Accuracy Enhanced Lung Cancer Prognosis for Improving Patient Survivability Using Proposed Gaussian Classifier System

Identifying cancer risks using spectral subset feature selection based on multi-layer perception neural network for premature treatment

Recently, human beings have been affected mainly by dreadful cancer diseases. Predicting cancer risk levels is a major challenge in biomedical research for feature selection and classification at the margins. To resolve this problem, we propose a Subset Clustering-Based Feature Selection using a Multi-Layer Perception Neural Network (SCFS-MLPNN). Initially, pre-processing is carried out with Intensive Mutual Disease Influence Rate (IMDIR) to identify the relational features. In addition, the Successive Disease Pattern Stimulus Rate (SDPSR) is carried out to create relative feature patterns. Based on the patterns, the features are selected and grouped into clustering. Inter-Class Sub-Space Clustering (ICSSC) is applied to split the features by class labels depending on the marginal rate. From the class labels, marginal features are obtained using spectral subset feature selection (SSFS). The selected features are then trained in a Multi-Layer Perception Neural Network (MLPNN) classifier to classify the patient features by risk. Its contribution is to exploit subset features to improve classification accuracy by clustering relational features. The proposed classifier yields higher classification accuracy than previous methods and observes cancer detection for early detection. Therefore, the proposed method achieved a risk analysis accuracy of 91.8% and an F-measure of 91.3% for early detection, which is recommended for early diagnosis.

SPIN-PM: a consensus framework to evaluate the presence of spin in studies on prediction models

OBJECTIVES

To develop a framework to identify and evaluate spin practices and its facilitators in studies on clinical prediction model regardless of the modeling technique.

STUDY DESIGN AND SETTING

We followed a three-phase consensus process: (1) premeeting literature review to generate items to be included; (2) a series of structured meetings to provide comments discussed and exchanged viewpoints on items to be included with a panel of experienced researchers; and (3) postmeeting review on final list of items and examples to be included. Through this iterative consensus process, a framework was derived after all panel's researchers agreed.

RESULTS

This consensus process involved a panel of eight researchers and resulted in SPIN-Prediction Models which consists of two categories of spin (misleading interpretation and misleading transportability), and within these categories, two forms of spin (spin practices and facilitators of spin). We provide criteria and examples.

CONCLUSION

We proposed this guidance aiming to facilitate not only the accurate reporting but also an accurate interpretation and extrapolation of clinical prediction models which will likely improve the reporting quality of subsequent research, as well as reduce research waste.

New perspectives on cancer clinical research in the era of big data and machine learning

In the 21st century, the development of medical science has entered the era of big data, and machine learning has become an essential tool for mining medical big data. The establishment of the SEER database has provided a wealth of epidemiological data for cancer clinical research, and the number of studies based on SEER and machine learning has been growing in recent years. This article reviews recent research based on SEER and machine learning and finds that the current focus of such studies is primarily on the development and validation of models using machine learning algorithms, with the main directions being lymph node metastasis prediction, distant metastasis prediction, and prognosis-related research. Compared to traditional models, machine learning algorithms have the advantage of stronger adaptability, but also suffer from disadvantages such as overfitting and poor interpretability, which need to be weighed in practical applications. At present, machine learning algorithms, as the foundation of artificial intelligence, have just begun to emerge in the field of cancer clinical research. The future development of oncology will enter a more precise era of cancer research, characterized by larger data, higher dimensions, and more frequent information exchange. Machine learning is bound to shine brightly in this field.

Predicting lung cancer survival based on clinical data using machine learning: A review

Machine learning has gained popularity in predicting survival time in the medical field. This review examines studies utilizing machine learning and data-mining techniques to predict lung cancer survival using clinical data. A systematic literature review searched MEDLINE, Scopus, and Google Scholar databases, following reporting guidelines and using the COVIDENCE system. Studies published from 2000 to 2023 employing machine learning for lung cancer survival prediction were included. Risk of bias assessment used the prediction model risk of bias assessment tool. Thirty studies were reviewed, with 13 (43.3%) using the surveillance, epidemiology, and end results database. Missing data handling was addressed in 12 (40%) studies, primarily through data transformation and conversion. Feature selection algorithms were used in 19 (63.3%) studies, with age, sex, and N stage being the most chosen features. Random forest was the predominant machine learning model, used in 17 (56.6%) studies. While the number of lung cancer survival prediction studies is limited, the use of machine learning models based on clinical data has grown since 2012. Consideration of diverse patient cohorts and data pre-processing are crucial. Notably, most studies did not account for missing data, normalization, scaling, or standardized data, potentially introducing bias. Therefore, a comprehensive study on lung cancer survival prediction using clinical data is needed, addressing these challenges.

Overinterpretation of findings in machine learning prediction model studies in oncology: a systematic review

OBJECTIVES

In biomedical research, spin is the overinterpretation of findings, and it is a growing concern. To date, the presence of spin has not been evaluated in prognostic model research in oncology, including studies developing and validating models for individualized risk prediction.

STUDY DESIGN AND SETTING

We conducted a systematic review, searching MEDLINE and EMBASE for oncology-related studies that developed and validated a prognostic model using machine learning published between 1st January, 2019, and 5th September, 2019. We used existing spin frameworks and described areas of highly suggestive spin practices.

RESULTS

We included 62 publications (including 152 developed models; 37 validated models). Reporting was inconsistent between methods and the results in 27% of studies due to additional analysis and selective reporting. Thirty-two studies (out of 36 applicable studies) reported comparisons between developed models in their discussion and predominantly used discrimination measures to support their claims (78%). Thirty-five studies (56%) used an overly strong or leading word in their title, abstract, results, discussion, or conclusion.

CONCLUSION

The potential for spin needs to be considered when reading, interpreting, and using studies that developed and validated prognostic models in oncology. Researchers should carefully report their prognostic model research using words that reflect their actual results and strength of evidence.

A systematic literature review for the prediction of anticancer drug response using various machine-learning and deep-learning techniques

Computational methods have gained prominence in healthcare research. The accessibility of healthcare data has greatly incited academicians and researchers to develop executions that help in prognosis of cancer drug response. Among various computational methods, machine-learning (ML) and deep-learning (DL) methods provide the most consistent and effectual approaches to handle the serious aftermaths of the deadly disease and drug administered to the patients. Hence, this systematic literature review has reviewed researches that have investigated drug discovery and prognosis of anticancer drug response using ML and DL algorithms. Fot this purpose, PRISMA guidelines have been followed to choose research papers from Google Scholar, PubMed, and Sciencedirect websites. A total count of 105 papers that align with the context of this review were chosen. Further, the review also presents accuracy of the existing ML and DL methods in the prediction of anticancer drug response. It has been found from the review that, amidst the availability of various studies, there are certain challenges associated with each method. Thus, future researchers can consider these limitations and challenges to develop a prominent anticancer drug response prediction method, and it would be greatly beneficial to the medical professionals in administering non-invasive treatment to the patients.

Subtyping and grading of lower-grade gliomas using integrated feature selection and support vector machine

Classifying lower-grade gliomas (LGGs) is a crucial step for accurate therapeutic intervention. The histopathological classification of various subtypes of LGG, including astrocytoma, oligodendroglioma and oligoastrocytoma, suffers from intraobserver and interobserver variability leading to inaccurate classification and greater risk to patient health. We designed an efficient machine learning-based classification framework to diagnose LGG subtypes and grades using transcriptome data. First, we developed an integrated feature selection method based on correlation and support vector machine (SVM) recursive feature elimination. Then, implementation of the SVM classifier achieved superior accuracy compared with other machine learning frameworks. Most importantly, we found that the accuracy of subtype classification is always high (>90%) in a specific grade rather than in mixed grade (~80%) cancer. Differential co-expression analysis revealed higher heterogeneity in mixed grade cancer, resulting in reduced prediction accuracy. Our findings suggest that it is necessary to identify cancer grades and subtypes to attain a higher classification accuracy. Our six-class classification model efficiently predicts the grades and subtypes with an average accuracy of 91% (±0.02). Furthermore, we identify several predictive biomarkers using co-expression, gene set enrichment and survival analysis, indicating our framework is biologically interpretable and can potentially support the clinician.

A Deep Learning-Based Framework for Supporting Clinical Diagnosis of Glioblastoma Subtypes

Understanding molecular features that facilitate aggressive phenotypes in glioblastoma multiforme (GBM) remains a major clinical challenge. Accurate diagnosis of GBM subtypes, namely classical, proneural, and mesenchymal, and identification of specific molecular features are crucial for clinicians for systematic treatment. We develop a biologically interpretable and highly efficient deep learning framework based on a convolutional neural network for subtype identification. The classifiers were generated from high-throughput data of different molecular levels, i.e., transcriptome and methylome. Furthermore, an integrated subsystem of transcriptome and methylome data was also used to build the biologically relevant model. Our results show that deep learning model outperforms the traditional machine learning algorithms. Furthermore, to evaluate the biological and clinical applicability of the classification, we performed weighted gene correlation network analysis, gene set enrichment, and survival analysis of the feature genes. We identified the genotype-phenotype relationship of GBM subtypes and the subtype-specific predictive biomarkers for potential diagnosis and treatment.

Methodological conduct of prognostic prediction models developed using machine learning in oncology: a systematic review

BACKGROUND

Describe and evaluate the methodological conduct of prognostic prediction models developed using machine learning methods in oncology.

METHODS

We conducted a systematic review in MEDLINE and Embase between 01/01/2019 and 05/09/2019, for studies developing a prognostic prediction model using machine learning methods in oncology. We used the Transparent Reporting of a multivariable prediction model for Individual Prognosis Or Diagnosis (TRIPOD) statement, Prediction model Risk Of Bias ASsessment Tool (PROBAST) and CHecklist for critical Appraisal and data extraction for systematic Reviews of prediction Modelling Studies (CHARMS) to assess the methodological conduct of included publications. Results were summarised by modelling type: regression-, non-regression-based and ensemble machine learning models.

RESULTS

Sixty-two publications met inclusion criteria developing 152 models across all publications. Forty-two models were regression-based, 71 were non-regression-based and 39 were ensemble models. A median of 647 individuals (IQR: 203 to 4059) and 195 events (IQR: 38 to 1269) were used for model development, and 553 individuals (IQR: 69 to 3069) and 50 events (IQR: 17.5 to 326.5) for model validation. A higher number of events per predictor was used for developing regression-based models (median: 8, IQR: 7.1 to 23.5), compared to alternative machine learning (median: 3.4, IQR: 1.1 to 19.1) and ensemble models (median: 1.7, IQR: 1.1 to 6). Sample size was rarely justified (n = 5/62; 8%). Some or all continuous predictors were categorised before modelling in 24 studies (39%). 46% (n = 24/62) of models reporting predictor selection before modelling used univariable analyses, and common method across all modelling types. Ten out of 24 models for time-to-event outcomes accounted for censoring (42%). A split sample approach was the most popular method for internal validation (n = 25/62, 40%). Calibration was reported in 11 studies. Less than half of models were reported or made available.

CONCLUSIONS

The methodological conduct of machine learning based clinical prediction models is poor. Guidance is urgently needed, with increased awareness and education of minimum prediction modelling standards. Particular focus is needed on sample size estimation, development and validation analysis methods, and ensuring the model is available for independent validation, to improve quality of machine learning based clinical prediction models.

A Review on Lung Cancer Diagnosis Using Data Mining Algorithms

Due to the serious consequences of lung cancer, medical associations use computer-aided diagnostic procedures to diagnose this disease more accurately. Despite the damaging effects of lung cancer on the body, the lifetime of cancer patients can be extended by early diagnosis. Data mining techniques are practical in diagnosing lung cancer in its first stages. This paper surveys a number of leading data mining-based cancer diagnosis approaches. Moreover, this review draws a comparison between data mining approaches in terms of selection criteria and presents the advantages and disadvantages of each method.

Identifying Lung Cancer Risk Factors in the Elderly Using Deep Neural Networks: Quantitative Analysis of Web-Based Survey Data

BACKGROUND

Lung cancer is one of the most dangerous malignant tumors, with the fastest-growing morbidity and mortality, especially in the elderly. With a rapid growth of the elderly population in recent years, lung cancer prevention and control are increasingly of fundamental importance, but are complicated by the fact that the pathogenesis of lung cancer is a complex process involving a variety of risk factors.

OBJECTIVE

This study aimed at identifying key risk factors of lung cancer incidence in the elderly and quantitatively analyzing these risk factors' degree of influence using a deep learning method.

METHODS

Based on Web-based survey data, we integrated multidisciplinary risk factors, including behavioral risk factors, disease history factors, environmental factors, and demographic factors, and then preprocessed these integrated data. We trained deep neural network models in a stratified elderly population. We then extracted risk factors of lung cancer in the elderly and conducted quantitative analyses of the degree of influence using the deep neural network models.

RESULTS

The proposed model quantitatively identified risk factors based on 235,673 adults. The proposed deep neural network models of 4 groups (age ≥65 years, women ≥65 years old, men ≥65 years old, and the whole population) achieved good performance in identifying lung cancer risk factors, with accuracy ranging from 0.927 (95% CI 0.223-0.525; P=.002) to 0.962 (95% CI 0.530-0.751; P=.002) and the area under curve ranging from 0.913 (95% CI 0.564-0.803) to 0.931(95% CI 0.499-0.593). Smoking frequency was the leading risk factor for lung cancer in men 65 years and older. Time since quitting and smoking at least 100 cigarettes in their lifetime were the main risk factors for lung cancer in women 65 years and older. Men 65 years and older had the highest lung cancer incidence among the stratified groups, particularly non-small cell lung cancer incidence. Lung cancer incidence decreased more obviously in men than in women with smoking rate decline.

CONCLUSIONS

This study demonstrated a quantitative method to identify risk factors of lung cancer in the elderly. The proposed models provided intervention indicators to prevent lung cancer, especially in older men. This approach might be used as a risk factor identification tool to apply in other cancers and help physicians make decisions on cancer prevention.

Survivability Prognosis for Lung Cancer Patients at Different Severity Stages by a Risk Factor-Based Bayesian Network Modeling

Lung cancer is a major reason of mortalities. Estimating the survivability for this disease has become a key issue to families, hospitals, and countries. A conditional Gaussian Bayesian network model was presented in this study. This model considered 15 risk factors to predict the survivability of a lung cancer patient at 4 severity stages. We surveyed 1075 patients. The presented model is constructed by using the demographic, diagnosed-based, and prior-utilization variables. The proposed model for the survivability prognosis at different four stages performed R² of 93.57%, 86.83%, 67.22%, and 52.94%, respectively. The model predicted the lung cancer survivability with high accuracy compared with the reported models. Our model also shows that it reached the ceiling of an ideal Bayesian network.