State-of-the-art methods for protein-protein interaction (PPI) extraction are primarily feature-based or kernel-based by leveraging lexical and syntactic information. But how to incorporate such knowledge in the recent deep learning methods remains an open question. In this paper, we propose a multichannel dependency-based convolutional neural network model (McDepCNN). It applies one channel to the embedding vector of each word in the sentence, and another channel to the embedding vector of the head of the corresponding word. Therefore, the model can use richer information obtained from different channels. Experiments on two public benchmarking datasets, AIMed and BioInfer, demonstrate that McDepCNN compares favorably to the state-of-the-art rich-feature and single-kernel based methods. In addition, McDepCNN achieves 24.4 relative improvement in F1-score over the state-of-the-art methods on cross-corpus evaluation and 12 improvement in F1-score over kernel-based methods on "difficult" instances. These results suggest that McDepCNN generalizes more easily over different corpora, and is capable of capturing long distance features in the sentences.
From the ML perspective, we formulate the PPI task as a binary classification problem where discriminative classifiers are trained with a set of positive and negative relation instances. In the last decade, ML-based methods for the PPI tasks have been dominated by two main types: the feature-based vs. kernel based method. The common characteristic of these methods is to transform relation instances into a set of features or rich structural representations like trees or graphs, by leveraging linguistic analysis and knowledge resources. Then a discriminative classifier is used, such as support vector machines @cite_48 or conditional random fields @cite_12 .
@cite_48 @cite_12
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This study assesses the relative performance characteristics of five established classification techniques on data collected using the P300 Speller paradigm, originally described by Farwell and Donchin (1988 Electroenceph. Clin. Neurophysiol. 70 510). Four linear methods: Pearson's correlation method (PCM), Fisher's linear discriminant (FLD), stepwise linear discriminant analysis (SWLDA) and a linear support vector machine (LSVM); and one nonlinear method: Gaussian kernel support vector machine (GSVM), are compared for classifying offline data from eight users. The relative performance of the classifiers is evaluated, along with the practical concerns regarding the implementation of the respective methods. The results indicate that while all methods attained acceptable performance levels, SWLDA and FLD provide the best overall performance and implementation characteristics for practical classification of P300 Speller data. 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. The essence of distantly supervised relation extraction is that it is an incomplete multi-label classification problem with sparse and noisy features. To tackle the sparsity and noise challenges, we propose solving the classification problem using matrix completion on factorized matrix of minimized rank. We formulate relation classification as completing the unknown labels of testing items (entity pairs) in a sparse matrix that concatenates training and testing textual features with training labels. Our algorithmic framework is based on the assumption that the rank of item-by-feature and item-by-label joint matrix is low. We apply two optimization models to recover the underlying low-rank matrix leveraging the sparsity of feature-label matrix. The matrix completion problem is then solved by the fixed point continuation (FPC) algorithm, which can find the global optimum. Experiments on two widely used datasets with different dimensions of textual features demonstrate that our low-rank matrix completion approach significantly outperforms the baseline and the state-of-the-art methods. In this work, we consider the task of classifying binary positive-unlabeled (PU) data. The existing discriminative learning based PU models attempt to seek an optimal reweighting strategy for U data, so that a decent decision boundary can be found. However, given limited P data, the conventional PU models tend to suffer from overfitting when adapted to very flexible deep neural networks. In contrast, we are the first to innovate a totally new paradigm to attack the binary PU task, from perspective of generative learning by leveraging the powerful generative adversarial networks (GAN). Our generative positive-unlabeled (GenPU) framework incorporates an array of discriminators and generators that are endowed with different roles in simultaneously producing positive and negative realistic samples. We provide theoretical analysis to justify that, at equilibrium, GenPU is capable of recovering both positive and negative data distributions. Moreover, we show GenPU is generalizable and closely related to the semi-supervised classification. Given rather limited P data, experiments on both synthetic and real-world dataset demonstrate the effectiveness of our proposed framework. With infinite realistic and diverse sample streams generated from GenPU, a very flexible classifier can then be trained using deep neural networks.