Identifying and extracting data elements such as study descriptors in publication full texts is a critical yet manual and labor-intensive step required in a number of tasks. In this paper we address the question of identifying data elements in an unsupervised manner. Specifically, provided a set of criteria describing specific study parameters, such as species, route of administration, and dosing regimen, we develop an unsupervised approach to identify text segments (sentences) relevant to the criteria. A binary classifier trained to identify publications that met the criteria performs better when trained on the candidate sentences than when trained on sentences randomly picked from the text, supporting the intuition that our method is able to accurately identify study descriptors.
A similar but distinct approach to unsupervised extraction is distant supervision. Similarly as unsupervised extraction methods, distant supervision methods don't require any labeled data, but make use of weakly labeled data, such as data extracted from a knowledge base. Distant supervision has been applied to relation extraction @cite_6 , extraction of gene interactions @cite_18 , PPI extraction @cite_3 @cite_4 , and identification of PICO elements @cite_10 . The advantage of our approach compared to the distantly supervised methods is that it does not require any underlying knowledge base or a similar source of data.
@cite_18 @cite_4 @cite_3 @cite_6 @cite_10
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In relation extraction, distant supervision seeks to extract relations between entities from text by using a knowledge base, such as Freebase, as a source of supervision. When a sentence and a knowledge base refer to the same entity pair, this approach heuristically labels the sentence with the corresponding relation in the knowledge base. However, this heuristic can fail with the result that some sentences are labeled wrongly. This noisy labeled data causes poor extraction performance. In this paper, we propose a method to reduce the number of wrong labels. We present a novel generative model that directly models the heuristic labeling process of distant supervision. The model predicts whether assigned labels are correct or wrong via its hidden variables. Our experimental results show that this model detected wrong labels with higher performance than baseline methods. In the experiment, we also found that our wrong label reduction boosted the performance of relation extraction. Distant supervision for relation extraction is an efficient method to scale relation extraction to very large corpora which contains thousands of relations. However, the existing approaches have flaws on selecting valid instances and lack of background knowledge about the entities. In this paper, we propose a sentence-level attention model to select the valid instances, which makes full use of the supervision information from knowledge bases. And we extract entity descriptions from Freebase and Wikipedia pages to supplement background knowledge for our task. The background knowledge not only provides more information for predicting relations, but also brings better entity representations for the attention module. We conduct three experiments on a widely used dataset and the experimental results show that our approach outperforms all the baseline systems significantly. Relation extraction is frequently and successfully addressed by machine learning methods. The downside of this approach is the need for annotated training data, typically generated in tedious manual, cost intensive work. Distantly supervised approaches make use of weakly annotated data, like automatically annotated corpora. Recent work in the biomedical domain has applied distant supervision for protein-protein interaction (PPI) with reasonable results making use of the IntAct database. Such data is typically noisy and heuristics to filter the data are commonly applied. We propose a constraint to increase the quality of data used for training based on the assumption that no self-interaction of real-world objects are described in sentences. In addition, we make use of the University of Kansas Proteomics Service (KUPS) database. These two steps show an increase of 7 percentage points (pp) for the PPI corpus AIMed. We demonstrate the broad applicability of our approach by using the same workflow for the analysis of drug-drug interactions, utilizing relationships available from the drug database DrugBank. We achieve 37.31 in F1 measure without manually annotated training data on an independent test set. Several recent works on relation extraction have been applying the distant supervision paradigm: instead of relying on annotated text to learn how to predict relations, they employ existing knowledge bases (KBs) as source of supervision. Crucially, these approaches are trained based on the assumption that each sentence which mentions the two related entities is an expression of the given relation. Here we argue that this leads to noisy patterns that hurt precision, in particular if the knowledge base is not directly related to the text we are working with. We present a novel approach to distant supervision that can alleviate this problem based on the following two ideas: First, we use a factor graph to explicitly model the decision whether two entities are related, and the decision whether this relation is mentioned in a given sentence; second, we apply constraint-driven semi-supervision to train this model without any knowledge about which sentences express the relations in our training KB. We apply our approach to extract relations from the New York Times corpus and use Freebase as knowledge base. When compared to a state-of-the-art approach for relation extraction under distant supervision, we achieve 31 error reduction.