Category: Projects of Machine Learning with Real Data
-
Machine Learning Project in Oncology 6 – Web Scraping for Cancer Omics Data
Web scraping is data scraping used for extracting data from websites. Why Scrape Cancer Omics data? Cancer Omics data is scattered around various resources, with most of them not providing a direct access to the data by using an API. This makes impossible to fetch the data programmatically and leaves with an option to scrape the data from […]
-
Machine Learning Project in Oncology 5 – Developing Convolutional Neural Networks for Classifying Breast Cancer Based on Histopathological Images
There are already some excellent blogs and papers on the topic (See [1]-[4] in References). The project was divided into 6 steps: 0. Raise A question and Prepare Data. Breast cancer is a malignant tumor that grows in or around the breast tissue (mainly in the milk ducts and glands). A tumor usually starts as […]
-
Machine Learning Project in Oncology 4 – Building Machine Learning Models in Subtyping Breast Cancer Tumors Based on Gene Expression of Biomarkers (Python version)
In Project 3, we built machine learning models in subtyping breast cancer tumors based on gene expression of biomarkers in R. Machine Learning Project 3 In this project, we will carry out the project in python, which is divided to 8 steps: 0. Prepare Data. We use the following datasets: BRCA_PAM50_Expression.txt : The gene expression […]
-
Machine Learning Project in Oncology 3 – Comparison of Five Machine Learning Methods in Subtyping Breast Cancer Tumors Based on Gene Expression of Biomarkers (R version)
Breast Cancer Is not one disease as most of us think. There are four main female breast cancer subtypes categorized according to hormone receptor (ER and PR) and HER2: Luminal A: HR+/HER2– Luminal B: HR+/HER2+ HER2-enriched: HR–/HER2+ Triple Negative: HR–/HER2– These biomrker proteins (HER2, ER, and PR), are encoded by three genes, including ERBB2 (Erb-B2 […]
-
Machine Learning Project in Oncology 2 – Developing A Multilayer Perceptron Neural Network for Breast Cancer Survival
According to Cancer.Net: Breast cancer has now surpassed lung cancer as the most commonly diagnosed cancer worldwide. An estimated over 2,20,000 new cases were diagnosed in women across the world in 2020. More women in the United States are diagnosed with breast cancer than any other type of cancer, besides skin cancer. The disease accounts […]
-
Machine Learning Project in Oncology 1 – Deep Learning-based Identification of Prostate Cancer using TCGA RNA-seq
Prostate cancer (PRAD) is the most common non-skin cancer in America. In the United States, 1 in 8 men will be diagnosed with prostate cancer in his lifetime. The challenge of classifying PRAD and normal tissues based on gene expression data has been tackled through the development of diverse machine learning methods, such as self-organizing […]