AIMC Topic: Deep Learning

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ViNe-Seg: deep-learning-assisted segmentation of visible neurons and subsequent analysis embedded in a graphical user interface.

Bioinformatics (Oxford, England)
SUMMARY: Segmentation of neural somata is a crucial and usually the most time-consuming step in the analysis of optical functional imaging of neuronal microcircuits. In recent years, multiple auto-segmentation tools have been developed to improve the...

Integrating physics in deep learning algorithms: a force field as a PyTorch module.

Bioinformatics (Oxford, England)
MOTIVATION: Deep learning algorithms applied to structural biology often struggle to converge to meaningful solutions when limited data is available, since they are required to learn complex physical rules from examples. State-of-the-art force-fields...

Advancing entity recognition in biomedicine via instruction tuning of large language models.

Bioinformatics (Oxford, England)
MOTIVATION: Large Language Models (LLMs) have the potential to revolutionize the field of Natural Language Processing, excelling not only in text generation and reasoning tasks but also in their ability for zero/few-shot learning, swiftly adapting to...

Clinical efficacy of motion-insensitive imaging technique with deep learning reconstruction to improve image quality in cervical spine MR imaging.

The British journal of radiology
OBJECTIVE: To demonstrate that a T2 periodically rotated overlapping parallel lines with enhanced reconstruction (PROPELLER) technique using deep learning reconstruction (DLR) will provide better image quality and decrease image noise.

Optimal fusion of genotype and drug embeddings in predicting cancer drug response.

Briefings in bioinformatics
Predicting cancer drug response using both genomics and drug features has shown some success compared to using genomics features alone. However, there has been limited research done on how best to combine or fuse the two types of features. Using a vi...

Contrastive learning for enhancing feature extraction in anticancer peptides.

Briefings in bioinformatics
Cancer, recognized as a primary cause of death worldwide, has profound health implications and incurs a substantial social burden. Numerous efforts have been made to develop cancer treatments, among which anticancer peptides (ACPs) are garnering reco...

Deep learning in structural bioinformatics: current applications and future perspectives.

Briefings in bioinformatics
In this review article, we explore the transformative impact of deep learning (DL) on structural bioinformatics, emphasizing its pivotal role in a scientific revolution driven by extensive data, accessible toolkits and robust computing resources. As ...

Genotypic-phenotypic landscape computation based on first principle and deep learning.

Briefings in bioinformatics
The relationship between genotype and fitness is fundamental to evolution, but quantitatively mapping genotypes to fitness has remained challenging. We propose the Phenotypic-Embedding theorem (P-E theorem) that bridges genotype-phenotype through an ...

BERT-TFBS: a novel BERT-based model for predicting transcription factor binding sites by transfer learning.

Briefings in bioinformatics
Transcription factors (TFs) are proteins essential for regulating genetic transcriptions by binding to transcription factor binding sites (TFBSs) in DNA sequences. Accurate predictions of TFBSs can contribute to the design and construction of metabol...

DeepKEGG: a multi-omics data integration framework with biological insights for cancer recurrence prediction and biomarker discovery.

Briefings in bioinformatics
Deep learning-based multi-omics data integration methods have the capability to reveal the mechanisms of cancer development, discover cancer biomarkers and identify pathogenic targets. However, current methods ignore the potential correlations betwee...