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.
: also uses manually defined and automatically generated rules from the training data to extract relations. Depending on the systems, the differences between pattern-based and ruled-based approaches can be minor. Ruled-based approaches not only use patterns but also, additional restraints to cover issues that are difficult to express by patterns, such as checking for the negation of the relations @cite_8 . Some ruled-based systems distance themselves from pattern-based approaches by replacing regular expressions with heuristic algorithms and sets of procedures @cite_14 . Similarly to pattern-based, ruled-based approaches tend to have poor recall, even though rules tend to be more flexible. The trade-off recall precision can be improved using automatic methods for rule creation @cite_37 .
@cite_37 @cite_14 @cite_8
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Action rules (or actionable patterns) describe possible transitions of objects from one state to another with respect to a distinguished attribute. Strategies for discovering them can be divided into two types: rule based and object based. Rule-based actionable patterns are built on the foundations of preexisting rules. This approach consists of two main steps: (1) a standard learning method is used to detect interesting patterns in the form of classification rules, association rules, or clusters; (2) the second step is to use an automatic or semiautomatic strategy to inspect such results and derive possible action strategies. These strategies provide an insight of how values of some attributes need to be changed so the desirable objects can be shifted to a desirable group. Object-based approach assumes that actionable patterns are extracted directly from a database. System DEAR, presented in this paper, is an example of a rule-based approach. System ARD and system for association rules mining are examples of an object-based approach. Music Information Retrieval (MIR) is taken as an application domain. We show how to manipulate the music score using action rules. © 2011 Wiley Periodicals, Inc. © 2011 Wiley Periodicals, Inc. In the field of infrastructures’ surveillance and protection, it is important to make decisions based on activities occurring in the environment and its local context and conditions. In this paper we use an active rule based event processing architecture in order to make sense of situations from the combination of different signals received by the rule engine. However obtaining some high level information automatically is not without risks, especially in sensitive environments, and detection mistakes can happen for various reasons: the signal’s source can be defective, whether it is human—miss-interpretation of the signal—or computed—material malfunction; the aggregation rules can be wrong syntaxically, for example when a rule will never be triggered or a situation never detected; the interpretation given to the combination of signals does not correspond to the reality on the field—because the knowledge of the rule designer is subjective or because the environment evolves over-time—the rules are therefore incorrect semantically. In this paper, a new approach is proposed to avoid the third kind of error sources. We present a hybrid machine learning technique adapted to the complexity of the rules’ representation, in order to create a system more conform to reality. The proposed approach uses a combination of an Association Rule Mining algorithm and Inductive Logic Programming for rule induction. Empirical studies on simulated datasets demonstrate how our method can contribute to sensible systems such as the security of a public or semi-public place. We propose an interpretable rule-based classification system based on ideas from Boolean compressed sensing. We represent the problem of learning individual conjunctive clauses or individual disjunctive clauses as a Boolean group testing problem, and apply a novel linear programming relaxation to find solutions. We derive results for exact rule recovery which parallel the conditions for exact recovery of sparse signals in the compressed sensing literature: although the general rule recovery problem is NP-hard, under some conditions on the Boolean 'sensing' matrix, the rule can be recovered exactly. This is an exciting development in rule learning where most prior work focused on heuristic solutions. Furthermore we construct rule sets from these learned clauses using set covering and boosting. We show competitive classification accuracy using the proposed approach. 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.