A wealth of genetic, demographic, clinical and biomarker data is collected from routine clinical care of HIV patients and exists in the form of medical records available among the medical care and research communities. Machine learning (ML) methods h...
BACKGROUND: Biomedical named entity recognition(BNER) is a crucial initial step of information extraction in biomedical domain. The task is typically modeled as a sequence labeling problem. Various machine learning algorithms, such as Conditional Ran...
BACKGROUND: Most state-of-the-art biomedical entity normalization systems, such as rule-based systems, merely rely on morphological information of entity mentions, but rarely consider their semantic information. In this paper, we introduce a novel co...
The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such texts. Annotation of biomedical documents wit...
BACKGROUND: In this paper we present the approach that we employed to deal with large scale multi-label semantic indexing of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge (2013-2017), a challenge conce...
BMC medical informatics and decision making
Jul 3, 2017
BACKGROUND: Understanding semantic relatedness and similarity between biomedical terms has a great impact on a variety of applications such as biomedical information retrieval, information extraction, and recommender systems. The objective of this st...
BACKGROUND: Extracting biomedical entities and their relations from text has important applications on biomedical research. Previous work primarily utilized feature-based pipeline models to process this task. Many efforts need to be made on feature e...
CPT: pharmacometrics & systems pharmacology
Mar 13, 2017
Despite the existence of various databases cataloging cancer drugs, there is an emerging need to support the development and application of personalized therapies, where an integrated understanding of the clinical factors and drug mechanism of action...
AMIA ... Annual Symposium proceedings. AMIA Symposium
Feb 10, 2017
Authors of biomedical articles use comparison sentences to communicate the findings of a study, and to compare the results of the current study with earlier studies. The Claim Framework defines a comparison claim as a sentence that includes at least ...
AMIA ... Annual Symposium proceedings. AMIA Symposium
Feb 10, 2017
Scientific reproducibility is key to scientific progress as it allows the research community to build on validated results, protect patients from potentially harmful trial drugs derived from incorrect results, and reduce wastage of valuable resources...