Classification models for early detection of prostate cancer

PyDTS: A Python Toolkit for Deep Learning Time Series Modelling

In this article, the topic of time series modelling is discussed. It highlights the criticality of analysing and forecasting time series data across various sectors, identifying five primary application areas: denoising, forecasting, nonlinear transient modelling, anomaly detection, and degradation modelling. It further outlines the mathematical frameworks employed in a time series modelling task, categorizing them into statistical, linear algebra, and machine- or deep-learning-based approaches, with each category serving distinct dimensions and complexities of time series problems. Additionally, the article reviews the extensive literature on time series modelling, covering statistical processes, state space representations, and machine and deep learning applications in various fields. The unique contribution of this work lies in its presentation of a Python-based toolkit for time series modelling (PyDTS) that integrates popular methodologies and offers practical examples and benchmarking across diverse datasets.

Discrimination between authentic and adulterated liquors by near-infrared spectroscopy and ensemble classification

Chinese liquor is one of the famous distilled spirits and counterfeit liquor is becoming a serious problem in the market. Especially, age liquor is facing the crisis of confidence because it is difficult for consumer to identify the marked age, which prompts unscrupulous traders to pose off low-grade liquors as high-grade liquors. An ideal method for authenticity confirmation of liquors should be non-invasive, non-destructive and timely. The combination of near-infrared spectroscopy with chemometrics proves to be a good way to reach these premises. A new strategy is proposed for classification and verification of the adulteration of liquors by using NIR spectroscopy and chemometric classification, i.e., ensemble support vector machines (SVM). Three measures, i.e., accuracy, sensitivity and specificity were used for performance evaluation. The results confirmed that the strategy can serve as a screening tool applied to verify adulteration of the liquor, that is, a prior step used to condition the sample to a deeper analysis only when a positive result for adulteration is obtained by the proposed methodology.

The diagnostics of diabetes mellitus based on ensemble modeling and hair/urine element level analysis

The aim of the present work focuses on exploring the feasibility of analyzing the relationship between diabetes mellitus and several element levels in hair/urine specimens by chemometrics. A dataset involving 211 specimens and eight element concentrations was used. The control group was divided into three age subsets in order to analyze the influence of age. It was found that the most obvious difference was the effect of age on the level of zinc and iron. The decline of iron concentration with age in hair was exactly consistent with the opposite trend in urine. Principal component analysis (PCA) was used as a tool for a preliminary evaluation of the data. Both ensemble and single support vector machine (SVM) algorithms were used as the classification tools. On average, the accuracy, sensitivity and specificity of ensemble SVM models were 99%, 100%, 99% and 97%, 89%, 99% for hair and urine samples, respectively. The findings indicate that hair samples are superior to urine samples. Even so, it can provide more valuable information for prevention, diagnostics, treatment and research of diabetes by simultaneously analyzing the hair and urine samples.

Ensemble modeling coupled with six element concentrations in human blood for cancer diagnosis

Six important metal contents (i.e., zinc, barium, magnesium, calcium, copper, and selenium) in blood samples coupled with an ensemble classification algorithm have been used for the classification of normal people and cancer patients. A dataset containing 42 healthy samples and 32 cancer samples was used for experiment. The prediction results from this method outperformed those from the newly developed support vector machine, i.e., a sensitivity of 100%, a specificity of 95.2%, and an overall accuracy of 98.6%. It seems that ELDA coupled with blood element analysis can serve as a valuable tool for diagnosing cancer in clinical practice.

Avoiding pitfalls in applying prediction models, as illustrated by the example of prostate cancer diagnosis

BACKGROUND

The use of different mathematical models to support medical decisions is accompanied by increasing uncertainties when they are applied in practice. Using prostate cancer (PCa) risk models as an example, we recommend requirements for model development and draw attention to possible pitfalls so as to avoid the uncritical use of these models.

CONTENT

We conducted MEDLINE searches for applications of multivariate models supporting the prediction of PCa risk. We critically reviewed the methodological aspects of model development and the biological and analytical variability of the parameters used for model development. In addition, we reviewed the role of prostate biopsy as the gold standard for confirming diagnoses. In addition, we analyzed different methods of model evaluation with respect to their application to different populations. When using models in clinical practice, one must validate the results with a population from the application field. Typical model characteristics (such as discrimination performance and calibration) and methods for assessing the risk of a decision should be used when evaluating a model's output. The choice of a model should be based on these results and on the practicality of its use.

SUMMARY

To avoid possible errors in applying prediction models (the risk of PCa, for example) requires examining the possible pitfalls of the underlying mathematical models in the context of the individual case. The main tools for this purpose are discrimination, calibration, and decision curve analysis.

Prediction of breast cancer using artificial neural networks

In this study, an artificial neural network (ANN) was developed to determine whether patients have breast cancer or not. Whether patients have cancer or not and if they have its type can be determined by using ANN and BI-RADS evaluation and based on the age of the patient, mass shape, mass border and mass density. Though this system cannot diagnose cancer conclusively, it helps physicians in deciding whether a biopsy is required by providing information about whether the patient has breast cancer or not. Data obtained from 800 patients who were diagnosed with cancer definitively through biopsy. The definitive diagnosis corresponding to each patient and the data from ANN model results were investigated using Confusion matrix and ROC analyses. In the test data of the ANN model that was implemented as a result of these analyses, disease prediction rate was 90.5% and the health ratio was 80.9%. It is seen from these high predictive values that the ANN model is fast, reliable and without any risks and therefore can be of great help to physicians.

Classification models for detection of lung cancer based on nine element distribution of urine samples

The detection of lung cancer has a special value in the diagnosis of cancer diseases. Based on nine elemental concentrations (i.e., chromium, iron, manganese, aluminum, cadmium, copper, zinc, nickel, and selenium) in urine samples and an ensemble linear discriminant analysis (ELDA), a detection method for lung cancer has been developed. A dataset containing 30 healthy samples and 27 lung cancer samples is used for experiment. The whole dataset was first split into a training set with 29 samples and a test set with 28 samples. The prediction results from the ELDA classifier were compared with those from single Fisher's discriminate analysis (FDA). On the test set, the ELDA classifier achieved better performance, that is, a sensitivity of 100%, a specificity of 86.7%, and an overall accuracy of 92.9%, while the FDA classifier had a sensitivity of 92.3%, a specificity of 93.3%, and an overall accuracy of 92.9%. The superiority of ELDA to FDA is ascribed to the fact that ELDA can model more nonlinear relationships through the cooperation of several single models, suggesting that ensemble modeling is more advisable in such a task.