scholarly journals Mixed Effects Machine Learning Models for Colon Cancer Metastasis Prediction using Spatially Localized Immuno-Oncology Markers

Author(s):  
Joshua J. Levy ◽  
Carly A. Bobak ◽  
Mustafa Nasir-Moin ◽  
Eren M. Veziroglu ◽  
Scott M. Palisoul ◽  
...  
2021 ◽  
Author(s):  
Joshua Levy ◽  
Carly Bobak ◽  
Mustafa Nasir-Moin ◽  
Eren M Veziroglu ◽  
Scott M Palisoul ◽  
...  

Spatially resolved characterization of the transcriptome and proteome promises to provide further clarity on cancer pathogenesis and etiology, which may inform future clinical practice through classifier development for clinical outcomes. However, batch effects may potentially obscure the ability of machine learning methods to derive complex associations within spatial omics data. Profiling thirty-five stage three colon cancer patients using the GeoMX Digital Spatial Profiler, we found that mixed-effects machine learning (MEML) methods may provide utility for overcoming significant batch effects to communicate key and complex disease associations from spatial information. These results point to further exploration and application of MEML methods within the algorithm development life cycle for clinical deployment.


2022 ◽  
Author(s):  
Aya Hage Chehade ◽  
Nassib Abdallah ◽  
Jean-Marie Marion ◽  
Mohamad Oueidat ◽  
Pierre Chauvet

Abstract Lung and colon cancers are the most common causes of death. Their simultaneous occurrence is uncommon, however, in the absence of early diagnosis, the metastasis of cancer cells is very high between these two organs. Currently, histopathological diagnosis and appropriate treatment are the only possibility to improve the chances of survival and reduce cancer mortality. Using artificial intelligence in the histopathological diagnosis of colon and lung cancer can provide significant help to specialists in identifying cases of colon and lung cancers with less effort, time and cost. The objective of this study is to set up a computer-aided diagnostic system that can accurately classify five types of colon and lung tissues (two classes for colon cancer and three classes for lung cancer) by analyzing their histopathological images. Using machine learning, features engineering and image processing techniques, the five models XGBoost, SVM, RF, LDA and MLP were used to perform the classification of histopathological images of lung and colon cancers that were acquired from the LC25000 dataset. The main advantage of using machine learning models is that they allow for better interpretability of the classification model since they are based on feature engineering; however, deep learning models are black box networks whose working is very difficult to understand due to the complex network design. The acquired experimental results show that machine learning models give satisfactory results and are very precise in identifying classes of lung and colon cancer subtypes. The XGBoost model gave the best performance with an accuracy of 99% and a F1-score of 98.8%. The implementation and the development of this model will help healthcare specialists identify types of colon and lung cancers. The code will be available upon request.


2020 ◽  
Vol 2 (1) ◽  
pp. 3-6
Author(s):  
Eric Holloway

Imagination Sampling is the usage of a person as an oracle for generating or improving machine learning models. Previous work demonstrated a general system for using Imagination Sampling for obtaining multibox models. Here, the possibility of importing such models as the starting point for further automatic enhancement is explored.


2021 ◽  
Author(s):  
Norberto Sánchez-Cruz ◽  
Jose L. Medina-Franco

<p>Epigenetic targets are a significant focus for drug discovery research, as demonstrated by the eight approved epigenetic drugs for treatment of cancer and the increasing availability of chemogenomic data related to epigenetics. This data represents a large amount of structure-activity relationships that has not been exploited thus far for the development of predictive models to support medicinal chemistry efforts. Herein, we report the first large-scale study of 26318 compounds with a quantitative measure of biological activity for 55 protein targets with epigenetic activity. Through a systematic comparison of machine learning models trained on molecular fingerprints of different design, we built predictive models with high accuracy for the epigenetic target profiling of small molecules. The models were thoroughly validated showing mean precisions up to 0.952 for the epigenetic target prediction task. Our results indicate that the herein reported models have considerable potential to identify small molecules with epigenetic activity. Therefore, our results were implemented as freely accessible and easy-to-use web application.</p>


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