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.
Modern models of relation extraction for tasks like ACE are based on supervised learning of relations from small hand-labeled corpora. We investigate an alternative paradigm that does not require labeled corpora, avoiding the domain dependence of ACE-style algorithms, and allowing the use of corpora of any size. Our experiments use Freebase, a large semantic database of several thousand relations, to provide distant supervision. For each pair of entities that appears in some Freebase relation, we find all sentences containing those entities in a large unlabeled corpus and extract textual features to train a relation classifier. Our algorithm combines the advantages of supervised IE (combining 400,000 noisy pattern features in a probabilistic classifier) and unsupervised IE (extracting large numbers of relations from large corpora of any domain). Our model is able to extract 10,000 instances of 102 relations at a precision of 67.6 . We also analyze feature performance, showing that syntactic parse features are particularly helpful for relations that are ambiguous or lexically distant in their expression. Recently, there has been much effort in making databases for Inolecular biology more accessible osld interoperable. However, information in text. form, such as MEDLINE records, remains a greatly underutilized source of biological information. We have begun a research effort aimed at automatically mapping information from text. sources into structured representations, such as knowledge bases. Our approach to this task is to use machine-learning methods to induce routines for extracting facts from text. We describe two learning methods that we have applied to this task -a statistical text classification method, and a relational learning method -and our initial experiments in learning such information-extraction routines. We also present an approach to decreasing the cost of learning information-extraction routines by learning from "weakly" labeled training data.