PubMed, a repository and search engine for biomedical literature, now indexes >1 million articles each year. This exceeds the processing capacity of human domain experts, limiting our ability to truly understand many diseases. We present Reach, a system for automated, large-scale machine reading of biomedical papers that can extract mechanistic descriptions of biological processes with relatively high precision at high throughput. We demonstrate that combining the extracted pathway fragments with existing biological data analysis algorithms that rely on curated models helps identify and explain a large number of previously unidentified mutually exclusive altered signaling pathways in seven different cancer types. This work shows that combining human-curated ‘big mechanisms’ with extracted ‘big data’ can lead to a causal, predictive understanding of cellular processes and unlock important downstream applications.

Lexical semantic models provide robust performance for question answering, but, in general, can only capitalize on direct evidence seen during training. For example, monolingual alignment models acquire term alignment probabilities from semi-structured data such as question-answer pairs; neural network language models learn term embeddings from unstructured text. All this knowledge is then used to estimate the semantic similarity between question and answer candidates. We introduce a higher-order formalism that allows all these lexical semantic models to chain direct evidence to construct indirect associations between question and answer texts, by casting the task as the traversal of graphs that encode direct term associations. Using a corpus of 10,000 questions from Yahoo! Answers, we experimentally demonstrate that higher-order methods are broadly applicable to alignment and language models, across both word and syntactic representations. We show that an important criterion for success is controlling for the semantic drift that accumulates during graph traversal. All in all, the proposed higher-order approach improves five out of the six lexical semantic models investigated, with relative gains of up to +13% over their first-order variants.

We describe the design, development, and API of ODIN (Open Domain INformer), a domainindependent, rule-based event extraction (EE) framework. The proposed EE approach is: simple (most events are captured with simple lexico-syntactic patterns), powerful (the language can capture complex constructs, such as events taking other events as arguments, and regular expressions over syntactic graphs), robust (to recover from syntactic parsing errors, syntactic patterns can be freely mixed with surface, token-based patterns), and fast (the runtime environment processes 110 sentences/second in a real-world domain with a grammar of over 200 rules). We used this framework to develop a grammar for the biochemical domain, which approached human performance. Our EE framework is accompanied by a web-based user interface for the rapid development of event grammars and visualization of matches. The ODIN framework and the domain-specific grammars are available as open-source code.

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We introduce a modular approach for literature-based discovery consisting of a machine reading and knowledge assembly component that together produce a graph of influence relations (e.g., "A promotes B") from a collection of publications. A search engine is used to explore direct and indirect influence chains. Query results are substantiated with textual evidence, ranked according to their relevance, and presented in both a table-based view, as well as a network graph visualization. Our approach operates in both domain-specific settings, where there are knowledge bases and ontologies available to guide reading, and in multi-domain settings where such resources are absent. We demonstrate that this deep reading and search system reduces the effort needed to uncover "undiscovered public knowledge", and that with the aid of this tool a domain expert was able to drastically reduce her model building time from months to two days.