AIMC Topic: Deep Learning

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iMFP-LG: Identify Novel Multi-functional Peptides Using Protein Language Models and Graph-based Deep Learning.

Genomics, proteomics & bioinformatics
Functional peptides are short amino acid fragments that have a wide range of beneficial functions for living organisms. The majority of previous studies have focused on mono-functional peptides, but an increasing number of multi-functional peptides h...

DeepMEns: an ensemble model for predicting sgRNA on-target activity based on multiple features.

Briefings in functional genomics
The CRISPR/Cas9 system developed from Streptococcus pyogenes (SpCas9) has high potential in gene editing. However, its successful application is hindered by the considerable variability in target efficiencies across different single guide RNAs (sgRNA...

Multimodal deep learning improves recurrence risk prediction in pediatric low-grade gliomas.

Neuro-oncology
BACKGROUND: Postoperative recurrence risk for pediatric low-grade gliomas (pLGGs) is challenging to predict by conventional clinical, radiographic, and genomic factors. We investigated if deep learning (DL) of magnetic resonance imaging (MRI) tumor f...

MRI-Seed-Wizard: combining deep learning algorithms with magnetic resonance imaging enables advanced seed phenotyping.

Journal of experimental botany
Evaluation of relevant seed traits is an essential part of most plant breeding and biotechnology programmes. There is a need for non-destructive, three-dimensional assessment of the morphometry, composition, and internal features of seeds. Here, we i...

[Value of the deep learning automated quantification of tumor-stroma ratio in predicting efficacy and prognosis of neoadjuvant therapy for breast cancer based on residual cancer burden grading].

Zhonghua bing li xue za zhi = Chinese journal of pathology
To investigate the prognostic value of deep learning-based automated quantification of tumor-stroma ratio (TSR) in patients undergoing neoadjuvant therapy (NAT) for breast cancer. Specimens were collected from 209 breast cancer patients who receive...

miRStart 2.0: enhancing miRNA regulatory insights through deep learning-based TSS identification.

Nucleic acids research
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by binding to the 3'-untranslated regions of target mRNAs, influencing various biological processes at the post-transcriptional level. Identifying miRNA transcription start si...

Automated Breast Density Assessment for Full-Field Digital Mammography and Digital Breast Tomosynthesis.

Cancer prevention research (Philadelphia, Pa.)
Mammographic density is a strong risk factor for breast cancer and is reported clinically as part of Breast Imaging Reporting and Data System (BI-RADS) results issued by radiologists. Automated assessment of density is needed that can be used for bot...

CGPDTA: An Explainable Transfer Learning-Based Predictor With Molecule Substructure Graph for Drug-Target Binding Affinity.

Journal of computational chemistry
Identifying interactions between drugs and targets is crucial for drug discovery and development. Nevertheless, the determination of drug-target binding affinities (DTAs) through traditional experimental methods is a time-consuming process. Conventio...

An efficient deep learning method for amino acid substitution model selection.

Journal of evolutionary biology
Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number of parameters; therefore, it is estimated from hundred...

Artificial Intelligence for Optical Coherence Tomography in Glaucoma.

Translational vision science & technology
PURPOSE: The integration of artificial intelligence (AI), particularly deep learning (DL), with optical coherence tomography (OCT) offers significant opportunities in the diagnosis and management of glaucoma. This article explores the application of ...