Can Machine Learning Models Detect and Predict Lymph Node Involvement in Prostate Cancer? A Comprehensive Systematic Review
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PROVIDER: S-EPMC10672480 | biostudies-literature | 2023 Nov
REPOSITORIES: biostudies-literature
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Project description:Background/objectivesExtended pelvic lymph node dissection is a crucial surgical technique for managing intermediate to high-risk prostate cancer. Accurately predicting lymph node metastasis before surgery can minimize unnecessary lymph node dissections and their associated complications. This study assessed the efficacy of various machine learning models for predicting lymph node metastasis in a cohort of Japanese patients who underwent robot-assisted laparoscopic radical prostatectomy.MethodsData from 625 patients who underwent extended pelvic lymph node dissection or standard dissection with lymph node metastasis between October 2010 and February 2023 were analyzed. Four machine learning models-Random Forest, Light Gradient-Boosting Machine, Logistic Regression, and Support Vector Machine-were used to predict lymph node metastasis. Their performance was assessed using receiver operating characteristic curves, a decision curve analysis, and predictive values at different thresholds.ResultsLymph node metastasis was observed in 34 patients (5.4%). The Light Gradient-Boosting Machine had the highest AUC of 0.924, followed by the Random Forest model with an AUC of 0.894. The decision curve analysis indicated substantial net benefits for both models, particularly at low threshold probabilities. The Light Gradient-Boosting Machine demonstrated superior accuracy, achieving 95.6% at the 0.05 threshold and 96.7% at the 0.10 threshold, outperforming other models and conventional nomograms in the validation dataset.ConclusionMachine learning models, especially Light Gradient-Boosting Machine and Random Forest, show significant potential for predicting lymph node metastasis in prostate cancer, thereby aiding in reducing unnecessary surgical interventions.
| S-EPMC11640458 | biostudies-literature
Project description:BackgroundThe presence of lymph node metastasis leads to a poor prognosis for prostate cancer (Pca). Recently, many studies have indicated that gene signatures may be able to predict the status of lymph nodes. The purpose of this study is to probe and validate a new tool to predict lymph node metastasis (LNM) based on alternative splicing (AS).MethodsGene expression profiles and clinical information of prostate adenocarcinoma cohort were retrieved from The Cancer Genome Atlas (TCGA) database, and the corresponding RNA-seq splicing events profiles were obtained from the TCGA SpliceSeq. Limma package was used to identify the differentially expressed alternative splicing (DEAS) events between LNM and non-LNM groups. Eight machine learning classifiers were built to train with stratified five-fold cross-validation. SHAP values was used to explain the model.Results333 differentially expressed alternative splicing (DEAS) events were identified. Using correlation filter and the least absolute shrinkage and selection operator (LASSO) method, a 96 AS signature was identified that had favorable discrimination in the training set and validated in the validation set. The linear discriminant analysis (LDA) was the best classifier after 100 iterations of training. The LDA classifier was able to distinguish between LNM and non-LNM with an area under the receiver operating curve of 0.962 ± 0.026 in the training set (D1 = 351) and 0.953 in the validation set (D2 = 62). The decision curve analysis plot proved the clinical application of the AS-based model.ConclusionMachine learning combined with AS data could robustly distinguish between LNM and non-LNM in Pca.
| S-EPMC9880415 | biostudies-literature
Project description:BackgroundFor patients with stage T1-T2 esophageal squamous cell carcinoma (ESCC), accurately predicting lymph node metastasis (LNM) remains challenging. We aimed to investigate the performance of machine learning (ML) models for predicting LNM in patients with stage T1-T2 ESCC.MethodsPatients with T1-T2 ESCC at three centers between January 2014 and December 2019 were included in this retrospective study and divided into training and external test sets. All patients underwent esophagectomy and were pathologically examined to determine the LNM status. Thirty-six ML models were developed using six modeling algorithms and six feature selection techniques. The optimal model was determined by the bootstrap method. An external test set was used to further assess the model's generalizability and effectiveness. To evaluate prediction performance, the area under the receiver operating characteristic curve (AUC) was applied.ResultsOf the 1097 included patients, 294 (26.8%) had LNM. The ML models based on clinical features showed good predictive performance for LNM status, with a median bootstrapped AUC of 0.659 (range: 0.592, 0.715). The optimal model using the naive Bayes algorithm with feature selection by determination coefficient had the highest AUC of 0.715 (95% CI: 0.671, 0.763). In the external test set, the optimal ML model achieved an AUC of 0.752 (95% CI: 0.674, 0.829), which was superior to that of T stage (0.624, 95% CI: 0.547, 0.701).ConclusionsML models provide good LNM prediction value for stage T1-T2 ESCC patients, and the naive Bayes algorithm with feature selection by determination coefficient performed best.
| S-EPMC9496653 | biostudies-literature
Project description:Prostate cancer (PCa) patients with lymph node involvement (LNI) constitute a single-risk group with varied prognoses. Existing studies on this group have focused solely on those who underwent prostatectomy (RP), using statistical models to predict prognosis. This study aimed to develop an easily accessible individual survival prediction tool based on multiple machine learning (ML) algorithms to predict survival probability for PCa patients with LNI. A total of 3280 PCa patients with LNI were identified from the Surveillance, Epidemiology, and End Results (SEER) database, covering the years 2000-2019. The primary endpoint was overall survival (OS). Gradient Boosting Survival Analysis (GBSA), Random Survival Forest (RSF), and Extra Survival Trees (EST) were used to develop prognosis models, which were compared to Cox regression. Discrimination was evaluated using the time-dependent areas under the receiver operating characteristic curve (time-dependent AUC) and the concordance index (c-index). Calibration was assessed using the time-dependent Brier score (time-dependent BS) and the integrated Brier score (IBS). Moreover, the beeswarm summary plot in SHAP (SHapley Additive exPlanations) was used to display the contribution of variables to the results. The 3280 patients were randomly split into a training cohort (n = 2624) and a validation cohort (n = 656). Nine variables including age at diagnosis, race, marital status, clinical T stage, prostate-specific antigen (PSA) level at diagnosis, Gleason Score (GS), number of positive lymph nodes, radical prostatectomy (RP), and radiotherapy (RT) were used to develop models. The mean time-dependent AUC for GBSA, RSF, and EST was 0.782 (95% confidence interval [CI] 0.779-0.783), 0.779 (95% CI 0.776-0.780), and 0.781 (95% CI 0.778-0.782), respectively, which were higher than the Cox regression model of 0.770 (95% CI 0.769-0.773). Additionally, all models demonstrated almost similar calibration, with low IBS. A web-based prediction tool was developed using the best-performing GBSA, which is accessible at https://pengzihexjtu-pca-n1.streamlit.app/ . ML algorithms showed better performance compared with Cox regression and we developed a web-based tool, which may help to guide patient treatment and follow-up.
| S-EPMC10611782 | biostudies-literature
Project description:BackgroundEndoscopic submucosal dissection has become the primary option of treatment for early gastric cancer. However, lymph node metastasis may lead to poor prognosis. We analyzed factors related to lymph node metastasis in EGC patients, and we developed a construction prediction model with machine learning using data from a retrospective series.MethodsTwo independent cohorts' series were evaluated including 305 patients with EGC from China as cohort I and 35 patients from Spain as cohort II. Five classifiers obtained from machine learning were selected to establish a robust prediction model for lymph node metastasis in EGC.ResultsThe clinical variables such as invasion depth, histologic type, ulceration, tumor location, tumor size, Lauren classification, and age were selected to establish the five prediction models: linear support vector classifier (Linear SVC), logistic regression model, extreme gradient boosting model (XGBoost), light gradient boosting machine model (LightGBM), and Gaussian process classification model. Interestingly, all prediction models of cohort I showed accuracy between 70 and 81%. Furthermore, the prediction models of the cohort II exhibited accuracy between 48 and 82%. The areas under curve (AUC) of the five models between cohort I and cohort II were between 0.736 and 0.830.ConclusionsOur results support that the machine learning method could be used to predict lymph node metastasis in early gastric cancer and perhaps provide another evaluation method to choose the suited treatment for patients.
| S-EPMC9751349 | biostudies-literature
Project description:BackgroundExisting models do poorly when it comes to quantifying the risk of Lymph node metastases (LNM). This study aimed to develop a machine learning model for LNM in patients with T1 esophageal squamous cell carcinoma (ESCC).Methods and resultsThe study is multicenter, and population based. Elastic net regression (ELR), random forest (RF), extreme gradient boosting (XGB), and a combined (ensemble) model of these was generated. The contribution to the model of each factor was calculated. The models all exhibited potent discriminating power. The Elastic net regression performed best with externally validated AUC of 0.803, whereas the NCCN guidelines identified patients with LNM with an AUC of 0.576 and logistic model with an AUC of 0. 670. The most important features were lymphatic and vascular invasion and depth of tumor invasion.ConclusionsModels created utilizing machine learning approaches had excellent performance estimating the likelihood of LNM in T1 ESCC.
| S-EPMC11634146 | biostudies-literature
Project description:BackgroundA more accurate preoperative prediction of lymph node involvement (LNI) in prostate cancer (PCa) would improve clinical treatment and follow-up strategies of this disease. We developed a predictive model based on machine learning (ML) combined with big data to achieve this.MethodsClinicopathological characteristics of 2,884 PCa patients who underwent extended pelvic lymph node dissection (ePLND) were collected from the U.S. National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) database from 2010 to 2015. Eight variables were included to establish an ML model. Model performance was evaluated by the receiver operating characteristic (ROC) curves and calibration plots for predictive accuracy. Decision curve analysis (DCA) and cutoff values were obtained to estimate its clinical utility.ResultsThree hundred and forty-four (11.9%) patients were identified with LNI. The five most important factors were the Gleason score, T stage of disease, percentage of positive cores, tumor size, and prostate-specific antigen levels with 158, 137, 128, 113, and 88 points, respectively. The XGBoost (XGB) model showed the best predictive performance and had the highest net benefit when compared with the other algorithms, achieving an area under the curve of 0.883. With a 5%~20% cutoff value, the XGB model performed best in reducing omissions and avoiding overtreatment of patients when dealing with LNI. This model also had a lower false-negative rate and a higher percentage of ePLND was avoided. In addition, DCA showed it has the highest net benefit across the whole range of threshold probabilities.ConclusionsWe established an ML model based on big data for predicting LNI in PCa, and it could lead to a reduction of approximately 50% of ePLND cases. In addition, only ≤3% of patients were misdiagnosed with a cutoff value ranging from 5% to 20%. This promising study warrants further validation by using a larger prospective dataset.
| S-EPMC8551611 | biostudies-literature
Project description:BackgroundWhether prophylactic central lymph node dissection is necessary for cN0 papillary thyroid microcarcinoma (PTMC) patients remains highly debatable. Surgeons desperately need a way to help with surgical decision-making. While traditional predictive models can better explain changes in variables, machine learning (ML) models may have better predictive performance. This study aims to develop models for predicting the risk of central lymph node metastasis (CLNM) by utilizing ML algorithms.MethodsThe clinical records of 1,121 patients with cN0 PTMC who underwent initial thyroid resection at our hospital between January 2014 and December 2018 were retrospectively retrieved. Univariate and multivariate analyses were performed to examine risk factors associated with CLNM. Six ML algorithms for predicting CLNM were established and internally validated. Indices including the area under the receiver operating characteristic (AUROC), sensitivity, specificity, accuracy, positive predictive value (PPV), and negative predictive value (NPV) were calculated to test the performance of the model.ResultsThe results showed 33.5% (376 out of 1,121) of patients had CLNM. In multivariate logistic regression (LR) analyses, gender, age, tumor size, multifocal lesions, and extrathyroidal extension (ETE) were all independent predictors of CLNM. The AUROC predictive values of the six ML algorithms were between 0.664 and 0.794, with the random forest (RF) model performing the best with an AUROC of 0.794. Therefore, we used the RF model and uploaded the results to a web-based risk calculator to predict an individual's probability of CLNM (https://xijing-thyroid.shinyapps.io/ptmc_clnm).ConclusionsDeveloping predictive models of CLNM in cN0 PTMC patients using the ML algorithm is a feasible method. Our online risk calculator based on the RF model may be a useful tool for surgical decisions.
| S-EPMC9469161 | biostudies-literature
Project description:BackgroundAccurate predictions of tumor dissemination risks and medical treatment outcomes are critical to personalize therapy. Patient-derived xenograft (PDX) models in mice have demonstrated high accuracy in predicting therapeutic outcomes, but methods for predicting tumor invasiveness and early stages of vascular/lymphatic dissemination are still lacking. Here we show that a zebrafish tumor xenograft (ZTX) platform based on implantation of PDX tissue fragments recapitulate both treatment outcome and tumor invasiveness/dissemination in patients, within an assay time of only 3 days.MethodsUsing a panel of 39 non-small cell lung cancer PDX models, we developed a combined mouse-zebrafish PDX platform based on direct implantation of cryopreserved PDX tissue fragments into zebrafish embryos, without the need for pre-culturing or expansion. Clinical proof-of-principle was established by direct implantation of tumor samples from four patients.ResultsThe resulting ZTX models responded to Erlotinib and Paclitaxel, with similar potency as in mouse-PDX models and the patients themselves, and resistant tumors similarly failed to respond to these drugs in the ZTX system. Drug response was coupled to elevated expression of EGFR, Mdm2, Ptch1 and Tsc1 (Erlotinib), or Nras and Ptch1 (Paclitaxel) and reduced expression of Egfr, Erbb2 and Foxa (Paclitaxel). Importantly, ZTX models retained the invasive phenotypes of the tumors and predicted lymph node involvement of the patients with 91% sensitivity and 62% specificity, which was superior to clinically used tests. The biopsies from all four patient tested implanted successfully, and treatment outcome and dissemination were quantified for all patients in only 3 days.ConclusionsWe conclude that the ZTX platform provide a fast, accurate, and clinically relevant system for evaluation of treatment outcome and invasion/dissemination of PDX models, providing an attractive platform for combined mouse-zebrafish PDX trials and personalized medicine.
| S-EPMC8827197 | biostudies-literature
Project description:ObjectivesA more accurate preoperative prediction of lymph node metastasis (LNM) plays a decisive role in the selection of treatment in patients with laryngeal carcinoma (LC). This study aimed to develop a machine learning (ML) prediction model for predicting LNM in patients with LC.MethodsWe collected and retrospectively analysed 4887 LC patients with detailed demographical characteristics including age at diagnosis, race, sex, primary site, histology, number of tumours, T-stage, grade, and tumour size in the National Institutes of Health (NIH) Surveillance, Epidemiology, and End Results (SEER) database from 2005 to 2015. A correlation analysis of all variables was evaluated by the Pearson correlation. Independent risk factors for LC patients with LNM were identified by univariate and multivariate logistic regression analyses. Afterward, patients were randomly divided into training and test sets in a ratio of 8 to 2. On this basis, we established logistic regression (LR), k-nearest neighbor (KNN), support vector machine (SVM), extreme gradient boosting (XGBoost), random forest (RF), and light gradient boosting machine (LightGBM) algorithm models based on ML. The area under the receiver operating characteristic curve (AUC) value, accuracy, precision, recall rate, F1-score, specificity, and Brier score was adopted to evaluate and compare the prediction performance of the models. Finally, the Shapley additive explanation (SHAP) method was used to interpret the association between each feature variable and target variables based on the best model.ResultsOf the 4887 total LC patients, 3409 were without LNM (69.76%), and 1478 had LNM (30.24%). The result of the Pearson correlation showed that variables were weakly correlated with each other. The independent risk factors for LC patients with LNM were age at diagnosis, race, primary site, number of tumours, tumour size, grade, and T-stage. Among six models, XGBoost displayed a better performance for predicting LNM, with five performance metrics outperforming other models in the training set (AUC: 0.791 (95% CI: 0.776-0.806), accuracy: 0.739, recall rate: 0.638, F1-score: 0.663, and Brier score: 0.165), and similar results were observed in the test set. Moreover, the SHAP value of XGBoost was calculated, and the result showed that the three features, T-stage, primary site, and grade, had the greatest impact on predicting the outcomes.ConclusionsThe XGBoost model performed better and can be applied to forecast the LNM of LC, offering a valuable and significant reference for clinicians in advanced decision-making.
| S-EPMC9675609 | biostudies-literature