Appendix B: Cross-Validation, the Jackknife, and the Bootstrap: Excess Error Estimation in Forward Logistic Regression

2006 ◽  
pp. 205-218
Author(s):  
Gail Gong
Keyword(s):  
Logistic Regression ◽  
Error Estimation ◽  
Cross Validation ◽  
Forward Logistic Regression

Genome-wide 5hmC profiles to enable cancer detection and tissue of origin classification in breast, colorectal, lung, ovarian, and pancreatic cancers.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 3044-3044
Author(s):  
David Haan ◽  
Anna Bergamaschi ◽  
Yuhong Ning ◽  
William Gibb ◽  
Michael Kesling ◽  
...  
Keyword(s):  
Logistic Regression ◽  
Cancer Detection ◽  
Normal Tissue ◽  
Cross Validation ◽  
Tissue Type ◽  
Normal Tissues ◽  
Pancreatic Cancers ◽  
Tissue Of Origin ◽  
Fold Cross Validation

3044 Background: Epigenomics assays have recently become popular tools for identification of molecular biomarkers, both in tissue and in plasma. In particular 5-hydroxymethyl-cytosine (5hmC) method, has been shown to enable the epigenomic regulation of gene expression and subsequent gene activity, with different patterns, across several tumor and normal tissues types. In this study we show that 5hmC profiles enable discrete classification of tumor and normal tissue for breast, colorectal, lung ovary and pancreas. Such classification was also recapitulated in cfDNA from patient with breast, colorectal, lung, ovarian and pancreatic cancers. Methods: DNA was isolated from 176 fresh frozen tissues from breast, colorectal, lung, ovary and pancreas (44 per tumor per tissue type and up to 11 tumor tissues for each stage (I-IV)) and up to 10 normal tissues per tissue type. cfDNA was isolated from plasma from 783 non-cancer individuals and 569 cancer patients. Plasma-isolated cfDNA and tumor genomic DNA, were enriched for the 5hmC fraction using chemical labelling, sequenced, and aligned to a reference genome to construct features sets of 5hmC patterns. Results: 5hmC multinomial logistic regression analysis was employed across tumor and normal tissues and identified a set of specific and discrete tumor and normal tissue gene-based features. This indicates that we can classify samples regardless of source, with a high degree of accuracy, based on tissue of origin and also distinguish between normal and tumor status.Next, we employed a stacked ensemble machine learning algorithm combining multiple logistic regression models across diverse feature sets to the cfDNA dataset composed of 783 non cancers and 569 cancers comprising 67 breast, 118 colorectal, 210 Lung, 71 ovarian and 100 pancreatic cancers. We identified a genomic signature that enable the classification of non-cancer versus cancers with an outer fold cross validation sensitivity of 49% (CI 45%-53%) at 99% specificity. Further, individual cancer outer fold cross validation sensitivity at 99% specificity, was measured as follows: breast 30% (CI 119% -42%); colorectal 41% (CI 32%-50%); lung 49% (CI 42%-56%); ovarian 72% (CI 60-82%); pancreatic 56% (CI 46%-66%). Conclusions: This study demonstrates that 5hmC profiles can distinguish cancer and normal tissues based on their origin. Further, 5hmC changes in cfDNA enables detection of the several cancer types: breast, colorectal, lung, ovarian and pancreatic cancers. Our technology provides a non-invasive tool for cancer detection with low risk sample collection enabling improved compliance than current screening methods. Among other utilities, we believe our technology could be applied to asymptomatic high-risk individuals thus enabling enrichment for those subjects that most need a diagnostic imaging follow up.

Αποτίμηση κινδύνων των ευρωπαϊκών τραπεζών και συστήματα έγκαιρης προειδοποίησης

2018 ◽  
Author(s):  
Παντελής Σταυρούλιας
Keyword(s):  
Logistic Regression ◽  
Discriminant Analysis ◽  
Cross Validation ◽  
Multinomial Logistic Regression ◽  
Classification Tree ◽  
Probit Regression ◽  
Macroprudential Policy ◽  
Policy Makers ◽  
Out Of Sample ◽  
Sample Testing

Οι έγκυρες προβλέψεις χρηματοοικονομικών κρίσεων διασφάλιζαν ανέκαθεν την σταθερότητα τόσο ολόκληρου του χρηματοοικονομικού οικοδομήματος γενικότερα, όσο και του τραπεζικού τομέα ειδικότερα. Με την παρούσα διατριβή επιτυγχάνεται η πρόβλεψη συστημικών τραπεζικών κρίσεων για χώρες της EE-14 αρκετά τρίμηνα προτού αυτές γίνουν αντιληπτές με την χρησιμοποίηση των πιο διαδεδομένων μεταβλητών (μακροοικονομικών, τραπεζικών και αγοράς) μέσω δύο προσεγγίσεων, της δυαδικής και της πολυεπίπεδης. Ακολουθώντας τη δυαδική προσέγγιση, εξάγονται μοντέλα ταξινόμησης με την εφαρμογή της Διακριτής Ανάλυσης (Discriminant Analysis), της Γραμμικής Παλινδρόμησης (Linear Regression), της Λογιστικής Παλινδρόμησης (Logistic Regression) και της Παλινδρόμησης Πιθανοομάδας (Probit Regression), για την έγκαιρη πρόβλεψη των κρίσεων -12 έως -7 τρίμηνα πριν την εμφάνισή τους. Επιπροσθέτως, συγκρίνεται η απόδοση της ανωτέρω ανάλυσης χρησιμοποιώντας τις νεότερες και πλέον υποσχόμενες μεθόδους του Δέντρου Ταξινόμησης (Classification Tree), του Τυχαίου Δάσους (Random Forest) και της C5. Ταυτόχρονα προτείνεται ένα νέο μέτρο επιλογής κατωφλίων και απόδοσης προσαρμογής (GoF) των μοντέλων πρόβλεψης και μια νέα συνδυαστική (combined) μέθοδος ταξινόμησης. Προκειμένου να διερευνηθεί η απόδοση της ανωτέρω ανάλυσης, χρησιμοποιείται ο εκτός του δείγματος έλεγχος (out-of-sample testing) με τη μέθοδο της ανά χώρα σταυρωτής επικύρωσης (country-blocked cross validation). Σύμφωνα με τη μέθοδο αυτή, πραγματοποιείται η ανάλυση και εξάγονται τα μοντέλα πρόβλεψης με τη χρήση των δεκατριών από τις δεκατέσσερις χώρες του δείγματος (in-sample), εφαρμόζονται τα εξαγόμενα μοντέλα για την δέκατη τέταρτη χώρα που είχε εξαιρεθεί από το αρχικό δείγμα (out-of-sample) και ελέγχονται τα αποτελέσματα πρόβλεψης με τα πραγματικά δεδομένα της χώρας αυτής. Η παραπάνω διαδικασία επαναλαμβάνεται δεκατέσσερις φορές, αφήνοντας δηλαδή κάθε φορά μια χώρα εκτός δείγματος και τελικά εξάγεται ο μέσος όρος των επαναλήψεων. Στην παρούσα διατριβή, και χρησιμοποιώντας τον εκτός του δείγματος έλεγχο, επιτυγχάνεται η κατά 82.4% σωστή ταξινόμηση (Ακρίβεια – Accuracy), 78.4% ποσοστό Αληθινών Θετικών (Τrue Ρositive Rate - TPR) και 80.6% ποσοστό Θετικής Τιμής Πρόβλεψης (Positive Predictive Value - PPV). Σύμφωνα με την πολυεπίπεδη προσέγγιση, διακρίνονται δύο επίπεδα-περίοδοι πρόβλεψης των Συστημικών Τραπεζικών Κρίσεων. Το πρώτο επίπεδο ονομάζεται έγκαιρη πρόβλεψη (early warning) και αφορά περίοδο -12 έως -7 τρίμηνα πριν την έλευση της κρίσης ενώ το δεύτερο επίπεδο ονομάζεται καθυστερημένη πρόβλεψη (late warning) και αφορά περίοδο -6 έως -1 τρίμηνα πριν την έλευση της κρίσης. Για την πολυεπίπεδη αυτή ταξινόμηση, γίνεται χρήση των Νευρωνικών Δικτύων (Neural Networks), της Πολυωνυμικής Λογιστικής Παλινδρόμησης (Multinomial Logistic Regression) και της Πολυεπίπεδης Γραμμικής Διακριτής Ανάλυσης (Multinomial Discriminant Analysis). Εφαρμόζοντας τον ίδιο εκτός του δείγματος έλεγχο με την πρώτη προσέγγιση επιτυγχάνεται η κατά 85.7% σωστή ταξινόμηση με την βέλτιστη μέθοδο που αποδεικνύεται ότι είναι η Πολυεπίπεδη Γραμμική Διακριτή Ανάλυση. Εφαρμόζοντας την ανωτέρω ανάλυση, οι ενδιαφερόμενοι φορείς άσκησης πολιτικής (policy makers) μπορούν να ανιχνεύσουν την ύπαρξης κρίσης σε βάθος χρόνου έως τριών ετών με τα προτεινόμενα μοντέλα, χρησιμοποιώντας μόνο δεδομένα που υπάρχουν ελεύθερα προσβάσιμα στο κοινό, ασκώντας με τον τρόπο αυτό την κατάλληλη ανά περίπτωση μακροπροληπτική πολιτική (macroprudential policy).

scholarly journals Prediction and Cross-Validation of Neural Networks Versus Logistic Regression: Using Hepatic Disorders as an Example

1998 ◽  
Vol 147 (4) ◽  
pp. 407-413 ◽  
Author(s):  
M.-S. Duh ◽  
A. M. Walker ◽  
M. Pagano ◽  
K. Kronlund
Keyword(s):  
Neural Networks ◽  
Logistic Regression ◽  
Cross Validation

scholarly journals Novel Ensemble of Multivariate Adaptive Regression Spline with Spatial Logistic Regression and Boosted Regression Tree for Gully Erosion Susceptibility

2020 ◽  
Vol 12 (20) ◽  
pp. 3284
Author(s):  
Paramita Roy ◽  
Subodh Chandra Pal ◽  
Alireza Arabameri ◽  
Rabin Chakrabortty ◽  
Biswajeet Pradhan ◽  
...  
Keyword(s):  
Logistic Regression ◽  
River Basin ◽  
Cross Validation ◽  
Gully Erosion ◽  
Multivariate Adaptive Regression Spline ◽  
Boosted Regression Tree ◽  
Regression Spline ◽  
Adaptive Regression ◽  
Fold Cross Validation ◽  
Very High

The extreme form of land degradation through different forms of erosion is one of the major problems in sub-tropical monsoon dominated region. The formation and development of gullies is the dominant form or active process of erosion in this region. So, identification of erosion prone regions is necessary for escaping this type of situation and maintaining the correspondence between different spheres of the environment. The major goal of this study is to evaluate the gully erosion susceptibility in the rugged topography of the Hinglo River Basin of eastern India, which ultimately contributes to sustainable land management practices. Due to the nature of data instability, the weakness of the classifier andthe ability to handle data, the accuracy of a single method is not very high. Thus, in this study, a novel resampling algorithm was considered to increase the robustness of the classifier and its accuracy. Gully erosion susceptibility maps have been prepared using boosted regression trees (BRT), multivariate adaptive regression spline (MARS) and spatial logistic regression (SLR) with proposed resampling techniques. The re-sampling algorithm was able to increase the efficiency of all predicted models by improving the nature of the classifier. Each variable in the gully inventory map was randomly allocated with 5-fold cross validation, 10-fold cross validation, bootstrap and optimism bootstrap, while each consisted of 30% of the database. The ensemble model was tested using 70% and validated with the other 30% using the K-fold cross validation (CV) method to evaluate the influence of the random selection of training and validation database. Here, all resampling methods are associated with higher accuracy, but SLR bootstrap optimism is more optimal than any other methods according to its robust nature. The AUC values of BRT optimism bootstrap, MARS optimism bootstrap and SLR optimism bootstrap are 87.40%, 90.40% and 90.60%, respectively. According to the SLR optimism bootstrap, the 107,771 km2 (27.51%) area of this region is associated with a very high to high susceptible to gully erosion. This potential developmental area of the gully was found primarily in the Hinglo River Basin, where lateral exposure was mainly observed with scarce vegetation. The outcome of this work can help policy-makers to implement remedial measures to minimize the damage caused by erosion of the gully.

scholarly journals Clinical risk factors and predictive tool of bacteremia in patients with cirrhosis

2020 ◽  
Vol 48 (5) ◽  
pp. 030006052091922
Author(s):  
Qiao Yang ◽  
Xian Zhong Jiang ◽  
Yong Fen Zhu ◽  
Fang Fang Lv
Keyword(s):  
Risk Factors ◽  
Risk Assessment ◽  
Logistic Regression ◽  
Cross Validation ◽  
Bloodstream Infections ◽  
Roc Curves ◽  
Predictive Tool ◽  
Reactive Protein ◽  
Significant Difference ◽  
Fold Cross Validation

Objective We aimed to analyze the risk factors and to establish a predictive tool for the occurrence of bloodstream infections (BSI) in patients with cirrhosis. Methods A total of 2888 patients with cirrhosis were retrospectively included. Multivariate analysis for risk factors of BSI were tested using logistic regression. Multivariate logistic regression was validated using five-fold cross-validation. Results Variables that were independently associated with incidence of BSI were white blood cell count (odds ratio [OR] = 1.094, 95% confidence interval [CI] 1.063–1.127)], C-reactive protein (OR = 1.005, 95% CI 1.002–1.008), total bilirubin (OR = 1.003, 95% CI 1.002–1.004), and previous antimicrobial exposure (OR = 4.556, 95% CI 3.369–6.160); albumin (OR = 0.904, 95% CI 0.883–0.926), platelet count (OR = 0.996, 95% CI 0.994–0.998), and serum creatinine (OR = 0.989, 95% CI 0.985–0.994) were associated with lower odds of BSI. The area under receiver operating characteristic (ROC) curve of the risk assessment scale was 0.850, and its sensitivity and specificity were 0.762 and 0.801, respectively. There was no significant difference between the ROC curves of cross-validation and risk assessment. Conclusions We developed a predictive tool for BSI in patients with cirrhosis, which could help with early identification of such episodes at admission, to improve outcome in these patients.

scholarly journals Comparison Decision Tree and Logistic Regression Machine Learning Classification Algorithms to determine Covid-19

SinkrOn ◽  
2022 ◽  
Vol 7 (1) ◽  
pp. 59-65
Author(s):  
Artika Arista
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Decision Tree ◽  
Cross Validation ◽  
Performance Testing ◽  
Signs And Symptoms ◽  
Classification Algorithms ◽  
Machine Learning Classification ◽  
Wide Range ◽  
Testing Performance

Many people today are unsure whether they have COVID-19. The frequent fever, dry cough, and sore throat are all signs and symptoms of COVID-19. If a person has signs or symptoms of coronavirus disease 2019 (COVID-19), he/she should see the doctor or go to a clinic as soon as possible. As a result, it's vital to learn and comprehend the fundamental differences. COVID-19 can cause a wide range of symptoms. The experiments were carried out using two Machine Learning Classification Algorithms, namely Decision Tree (DT) and Logistic Regression (LR). Both algorithms were written and analyzed using the Python program in Jupyter Notebook 6.4.5. From the results obtained in the experiments of covid symptoms dataset, on average, the DT model has obtained the best cross-validation average and the testing performance average compared to the LR machine learning models. For cross-validation results, the DT model has achieved an accuracy of 98.0%. For performance testing, the DT model has achieved an accuracy of 98.0%. The LR has obtained the second-best result on the average of cross-validation performance and the testing results. For cross-validation results, the LR model has achieved an accuracy of 96.0%. For performance testing, the LR model has achieved an accuracy of 97.0%. Consequently, the DT for the COVID-19 symptoms dataset is outperforming the LR for cross-validation and testing results.

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