic segmentation algorithm for segment-based speech recognition. A high-quality segmentation algorithm produces a sparse network of segments that contains most of the actual segments in the speech utterance. A real-time algorithm implies that it is fast, and that it is able to produce an output in a pipelined manner. The approach taken in this thesis is to adopt the framework of a state-of-the-art algorithm that does not operate in real-time, and to make the modifications necessary to enable it to run in real-time. The algorithm adopted as the starting point for this work makes use of a for...

Active learning is well-suited to many problems in natural language processing, where unlabeled data may be abundant but annotation is slow and expensive. This paper aims to shed light on the best active learning approaches for sequence labeling tasks such as information extraction and document segmentation. We survey previously used query selection strategies for sequence models, and propose several novel algorithms to address their shortcomings. We also conduct a large-scale empirical comparison using multiple corpora, which demonstrates that our proposed methods advance the state of the art.

In this paper, we describe a system which is capable of utilizing a variety of knowledge sources to select the most appropriate parse for a spoken sentence. These knowledge sources include syntax, semantics, and contextual information. We discuss one way to utilize contextual information when determining the parse for a sentence. At its simplest level, the system can be thought of as a generalpurpose query answering system for multiple topical databases. The user's input would be processed by the language processor which interfaces to the databases with the goal of interacting with the correct database in order to provide a reasonable answer to the user's spoken request. Initially, it analyzes a word graph of sentence hypotheses provided by a speech recognizer using general syntactic and semantic rules. Then, if the utterance is still ambiguous, it utilizes contextspecific constraints to further refine the analysis. This brings us closer to developing a more general purpose interface f...