AI Medical Compendium Topic:
Genomics

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Deep-Learning Model for Tumor-Type Prediction Using Targeted Clinical Genomic Sequencing Data.

Cancer discovery
UNLABELLED: Tumor type guides clinical treatment decisions in cancer, but histology-based diagnosis remains challenging. Genomic alterations are highly diagnostic of tumor type, and tumor-type classifiers trained on genomic features have been explore...

A novel deep learning framework for accurate melanoma diagnosis integrating imaging and genomic data for improved patient outcomes.

Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)
BACKGROUND: Melanoma is one of the most malignant forms of skin cancer, with a high mortality rate in the advanced stages. Therefore, early and accurate detection of melanoma plays an important role in improving patients' prognosis. Biopsy is the tra...

Advancing drug-response prediction using multi-modal and -omics machine learning integration (MOMLIN): a case study on breast cancer clinical data.

Briefings in bioinformatics
The inherent heterogeneity of cancer contributes to highly variable responses to any anticancer treatments. This underscores the need to first identify precise biomarkers through complex multi-omics datasets that are now available. Although much rese...

Omics-based deep learning approaches for lung cancer decision-making and therapeutics development.

Briefings in functional genomics
Lung cancer has been the most common and the leading cause of cancer deaths globally. Besides clinicopathological observations and traditional molecular tests, the advent of robust and scalable techniques for nucleic acid analysis has revolutionized ...

Interpreting generative adversarial networks to infer natural selection from genetic data.

Genetics
Understanding natural selection and other forms of non-neutrality is a major focus for the use of machine learning in population genetics. Existing methods rely on computationally intensive simulated training data. Unlike efficient neutral coalescent...

Coding genomes with gapped pattern graph convolutional network.

Bioinformatics (Oxford, England)
MOTIVATION: Genome sequencing technologies reveal a huge amount of genomic sequences. Neural network-based methods can be prime candidates for retrieving insights from these sequences because of their applicability to large and diverse datasets. Howe...

Improving the performance of supervised deep learning for regulatory genomics using phylogenetic augmentation.

Bioinformatics (Oxford, England)
MOTIVATION: Supervised deep learning is used to model the complex relationship between genomic sequence and regulatory function. Understanding how these models make predictions can provide biological insight into regulatory functions. Given the compl...

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...

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...

Prior knowledge-guided multilevel graph neural network for tumor risk prediction and interpretation via multi-omics data integration.

Briefings in bioinformatics
The interrelation and complementary nature of multi-omics data can provide valuable insights into the intricate molecular mechanisms underlying diseases. However, challenges such as limited sample size, high data dimensionality and differences in omi...