scholarly journals The impact coenzyme Q10 supplementation on the inflammatory indices of women with breast cancer using A machine learning prediction model

2021 ◽  
pp. 100614
Author(s):  
Amir Jamshidnezhad ◽  
Zohreh Anjomshoa ◽  
Sayed Ahmad Hosseini ◽  
Ahmad Azizi
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Prediction Model ◽  
Coenzyme Q10 ◽  
The Impact ◽  
Coenzyme Q10 Supplementation

scholarly journals A Review of Computer-Aided Expert Systems for Breast Cancer Diagnosis

Cancers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 2764
Author(s):  
Xin Yu Liew ◽  
Nazia Hameed ◽  
Jeremie Clos
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Deep Learning ◽  
Main Process ◽  
Learning Approaches ◽  
Learning Methods ◽  
Advantages And Disadvantages ◽  
Computer Aided ◽  
Conventional Methods ◽  
The Impact

A computer-aided diagnosis (CAD) expert system is a powerful tool to efficiently assist a pathologist in achieving an early diagnosis of breast cancer. This process identifies the presence of cancer in breast tissue samples and the distinct type of cancer stages. In a standard CAD system, the main process involves image pre-processing, segmentation, feature extraction, feature selection, classification, and performance evaluation. In this review paper, we reviewed the existing state-of-the-art machine learning approaches applied at each stage involving conventional methods and deep learning methods, the comparisons within methods, and we provide technical details with advantages and disadvantages. The aims are to investigate the impact of CAD systems using histopathology images, investigate deep learning methods that outperform conventional methods, and provide a summary for future researchers to analyse and improve the existing techniques used. Lastly, we will discuss the research gaps of existing machine learning approaches for implementation and propose future direction guidelines for upcoming researchers.

scholarly journals Explainable machine learning can outperform Cox regression predictions and provide insights in breast cancer survival

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arturo Moncada-Torres ◽  
Marissa C. van Maaren ◽  
Mathijs P. Hendriks ◽  
Sabine Siesling ◽  
Gijs Geleijnse
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Explicit Knowledge ◽  
Cox Regression ◽  
Metastatic Breast ◽  
Gradient Boosting ◽  
Support Vector ◽  
Netherlands Cancer Registry ◽  
Extreme Gradient Boosting ◽  
The Impact

AbstractCox Proportional Hazards (CPH) analysis is the standard for survival analysis in oncology. Recently, several machine learning (ML) techniques have been adapted for this task. Although they have shown to yield results at least as good as classical methods, they are often disregarded because of their lack of transparency and little to no explainability, which are key for their adoption in clinical settings. In this paper, we used data from the Netherlands Cancer Registry of 36,658 non-metastatic breast cancer patients to compare the performance of CPH with ML techniques (Random Survival Forests, Survival Support Vector Machines, and Extreme Gradient Boosting [XGB]) in predicting survival using the $$c$$ c -index. We demonstrated that in our dataset, ML-based models can perform at least as good as the classical CPH regression ($$c$$ c -index $$\sim \,0.63$$ ∼ 0.63 ), and in the case of XGB even better ($$c$$ c -index $$\sim 0.73$$ ∼ 0.73 ). Furthermore, we used Shapley Additive Explanation (SHAP) values to explain the models’ predictions. We concluded that the difference in performance can be attributed to XGB’s ability to model nonlinearities and complex interactions. We also investigated the impact of specific features on the models’ predictions as well as their corresponding insights. Lastly, we showed that explainable ML can generate explicit knowledge of how models make their predictions, which is crucial in increasing the trust and adoption of innovative ML techniques in oncology and healthcare overall.

scholarly journals Retweet Prediction Based on User Behavior

2021 ◽  
Author(s):  
Syeda Nadia Firdaus
Keyword(s):  
Machine Learning ◽  
Social Networks ◽  
Social Network ◽  
Prediction Model ◽  
Matrix Factorization ◽  
Information Diffusion ◽  
User Behavior ◽  
Past Research ◽  
The Difference ◽  
The Impact

Social network is a hot topic of interest for researchers in the field of computer science in recent years. These social networks such as Facebook, Twitter, Instagram play an important role in information diffusion. Social network data are created by its users. Users’ online activities and behavior have been studied in various past research efforts in order to get a better understanding on how information is diffused on social networks. In this study, we focus on Twitter and we explore the impact of user behavior on their retweet activity. To represent a user’s behavior for predicting their retweet decision, we introduce 10-dimentional emotion and 35-dimensional personality related features. We consider the difference of a user being an author and a retweeter in terms of their behaviors, and propose a machine learning based retweet prediction model considering this difference. We also propose two approaches for matrix factorization retweet prediction model which learns the latent relation between users and tweets to predict the user’s retweet decision. In the experiment, we have tested our proposed models. We find that models based on user behavior related features provide good improvement (3% - 6% in terms of F1- score) over baseline models. By only considering user’s behavior as a retweeter, the data processing time is reduced while the prediction accuracy is comparable to the case when both retweeting and posting behaviors are considered. In the proposed matrix factorization models, we include tweet features into the basic factorization model through newly defined regularization terms and improve the performance by 3% - 4% in terms of F1-score. Finally, we compare the performance of machine learning and matrix factorization models for retweet prediction and find that none of the models is superior to the other in all occasions. Therefore, different models should be used depending on how prediction results will be used. Machine learning model is preferable when a model’s performance quality is important such as for tweet re-ranking and tweet recommendation. Matrix factorization is a preferred option when model’s positive retweet prediction capability is more important such as for marketing campaign and finding potential retweeters.

scholarly journals Retweet Prediction Based on User Behavior

2021 ◽  
Author(s):  
Syeda Nadia Firdaus
Keyword(s):  
Machine Learning ◽  
Social Networks ◽  
Social Network ◽  
Prediction Model ◽  
Matrix Factorization ◽  
Information Diffusion ◽  
User Behavior ◽  
Past Research ◽  
The Difference ◽  
The Impact

Social network is a hot topic of interest for researchers in the field of computer science in recent years. These social networks such as Facebook, Twitter, Instagram play an important role in information diffusion. Social network data are created by its users. Users’ online activities and behavior have been studied in various past research efforts in order to get a better understanding on how information is diffused on social networks. In this study, we focus on Twitter and we explore the impact of user behavior on their retweet activity. To represent a user’s behavior for predicting their retweet decision, we introduce 10-dimentional emotion and 35-dimensional personality related features. We consider the difference of a user being an author and a retweeter in terms of their behaviors, and propose a machine learning based retweet prediction model considering this difference. We also propose two approaches for matrix factorization retweet prediction model which learns the latent relation between users and tweets to predict the user’s retweet decision. In the experiment, we have tested our proposed models. We find that models based on user behavior related features provide good improvement (3% - 6% in terms of F1- score) over baseline models. By only considering user’s behavior as a retweeter, the data processing time is reduced while the prediction accuracy is comparable to the case when both retweeting and posting behaviors are considered. In the proposed matrix factorization models, we include tweet features into the basic factorization model through newly defined regularization terms and improve the performance by 3% - 4% in terms of F1-score. Finally, we compare the performance of machine learning and matrix factorization models for retweet prediction and find that none of the models is superior to the other in all occasions. Therefore, different models should be used depending on how prediction results will be used. Machine learning model is preferable when a model’s performance quality is important such as for tweet re-ranking and tweet recommendation. Matrix factorization is a preferred option when model’s positive retweet prediction capability is more important such as for marketing campaign and finding potential retweeters.

scholarly journals CPEM: Accurate cancer type classification based on somatic alterations using an ensemble of a random forest and a deep neural network

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kanggeun Lee ◽  
Hyoung-oh Jeong ◽  
Semin Lee ◽  
Won-Ki Jeong
Keyword(s):  
Machine Learning ◽  
Prediction Model ◽  
Genomic Data ◽  
The Cancer Genome Atlas ◽  
Cancer Type ◽  
Machine Learning Classifiers ◽  
Learning Classifiers ◽  
Somatic Alterations ◽  
The Impact ◽  
Type Classification

AbstractWith recent advances in DNA sequencing technologies, fast acquisition of large-scale genomic data has become commonplace. For cancer studies, in particular, there is an increasing need for the classification of cancer type based on somatic alterations detected from sequencing analyses. However, the ever-increasing size and complexity of the data make the classification task extremely challenging. In this study, we evaluate the contributions of various input features, such as mutation profiles, mutation rates, mutation spectra and signatures, and somatic copy number alterations that can be derived from genomic data, and further utilize them for accurate cancer type classification. We introduce a novel ensemble of machine learning classifiers, called CPEM (Cancer Predictor using an Ensemble Model), which is tested on 7,002 samples representing over 31 different cancer types collected from The Cancer Genome Atlas (TCGA) database. We first systematically examined the impact of the input features. Features known to be associated with specific cancers had relatively high importance in our initial prediction model. We further investigated various machine learning classifiers and feature selection methods to derive the ensemble-based cancer type prediction model achieving up to 84% classification accuracy in the nested 10-fold cross-validation. Finally, we narrowed down the target cancers to the six most common types and achieved up to 94% accuracy.

scholarly journals A Complete VADER-Based Sentiment Analysis of Bitcoin (BTC) Tweets during the Era of COVID-19

2020 ◽  
Vol 4 (4) ◽  
pp. 33
Author(s):  
Toni Pano ◽  
Rasha Kashef
Keyword(s):  
Machine Learning ◽  
Social Media ◽  
Prediction Model ◽  
Sentiment Analysis ◽  
Significant Role ◽  
Prediction Models ◽  
Financial Sector ◽  
Research Gap ◽  
Text Preprocessing ◽  
The Impact

During the COVID-19 pandemic, many research studies have been conducted to examine the impact of the outbreak on the financial sector, especially on cryptocurrencies. Social media, such as Twitter, plays a significant role as a meaningful indicator in forecasting the Bitcoin (BTC) prices. However, there is a research gap in determining the optimal preprocessing strategy in BTC tweets to develop an accurate machine learning prediction model for bitcoin prices. This paper develops different text preprocessing strategies for correlating the sentiment scores of Twitter text with Bitcoin prices during the COVID-19 pandemic. We explore the effect of different preprocessing functions, features, and time lengths of data on the correlation results. Out of 13 strategies, we discover that splitting sentences, removing Twitter-specific tags, or their combination generally improve the correlation of sentiment scores and volume polarity scores with Bitcoin prices. The prices only correlate well with sentiment scores over shorter timespans. Selecting the optimum preprocessing strategy would prompt machine learning prediction models to achieve better accuracy as compared to the actual prices.

scholarly journals Analysis of the TP53 Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach

2019 ◽  
Vol 20 (12) ◽  
pp. 2962 ◽  
Author(s):  
Kumaraswamy Naidu Chitrala ◽  
Mitzi Nagarkatti ◽  
Prakash Nagarkatti ◽  
Suneetha Yeguvapalli
Keyword(s):  
Breast Cancer ◽  
Machine Learning ◽  
Risk Factors ◽  
Estrogen Receptor ◽  
Estrogen Receptor Alpha ◽  
Large Deviation ◽  
The Other ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
The Impact

Breast cancer is a leading cancer type and one of the major health issues faced by women around the world. Some of its major risk factors include body mass index, hormone replacement therapy, family history and germline mutations. Of these risk factors, estrogen levels play a crucial role. Among the estrogen receptors, estrogen receptor alpha (ERα) is known to interact with tumor suppressor protein p53 directly thereby repressing its function. Previously, we have studied the impact of deleterious breast cancer-associated non-synonymous single nucleotide polymorphisms (nsnps) rs11540654 (R110P), rs17849781 (P278A) and rs28934874 (P151T) in TP53 gene on the p53 DNA-binding core domain. In the present study, we aimed to analyze the impact of these mutations on p53–ERα interaction. To this end, we, have modelled the full-length structure of human p53 and validated its quality using PROCHECK and subjected it to energy minimization using NOMAD-Ref web server. Three-dimensional structure of ERα activation function-2 (AF-2) domain was downloaded from the protein data bank. Interactions between the modelled native and mutant (R110P, P278A, P151T) p53 with ERα was studied using ZDOCK. Machine learning predictions on the interactions were performed using Weka software. Results from the protein–protein docking showed that the atoms, residues and solvent accessibility surface area (SASA) at the interface was increased in both p53 and ERα for R110P mutation compared to the native complexes indicating that the mutation R110P has more impact on the p53–ERα interaction compared to the other two mutants. Mutations P151T and P278A, on the other hand, showed a large deviation from the native p53-ERα complex in atoms and residues at the surface. Further, results from artificial neural network analysis showed that these structural features are important for predicting the impact of these three mutations on p53–ERα interaction. Overall, these three mutations showed a large deviation in total SASA in both p53 and ERα. In conclusion, results from our study will be crucial in making the decisions for hormone-based therapies against breast cancer.

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