Discovering Power Laws in Entity Length

This paper presents a discovery that the length of the entities in various datasets follows a family of scale-free power law distributions. The concept of entity here broadly includes the named entity, entity mention, time expression, aspect term, and domain-specific entity that are well investigated in natural language processing and related areas. The entity length denotes the number of words in an entity. The power law distributions in entity length possess the scale-free property and have well-defined means and finite variances. We explain the phenomenon of power laws in entity length by the principle of least effort in communication and the preferential mechanism

A System for Identifying Named Entities in Biomedical Text: how Results From two Evaluations Reflect on Both the System and the Evaluations

We present a maximum entropy-based system for identifying named entities (NEs) in biomedical abstracts and present its performance in the only two biomedical named entity recognition (NER) comparative evaluations that have been held to date, namely BioCreative and Coling BioNLP. Our system obtained an exact match F-score of 83.2% in the BioCreative evaluation and 70.1% in the BioNLP evaluation. We discuss our system in detail, including its rich use of local features, attention to correct boundary identification, innovative use of external knowledge resources, including parsing and web searches, and rapid adaptation to new NE sets. We also discuss in depth problems with data annotation in the evaluations which caused the final performance to be lower than optimal

Opportunities for Business Intelligence and Big Data Analytics in Evidence Based Medicine

Evidence based medicine (EBM) is the conscientious, explicit, and judicious use of current best evidence in making decisions about the care of individual patients. Each year, a significant number of research studies (potentially serving as evidence) are reported in the literature at an ever-increasing rate outpacing the translation of research findings into practice. Coupled with the proliferation of electronic health records, and consumer health information, researchers and practitioners are challenged to leverage the full potential of EBM. In this paper we present a research agenda for leveraging business intelligence and big data analytics in evidence based medicine, and illustrate how analytics can be used to support EBM

A Survey of Biological Entity Recognition Approaches

There has been growing interest in the task of Named Entity Recognition (NER) and a lot of research has been done in this direction in last two decades. Particularly, a lot of progress has been made in the biomedical domain with emphasis on identifying domain-specific entities and often the task being known as Biological Named Entity Recognition (BER). The task of biological entity recognition (BER) has been proved to be a challenging task due to several reasons as identified by many researchers. The recognition of biological entities in text and the extraction of relationships between them have paved the way for doing more complex text-mining tasks and building further applications. This paper looks at the challenges perceived by the researchers in BER task and investigates the works done in the domain of BER by using the multiple approaches available for the task

Recognition of medication information from discharge summaries using ensembles of classifiers

BACKGROUND: Extraction of clinical information such as medications or problems from clinical text is an important task of clinical natural language processing (NLP). Rule-based methods are often used in clinical NLP systems because they are easy to adapt and customize. Recently, supervised machine learning methods have proven to be effective in clinical NLP as well. However, combining different classifiers to further improve the performance of clinical entity recognition systems has not been investigated extensively. Combining classifiers into an ensemble classifier presents both challenges and opportunities to improve performance in such NLP tasks. METHODS: We investigated ensemble classifiers that used different voting strategies to combine outputs from three individual classifiers: a rule-based system, a support vector machine (SVM) based system, and a conditional random field (CRF) based system. Three voting methods were proposed and evaluated using the annotated data sets from the 2009 i2b2 NLP challenge: simple majority, local SVM-based voting, and local CRF-based voting. RESULTS: Evaluation on 268 manually annotated discharge summaries from the i2b2 challenge showed that the local CRF-based voting method achieved the best F-score of 90.84% (94.11% Precision, 87.81% Recall) for 10-fold cross-validation. We then compared our systems with the first-ranked system in the challenge by using the same training and test sets. Our system based on majority voting achieved a better F-score of 89.65% (93.91% Precision, 85.76% Recall) than the previously reported F-score of 89.19% (93.78% Precision, 85.03% Recall) by the first-ranked system in the challenge. CONCLUSIONS: Our experimental results using the 2009 i2b2 challenge datasets showed that ensemble classifiers that combine individual classifiers into a voting system could achieve better performance than a single classifier in recognizing medication information from clinical text. It suggests that simple strategies that can be easily implemented such as majority voting could have the potential to significantly improve clinical entity recognition

Bio-Medical Entity Extraction Using Support Vector Machines

Support Vector Machines have achieved state of the art performance in several classification tasks. In this article we apply them to the identification and semantic annotation of scientific and technical terminology in the domain of molecular biology