We propose a novel neural method to extract drug-drug interactions (DDIs) from texts using external drug molecular structure information. We encode textual drug pairs with convolutional neural networks and their molecular pairs with graph convolutional networks (GCNs), and then we concatenate the outputs of these two networks. In the experiments, we show that GCNs can predict DDIs from the molecular structures of drugs in high accuracy and the molecular information can enhance text-based DDI extraction by 2.39 percent points in the F-score on the DDIExtraction 2013 shared task data set.
Various feature-based methods have been proposed during and after the DDIExtraction-2013 shared task @cite_10 . proposed a two-phase SVM-based approach that employed a linear SVM with rich features that consist of word, word pair, dependency graph, parse tree, and noun phrase-based constrained coordination features. proposed a context vector graph kernel to exploit various types of contexts. also employed a two-phase SVM-based approach using non-linear kernels and they proposed five groups of features: word, drug, pair of drug, main verb and negative sentence features. Our model does not use any features or kernels.
@cite_10
2060515712 2105644991 2169272853 2110142955
The wealth of interaction information provided in biomedical articles motivated the implementation of text mining approaches to automatically extract biomedical relations. This paper presents an unsupervised method based on pattern clustering and sentence parsing to deal with biomedical relation extraction. Pattern clustering algorithm is based on Polynomial Kernel method, which identifies interaction words from unlabeled data; these interaction words are then used in relation extraction between entity pairs. Dependency parsing and phrase structure parsing are combined for relation extraction. Based on the semi-supervised KNN algorithm, we extend the proposed unsupervised approach to a semi-supervised approach by combining pattern clustering, dependency parsing and phrase structure parsing rules. We evaluated the approaches on two different tasks: (1) Protein–protein interactions extraction, and (2) Gene–suicide association extraction. The evaluation of task (1) on the benchmark dataset (AImed corpus) showed that our proposed unsupervised approach outperformed three supervised methods. The three supervised methods are rule based, SVM based, and Kernel based separately. The proposed semi-supervised approach is superior to the existing semi-supervised methods. The evaluation on gene–suicide association extraction on a smaller dataset from Genetic Association Database and a larger dataset from publicly available PubMed showed that the proposed unsupervised and semi-supervised methods achieved much higher F-scores than co-occurrence based method. In typical classification tasks, we seek a function which assigns a label to a single object. Kernel-based approaches, such as support vector machines (SVMs), which maximize the margin of confidence of the classifier, are the method of choice for many such tasks. Their popularity stems both from the ability to use high-dimensional feature spaces, and from their strong theoretical guarantees. However, many real-world tasks involve sequential, spatial, or structured data, where multiple labels must be assigned. Existing kernel-based methods ignore structure in the problem, assigning labels independently to each object, losing much useful information. Conversely, probabilistic graphical models, such as Markov networks, can represent correlations between labels, by exploiting problem structure, but cannot handle high-dimensional feature spaces, and lack strong theoretical generalization guarantees. In this paper, we present a new framework that combines the advantages of both approaches: Maximum margin Markov (M3) networks incorporate both kernels, which efficiently deal with high-dimensional features, and the ability to capture correlations in structured data. We present an efficient algorithm for learning M3 networks based on a compact quadratic program formulation. We provide a new theoretical bound for generalization in structured domains. Experiments on the task of handwritten character recognition and collective hypertext classification demonstrate very significant gains over previous approaches. Using discriminative classifiers, such as Support Vector Machines (SVMs) in combination with, or as an alternative to, Hidden Markov Models (HMMs) has a number of advantages for difficult speech recognition tasks. For example, the models can make use of additional dependencies in the observation sequences than HMMs provided the appropriate form of kernel is used. However standard SVMs are binary classifiers, and speech is a multi-class problem. Furthermore, to train SVMs to distinguish word pairs requires that each word appears in the training data. This paper examines both of these limitations. Tree-based reduction approaches for multiclass classification are described, as well as some of the issues in applying them to dynamic data, such as speech. To address the training data issues, a simplified version of HMM-based synthesis can be used, which allows data for any word-pair to be generated. These approaches are evaluated on two noise corrupted digit sequence tasks: AURORA 2.0; and actual in-car collected data. In this paper, we present a novel approach for automatically learning a compact and yet discriminative appearance-based human action model. A video sequence is represented by a bag of spatiotemporal features called video-words by quantizing the extracted 3D interest points (cuboids) from the videos. Our proposed approach is able to automatically discover the optimal number of video-word clusters by utilizing maximization of mutual information(MMI). Unlike the k-means algorithm, which is typically used to cluster spatiotemporal cuboids into video words based on their appearance similarity, MMI clustering further groups the video-words, which are highly correlated to some group of actions. To capture the structural information of the learnt optimal video-word clusters, we explore the correlation of the compact video-word clusters. We use the modified correlogram, which is not only translation and rotation invariant, but also somewhat scale invariant. We extensively test our proposed approach on two publicly available challenging datasets: the KTH dataset and IXMAS multiview dataset. To the best of our knowledge, we are the first to try the bag of video-words related approach on the multiview dataset. We have obtained very impressive results on both datasets.