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Integrated Multi-omics Analysis Using Variational Autoencoders: Application to Pan-cancer Classification

arXiv.org Machine Learning

Different aspects of a clinical sample can be revealed by multiple types of omics data. Integrated analysis of multi-omics data provides a comprehensive view of patients, which has the potential to facilitate more accurate clinical decision making. However, omics data are normally high dimensional with large number of molecular features and relatively small number of available samples with clinical labels. The "dimensionality curse" makes it challenging to train a machine learning model using high dimensional omics data like DNA methylation and gene expression profiles. Here we propose an end-to-end deep learning model called OmiVAE to extract low dimensional features and classify samples from multi-omics data. OmiVAE combines the basic structure of variational autoencoders with a classification network to achieve task-oriented feature extraction and multi-class classification. The training procedure of OmiVAE is comprised of an unsupervised phase without the classifier and a supervised phase with the classifier. During the unsupervised phase, a hierarchical cluster structure of samples can be automatically formed without the need for labels. And in the supervised phase, OmiVAE achieved an average classification accuracy of 97.49% after 10-fold cross-validation among 33 tumour types and normal samples, which shows better performance than other existing methods. The OmiVAE model learned from multi-omics data outperformed that using only one type of omics data, which indicates that the complementary information from different omics datatypes provides useful insights for biomedical tasks like cancer classification.


Her2 Challenge Contest: A Detailed Assessment of Automated Her2 Scoring Algorithms in Whole Slide Images of Breast Cancer Tissues

arXiv.org Artificial Intelligence

Evaluating expression of the Human epidermal growth factor receptor 2 (Her2) by visual examination of immunohistochemistry (IHC) on invasive breast cancer (BCa) is a key part of the diagnostic assessment of BCa due to its recognised importance as a predictive and prognostic marker in clinical practice. However, visual scoring of Her2 is subjective and consequently prone to inter-observer variability. Given the prognostic and therapeutic implications of Her2 scoring, a more objective method is required. In this paper, we report on a recent automated Her2 scoring contest, held in conjunction with the annual PathSoc meeting held in Nottingham in June 2016, aimed at systematically comparing and advancing the state-of-the-art Artificial Intelligence (AI) based automated methods for Her2 scoring. The contest dataset comprised of digitised whole slide images (WSI) of sections from 86 cases of invasive breast carcinoma stained with both Haematoxylin & Eosin (H&E) and IHC for Her2. The contesting algorithms automatically predicted scores of the IHC slides for an unseen subset of the dataset and the predicted scores were compared with the 'ground truth' (a consensus score from at least two experts). We also report on a simple Man vs Machine contest for the scoring of Her2 and show that the automated methods could beat the pathology experts on this contest dataset. This paper presents a benchmark for comparing the performance of automated algorithms for scoring of Her2. It also demonstrates the enormous potential of automated algorithms in assisting the pathologist with objective IHC scoring.


Starting an extreme diet before chemotherapy could improve outcomes

Daily Mail - Science & tech

An extreme diet involving fasting before a patient starts chemotherapy could improve the outcome for breast cancer patients, a new study shows. The randomised controlled study by Leiden University Medical Center in the Netherlands had 129 patients with breast cancer follow different types of diets. Stage two and three breast cancer patients on a'fasting mimicking' diet - that is a low-calorie, low-protein diet - had a better response to the chemotherapy treatment. Fasting mimicking diets were developed to elicit similar metabolic responses to water-only fasting, but also providing necessary sustenance and proteins. The diet works to make cancerous cells more susceptible to chemotherapy while helping to protect healthy cells in breast cancer patients, the authors found.


How AI is improving cancer diagnostics

#artificialintelligence

When a young girl came to New York University (NYU) Langone Health for a routine follow-up, tests seemed to show that the medulloblastoma for which she had been treated a few years earlier had returned. The girl's recurrent cancer was found in the same part of brain as before, and the biopsy seemed to confirm medulloblastoma. With this diagnosis, the girl would begin a specific course of radiotherapy and chemotherapy. But just as neuropathologist Matija Snuderl was about to sign off on the diagnosis and set her on that treatment path, he hesitated. The biopsy was slightly unusual, he thought, and he remembered a previous case in which what was thought to be medulloblastoma turned out to be something else. So, to help him make up his mind, Snuderl turned to a computer.


Cost-sensitive detection with variational autoencoders for environmental acoustic sensing

arXiv.org Machine Learning

Environmental acoustic sensing involves the retrieval and processing of audio signals to better understand our surroundings. While large-scale acoustic data make manual analysis infeasible, they provide a suitable playground for machine learning approaches. Most existing machine learning techniques developed for environmental acoustic sensing do not provide flexible control of the trade-off between the false positive rate and the false negative rate. This paper presents a cost-sensitive classification paradigm, in which the hyper-parameters of classifiers and the structure of variational autoencoders are selected in a principled Neyman-Pearson framework. We examine the performance of the proposed approach using a dataset from the HumBug project which aims to detect the presence of mosquitoes using sound collected by simple embedded devices.