Semi-supervised prediction of protein interaction sentences exploiting semantically encoded metrics

Protein-protein interaction (PPI) identification is an integral component of many biomedical research and database curation tools. Automation of this task through classification is one of the key goals of text mining (TM). However, labelled PPI corpora required to train classifiers are generally small. In order to overcome this sparsity in the training data, we propose a novel method of integrating corpora that do not contain relevance judgements. Our approach uses a semantic language model to gather word similarity from a large unlabelled corpus. This additional information is integrated into the sentence classification process using kernel transformations and has a re-weighting effect on the training features that leads to an 8% improvement in F-score over the baseline results. Furthermore, we discover that some words which are generally considered indicative of interactions are actually neutralised by this process

From Frequency to Meaning: Vector Space Models of Semantics

Computers understand very little of the meaning of human language. This profoundly limits our ability to give instructions to computers, the ability of computers to explain their actions to us, and the ability of computers to analyse and process text. Vector space models (VSMs) of semantics are beginning to address these limits. This paper surveys the use of VSMs for semantic processing of text. We organize the literature on VSMs according to the structure of the matrix in a VSM. There are currently three broad classes of VSMs, based on term-document, word-context, and pair-pattern matrices, yielding three classes of applications. We survey a broad range of applications in these three categories and we take a detailed look at a specific open source project in each category. Our goal in this survey is to show the breadth of applications of VSMs for semantics, to provide a new perspective on VSMs for those who are already familiar with the area, and to provide pointers into the literature for those who are less familiar with the field

Topic-based mixture language modelling

This paper describes an approach for constructing a mixture of language models based on simple statistical notions of semantics using probabilistic models developed for information retrieval. The approach encapsulates corpus-derived semantic information and is able to model varying styles of text. Using such information, the corpus texts are clustered in an unsupervised manner and a mixture of topic-specific language models is automatically created. The principal contribution of this work is to characterise the document space resulting from information retrieval techniques and to demonstrate the approach for mixture language modelling. A comparison is made between manual and automatic clustering in order to elucidate how the global content information is expressed in the space. We also compare (in terms of association with manual clustering and language modelling accuracy) alternative term-weighting schemes and the effect of singular value decomposition dimension reduction (latent semantic analysis). Test set perplexity results using the British National Corpus indicate that the approach can improve the potential of statistical language modelling. Using an adaptive procedure, the conventional model may be tuned to track text data with a slight increase in computational cost