Comparing machine learning algorithms to predict 5-year survival in patients with chronic myeloid leukemia

Identification of relevant features using SEQENS to improve supervised machine learning models predicting AML treatment outcome

BACKGROUND AND OBJECTIVE

This study has two main objectives. First, to evaluate a feature selection methodology based on SEQENS, an algorithm for identifying relevant variables. Second, to validate machine learning models that predict the risk of complications in patients with acute myeloid leukemia (AML) using data available at diagnosis. Predictions are made at three time points: 90 days, six months, and one year post-diagnosis. These objectives represent fundamental steps toward the development of a tool to assist clinicians in therapeutic decision-making and provide insights into the risk factors associated with AML complications.

METHODS

A dataset of 568 patients, including demographic, clinical, genetic (VAF), and cytogenetic information, was created by combining data from Hospital 12 de Octubre (Madrid, Spain) and Instituto de Investigación Sanitaria La Fe (Valencia, Spain). Feature selection based on an enhanced version of SEQENS was conducted for each time point, followed by the comparison of four classifiers (XGBoost, Multi-Layer Perceptron, Logistic Regression and Decision Tree) to assess the impact of feature selection on model performance.

RESULTS

SEQENS identified different relevant features for each prediction horizon, with Age, TP53, - 7/7Q, and EZH2 consistently relevant across all time points. The models were evaluated using 5-fold cross-validation, XGBoost achieve the highest average ROC-AUC scores of 0.81, 0.84, and 0.82 for 90-day, 6-month, and 1-year predictions, respectively. Generally, performance remained stable or improved after applying SEQENS-based feature selection. Evaluation on an external test set of 54 patients yielded ROC-AUC scores of 0.72 (90-day), 0.75 (6-month), and 0.68 (1-year).

CONCLUSIONS

The models achieved performance levels that suggest they could serve as therapeutic decision support tools at different times after diagnosis. The selected variables align with the European LeukemiaNet (ELN) 2022 risk classification, and the SEQENS-based feature selection effectively reduced the feature set while maintaining prediction accuracy.

Utilization of Machine Learning in the Prediction, Diagnosis, Prognosis, and Management of Chronic Myeloid Leukemia

Chronic myeloid leukemia is a clonal hematologic disease characterized by the presence of the Philadelphia chromosome and the BCR::ABL1 fusion protein. Integrating different molecular, genetic, clinical, and laboratory data would improve the diagnostic, prognostic, and predictive sensitivity of chronic myeloid leukemia. However, without artificial intelligence support, managing such a vast volume of data would be impossible. Considering the advancements and growth in machine learning throughout the years, several models and algorithms have been proposed for the management of chronic myeloid leukemia. Here, we provide an overview of recent research that used specific algorithms on patients with chronic myeloid leukemia, highlighting the potential benefits of adopting machine learning in therapeutic contexts as well as its drawbacks. Our analysis demonstrated the great potential for advancing precision treatment in CML through the combination of clinical and genetic data, laboratory testing, and machine learning. We can use these powerful research instruments to unravel the molecular and spatial puzzles of CML by overcoming the current obstacles. A new age of patient-centered hematology care will be ushered in by this, opening the door for improved diagnosis accuracy, sophisticated risk assessment, and customized treatment plans.

Application of artificial intelligence in chronic myeloid leukemia (CML) disease prediction and management: a scoping review

BACKGROUND

Navigating the complexity of chronic myeloid leukemia (CML) diagnosis and management poses significant challenges, including the need for accurate prediction of disease progression and response to treatment. Artificial intelligence (AI) presents a transformative approach that enables the development of sophisticated predictive models and personalized treatment strategies that enhance early detection and improve therapeutic interventions for better patient outcomes.

METHODS

An extensive search was conducted to retrieve relevant articles from PubMed, Scopus, and Web of Science databases up to April 24, 2023. Data were collected using a standardized extraction form, and the results are presented in tables and graphs, showing frequencies and percentages. The authors adhered to the PRISMA-ScR checklist to ensure transparent reporting of the study.

RESULTS

Of the 176 articles initially identified, 12 were selected for our study after removing duplicates and applying the inclusion and exclusion criteria. AI's primary applications of AI in managing CML included tumor diagnosis/classification (n = 9, 75%), prediction/prognosis (n = 2, 17%), and treatment (n = 1, 8%). For tumor diagnosis, AI is categorized into blood smear image-based (n = 5), clinical parameter-based (n = 2), and gene profiling-based (n = 2) approaches. The most commonly employed AI models include Support Vector Machine (SVM) (n = 5), eXtreme Gradient Boosting (XGBoost) (n = 4), and various neural network methods, such as Artificial Neural Network (ANN) (n = 3). Furthermore, Hybrid Convolutional Neural Network with Interactive Autodidactic School (HCNN-IAS) achieved 100% accuracy and sensitivity in organizing leukemia data types, whereas MayGAN attained 99.8% accuracy and high performance in diagnosing CML from blood smear images.

CONCLUSIONS

AI offers groundbreaking insights and tools for enhancing prediction, prognosis, and personalized treatment in chronic myeloid leukemia. Integrated AI systems empower healthcare practitioners with advanced analytics, optimizing patient care and improving clinical outcomes in CML management.

Balancing aquaculture and estuarine ecosystems: machine learning-based water quality indices for effective management

This study delves into the environmental impact of inland aquaculture on estuarine ecosystems by examining the water quality of four estuarine streams within the key inland aquaculture zone of South India. In this region, extensive and intensive aquaculture practices are common, posing potential challenges to estuarine health. The research explores the predictive capabilities of the Gaussian elimination method (GEM) and machine learning techniques, specifically multi-linear regression (MLR) and support vector regressor (SVR), in forecasting the water quality index of these streams. Through comprehensive evaluation using performance metrics such as coefficient of determination (R2) and average mean absolute percentage error (MAPE), MLR and SVR demonstrate higher prediction efficiency. Notably, employing key water parameters as inputs in machine learning models is also more effective. Biochemical oxygen demand (BOD) emerges as a critical water parameter, identified by both MLR and SVR, exhibiting high specificity in predicting water quality. This suggests that MLR and SVR, incorporating key water parameters, should be prioritized for future water quality monitoring in intensive aquaculture zones, facilitating timely warnings and interventions to safeguard water quality.

Artificial Intelligence-Based Management of Adult Chronic Myeloid Leukemia: Where Are We and Where Are We Going?

Artificial intelligence (AI) is emerging as a discipline capable of providing significant added value in Medicine, in particular in radiomic, imaging analysis, big dataset analysis, and also for generating virtual cohort of patients. However, in coping with chronic myeloid leukemia (CML), considered an easily managed malignancy after the introduction of TKIs which strongly improved the life expectancy of patients, AI is still in its infancy. Noteworthy, the findings of initial trials are intriguing and encouraging, both in terms of performance and adaptability to different contexts in which AI can be applied. Indeed, the improvement of diagnosis and prognosis by leveraging biochemical, biomolecular, imaging, and clinical data can be crucial for the implementation of the personalized medicine paradigm or the streamlining of procedures and services. In this review, we present the state of the art of AI applications in the field of CML, describing the techniques and objectives, and with a general focus that goes beyond Machine Learning (ML), but instead embraces the wider AI field. The present scooping review spans on publications reported in Pubmed from 2003 to 2023, and resulting by searching "chronic myeloid leukemia" and "artificial intelligence". The time frame reflects the real literature production and was not restricted. We also take the opportunity for discussing the main pitfalls and key points to which AI must respond, especially considering the critical role of the 'human' factor, which remains key in this domain.

Artificial Intelligence-Assisted Diagnostic Cytology and Genomic Testing for Hematologic Disorders

Artificial intelligence (AI) is a rapidly evolving field of computer science that involves the development of computational programs that can mimic human intelligence. In particular, machine learning and deep learning models have enabled the identification and grouping of patterns within data, leading to the development of AI systems that have been applied in various areas of hematology, including digital pathology, alpha thalassemia patient screening, cytogenetics, immunophenotyping, and sequencing. These AI-assisted methods have shown promise in improving diagnostic accuracy and efficiency, identifying novel biomarkers, and predicting treatment outcomes. However, limitations such as limited databases, lack of validation and standardization, systematic errors, and bias prevent AI from completely replacing manual diagnosis in hematology. In addition, the processing of large amounts of patient data and personal information by AI poses potential data privacy issues, necessitating the development of regulations to evaluate AI systems and address ethical concerns in clinical AI systems. Nonetheless, with continued research and development, AI has the potential to revolutionize the field of hematology and improve patient outcomes. To fully realize this potential, however, the challenges facing AI in hematology must be addressed and overcome.

Predicting the Activity of Oral Lichen Planus with Glycolysis-related Molecules: A Scikit-learn-based Function

OBJECTIVE

Oral lichen planus (OLP) is one of the most common oral mucosa diseases, and is mainly mediated by T lymphocytes. The metabolic reprogramming of activated T cells has been shown to transform from oxidative phosphorylation to aerobic glycolysis. The present study investigated the serum levels of glycolysis-related molecules (lactate dehydrogenase, LDH; pyruvic acid, PA; lactic acid, LAC) in OLP, and the correlation with OLP activity was assessed using the reticular, atrophic and erosive lesion (RAE) scoring system.

METHODS

Univariate and multivariate linear regression functions based on scikit-learn were designed to predict the RAE scores in OLP patients, and the performance of these two machine learning functions was compared.

RESULTS

The results revealed that the serum levels of PA and LAC were upregulated in erosive OLP (EOLP) patients, when compared to healthy volunteers. Furthermore, the LDH and LAC levels were significantly higher in the EOLP group than in the nonerosive OLP (NEOLP) group. All glycolysis-related molecules were positively correlated to the RAE scores. Among these, LAC had a strong correlation. The univariate function that involved the LAC level and the multivariate function that involved all glycolysis-related molecules presented comparable prediction accuracy and stability, but the latter was more time-consuming.

CONCLUSION

It can be concluded that the serum LAC level can be a user-friendly biomarker to monitor the OLP activity, based on the univariate function developed in the present study. The intervention of the glycolytic pathway may provide a potential therapeutic strategy.

Applications of Machine Learning in Chronic Myeloid Leukemia

Chronic myeloid leukemia (CML) is a myeloproliferative neoplasm characterized by dysregulated growth and the proliferation of myeloid cells in the bone marrow caused by the BCR-ABL1 fusion gene. Clinically, CML demonstrates an increased production of mature and maturing granulocytes, mainly neutrophils. When a patient is suspected to have CML, peripheral blood smears and bone marrow biopsies may be manually examined by a hematologist. However, confirmatory testing for the BCR-ABL1 gene is still needed to confirm the diagnosis. Despite tyrosine kinase inhibitors (TKIs) being the mainstay of treatment for patients with CML, different agents should be used in different patients given their stage of disease and comorbidities. Moreover, some patients do not respond well to certain agents and some need more aggressive courses of therapy. Given the innovations and development that machine learning (ML) and artificial intelligence (AI) have undergone over the years, multiple models and algorithms have been put forward to help in the assessment and treatment of CML. In this review, we summarize the recent studies utilizing ML algorithms in patients with CML. The search was conducted on the PubMed/Medline and Embase databases and yielded 66 full-text articles and abstracts, out of which 11 studies were included after screening against the inclusion criteria. The studies included show potential for the clinical implementation of ML models in the diagnosis, risk assessment, and treatment processes of patients with CML.

Prediction of acute organophosphate poisoning severity using machine learning techniques

Poisoning with organophosphate compounds is a significant public health risk, especially in developing countries. Considering the importance of early and accurate prediction of organophosphate poisoning prognosis, the aim of this study was to develop a machine learning-based prediction model to predict the severity of organophosphate poisoning. The data of patients with organophosphate poisoning were retrospectively extracted and split into training and test sets in a ratio of 70:30. The feature selection was done by least absolute shrinkage and selection operator method. Selected features were fed into five machine learning techniques, including Histogram Boosting Gradient, eXtreme Gradient Boosting, K-Nearest Neighborhood, Support Vector Machine (SVM) (kernel = linear), and Random Forest. The Scikit-learn library in Python programming language was used to implement the models. Finally, the performance of developed models was measured using ten-fold cross-validation methods and some evaluation criteria with 95 % confidence intervals. A total of 1237 patients were used to train and test the machine learning models. According to the criteria determining severe organophosphate poisoning, 732 patients were assigned to group 1 (patients with mild to moderate poisoning) and 505 patients were assigned to group 2 (patients with severe poisoning). With an AUC value of 0.907 (95 % CI 0.89-0.92), the model developed using XGBoost outperformed other models. Feature importance evaluation found that venous blood gas-pH, white blood cells, and plasma cholinesterase activity were the top three variables that contribute the most to the prediction performance of the prognosis in patients with organophosphate poisoning. XGBoost model yield an accuracy of 90.1 % (95 % CI 0.891-0.918), specificity of 91.4 % (95 % CI 0.90-0.92), a sensitivity of 89.5 % (95 % CI 0.87-0.91), F-measure of 91.2 % (95 % CI 0.90-0.921), and Kappa statistic of 91.2 % (95 % CI 0.90-0.92). The machine learning-based prediction models can accurately predict the severity of organophosphate poisoning. Based on feature selection techniques, the most important predictors of organophosphate poisoning were VBG-pH, white blood cell count, plasma cholinesterase activity, VBG-BE, and age. The best algorithm with the highest predictive performance was the XGBoost classifier.