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

On the Reproducibility and Generalisation of the Linear Transformation of Word Embeddings

Linear transformation is a way to learn a linear relationship between two word embeddings, such that words in the two different embedding spaces can be semantically related. In this paper, we examine the reproducibility and generalisation of the linear transformation of word embeddings. Linear transformation is particularly useful when translating word embedding models in different languages, since it can capture the semantic relationships between two models. We first reproduce two linear transformation approaches, a recent one using orthogonal transformation and the original one using simple matrix transformation. Previous findings on a machine translation task are re-examined, validating that linear transformation is indeed an effective way to transform word embedding models in different languages. In particular, we show that the orthogonal transformation can better relate the different embedding models. Following the verification of previous findings, we then study the generalisation of linear transformation in a multi-language Twitter election classification task. We observe that the orthogonal transformation outperforms the matrix transformation. In particular, it significantly outperforms the random classifier by at least 10% under the F1 metric across English and Spanish datasets. In addition, we also provide best practices when using linear transformation for multi-language Twitter election classification