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We propose a neural-based approach for rule synthesis designed to help bridge the gap between the interpretability, precision and maintainability exhibited by rule-based information extraction systems with the scalability and convenience of statistical information extraction systems. This is achieved by avoiding placing the burden of learning another specialized language on domain experts and instead asking them to provide a small set of examples in the form of highlighted spans of text. We introduce a transformer-based architecture that drives a rule synthesis system that leverages a self-supervised approach for pre-training a large-scale language model complemented by an analysis of different loss functions and aggregation mechanisms for variable length sequences of user-annotated spans of text. The results are encouraging and point to different desirable properties, such as speed and quality, depending on the choice of loss and aggregation method. 

We propose a system that assists a user in constructing transparent information extraction models, consisting of patterns (or rules) written in a declarative language, through program synthesis. Users of our system can specify their requirements through the use of examples, which are collected with a search interface. The rule-synthesis system proposes rule candidates and the results of applying them on a textual corpus; the user has the option to accept the candidate, request another option, or adjust the examples provided to the system. Through an interactive evaluation, we show that our approach generates high-precision rules even in a 1-shot setting. On a second evaluation on a widely-used relation extraction dataset (TACRED), our method generates rules that outperform considerably manually written patterns. Our code, demo, and documentation is available at https://clulab.github.io/odinsynth/. 

An important task in the machine reading of biochemical events expressed in biomedical texts is correctly reading the polarity, i.e., attributing whether the biochemical event is a promotion or an inhibition. Here we present a novel dataset for studying polarity attribution accuracy. We use this dataset to train and evaluate several deep learning models for polarity identification, and compare these to a linguistically-informed model. The best performing deep learning architecture achieves 0.968 average F1 performance in a five-fold cross-validation study, a considerable improvement over the linguistically informed model average F1 of 0.862. 

Recent efforts in bioinformatics have achieved tremendous progress in the machine reading of biomedical literature, and the assembly of the extracted biochemical interactions into large-scale models such as protein signaling pathways. However, batch machine reading of literature at today’s scale (PubMed alone indexes over 1 million papers per year) is unfeasible due to both cost and processing overhead. In this work, we introduce a focused reading approach to guide the machine reading of biomedical literature towards what literature should be read to answer a biomedical query as efficiently as possible. We introduce a family of algorithms for focused reading, including an intuitive, strong baseline, and a second approach which uses a reinforcement learning (RL) framework that learns when to explore (widen the search) or exploit (narrow it). We demonstrate that the RL approach is capable of answering more queries than the baseline, while being more efficient, i.e., reading fewer documents.