AIMC Topic: Software

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PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning.

GigaScience
BACKGROUND: Phages and plasmids are the major components of mobile genetic elements, and fragments from such elements generally co-exist with chromosome-derived fragments in sequenced metagenomic data. However, there is a lack of efficient methods th...

Deep transfer learning-based prostate cancer classification using 3 Tesla multi-parametric MRI.

Abdominal radiology (New York)
PURPOSE: The purpose of the study was to propose a deep transfer learning (DTL)-based model to distinguish indolent from clinically significant prostate cancer (PCa) lesions and to compare the DTL-based model with a deep learning (DL) model without t...

Identifying antimicrobial peptides using word embedding with deep recurrent neural networks.

Bioinformatics (Oxford, England)
MOTIVATION: Antibiotic resistance constitutes a major public health crisis, and finding new sources of antimicrobial drugs is crucial to solving it. Bacteriocins, which are bacterially produced antimicrobial peptide products, are candidates for broad...

DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence.

Bioinformatics (Oxford, England)
MOTIVATION: Various bacterial pathogens can deliver their secreted substrates also called effectors through Type III secretion systems (T3SSs) into host cells and cause diseases. Since T3SS secreted effectors (T3SEs) play important roles in pathogen-...

Antibody interface prediction with 3D Zernike descriptors and SVM.

Bioinformatics (Oxford, England)
MOTIVATION: Antibodies are a class of proteins capable of specifically recognizing and binding to a virtually infinite number of antigens. This binding malleability makes them the most valuable category of biopharmaceuticals for both diagnostic and t...

Bastion3: a two-layer ensemble predictor of type III secreted effectors.

Bioinformatics (Oxford, England)
MOTIVATION: Type III secreted effectors (T3SEs) can be injected into host cell cytoplasm via type III secretion systems (T3SSs) to modulate interactions between Gram-negative bacterial pathogens and their hosts. Due to their relevance in pathogen-hos...

Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction.

Bioinformatics (Oxford, England)
MOTIVATION: With the accumulation of DNA sequencing data, convolution neural network (CNN) based methods such as DeepBind and DeepSEA have achieved great success for predicting the function of primary DNA sequences. Previous studies confirm the impor...

Impact of Data Presentation on Physician Performance Utilizing Artificial Intelligence-Based Computer-Aided Diagnosis and Decision Support Systems.

Journal of digital imaging
Ultrasound (US) is a valuable imaging modality used to detect primary breast malignancy. However, radiologists have a limited ability to distinguish between benign and malignant lesions on US, leading to false-positive and false-negative results, whi...

Cross-type biomedical named entity recognition with deep multi-task learning.

Bioinformatics (Oxford, England)
MOTIVATION: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network models for...