Development and head-to-head comparison of machine-learning models to identify patients requiring prostate biopsy

Risk calculators for the detection of prostate cancer: a systematic review

BACKGROUND

Prostate cancer (PCa) (early) detection poses significant challenges, including unnecessary testing and the risk of potential overdiagnosis. The European Association of Urology therefore suggests an individual risk-adapted approach, incorporating risk calculators (RCs) into the PCa detection pathway. In the context of 'The PRostate Cancer Awareness and Initiative for Screening in the European Union' (PRAISE-U) project ( https://uroweb.org/praise-u ), we aim to provide an overview of the currently available clinical RCs applicable in an early PCa detection algorithm.

METHODS

We performed a systematic review to identify RCs predicting detection of clinically significant PCa at biopsy. A search was performed in the databases Medline ALL, Embase, Web of Science Core Collection, Cochrane Central Register of Controlled Trials and Google Scholar for publications between January 2010 and July 2023. We retrieved relevant literature by using the terms "prostate cancer", "screening/diagnosis" and "predictive model". Inclusion criteria included systematic reviews, meta-analyses, and clinical trials. Exclusion criteria applied to studies involving pre-targeted high-risk populations, diagnosed PCa patients, or a sample sizes under 50 men.

RESULTS

We identified 6474 articles, of which 140 were included after screening abstracts and full texts. In total, we identified 96 unique RCs. Among these, 45 underwent external validation, with 28 validated in multiple cohorts. Of the externally validated RCs, 17 are based on clinical factors, 19 incorporate clinical factors along with MRI details, 4 were based on blood biomarkers alone or in combination with clinical factors, and 5 included urinary biomarkers. The median AUC of externally validated RCs ranged from 0.63 to 0.93.

CONCLUSIONS

This systematic review offers an extensive analysis of currently available RCs, their variable utilization, and performance within validation cohorts. RCs have consistently demonstrated their capacity to mitigate the limitations associated with early detection and have been integrated into modern practice and screening trials. Nevertheless, the lack of external validation data raises concerns about numerous RCs, and it is crucial to factor in this omission when evaluating whether a specific RC is applicable to one's target population.

iPCa-Net: A CNN-based framework for predicting incidental prostate cancer using multiparametric MRI

Incidental prostate cancer (iPCa) is an early stage of clinically significant prostate cancer (csPCa) and is typically asymptomatic, making it difficult to detect in clinical practice. The objective of this study is to predict iPCa by analyzing prostatic MRIs using deep convolutional neural network (CNN). While CNN-based models in medical image analysis have made significant advancements, the iPCa prediction task presents two challenging problems: subtler differences in MRIs that are imperceptible to human eyes and a lower incidence rate, resulting in a more pronounced sample imbalance compared to routine cancer prediction. To address these two challenges, we propose a new CNN-based framework called iPCa-Net, which is designed to jointly optimize two tasks: prostate transition zone segmentation and iPCa prediction. To evaluate the performance of our model, we construct a prostatic MRI dataset comprising 9536 prostate MRI slices from 448 patients diagnosed with benign prostatic hyperplasia (BPH) at our institution. In our study, the incidence rate of iPCa is 5.13% (23 out of 448) . We compare our model with eight state-of-the-art methods for segmentation task and nine established methods for prediction task respectively using our dataset, and experimental results demonstrate the superior performance of our model. Specifically, in the prostate transition zone segmentation task, our iPCa-Net outperforms the top-performing method by 1.23% with respect to mIoU. In the iPCa prediction task, our iPCa-Net surpasses the top-performing method by 2.06% with respect to F1 score. In conclusion, our iPCa-Net demonstrates superior performance in the early identification of iPCa patients compared to state-of-the-art methods. This advancement holds great significance for appropriate disease management and is highly beneficial for patients.

Joint models for dynamic prediction in localised prostate cancer: a literature review

BACKGROUND

Prostate cancer is a very prevalent disease in men. Patients are monitored regularly during and after treatment with repeated assessment of prostate-specific antigen (PSA) levels. Prognosis of localised prostate cancer is generally good after treatment, and the risk of having a recurrence is usually estimated based on factors measured at diagnosis. Incorporating PSA measurements over time in a dynamic prediction joint model enables updates of patients' risk as new information becomes available. We review joint model strategies that have been applied to model time-dependent PSA trajectories to predict time-to-event outcomes in localised prostate cancer.

METHODS

We identify articles that developed joint models for prediction of localised prostate cancer recurrence over the last two decades. We report, compare, and summarise the methodological approaches and applications that use joint modelling accounting for two processes: the longitudinal model (PSA), and the time-to-event process (clinical failure). The methods explored differ in how they specify the association between these two processes.

RESULTS

Twelve relevant articles were identified. A range of methodological frameworks were found, and we describe in detail shared-parameter joint models (9 of 12, 75%) and joint latent class models (3 of 12, 25%). Within each framework, these articles presented model development, estimation of dynamic predictions and model validations.

CONCLUSIONS

Each framework has its unique principles with corresponding advantages and differing interpretations. Regardless of the framework used, dynamic prediction models enable real-time prediction of individual patient prognosis. They utilise all available longitudinal information, in addition to baseline prognostic risk factors, and are superior to traditional baseline-only prediction models.

Machine Learning-Based Models Enhance the Prediction of Prostate Cancer

Purpose

PSA is currently the most commonly used screening indicator for prostate cancer. However, it has limited specificity for the diagnosis of prostate cancer. We aim to construct machine learning-based models and enhance the prediction of prostate cancer.

Methods

The data of 551 patients who underwent prostate biopsy were retrospectively retrieved and divided into training and test datasets in a 3:1 ratio. We constructed five PCa prediction models with four supervised machine learning algorithms, including tPSA univariate logistic regression (LR), multivariate LR, decision tree (DT), random forest (RF), and support vector machine (SVM). The five prediction models were compared based on model performance metrics, such as the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, specificity, calibration curve, and clinical decision curve analysis (DCA).

Results

All five models had good calibration in the training dataset. In the training dataset, the RF, DT, and multivariate LR models showed better discrimination, with AUCs of 1.0, 0.922 and 0.91, respectively, than the tPSA univariate LR and SVM models. In the test dataset, the multivariate LR model exhibited the best discrimination (AUC=0.918). The multivariate LR model and SVM model had better extrapolation and generalizability, with little change in performance between the training and test datasets. Compared with the DCA curves of the tPSA LR model, the other four models exhibited better net clinical benefits.

Conclusion

The results of the current retrospective study suggest that machine learning techniques can predict prostate cancer with significantly better AUC, accuracy, and net clinical benefits.

Anti-Ebola: an initiative to predict Ebola virus inhibitors through machine learning

Ebola virus is a deadly pathogen responsible for a frequent series of outbreaks since 1976. Despite various efforts from researchers worldwide, its mortality and fatality are quite high. For antiviral drug discovery, the computational efforts are considered highly useful. Therefore, we have developed an 'anti-Ebola' web server, through quantitative structure-activity relationship information of available molecules with experimental anti-Ebola activities. Three hundred and five unique anti-Ebola compounds with their respective IC₅₀ values were extracted from the 'DrugRepV' database. Later, the compounds were used to extract the molecular descriptors, which were subjected to regression-based model development. The robust machine learning techniques, namely support vector machine, random forest and artificial neural network, were employed using tenfold cross-validation. After a randomization approach, the best predictive model showed Pearson's correlation coefficient ranges from 0.83 to 0.98 on training/testing (T²⁷⁴) dataset. The robustness of the developed models was cross-evaluated using William's plot. The highly robust computational models are integrated into the web server. The 'anti-Ebola' web server is freely available at https://bioinfo.imtech.res.in/manojk/antiebola . We anticipate this will serve the scientific community for developing effective inhibitors against the Ebola virus.