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.
: assumes that if two entities are mentioned in the same sentence (co-occur), it is likely that they are related. Usually, the application of this approach results in a higher recall (most of the entities co-occurring in a sentence participate in a relation), and lower precision. Some methods use frequency-based scoring schemes to eliminate relations identified by chance @cite_47 . Nowadays, most applications use co-occurrence as a baseline against more complex approaches @cite_45 .
@cite_47 @cite_45
1632875369 110692952 2138627627 2466190630
Entity Linking (EL) has received considerable attention in recent years. Given many name mentions in a document, the goal of EL is to predict their referent entities in a knowledge base. Traditionally, there have been two distinct directions of EL research: one focusing on the effects of mention's context compatibility, assuming that "the referent entity of a mention is reflected by its context"; the other dealing with the effects of document's topic coherence, assuming that "a mention's referent entity should be coherent with the document's main topics". In this paper, we propose a generative model -- called entity-topic model, to effectively join the above two complementary directions together. By jointly modeling and exploiting the context compatibility, the topic coherence and the correlation between them, our model can accurately link all mentions in a document using both the local information (including the words and the mentions in a document) and the global knowledge (including the topic knowledge, the entity context knowledge and the entity name knowledge). Experimental results demonstrate the effectiveness of the proposed model. In natural language relationships between entities can asserted within a single sentence or over many sentences in a document. Many information extraction systems are constrained to extracting binary relations that are asserted within a single sentence (single-sentence relations) and this limits the proportion of relations they can extract since those expressed across multiple sentences (inter-sentential relations) are not considered. The analysis in this paper focuses on finding the distribution of inter-sentential and single-sentence relations in two corpora used for the evaluation of information extraction systems: the MUC6 corpus and the ACE corpus from 2003. In order to carry out this analysis we had to manually mark up all the management succession relations described in the MUC6 corpus. It was found that inter-sentential relations constitute 28.5 and 9.4 of the total number of relations in MUC6 and ACE03 respectively. This places upper bounds on the recall of information extraction systems that do not consider relations that are asserted across multiple sentences (71.5 and 90.6 respectively). We present a novel approach to relation extraction, based on the observation that the information required to assert a relationship between two named entities in the same sentence is typically captured by the shortest path between the two entities in the dependency graph. Experiments on extracting top-level relations from the ACE (Automated Content Extraction) newspaper corpus show that the new shortest path dependency kernel outperforms a recent approach based on dependency tree kernels. We propose Feedback-query-expansion and Re-ranking methods which model the semantic relatedness of entities in one document.We demonstrate the effectiveness of our methods by comparing with the baseline systems on three data sets.Our team has scored in the top 3 teams across multiple metrics for the English EDL task in TAC2014. Entity disambiguation is a fundamental task of semantic Web annotation. Entity Linking (EL) is an essential procedure in entity disambiguation, which aims to link a mention appearing in a plain text to a structured or semi-structured knowledge base, such as Wikipedia. Existing research on EL usually annotates the mentions in a text one by one and treats entities independent to each other. However this might not be true in many application scenarios. For example, if two mentions appear in one text, they are likely to have certain intrinsic relationships. In this paper, we first propose a novel query expansion method for candidate generation utilizing the information of co-occurrences of mentions. We further propose a re-ranking model which can be iteratively adjusted based on the prediction in the previous round. Experiments on real-world data demonstrate the effectiveness of our proposed methods for entity disambiguation.