Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been proposed to identify relations between concepts in biomedical literature, namely using neural networks algorithms. The use of multichannel architectures composed of multiple data representations, as in deep neural networks, is leading to state-of-the-art results. The right combination of data representations can eventually lead us to even higher evaluation scores in relation extraction tasks. Thus, biomedical ontologies play a fundamental role by providing semantic and ancestry information about an entity. The incorporation of biomedical ontologies has already been proved to enhance previous state-of-the-art results.
: usually makes use of large annotated biomedical corpora (supervised learning) to perform RE. These corpora are pre-processed using NLP tools and then used to train classification models. Beyond Neural Networks, described in detail in Section 3 3 , it is possible to categorize ML methods into two main approaches, Feature-based and Kernel-based. represent each instance (e.g., sentence) as a vector in an n-dimensional space. Support Vector Machines (SVM) classifiers tend to be used to solve problems of binary classification, and are considered because there is no interference of the user in the classification process. These classifiers can use different features that are meant to represent the data characteristics (e.g., shortest path, bag-of-words (BOW), and POS tagging) @cite_13 . main idea is to quantify the similarity between the different instances in a data-set by computing the similarities of their representations @cite_48 . Kernel-based approaches add the structural representation of instances (e.g., by using parse trees). These methods can use one kernel or a combination of kernels (e.g., graph, sub-tree (ST), and shallow linguistic (SL)).
@cite_48 @cite_13
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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. In this paper we have designed and experimented novel convolution kernels for automatic classification of predicate arguments. Their main property is the ability to process structured representations. Support Vector Machines (SVMs), using a combination of such kernels and the flat feature kernel, classify Prop-Bank predicate arguments with accuracy higher than the current argument classification state-of-the-art.Additionally, experiments on FrameNet data have shown that SVMs are appealing for the classification of semantic roles even if the proposed kernels do not produce any improvement. 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. Support vector machines (SVM) have been highly successful in many machine learning problems. Recently, it is also used for multi-instance (MI) learning by employing a kernel that is defined directly on the bags. As only the bags (but not the instances) have known labels, this MI kernel implicitly assumes all instances in the bag to be equally important. However, a fundamental property of MI learning is that not all instances in a positive bag necessarily belong to the positive class, and thus different instances in the same bag should have different contributions to the kernel. In this paper, we address this instance label ambiguity by using the method of marginalized kernels. It first assumes that all the instance labels are available and defines a label-dependent kernel on the instances. By integrating out the unknown instance labels, a marginalized kernel defined on the bags can then be obtained. A desirable property is that this kernel weights the instance pairs by the consistencies of their probabilistic instance labels. Experiments on both classification and regression data sets show that this marginalized MI kernel, when used in a standard SVM, performs consistently better than the original MI kernel. It also outperforms a number of traditional MI learning methods.