AIMC Topic: Software

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ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data.

GigaScience
BACKGROUND: Classification algorithms assign observations to groups based on patterns in data. The machine-learning community have developed myriad classification algorithms, which are used in diverse life science research domains. Algorithm choice c...

Prediction of mutation effects using a deep temporal convolutional network.

Bioinformatics (Oxford, England)
MOTIVATION: Accurate prediction of the effects of genetic variation is a major goal in biological research. Towards this goal, numerous machine learning models have been developed to learn information from evolutionary sequence data. The most effecti...

DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins.

Bioinformatics (Oxford, England)
MOTIVATION: The success of genome sequencing techniques has resulted in rapid explosion of protein sequences. Collections of multiple homologous sequences can provide critical information to the modeling of structure and function of unknown proteins....

Can artificial intelligence replace manual search for systematic literature? Review on cutaneous manifestations in primary Sjögren's syndrome.

Rheumatology (Oxford, England)
OBJECTIVES: Manual systematic literature reviews are becoming increasingly challenging due to the sharp rise in publications. The primary objective of this literature review was to compare manual and computer software using artificial intelligence re...

MLCD: A Unified Software Package for Cancer Diagnosis.

JCO clinical cancer informatics
PURPOSE: Machine Learning Package for Cancer Diagnosis (MLCD) is the result of a National Institutes of Health/National Cancer Institute (NIH/NCI)-sponsored project for developing a unified software package from state-of-the-art breast cancer biopsy ...

OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data.

JCO clinical cancer informatics
PURPOSE: The purpose of OncoMX knowledgebase development was to integrate cancer biomarker and relevant data types into a meta-portal, enabling the research of cancer biomarkers side by side with other pertinent multidimensional data types.

DeepPod: a convolutional neural network based quantification of fruit number in Arabidopsis.

GigaScience
BACKGROUND: High-throughput phenotyping based on non-destructive imaging has great potential in plant biology and breeding programs. However, efficient feature extraction and quantification from image data remains a bottleneck that needs to be addres...

medExtractR: A targeted, customizable approach to medication extraction from electronic health records.

Journal of the American Medical Informatics Association : JAMIA
OBJECTIVE: We developed medExtractR, a natural language processing system to extract medication information from clinical notes. Using a targeted approach, medExtractR focuses on individual drugs to facilitate creation of medication-specific research...

Deep-learning approach to identifying cancer subtypes using high-dimensional genomic data.

Bioinformatics (Oxford, England)
MOTIVATION: Cancer subtype classification has the potential to significantly improve disease prognosis and develop individualized patient management. Existing methods are limited by their ability to handle extremely high-dimensional data and by the i...

Multi-scale structural analysis of proteins by deep semantic segmentation.

Bioinformatics (Oxford, England)
MOTIVATION: Recent advances in computational methods have facilitated large-scale sampling of protein structures, leading to breakthroughs in protein structural prediction and enabling de novo protein design. Establishing methods to identify candidat...