Deep transfer learning for clinical decision-making based on high-throughput data: comprehensive survey with benchmark results.

The rapid growth of omics-based data has revolutionized biomedical research and precision medicine, allowing machine learning models to be developed for cutting-edge performance. However, despite the wealth of high-throughput data available, the performance of these models is hindered by the lack of sufficient training data, particularly in clinical research (in vivo experiments). As a result, translating this knowledge into clinical practice, such as predicting drug responses, remains a challenging task. Transfer learning is a promising tool that bridges the gap between data domains by transferring knowledge from the source to the target domain. Researchers have proposed transfer learning to predict clinical outcomes by leveraging pre-clinical data (mouse, zebrafish), highlighting its vast potential. In this work, we present a comprehensive literature review of deep transfer learning methods for health informatics and clinical decision-making, focusing on high-throughput molecular data. Previous reviews mostly covered image-based transfer learning works, while we present a more detailed analysis of transfer learning papers. Furthermore, we evaluated original studies based on different evaluation settings across cross-validations, data splits and model architectures. The result shows that those transfer learning methods have great potential; high-throughput sequencing data and state-of-the-art deep learning models lead to significant insights and conclusions. Additionally, we explored various datasets in transfer learning papers with statistics and visualization.

CancerEMC: frontline non-invasive cancer screening from circulating protein biomarkers and mutations in cell-free DNA.

MOTIVATION: The early detection of cancer through accessible blood tests can foster early patient interventions. Although there are developments in cancer detection from cell-free DNA (cfDNA), its accuracy remains speculative. Given its central importance with broad impacts, we aspire to address the challenge. METHOD: A bagging Ensemble Meta Classifier (CancerEMC) is proposed for early cancer detection based on circulating protein biomarkers and mutations in cfDNA from blood. CancerEMC is generally designed for both binary cancer detection and multi-class cancer type localization. It can address the class imbalance problem in multi-analyte blood test data based on robust oversampling and adaptive synthesis techniques. RESULTS: Based on the clinical blood test data, we observe that the proposed CancerEMC has outperformed other algorithms and state-of-the-arts studies (including CancerSEEK) for cancer detection. The results reveal that our proposed method (i.e. CancerEMC) can achieve the best performance result for both binary cancer classification with 99.17% accuracy (AUC = 0.999) and localized multiple cancer detection with 74.12% accuracy (AUC = 0.938). Addressing the data imbalance issue with oversampling techniques, the accuracy can be increased to 91.50% (AUC = 0.992), where the state-of-the-art method can only be estimated at 69.64% (AUC = 0.921). Similar results can also be observed on independent and isolated testing data. AVAILABILITY: https://github.com/saifurcubd/Cancer-Detection. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A Belief Degree-Associated Fuzzy Multifactor Dimensionality Reduction Framework for Epistasis Detection.

Epistasis is a challenge in prediction, classification, and suspicion of human genetic diseases. Many technologies, methods, and tools have been developed for epistasis detection. Multifactor dimensionality reduction (MDR) is the method commonly used in epistasis detection. It uses two class groups-high risk and low risk-in human genetic disease and complex genetic traits. However, it cannot handle uncertainties from genetic information. This chapter describes the fuzzy sigmoid membership-based MDR (FSMDR) method of epistasis detection. The algorithmic steps in FSMDR are also elaborated with simulated data generated from GAMETES and a real coronary artery disease patient epistasis data set obtained from the Wellcome Trust Case Control Consortium (WTCCC). Moreover, a belief degree-associated fuzzy MDR framework is also proposed for epistasis detection, which can overcome the uncertainties of MDR-based methods. This framework improves the detection efficiency. It works like fuzzy set-based MDR methods. Simulated epistasis data sets are used to compare different MDR-based methods. Belief degree-associated fuzzy MDR was shown to gives good results by taking into account the uncertainly of the high/low risk classification.

Machine Learning Protocols in Early Cancer Detection Based on Liquid Biopsy: A Survey.

With the advances of liquid biopsy technology, there is increasing evidence that body fluid such as blood, urine, and saliva could harbor the potential biomarkers associated with tumor origin. Traditional correlation analysis methods are no longer sufficient to capture the high-resolution complex relationships between biomarkers and cancer subtype heterogeneity. To address the challenge, researchers proposed machine learning techniques with liquid biopsy data to explore the essence of tumor origin together. In this survey, we review the machine learning protocols and provide corresponding code demos for the approaches mentioned. We discuss algorithmic principles and frameworks extensively developed to reveal cancer mechanisms and consider the future prospects in biomarker exploration and cancer diagnostics.