ObjectiveTo create annotated clinical narratives with layers of syntactic and semantic labels to facilitate advances in clinical natural language processing (NLP). To develop NLP algorithms and open source components.MethodsManual annotation of a clinical narrative corpus of 127 606 tokens following the Treebank schema for syntactic information, PropBank schema for predicate-argument structures, and the Unified Medical Language System (UMLS) schema for semantic information. NLP components were developed.ResultsThe final corpus consists of 13 091 sentences containing 1772 distinct predicate lemmas. Of the 766 newly created PropBank frames, 74 are verbs. There are 28 539 named entity (NE) annotations spread over 15 UMLS semantic groups, one UMLS semantic type, and the Person semantic category. The most frequent annotations belong to the UMLS semantic groups of Procedures (15.71%), Disorders (14.74%), Concepts and Ideas (15.10%), Anatomy (12.80%), Chemicals and Drugs (7.49%), and the UMLS semantic type of Sign or Symptom (12.46%). Inter-annotator agreement results: Treebank (0.926), PropBank (0.891–0.931), NE (0.697–0.750). The part-of-speech tagger, constituency parser, dependency parser, and semantic role labeler are built from the corpus and released open source. A significant limitation uncovered by this project is the need for the NLP community to develop a widely agreed-upon schema for the annotation of clinical concepts and their relations.ConclusionsThis project takes a foundational step towards bringing the field of clinical NLP up to par with NLP in the general domain. The corpus creation and NLP components provide a resource for research and application development that would have been previously impossible.

Abstract. The natural language processing community has recently experienced a growth of interest in domain independent shallow semantic parsing-the process of assigning a WHO did WHAT to WHOM, WHEN, WHERE, WHY, HOW etc. structure to plain text. This process entails identifying groups of words in a sentence that represent these semantic arguments and assigning specific labels to them. It could play a key role in NLP tasks like Information Extraction, Question Answering and Summarization. We propose a machine learning algorithm for semantic role parsing, extending the work of Gildea and Jurafsky (2002), Surdeanu et al. (2003) and others. Our algorithm is based on Support Vector Machines which we show give large improvement in performance over earlier classifiers. We show performance improvements through a number of new features designed to improve generalization to unseen data, such as automatic clustering of verbs. We also report on various analytic studies examining which features are most important, comparing our classifier to other machine learning algorithms in the literature, and testing its generalization to new test set from different genre. On the task of assigning semantic labels to the PropBank (Kingsbury, Palmer, & Marcus, 2002) corpus, our final system has a precision of 84% and a recall of 75%, which are the best results currently reported for this task. Finally, we explore a completely different architecture which does not requires a deep syntactic parse. We reformulate the task as a combined chunking and classification problem, thus allowing our algorithm to be applied to new languages or genres of text for which statistical syntactic parsers may not be available.

Semantic role labeling is the process of annotating the predicate-argument structure in text with semantic labels. In this paper we present a state-of-the-art baseline semantic role labeling system based on Support Vector Machine classifiers. We show improvements on this system by: i) adding new features including features extracted from dependency parses, ii) performing feature selection and calibration and iii) combining parses obtained from semantic parsers trained using different syntactic views. Error analysis of the baseline system showed that approximately half of the argument identification errors resulted from parse errors in which there was no syntactic constituent that aligned with the correct argument. In order to address this problem, we combined semantic parses from a Minipar syntactic parse and from a chunked syntactic representation with our original baseline system which was based on Charniak parses. All of the reported techniques resulted in performance improvements.

Correctly predicting the direction that branches will take is increasingly important in today's wide-issue computer architectures. The name program-based branch prediction is given to static branch prediction techniques that base their prediction on a program's structure. In this article, we investigate a new approach to program-based branch prediction that uses a body of existing programs to predict the branch behavior in a new program. We call this approach to program-based branch prediction evidence-based static prediction, or ESP. The main idea of ESP is that the behavior of a corpus of programs can be used to infer the behavior of new programs. In this article, we use neural networks and decision trees to map static features associated with each branch to a prediction that the branch will be taken. ESP shows significant advantages over other prediction mechanisms. Specifically, it is a program-based technique; it is effective across a range of programming languages and programming styles; and it does not rely on the use of expert-defined heuristics. In this article, we describe the application of ESP to the problem of static branch prediction and compare our results to existing program-based branch predictors. We also investigate the applicability of ESP across computer architectures, programming languages, compilers, and run-time systems. We provide results showing how sensitive ESP is to the number and type of static features and programs included in the ESP training sets, and we compare the efficacy of static branch prediction for subroutine libraries. Averaging over a body of 43 C and Fortran programs, ESP branch prediction results in a miss rate of 20%, as compared with the 25% miss rate obtained using the best existing program-based heuristics.