AIMC Topic: Software

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Improving the Quality of Synthetic FLAIR Images with Deep Learning Using a Conditional Generative Adversarial Network for Pixel-by-Pixel Image Translation.

AJNR. American journal of neuroradiology
BACKGROUND AND PURPOSE: Synthetic FLAIR images are of lower quality than conventional FLAIR images. Here, we aimed to improve the synthetic FLAIR image quality using deep learning with pixel-by-pixel translation through conditional generative adversa...

BO-LSTM: classifying relations via long short-term memory networks along biomedical ontologies.

BMC bioinformatics
BACKGROUND: Recent studies have proposed deep learning techniques, namely recurrent neural networks, to improve biomedical text mining tasks. However, these techniques rarely take advantage of existing domain-specific resources, such as ontologies. I...

funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model.

BMC genetics
BACKGROUND: Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA barcoding technique can be empl...

OMeta: an ontology-based, data-driven metadata tracking system.

BMC bioinformatics
BACKGROUND: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association stu...

Artificial intelligence for sex determination of skeletal remains: Application of a deep learning artificial neural network to human skulls.

Journal of forensic and legal medicine
A deep learning artificial neural network was adapted to the task of sex determination of skeletal remains. The neural network was trained on images of 900 skulls virtually reconstructed from hospital CT scans. When tested on previously unseen images...

Artificial intelligence-based decision-making for age-related macular degeneration.

Theranostics
Artificial intelligence (AI) based on convolutional neural networks (CNNs) has a great potential to enhance medical workflow and improve health care quality. Of particular interest is practical implementation of such AI-based software as a cloud-base...

Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering.

Database : the journal of biological databases and curation
Information about the interactions between chemical compounds and proteins is indispensable for understanding the regulation of biological processes and the development of therapeutic drugs. Manually extracting such information from biomedical litera...

Combining relation extraction with function detection for BEL statement extraction.

Database : the journal of biological databases and curation
The BioCreative-V community proposed a challenging task of automatic extraction of causal relation network in Biological Expression Language (BEL) from the biomedical literature. Previous studies on this task largely used models induced from other re...

MITK Phenotyping: An open-source toolchain for image-based personalized medicine with radiomics.

Radiotherapy and oncology : journal of the European Society for Therapeutic Radiology and Oncology
Radiomics - The extraction of quantitative features from radiologic images - shows increasing potential in contributing to modern personalized medicine approaches. MITK Phenotyping is an openly distributed radiomics framework implementing an exhausti...

Polypharmacology Browser PPB2: Target Prediction Combining Nearest Neighbors with Machine Learning.

Journal of chemical information and modeling
Here we report PPB2 as a target prediction tool assigning targets to a query molecule based on ChEMBL data. PPB2 computes ligand similarities using molecular fingerprints encoding composition (MQN), molecular shape and pharmacophores (Xfp), and subst...