AIMC Topic: Neoplasms

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Towards the genomic sequence code of DNA fragility for machine learning.

Nucleic acids research
Genomic DNA breakages and the subsequent insertion and deletion mutations are important contributors to genome instability and linked diseases. Unlike the research in point mutations, the relationship between DNA sequence context and the propensity f...

Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.

Briefings in bioinformatics
Existing algorithms for assessing tumor purity are limited to a single omics data, such as gene expression, somatic copy number variations, somatic mutations, and DNA methylation. Here we proposed the machine learning Multi-omics Tumor Purity predict...

Multi-view multi-level contrastive graph convolutional network for cancer subtyping on multi-omics data.

Briefings in bioinformatics
Cancer is a highly diverse group of diseases, and each type of cancer can be further divided into various subtypes according to specific characteristics, cellular origins, and molecular markers. Subtyping helps in tailoring treatment and prognosis ac...

Predicting transcriptional changes induced by molecules with MiTCP.

Briefings in bioinformatics
Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of cellular state alterations and response mechanisms under chemical perturbations, which plays a crucial role in drug di...

DD-PRiSM: a deep learning framework for decomposition and prediction of synergistic drug combinations.

Briefings in bioinformatics
Combination therapies have emerged as a promising approach for treating complex diseases, particularly cancer. However, predicting the efficacy and safety profiles of these therapies remains a significant challenge, primarily because of the complex i...

Multimodal deep learning approaches for precision oncology: a comprehensive review.

Briefings in bioinformatics
The burgeoning accumulation of large-scale biomedical data in oncology, alongside significant strides in deep learning (DL) technologies, has established multimodal DL (MDL) as a cornerstone of precision oncology. This review provides an overview of ...

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...

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...

Leveraging Cancer Therapy Peptide Data: A Case Study on Machine Learning Application in Accelerating Cancer Research.

Studies in health technology and informatics
This study leverages the DCTPep database, a comprehensive repository of cancer therapy peptides, to explore the application of machine learning in accelerating cancer research. We applied Principal Component Analysis (PCA) and K-means clustering to c...

Development of a Serum Metabolome-Based Test for Early-Stage Detection of Multiple Cancers.

Cancer reports (Hoboken, N.J.)
BACKGROUND: Detection of cancer at the early stage currently offers the only viable strategy for reducing disease-related morbidity and mortality. Various approaches for multi-cancer early detection are being explored, which largely rely on capturing...