Sean Finan


Extracting Relations between Radiotherapy Treatment Details
Danielle Bitterman | Timothy Miller | David Harris | Chen Lin | Sean Finan | Jeremy Warner | Raymond Mak | Guergana Savova
Proceedings of the 3rd Clinical Natural Language Processing Workshop

We present work on extraction of radiotherapy treatment information from the clinical narrative in the electronic medical records. Radiotherapy is a central component of the treatment of most solid cancers. Its details are described in non-standardized fashions using jargon not found in other medical specialties, complicating the already difficult task of manual data extraction. We examine the performance of several state-of-the-art neural methods for relation extraction of radiotherapy treatment details, with a goal of automating detailed information extraction. The neural systems perform at 0.82-0.88 macro-average F1, which approximates or in some cases exceeds the inter-annotator agreement. To the best of our knowledge, this is the first effort to develop models for radiotherapy relation extraction and one of the few efforts for relation extraction to describe cancer treatment in general.


Temporal Annotation in the Clinical Domain
William F. Styler IV | Steven Bethard | Sean Finan | Martha Palmer | Sameer Pradhan | Piet C de Groen | Brad Erickson | Timothy Miller | Chen Lin | Guergana Savova | James Pustejovsky
Transactions of the Association for Computational Linguistics, Volume 2

This article discusses the requirements of a formal specification for the annotation of temporal information in clinical narratives. We discuss the implementation and extension of ISO-TimeML for annotating a corpus of clinical notes, known as the THYME corpus. To reflect the information task and the heavily inference-based reasoning demands in the domain, a new annotation guideline has been developed, “the THYME Guidelines to ISO-TimeML (THYME-TimeML)”. To clarify what relations merit annotation, we distinguish between linguistically-derived and inferentially-derived temporal orderings in the text. We also apply a top performing TempEval 2013 system against this new resource to measure the difficulty of adapting systems to the clinical domain. The corpus is available to the community and has been proposed for use in a SemEval 2015 task.