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Evaluating generalizability of oncology trial results to real-world patients using machine learning-based trial emulations.

Nature medicine
Randomized controlled trials (RCTs) evaluating anti-cancer agents often lack generalizability to real-world oncology patients. Although restrictive eligibility criteria contribute to this issue, the role of selection bias related to prognostic risk r...

Artificial Intelligence and Cancer Health Equity: Bridging the Divide or Widening the Gap.

Current oncology reports
PURPOSE OF REVIEW: This review aims to evaluate the impact of artificial intelligence (AI) on cancer health equity, specifically investigating whether AI is addressing or widening disparities in cancer outcomes.

Classification of non-TCGA cancer samples to TCGA molecular subtypes using compact feature sets.

Cancer cell
Molecular subtypes, such as defined by The Cancer Genome Atlas (TCGA), delineate a cancer's underlying biology, bringing hope to inform a patient's prognosis and treatment plan. However, most approaches used in the discovery of subtypes are not suita...

pACP-HybDeep: predicting anticancer peptides using binary tree growth based transformer and structural feature encoding with deep-hybrid learning.

Scientific reports
Worldwide, Cancer remains a significant health concern due to its high mortality rates. Despite numerous traditional therapies and wet-laboratory methods for treating cancer-affected cells, these approaches often face limitations, including high cost...

Drug discovery and mechanism prediction with explainable graph neural networks.

Scientific reports
Apprehension of drug action mechanism is paramount for drug response prediction and precision medicine. The unprecedented development of machine learning and deep learning algorithms has expedited the drug response prediction research. However, exist...

A deep multiple instance learning framework improves microsatellite instability detection from tumor next generation sequencing.

Nature communications
Microsatellite instability (MSI) is a critical phenotype of cancer genomes and an FDA-recognized biomarker that can guide treatment with immune checkpoint inhibitors. Previous work has demonstrated that next-generation sequencing data can be used to ...

Multi-Modal Federated Learning for Cancer Staging Over Non-IID Datasets With Unbalanced Modalities.

IEEE transactions on medical imaging
The use of machine learning (ML) for cancer staging through medical image analysis has gained substantial interest across medical disciplines. When accompanied by the innovative federated learning (FL) framework, ML techniques can further overcome pr...

FR-MIL: Distribution Re-Calibration-Based Multiple Instance Learning With Transformer for Whole Slide Image Classification.

IEEE transactions on medical imaging
In digital pathology, whole slide images (WSI) are crucial for cancer prognostication and treatment planning. WSI classification is generally addressed using multiple instance learning (MIL), alleviating the challenge of processing billions of pixels...

Spatially-Constrained and -Unconstrained Bi-Graph Interaction Network for Multi-Organ Pathology Image Classification.

IEEE transactions on medical imaging
In computational pathology, graphs have shown to be promising for pathology image analysis. There exist various graph structures that can discover differing features of pathology images. However, the combination and interaction between differing grap...

An appropriate DNA input for bisulfite conversion reveals LINE-1 and Alu hypermethylation in tissues and circulating cell-free DNA from cancers.

PloS one
The autonomous and active Long-Interspersed Element-1 (LINE-1, L1) and the non-autonomous Alu retrotransposon elements, contributing to 30% of the human genome, are the most abundant repeated sequences. With more than 90% of their sequences being met...