scholarly journals Identification of a Transcriptomic Prognostic Signature by Machine Learning Using a Combination of Small Cohorts of Prostate Cancer

2020 ◽  
Vol 11 ◽  
Author(s):  
Benjamin Vittrant ◽  
Mickael Leclercq ◽  
Marie-Laure Martin-Magniette ◽  
Colin Collins ◽  
Alain Bergeron ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Machine Learning ◽  
Specific Antigen ◽  
Gene Signature ◽  
Learning Approach ◽  
Gleason Grade ◽  
Rna Seq ◽  
Number Of Patients ◽  
Heterogeneous Datasets ◽  
Machine Learning Approach

Determining which treatment to provide to men with prostate cancer (PCa) is a major challenge for clinicians. Currently, the clinical risk-stratification for PCa is based on clinico-pathological variables such as Gleason grade, stage and prostate specific antigen (PSA) levels. But transcriptomic data have the potential to enable the development of more precise approaches to predict evolution of the disease. However, high quality RNA sequencing (RNA-seq) datasets along with clinical data with long follow-up allowing discovery of biochemical recurrence (BCR) biomarkers are small and rare. In this study, we propose a machine learning approach that is robust to batch effect and enables the discovery of highly predictive signatures despite using small datasets. Gene expression data were extracted from three RNA-Seq datasets cumulating a total of 171 PCa patients. Data were re-analyzed using a unique pipeline to ensure uniformity. Using a machine learning approach, a total of 14 classifiers were tested with various parameters to identify the best model and gene signature to predict BCR. Using a random forest model, we have identified a signature composed of only three genes (JUN, HES4, PPDPF) predicting BCR with better accuracy [74.2%, balanced error rate (BER) = 27%] than the clinico-pathological variables (69.2%, BER = 32%) currently in use to predict PCa evolution. This score is in the range of the studies that predicted BCR in single-cohort with a higher number of patients. We showed that it is possible to merge and analyze different small and heterogeneous datasets altogether to obtain a better signature than if they were analyzed individually, thus reducing the need for very large cohorts. This study demonstrates the feasibility to regroup different small datasets in one larger to identify a predictive genomic signature that would benefit PCa patients.

Machine Learning Approach for Confirmation of COVID-19 Cases: Positive, Negative, Death and Release (Preprint)

2020 ◽  
Author(s):  
Samir Bandyopadhyay Sr ◽  
SHAWNI DUTTA ◽  
SHAWNI DUTTA ◽  
SHAWNI DUTTA
Keyword(s):  
Machine Learning ◽  
Short Term Memory ◽  
Health Workers ◽  
Original Data ◽  
High Rate ◽  
Learning Approach ◽  
Good Decision ◽  
Number Of Patients ◽  
Machine Learning Approach ◽  
Death Cases

BACKGROUND In recent days, Covid-19 coronavirus has been an immense impact on social, economic fields in the world. The objective of this study determines if it is feasible to use machine learning method to evaluate how much prediction results are close to original data related to Confirmed-Negative-Released-Death cases of Covid-19. For this purpose, a verification method is proposed in this paper that uses the concept of Deep-learning Neural Network. In this framework, Long short-term memory (LSTM) and Gated Recurrent Unit (GRU) are also assimilated finally for training the dataset and the prediction results are tally with the results predicted by clinical doctors. The prediction results are validated against the original data based on some predefined metric. The experimental results showcase that the proposed approach is useful in generating suitable results based on the critical disease outbreak. It also helps doctors to recheck further verification of virus by the proposed method. The outbreak of Coronavirus has the nature of exponential growth and so it is difficult to control with limited clinical persons for handling a huge number of patients with in a reasonable time. So it is necessary to build an automated model, based on machine learning approach, for corrective measure after the decision of clinical doctors. It could be a promising supplementary confirmation method for frontline clinical doctors. The proposed method has a high prediction rate and works fast for probable accurate identification of the disease. The performance analysis shows that a high rate of accuracy is obtained by the proposed method. OBJECTIVE Validation of COVID-19 disease METHODS Machine Learning RESULTS 90% CONCLUSIONS The combined LSTM-GRU based RNN model provides a comparatively better results in terms of prediction of confirmed, released, negative, death cases on the data. This paper presented a novel method that could recheck occurred cases of COVID-19 automatically. The data driven RNN based model is capable of providing automated tool for confirming, estimating the current position of this pandemic, assessing the severity, and assisting government and health workers to act for good decision making policy. It could be a promising supplementary rechecking method for frontline clinical doctors. It is now essential for improving the accuracy of detection process. CLINICALTRIAL 2020-04-03 3:22:36 PM

scholarly journals Identification of five important genes to predict GBM subtypes

2021 ◽  
Author(s):  
Yang Tang ◽  
Maleeha A Qazi ◽  
Kevin R Brown ◽  
Nicholas Mikolajewicz ◽  
Jason Moffat ◽  
...  
Keyword(s):  
Machine Learning ◽  
Gene Signature ◽  
Supervised Machine Learning ◽  
Gradient Boosting ◽  
Tissue Cell ◽  
Learning Approach ◽  
Gene Set ◽  
Primary Brain Tumour ◽  
Extreme Gradient Boosting ◽  
Machine Learning Approach

Abstract Background Glioblastoma (GBM), the most common and aggressive primary brain tumour in adults, has been classified into three subtypes: classical, mesenchymal and proneural. While the original classification relied on an 840 gene-set, further clarification on true GBM subtypes uses a 150-gene signature to accurately classify GBM into the three subtypes. We hypothesized whether a machine learning approach could be used to identify a smaller gene-set to accurately predict GBM subtype. Methods Using a supervised machine learning approach, extreme gradient boosting (XGBoost), we developed a classifier to predict the three subtypes of glioblastoma (GBM): classical, mesenchymal and proneural. We tested the classifier on in-house GBM tissue, cell lines and xenograft samples to predict their subtype. Results We identified the five most important genes for characterizing the three subtypes based on genes that often exhibited high Importance Scores in our XGBoost analyses. On average, this approach achieved 80.12% accuracy in predicting these three subtypes of GBM. Furthermore, we applied our five-gene classifier to successfully predict the subtype of GBM samples at our centre. Conclusion Our 5-gene set classifier is the smallest classifier to date that can predict GBM subtypes with high accuracy, which could facilitate the future development of a five-gene subtype diagnostic biomarker for routine assays in GBM samples.

scholarly journals Machine learning approach for confirmation of COVID-19 cases: positive, negative, death and release

2020 ◽  
Vol 2 (3) ◽  
pp. 172-177
Author(s):  
Shawni Dutta ◽  
◽  
Samir Kumar Bandyopadhyay ◽  
Keyword(s):  
Infectious Disease ◽  
Machine Learning ◽  
Original Data ◽  
World Health ◽  
Learning Approach ◽  
Human Beings ◽  
Verification Method ◽  
Number Of Patients ◽  
Machine Learning Approach ◽  
The World

Introduction: Corona Virus Infectious Disease (COVID-19) is the infectious disease. The COVID-19 disease came to earth in early 2019. It is expanding exponentially throughout the world and affected an enormous number of human beings starting from the last month. The World Health Organization (WHO) on March 11, 2020 declared COVID-19 was characterized as “Pandemic”. This paper proposed approach for confirmation of COVID-19 cases after the diagnosis of doctors. The objective of this study uses machine learning method to evaluate how much predicted results are close to original data related to Confirmed-Negative-Released-Death cases of COVID-19. Materials and methods: For this purpose, a verification method is proposed in this paper that uses the concept of Deep-learning Neural Network. In this framework, Long shrt-term memory (LSTM) and Gated Recurrent Unit (GRU) are also assimilated finally for training the dataset. The prediction results are tally with the results predicted by clinical doctors. Results: The results are obtained from the proposed method with accuracy 87 % for the “confirmed Cases”, 67.8 % for “Negative Cases”, 62% for “Deceased Case” and 40.5 % for “Released Case”. Another important parameter i.e. RMSE shows 30.15% for Confirmed Case, 49.4 % for Negative Cases, 4.16 % for Deceased Case and 13.72 % for Released Case. Conclusions: The outbreak of Coronavirus has the nature of exponential growth and so it is difficult to control with limited clinical persons for handling a huge number of patients within a reasonable time. So it is necessary to build an automated model, based on machine learning approach, for corrective measure after the decision of clinical doctors.

scholarly journals Consensus Machine Learning for Gene Target Selection in Pediatric AML Risk

2019 ◽  
Author(s):  
Jenny Smith ◽  
Sean K. Maden ◽  
David Lee ◽  
Ronald Buie ◽  
Vikas Peddu ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Expression Patterns ◽  
Specific Gene ◽  
Molecular Heterogeneity ◽  
Learning Approach ◽  
Rna Seq ◽  
Gene Target ◽  
Machine Learning Approach ◽  
Pediatric Aml

AbstractAcute myeloid leukemia (AML) is a cancer of hematopoietic systems that poses high population burden, especially among pediatric populations. AML presents with high molecular heterogeneity, complicating patient risk stratification and treatment planning. While molecular and cytogenetic subtypes of AML are well described, significance of subtype-specific gene expression patterns is poorly understood and effective modeling of these patterns with individual algorithms is challenging. Using a novel consensus machine learning approach, we analyzed public RNA-seq and clinical data from pediatric AML patients (N = 137 patients) enrolled in the TARGET project.We used a binary risk classifier (Low vs. Not-Low Risk) to study risk-specific expression patterns in pediatric AML. We applied the following workflow to identify important gene targets from RNA-seq data: (1) Reduce data dimensionality by identification of differentially expressed genes for AML risk (N = 1984 loci); (2) Optimize algorithm hyperparameters for each of 4 algorithm types (lasso, XGBoost, random forest, and SVM); (3) Study ablation test results for penalized methods (lasso and XGBoost); (4) Bootstrap Boruta permutations with a novel consensus importance metric.We observed recurrently selected features across hyperparameter optimizations, ablation tests, and Boruta permutation bootstrap iterations, including HOXA9 and putative cofactors including MEIS1. Consensus feature selection from Boruta bootstraps identified a larger gene set than single penalized algorithm runs (lasso or XGBoost), while also including correlated and predictive genes from ablation tests.We present a consensus machine learning approach to identify gene targets of likely importance for pediatric AML risk. The approach identified a moderately sized set of recurrent important genes from across 4 algorithm types, including genes identified across ablation tests with penalized algorithms (HOXA9 and MEIS1). Our approach mitigates exclusion biases of penalized algorithms (lasso and XGBoost) while obviating arbitrary importance cutoffs for other types (SVM and random forest). This approach is readily generalizable for research of other heterogeneous diseases, single-assay experiments, and high-dimensional data. Resources and code to recreate our findings are available online.

scholarly journals Machine Learning Approach for Confirmation of COVID-19 Cases: Positive, Negative, Death and Release

2020 ◽  
Author(s):  
Shawni Dutta ◽  
Samir Kumar Bandyopadhyay
Keyword(s):  
Machine Learning ◽  
Short Term Memory ◽  
Original Data ◽  
High Rate ◽  
Learning Approach ◽  
Accurate Identification ◽  
Verification Method ◽  
Number Of Patients ◽  
Machine Learning Approach ◽  
Deep Learning Neural Network

AbstractIn recent days, Covid-19 coronavirus has been an immense impact on social, economic fields in the world. The objective of this study determines if it is feasible to use machine learning method to evaluate how much prediction results are close to original data related to Confirmed-Negative-Released-Death cases of Covid-19. For this purpose, a verification method is proposed in this paper that uses the concept of Deep-learning Neural Network. In this framework, Long short-term memory (LSTM) and Gated Recurrent Unit (GRU) are also assimilated finally for training the dataset and the prediction results are tally with the results predicted by clinical doctors. The prediction results are validated against the original data based on some predefined metric. The experimental results showcase that the proposed approach is useful in generating suitable results based on the critical disease outbreak. It also helps doctors to recheck further verification of virus by the proposed method. The outbreak of Coronavirus has the nature of exponential growth and so it is difficult to control with limited clinical persons for handling a huge number of patients with in a reasonable time. So it is necessary to build an automated model, based on machine learning approach, for corrective measure after the decision of clinical doctors. It could be a promising supplementary confirmation method for frontline clinical doctors. The proposed method has a high prediction rate and works fast for probable accurate identification of the disease. The performance analysis shows that a high rate of accuracy is obtained by the proposed method.

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