Classification of protein interaction sentences via gaussian processes

The increase in the availability of protein interaction studies in textual format coupled with the demand for easier access to the key results has lead to a need for text mining solutions. In the text processing pipeline, classification is a key step for extraction of small sections of relevant text. Consequently, for the task of locating protein-protein interaction sentences, we examine the use of a classifier which has rarely been applied to text, the Gaussian processes (GPs). GPs are a non-parametric probabilistic analogue to the more popular support vector machines (SVMs). We find that GPs outperform the SVM and na\"ive Bayes classifiers on binary sentence data, whilst showing equivalent performance on abstract and multiclass sentence corpora. In addition, the lack of the margin parameter, which requires costly tuning, along with the principled multiclass extensions enabled by the probabilistic framework make GPs an appealing alternative worth of further adoption

Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks

We participated in three of the protein-protein interaction subtasks of the Second BioCreative Challenge: classification of abstracts relevant for protein-protein interaction (IAS), discovery of protein pairs (IPS) and text passages characterizing protein interaction (ISS) in full text documents. We approached the abstract classification task with a novel, lightweight linear model inspired by spam-detection techniques, as well as an uncertainty-based integration scheme. We also used a Support Vector Machine and the Singular Value Decomposition on the same features for comparison purposes. Our approach to the full text subtasks (protein pair and passage identification) includes a feature expansion method based on word-proximity networks. Our approach to the abstract classification task (IAS) was among the top submissions for this task in terms of the measures of performance used in the challenge evaluation (accuracy, F-score and AUC). We also report on a web-tool we produced using our approach: the Protein Interaction Abstract Relevance Evaluator (PIARE). Our approach to the full text tasks resulted in one of the highest recall rates as well as mean reciprocal rank of correct passages. Our approach to abstract classification shows that a simple linear model, using relatively few features, is capable of generalizing and uncovering the conceptual nature of protein-protein interaction from the bibliome. Since the novel approach is based on a very lightweight linear model, it can be easily ported and applied to similar problems. In full text problems, the expansion of word features with word-proximity networks is shown to be useful, though the need for some improvements is discussed

Kernelized Hashcode Representations for Relation Extraction

Kernel methods have produced state-of-the-art results for a number of NLP tasks such as relation extraction, but suffer from poor scalability due to the high cost of computing kernel similarities between natural language structures. A recently proposed technique, kernelized locality-sensitive hashing (KLSH), can significantly reduce the computational cost, but is only applicable to classifiers operating on kNN graphs. Here we propose to use random subspaces of KLSH codes for efficiently constructing an explicit representation of NLP structures suitable for general classification methods. Further, we propose an approach for optimizing the KLSH model for classification problems by maximizing an approximation of mutual information between the KLSH codes (feature vectors) and the class labels. We evaluate the proposed approach on biomedical relation extraction datasets, and observe significant and robust improvements in accuracy w.r.t. state-of-the-art classifiers, along with drastic (orders-of-magnitude) speedup compared to conventional kernel methods.Comment: To appear in the proceedings of conference, AAAI-1