AIMC Topic: Neural Networks, Computer

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Increasing a microscope's effective field of view via overlapped imaging and machine learning.

Optics express
This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morpholog...

Scan-less machine-learning-enabled incoherent microscopy for minimally-invasive deep-brain imaging.

Optics express
Deep-brain microscopy is strongly limited by the size of the imaging probe, both in terms of achievable resolution and potential trauma due to surgery. Here, we show that a segment of an ultra-thin multi-mode fiber (cannula) can replace the bulky mic...

Active disease-related compound identification based on capsule network.

Briefings in bioinformatics
Pneumonia, especially corona virus disease 2019 (COVID-19), can lead to serious acute lung injury, acute respiratory distress syndrome, multiple organ failure and even death. Thus it is an urgent task for developing high-efficiency, low-toxicity and ...

Detection of transcription factors binding to methylated DNA by deep recurrent neural network.

Briefings in bioinformatics
Transcription factors (TFs) are proteins specifically involved in gene expression regulation. It is generally accepted in epigenetics that methylated nucleotides could prevent the TFs from binding to DNA fragments. However, recent studies have confir...

SIGNET: single-cell RNA-seq-based gene regulatory network prediction using multiple-layer perceptron bagging.

Briefings in bioinformatics
High-throughput single-cell RNA-seq data have provided unprecedented opportunities for deciphering the regulatory interactions among genes. However, such interactions are complex and often nonlinear or nonmonotonic, which makes their inference using ...

Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design.

Briefings in bioinformatics
Artificial intelligence (AI)-based drug design has great promise to fundamentally change the landscape of the pharmaceutical industry. Even though there are great progress from handcrafted feature-based machine learning models, 3D convolutional neura...

DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning.

Briefings in bioinformatics
Proteins with intrinsically disordered regions (IDRs) are common among eukaryotes. Many IDRs interact with nucleic acids and proteins. Annotation of these interactions is supported by computational predictors, but to date, only one tool that predicts...

HINGRL: predicting drug-disease associations with graph representation learning on heterogeneous information networks.

Briefings in bioinformatics
Identifying new indications for drugs plays an essential role at many phases of drug research and development. Computational methods are regarded as an effective way to associate drugs with new indications. However, most of them complete their tasks ...

LR-GNN: a graph neural network based on link representation for predicting molecular associations.

Briefings in bioinformatics
In biomedical networks, molecular associations are important to understand biological processes and functions. Many computational methods, such as link prediction methods based on graph neural networks (GNNs), have been successfully applied in discov...

SGNNMD: signed graph neural network for predicting deregulation types of miRNA-disease associations.

Briefings in bioinformatics
MiRNAs are a class of small non-coding RNA molecules that play an important role in many biological processes, and determining miRNA-disease associations can benefit drug development and clinical diagnosis. Although great efforts have been made to de...