AIMC Topic: Neural Networks, Computer

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SPDesign: protein sequence designer based on structural sequence profile using ultrafast shape recognition.

Briefings in bioinformatics
Protein sequence design can provide valuable insights into biopharmaceuticals and disease treatments. Currently, most protein sequence design methods based on deep learning focus on network architecture optimization, while ignoring protein-specific p...

HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data.

Briefings in bioinformatics
Reliable cell type annotations are crucial for investigating cellular heterogeneity in single-cell omics data. Although various computational approaches have been proposed for single-cell RNA sequencing (scRNA-seq) annotation, high-quality cell label...

MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning.

Briefings in bioinformatics
MOTIVATION: Accurately predicting molecular metabolic stability is of great significance to drug research and development, ensuring drug safety and effectiveness. Existing deep learning methods, especially graph neural networks, can reveal the molecu...

A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts.

Briefings in bioinformatics
Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and h...

scNovel: a scalable deep learning-based network for novel rare cell discovery in single-cell transcriptomics.

Briefings in bioinformatics
Single-cell RNA sequencing has achieved massive success in biological research fields. Discovering novel cell types from single-cell transcriptomics has been demonstrated to be essential in the field of biomedicine, yet is time-consuming and needs pr...

Arrhythmia classification based on multi-feature multi-path parallel deep convolutional neural networks and improved focal loss.

Mathematical biosciences and engineering : MBE
Early diagnosis of abnormal electrocardiogram (ECG) signals can provide useful information for the prevention and detection of arrhythmia diseases. Due to the similarities in Normal beat (N) and Supraventricular Premature Beat (S) categories and imba...

Probing the Structure and Functional Properties of the Dropout-Induced Correlated Variability in Convolutional Neural Networks.

Neural computation
Computational neuroscience studies have shown that the structure of neural variability to an unchanged stimulus affects the amount of information encoded. Some artificial deep neural networks, such as those with Monte Carlo dropout layers, also have ...

Lateral Connections Improve Generalizability of Learning in a Simple Neural Network.

Neural computation
To navigate the world around us, neural circuits rapidly adapt to their environment learning generalizable strategies to decode information. When modeling these learning strategies, network models find the optimal solution to satisfy one task conditi...

EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks.

Nucleic acids research
Protein language models (pLMs) trained on a large corpus of protein sequences have shown unprecedented scalability and broad generalizability in a wide range of predictive modeling tasks, but their power has not yet been harnessed for predicting prot...

[Fully Automatic Glioma Segmentation Algorithm of Magnetic Resonance Imaging Based on 3D-UNet With More Global Contextual Feature Extraction: An Improvement on Insufficient Extraction of Global Features].

Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition
OBJECTIVE: The fully automatic segmentation of glioma and its subregions is fundamental for computer-aided clinical diagnosis of tumors. In the segmentation process of brain magnetic resonance imaging (MRI), convolutional neural networks with small c...