Dataset Information

Deep Neural Networks Outperform the CAPRA Score in Predicting Biochemical Recurrence After Prostatectomy.

ABSTRACT:

Background

Use of predictive models for the prediction of biochemical recurrence (BCR) is gaining attention for prostate cancer (PCa). Specifically, BCR occurs in approximately 20-40% of patients five years after radical prostatectomy (RP) and the ability to predict BCR may help clinicians to make better treatment decisions. We aim to investigate the accuracy of CAPRA score compared to others models in predicting the 3-year BCR of PCa patients.

Material and methods

A total of 5043 men who underwent RP were analyzed retrospectively. The accuracy of CAPRA score, Cox regression analysis, logistic regression, K-nearest neighbor (KNN), random forest (RF) and a densely connected feed-forward neural network (DNN) classifier were compared in terms of 3-year BCR predictive value. The area under the receiver operating characteristic curve was mainly used to assess the performance of the predictive models in predicting the 3 years BCR of PCa patients. Pre-operative data such as PSA level, Gleason grade, and T stage were included in the multivariate analysis. To measure potential improvements to the model performance due to additional data, each model was trained once more with an additional set of post-operative surgical data from definitive pathology.

Results

Using the CAPRA score variables, DNN predictive model showed the highest AUC value of 0.7 comparing to the CAPRA score, logistic regression, KNN, RF, and cox regression with 0.63, 0.63, 0.55, 0.64, and 0.64, respectively. After including the post-operative variables to the model, the AUC values based on KNN, RF, and cox regression and DNN were improved to 0.77, 0.74, 0.75, and 0.84, respectively.

Conclusions

Our results showed that the DNN has the potential to predict the 3-year BCR and outperformed the CAPRA score and other predictive models.

SUBMITTER: Sargos P

PROVIDER: S-EPMC7906005 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Publications

Deep Neural Networks Outperform the CAPRA Score in Predicting Biochemical Recurrence After Prostatectomy.

Sargos Paul P Leduc Nicolas N Giraud Nicolas N Gandaglia Giorgio G Roumiguié Mathieu M Ploussard Guillaume G Rozet Francois F Soulié Michel M Mathieu Romain R Artus Pierre Mongiat PM Niazi Tamim T Vinh-Hung Vincent V Beauval Jean-Baptiste JB

Frontiers in oncology 20210211

<h4>Background</h4>Use of predictive models for the prediction of biochemical recurrence (BCR) is gaining attention for prostate cancer (PCa). Specifically, BCR occurs in approximately 20-40% of patients five years after radical prostatectomy (RP) and the ability to predict BCR may help clinicians to make better treatment decisions. We aim to investigate the accuracy of CAPRA score compared to others models in predicting the 3-year BCR of PCa patients.<h4>Material and methods</h4>A total of 5043 ...[more]

PMID: 33643910

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Project description:Accurate estimation of recurrence risk is needed for optimal treatment of clinically localized prostate cancer (PCa) patients. We combined classical clinicopathological predictors of biochemical recurrence (BCR) and molecular markers into a new risk score for predicting BCR after radical prostatectomy (RP). A retrospective study which included 122 PCa patients who attended our department between 2000 and 2007 was conducted. Total RNA was isolated from formalin-fixed paraffin embedded PCa tissue. Gene expression patterns were analyzed in 21 selected samples from 7 localized, 6 locally advanced, and 8 metastatic PCa patients using Illumina microarrays. Expression levels of 41 genes were validated by quantitative PCR in an independent retrospective series of 101 patients with ≥ 10 years follow-up who underwent RP for clinically localized PCa. Univariate and multivariate logistic regression analysis were used to identify individual predictors of BCR. A risk score (RS) for predicting BCR including clinicopathological and gene expression data was developed and Kaplan-Meier curves were generated. Interaction networks between the genes of the model were built by GeneMANIA Cytoscape plugin. In a median follow-up of 120 months (range 3-190), 37 patients developed BCR (36.6%). Expression levels of 7,930 transcripts differed between clinically localized and locally advanced-metastatic PCa groups (FDR<0.1). A set of 41 genes were validated by quantitative PCR. Regression analysis showed that expression of ASF1B and MCL1 as well as Gleason score, extracapsular extension, seminal vesicle invasion and positive margins were independent prognostic factors of BCR. A RS generated using these gene expression and clinicopathological variables was able to discriminate between two groups of patients with a significantly different probability of BCR (HR 6.24; CI 3.23-12.4, p<0.01), improving the individual discriminative performance of each of these variables on their own. Direct interactions between the two genes of the model were not found. In conclusion, identification of new gene expression patterns associated with a high probability of BCR in clinically localized PCa patients treated with RP, and their combination with clinicopathological variables in a robust, easy-to-use and reliable classifier may contribute to improve PCa risk stratification and, consequently, to tailor treatment and surveillance strategies in these patients.

Project description:The increase of publicly available bioactivity data in recent years has fueled and catalyzed research in chemogenomics, data mining, and modeling approaches. As a direct result, over the past few years a multitude of different methods have been reported and evaluated, such as target fishing, nearest neighbor similarity-based methods, and Quantitative Structure Activity Relationship (QSAR)-based protocols. However, such studies are typically conducted on different datasets, using different validation strategies, and different metrics. In this study, different methods were compared using one single standardized dataset obtained from ChEMBL, which is made available to the public, using standardized metrics (BEDROC and Matthews Correlation Coefficient). Specifically, the performance of Naïve Bayes, Random Forests, Support Vector Machines, Logistic Regression, and Deep Neural Networks was assessed using QSAR and proteochemometric (PCM) methods. All methods were validated using both a random split validation and a temporal validation, with the latter being a more realistic benchmark of expected prospective execution. Deep Neural Networks are the top performing classifiers, highlighting the added value of Deep Neural Networks over other more conventional methods. Moreover, the best method ('DNN_PCM') performed significantly better at almost one standard deviation higher than the mean performance. Furthermore, Multi-task and PCM implementations were shown to improve performance over single task Deep Neural Networks. Conversely, target prediction performed almost two standard deviations under the mean performance. Random Forests, Support Vector Machines, and Logistic Regression performed around mean performance. Finally, using an ensemble of DNNs, alongside additional tuning, enhanced the relative performance by another 27% (compared with unoptimized 'DNN_PCM'). Here, a standardized set to test and evaluate different machine learning algorithms in the context of multi-task learning is offered by providing the data and the protocols. Graphical Abstract .

Project description:BACKGROUND:To determine the added value of preoperative prostate multiparametric MRI (mpMRI) supplementary to clinical variables and their role in predicting post prostatectomy adverse findings and biochemically recurrent cancer (BCR). METHODS:All consecutive patients treated at HUS Helsinki University Hospital with robot assisted radical prostatectomy (RALP) between 2014 and 2015 were included in the analysis. The mpMRI data, clinical variables, histopathological characteristics, and follow-up information were collected. Study end-points were adverse RALP findings: extraprostatic extension, seminal vesicle invasion, lymph node involvement, and BCR. The Memorial Sloan Kettering Cancer Center (MSKCC) nomogram, Cancer of the Prostate Risk Assessment (CAPRA) score and the Partin score were combined with any adverse findings at mpMRI. Predictive accuracy for adverse RALP findings by the regression models was estimated before and after the addition of MRI results. Logistic regression, area under curve (AUC), decision curve analyses, Kaplan-Meier survival curves and Cox proportional hazard models were used. RESULTS:Preoperative mpMRI data from 387 patients were available for analysis. Clinical variables alone, MSKCC nomogram or Partin tables were outperformed by models with mpMRI for the prediction of any adverse finding at RP. AUC for clinical parameters versus clinical parameters and mpMRI variables were 0.77 versus 0.82 for any adverse finding. For MSKCC nomogram versus MSKCC nomogram and mpMRI variables the AUCs were 0.71 and 0.78 for any adverse finding. For Partin tables versus Partin tables and mpMRI variables the AUCs were 0.62 and 0.73 for any adverse finding. In survival analysis, mpMRI-projected adverse RP findings stratify CAPRA and MSKCC high-risk patients into groups with distinct probability for BCR. CONCLUSIONS:Preoperative mpMRI improves the predictive value of commonly used clinical variables for pathological stage at RP and time to BCR. mpMRI is available for risk stratification prebiopsy, and should be considered as additional source of information to the standard predictive nomograms.

Dataset Information

Deep Neural Networks Outperform the CAPRA Score in Predicting Biochemical Recurrence After Prostatectomy.

Background

Material and methods

Results

Conclusions

Publications

Deep Neural Networks Outperform the CAPRA Score in Predicting Biochemical Recurrence After Prostatectomy.

Similar Datasets

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