AIMC Topic: Algorithms

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Phantom evaluation of feasibility and applicability of artificial intelligence based pulmonary nodule detection in chest radiographs.

Medicine
The aim of our study was to evaluate the specific performance of an artificial intelligence (AI) algorithm for lung nodule detection in chest radiography for a larger number of nodules of different sizes and densities using a standardized phantom app...

A framework of multi-view machine learning for biological spectral unmixing of fluorophores with overlapping excitation and emission spectra.

Briefings in bioinformatics
The accuracy of assigning fluorophore identity and abundance, known as spectral unmixing, in biological fluorescence microscopy images remains a significant challenge due to the substantial overlap in emission spectra among fluorophores. In tradition...

Towards simplified graph neural networks for identifying cancer driver genes in heterophilic networks.

Briefings in bioinformatics
The identification of cancer driver genes is crucial for understanding the complex processes involved in cancer development, progression, and therapeutic strategies. Multi-omics data and biological networks provided by numerous databases enable the a...

A transformer-based deep learning survival prediction model and an explainable XGBoost anti-PD-1/PD-L1 outcome prediction model based on the cGAS-STING-centered pathways in hepatocellular carcinoma.

Briefings in bioinformatics
Recent studies suggest cGAS-STING pathway may play a crucial role in the genesis and development of hepatocellular carcinoma (HCC), closely associated with classical pathways and tumor immunity. We aimed to develop models predicting survival and anti...

Dual-stage optimizer for systematic overestimation adjustment applied to multi-objective genetic algorithms for biomarker selection.

Briefings in bioinformatics
The selection of biomarker panels in omics data, challenged by numerous molecular features and limited samples, often requires the use of machine learning methods paired with wrapper feature selection techniques, like genetic algorithms. They test va...

Predicting phage-host interactions via feature augmentation and regional graph convolution.

Briefings in bioinformatics
Identifying phage-host interactions (PHIs) is a crucial step in developing phage therapy, which is the promising solution to addressing the issue of antibiotic resistance in superbugs. However, the lifestyle of phages, which strongly depends on their...

scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learning.

Briefings in bioinformatics
Cell type annotation is a critical step in analyzing single-cell RNA sequencing (scRNA-seq) data. A large number of deep learning (DL)-based methods have been proposed to annotate cell types of scRNA-seq data and have achieved impressive results. How...

A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks.

Briefings in bioinformatics
The interactions between transcription factors (TFs) and the target genes could provide a basis for constructing gene regulatory networks (GRNs) for mechanistic understanding of various biological complex processes. From gene expression data, particu...

Augmenting small biomedical datasets using generative AI methods based on self-organizing neural networks.

Briefings in bioinformatics
Small sample sizes in biomedical research often led to poor reproducibility and challenges in translating findings into clinical applications. This problem stems from limited study resources, rare diseases, ethical considerations in animal studies, c...

Comprehensive bioinformatics and machine learning analyses for breast cancer staging using TCGA dataset.

Briefings in bioinformatics
Breast cancer is an alarming global health concern, including a vast and varied set of illnesses with different molecular characteristics. The fusion of sophisticated computational methodologies with extensive biological datasets has emerged as an ef...