AIMC Topic: Software

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Evaluation of PHI Hunter in Natural Language Processing Research.

Perspectives in health information management
OBJECTIVES: We introduce and evaluate a new, easily accessible tool using a common statistical analysis and business analytics software suite, SAS, which can be programmed to remove specific protected health information (PHI) from a text document. Re...

Link-topic model for biomedical abbreviation disambiguation.

Journal of biomedical informatics
INTRODUCTION: The ambiguity of biomedical abbreviations is one of the challenges in biomedical text mining systems. In particular, the handling of term variants and abbreviations without nearby definitions is a critical issue. In this study, we adopt...

LinkRbrain: multi-scale data integrator of the brain.

Journal of neuroscience methods
BACKGROUND: LinkRbrain is an open-access web platform for multi-scale data integration and visualization of human brain data. This platform integrates anatomical, functional, and genetic knowledge produced by the scientific community.

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects.

Bioinformatics (Oxford, England)
UNLABELLED: In order to develop powerful computational predictors for identifying the biological features or attributes of DNAs, one of the most challenging problems is to find a suitable approach to effectively represent the DNA sequences. To facili...

A low cost real-time motion tracking approach using webcam technology.

Journal of biomechanics
Physical therapy is an important component of gait recovery for individuals with locomotor dysfunction. There is a growing body of evidence that suggests that incorporating a motor learning task through visual feedback of movement trajectory is a use...

flowCL: ontology-based cell population labelling in flow cytometry.

Bioinformatics (Oxford, England)
MOTIVATION: Finding one or more cell populations of interest, such as those correlating to a specific disease, is critical when analysing flow cytometry data. However, labelling of cell populations is not well defined, making it difficult to integrat...

Approximate kernel competitive learning.

Neural networks : the official journal of the International Neural Network Society
Kernel competitive learning has been successfully used to achieve robust clustering. However, kernel competitive learning (KCL) is not scalable for large scale data processing, because (1) it has to calculate and store the full kernel matrix that is ...

MetaVelvet-SL: an extension of the Velvet assembler to a de novo metagenomic assembler utilizing supervised learning.

DNA research : an international journal for rapid publication of reports on genes and genomes
The assembly of multiple genomes from mixed sequence reads is a bottleneck in metagenomic analysis. A single-genome assembly program (assembler) is not capable of resolving metagenome sequences, so assemblers designed specifically for metagenomics ha...

Secondary use of electronic health records for building cohort studies through top-down information extraction.

Journal of biomedical informatics
Controlled clinical trials are usually supported with an in-front data aggregation system, which supports the storage of relevant information according to the trial context within a highly structured environment. In contrast to the documentation of c...