A deep semantic matching approach for identifying relevant messages for social media analysis.

There is a growing interest in using social media content for Natural Language Processing applications. However, it is not easy to computationally identify the most relevant set of tweets related to any specific event. Challenging semantics coupled with different ways for using natural language in social media make it difficult for retrieving the most relevant set of data from any social media outlet.

A Gated Recurrent Unit based architecture for recognizing ontology concepts from biological literature.

Background: Annotating scientific literature with ontology concepts is a critical task in biology and several other domains for knowledge discovery. Ontology based annotations can power large-scale comparative analyses in a wide range of applications ranging from evolutionary phenotypes to rare human diseases to the study of protein functions. Computational methods that can tag scientific text with ontology terms have included lexical/syntactic methods, traditional machine learning, and most recently, deep learning.

Using EHR Data to Identify Patient Frailty and Risk for ICU Transfer.

The predictive properties of four definitions of a frailty risk score (FRS) constructed using combinations of nursing flowsheet data, laboratory tests, and ICD-10 codes were examined for time to first intensive care unit (ICU) transfer in medical-surgical inpatients ≥50 years of age. Cox regression modeled time to first ICU transfer and Schemper-Henderson explained variance summarized predictive accuracy of FRS combinations. Modeling by age group and controlling for sex, all FRS measures significantly predicted time to first ICU transfer.

Machine learning for predicting readmission risk among the frail: Explainable AI for healthcare.

Healthcare costs due to unplanned readmissions are high and negatively affect health and wellness of patients. Hospital readmission is an undesirable outcome for elderly patients. Here, we present readmission risk prediction using five machine learning approaches for predicting 30-day unplanned readmission for elderly patients (age ≥ 50 years).

Frailty and In-Hospital Mortality Risk Using EHR Nursing Data.

PurposeThe purpose of this study was to evaluate four definitions of a Frailty Risk Score (FRS) derived from EHR data that includes combinations of biopsychosocial risk factors using nursing flowsheet data or International Classification of Disease, 10th revision (ICD-10) codes and blood biomarkers and its predictive properties for in-hospital mortality in adults ≥50 years admitted to medical-surgical units. In this retrospective observational study and secondary analysis of an EHR dataset, survival analysis and Cox regression models were performed with sociodemographic and clinical covariates. Integrated area under the ROC curve (iAUC) across follow-up time based on Cox modeling was estimated.

Hospital Readmission Outcomes by Frailty Risk in Adults in Behavioral Health Acute Care.

The purpose of the current retrospective study was to determine whether frailty is predictive of 30-day readmission in adults aged ≥50 years who were admitted with a psychiatric diagnosis to a behavioral health hospital from 2013 to 2017. A total of 1,063 patients were included. A 26-item frailty risk score (FRS-26-ICD) was constructed from electronic health record (EHR) data.

Comparison of a Frailty Risk Score and Comorbidity Indices for Hospital Readmission Using Electronic Health Record Data.

The purpose of the current study was to investigate the predictive properties of five definitions of a frailty risk score (FRS) and three comorbidity indices using data from electronic health records (EHRs) of hospitalized adults aged ≥50 years for 3-day, 7-day, and 30-day readmission, and to identify an optimal model for a FRS and comorbidity combination. Retrospective analysis of the EHR dataset was performed, and multivariable logistic regression and area under the curve (AUC) were used to examine readmission for frailty and comorbidity. The sample ( = 55,778) was mostly female (53%), non-Hispanic White (73%), married (53%), and on Medicare (55%).

Using Manual and Computer-Based Text-Mining to Uncover Research Trends for .

Honey bee research is believed to be influenced dramatically by colony collapse disorder (CCD) and the sequenced genome release in 2006, but this assertion has never been tested. By employing text-mining approaches, research trends were tested by analyzing over 14,000 publications during the period of 1957 to 2017. Quantitatively, the data revealed an exponential growth until 2010 when the number of articles published per year ceased following the trend.

Avoiding "conflicts of interest": a computational approach to scheduling parallel conference tracks and its human evaluation.

Conferences with contributed talks grouped into multiple concurrent sessions pose an interesting scheduling problem. From an attendee's perspective, choosing which talks to visit when there are many concurrent sessions is challenging since an individual may be interested in topics that are discussed in different sessions simultaneously. The frequency of topically similar talks in different concurrent sessions is, in fact, a common cause for complaint in post-conference surveys.

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems.

Natural language descriptions of organismal phenotypes, a principal object of study in biology, are abundant in the biological literature. Expressing these phenotypes as logical statements using ontologies would enable large-scale analysis on phenotypic information from diverse systems. However, considerable human effort is required to make these phenotype descriptions amenable to machine reasoning.

INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.

There is growing use of ontologies for the measurement of cross-species phenotype similarity. Such similarity measurements contribute to diverse applications, such as identifying genetic models for human diseases, transferring knowledge among model organisms, and studying the genetic basis of evolutionary innovations. Two organismal features, whether genes, anatomical parts, or any other inherited feature, are considered to be homologous when they are evolutionarily derived from a single feature in a common ancestor.

The digital revolution in phenotyping.

Phenotypes have gained increased notoriety in the clinical and biological domain owing to their application in numerous areas such as the discovery of disease genes and drug targets, phylogenetics and pharmacogenomics. Phenotypes, defined as observable characteristics of organisms, can be seen as one of the bridges that lead to a translation of experimental findings into clinical applications and thereby support 'bench to bedside' efforts. However, to build this translational bridge, a common and universal understanding of phenotypes is required that goes beyond domain-specific definitions.

Using the phenoscape knowledgebase to relate genetic perturbations to phenotypic evolution.

The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms.

Interestingness measures and strategies for mining multi-ontology multi-level association rules from gene ontology annotations for the discovery of new GO relationships.

The Gene Ontology (GO), a set of three sub-ontologies, is one of the most popular bio-ontologies used for describing gene product characteristics. GO annotation data containing terms from multiple sub-ontologies and at different levels in the ontologies is an important source of implicit relationships between terms from the three sub-ontologies. Data mining techniques such as association rule mining that are tailored to mine from multiple ontologies at multiple levels of abstraction are required for effective knowledge discovery from GO annotation data.

Cross-Ontology multi-level association rule mining in the Gene Ontology.

The Gene Ontology (GO) has become the internationally accepted standard for representing function, process, and location aspects of gene products. The wealth of GO annotation data provides a valuable source of implicit knowledge of relationships among these aspects. We describe a new method for association rule mining to discover implicit co-occurrence relationships across the GO sub-ontologies at multiple levels of abstraction.

AgBase: supporting functional modeling in agricultural organisms.

AgBase (http://www.agbase.msstate.

GOModeler--a tool for hypothesis-testing of functional genomics datasets.

Background: Functional genomics technologies that measure genome expression at a global scale are accelerating biological knowledge discovery. Generating these high throughput datasets is relatively easy compared to the downstream functional modelling necessary for elucidating the molecular mechanisms that govern the biology under investigation. A number of publicly available 'discovery-based' computational tools use the computationally amenable Gene Ontology (GO) for hypothesis generation.

Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data.

Unlabelled: The widespread availability of microarray technology has driven functional genomics to the forefront as scientists seek to draw meaningful biological conclusions from their microarray results. Gene annotation enrichment analysis is a functional analysis technique that has gained widespread attention and for which many tools have been developed. Unfortunately, most of these tools have limited support for agricultural species.