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Prognostic studies of breast cancer survivability have been aided by machine learning algorithms, which can predict the survival of a particular patient based on historical patient data. However, it is not easy to collect labeled patient records. It takes at least 5 years to label a patient record as 'survived' or 'not survived'. Unguided trials of numerous types of oncology therapies are also very expensive. Confidentiality agreements with doctors and [...]

Detecting complex patterns of association between genetic or environmental risk factors and disease risk has become an important target for epidemiological research. In particular, strategies that provide multifactor interactions or heterogeneous patterns of association can offer new insights into association studies for which traditional analytic tools have had limited success.

To create an end-to-end system to identify temporal relation in discharge summaries for the 2012 i2b2 challenge. The challenge includes event extraction, timex extraction, and temporal relation identification.

An enduring challenge in personalized medicine lies in selecting the right drug for each individual patient. While testing of drugs on patients in large trials is the only way to assess their clinical efficacy and toxicity, we dramatically lack resources to test the hundreds of drugs currently under development. Therefore the use of preclinical model systems has been intensively investigated as this approach enables response to hundreds of drugs to [...]

While genome-wide association studies (GWAS) of complex traits have revealed thousands of reproducible genetic associations to date, these loci collectively confer very little of the heritability of their respective diseases and, in general, have contributed little to our understanding the underlying disease biology. Physical protein interactions have been utilized to increase our understanding of human Mendelian disease loci but have yet to be fully exploited for complex traits.

The goal of this work was to evaluate machine learning methods, binary classification and sequence labeling, for medication-attribute linkage detection in two clinical corpora.

The integration of electronic health records (EHRs) across care settings including residential care facilities (RCFs) promises to reduce medical errors and improve coordination of services. Using data from the 2010 National Survey of Residential Care Facilities (n=2302), this study examines the association between facility structural characteristics and the use of EHRs in RCFs. Findings indicate that in 2010, only 3% of RCFs nationwide were using an EHR. However, 55% of [...]

Epistasis has been historically used to describe the phenomenon that the effect of a given gene on a phenotype can be dependent on one or more other genes, and is an essential element for understanding the association between genetic and phenotypic variations. Quantifying epistasis of orders higher than two is very challenging due to both the computational complexity of enumerating all possible combinations in genome-wide data and the lack of [...]

This study was to assess whether active learning strategies can be integrated with supervised word sense disambiguation (WSD) methods, thus reducing the number of annotated samples, while keeping or improving the quality of disambiguation models.

Effective clinical communication is critical to providing high-quality patient care. Hospitals have used different types of interventions to improve communication between care teams, but there have been few studies of their effectiveness.