AIMC Topic: Software

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MIIC online: a web server to reconstruct causal or non-causal networks from non-perturbative data.

Bioinformatics (Oxford, England)
SUMMARY: We present a web server running the MIIC algorithm, a network learning method combining constraint-based and information-theoretic frameworks to reconstruct causal, non-causal or mixed networks from non-perturbative data, without the need fo...

L1000FWD: fireworks visualization of drug-induced transcriptomic signatures.

Bioinformatics (Oxford, England)
MOTIVATION: As part of the NIH Library of Integrated Network-based Cellular Signatures program, hundreds of thousands of transcriptomic signatures were generated with the L1000 technology, profiling the response of human cell lines to over 20 000 sma...

Arash: A social robot buddy to support children with cancer in a hospital environment.

Proceedings of the Institution of Mechanical Engineers. Part H, Journal of engineering in medicine
This article presents the thorough design procedure, specifications, and performance of a mobile social robot friend Arash for educational and therapeutic involvement of children with cancer based on their interests and needs. Our research focuses on...

Enhanced functionalities for annotating and indexing clinical text with the NCBO Annotator.

Bioinformatics (Oxford, England)
SUMMARY: Second use of clinical data commonly involves annotating biomedical text with terminologies and ontologies. The National Center for Biomedical Ontology Annotator is a frequently used annotation service, originally designed for biomedical dat...

Feature specific quantile normalization enables cross-platform classification of molecular subtypes using gene expression data.

Bioinformatics (Oxford, England)
MOTIVATION: Molecular subtypes of cancers and autoimmune disease, defined by transcriptomic profiling, have provided insight into disease pathogenesis, molecular heterogeneity and therapeutic responses. However, technical biases inherent to different...

Expanding a radiology lexicon using contextual patterns in radiology reports.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: Distributional semantics algorithms, which learn vector space representations of words and phrases from large corpora, identify related terms based on contextual usage patterns. We hypothesize that distributional semantics can speed up lex...

LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks.

Bioinformatics (Oxford, England)
MOTIVATION: Nucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets o...

DeepSig: deep learning improves signal peptide detection in proteins.

Bioinformatics (Oxford, England)
MOTIVATION: The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization.

Technical note: an R package for fitting sparse neural networks with application in animal breeding.

Journal of animal science
Neural networks (NNs) have emerged as a new tool for genomic selection (GS) in animal breeding. However, the properties of NN used in GS for the prediction of phenotypic outcomes are not well characterized due to the problem of over-parameterization ...