We present SwellShark, a framework for building biomedical named entity recognition (NER) systems quickly and without hand-labeled data. Our approach views biomedical resources like lexicons as function primitives for autogenerating weak supervision. We then use a generative model to unify and denoise this supervision and construct large-scale, probabilistically labeled datasets for training high-accuracy NER taggers. In three biomedical NER tasks, SwellShark achieves competitive scores with state-of-the-art supervised benchmarks using no hand-labeled training data. In a drug name extraction task using patient medical records, one domain expert using SwellShark achieved within 5.1 of a crowdsourced annotation approach -- which originally utilized 20 teams over the course of several weeks -- in 24 hours.
Leveraging existing resources to heuristically label data has received considerable research interest. Distant supervision @cite_11 @cite_7 uses knowledge bases to supervise relation extraction tasks. Recent methods incorporate more generalized knowledge into extraction systems. used Markov Logic Networks to encode commonsense domain knowledge like home teams are more likely to win a game" and generate weak training examples. is informed by these methods, but uses a generative model to unify and model noise across different supervision sources.
@cite_7 @cite_11
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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. 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. Distant supervision, heuristically labeling a corpus using a knowledge base, has emerged as a popular choice for training relation extractors. In this paper, we show that a significant number of “negative“ examples generated by the labeling process are false negatives because the knowledge base is incomplete. Therefore the heuristic for generating negative examples has a seriousflaw. Building on a state-of-the-art distantly-supervised extraction algorithm, we proposed an algorithm that learns from only positive and unlabeled labels at the pair-of-entity level. Experimental results demonstrate its advantage over existing algorithms. Two problems arise when using distant supervision for relation extraction. First, in this method, an already existing knowledge base is heuristically aligned to texts, and the alignment results are treated as labeled data. However, the heuristic alignment can fail, resulting in wrong label problem. In addition, in previous approaches, statistical models have typically been applied to ad hoc features. The noise that originates from the feature extraction process can cause poor performance. In this paper, we propose a novel model dubbed the Piecewise Convolutional Neural Networks (PCNNs) with multi-instance learning to address these two problems. To solve the first problem, distant supervised relation extraction is treated as a multi-instance problem in which the uncertainty of instance labels is taken into account. To address the latter problem, we avoid feature engineering and instead adopt convolutional architecture with piecewise max pooling to automatically learn relevant features. Experiments show that our method is effective and outperforms several competitive baseline methods.