Explainable AI in Diagnosing and Anticipating Leukemia Using Transfer Learning Method

SurvIAE: Survival prediction with Interpretable Autoencoders from Diffuse Large B-Cells Lymphoma gene expression data

BACKGROUND

In Diffuse Large B-Cell Lymphoma (DLBCL), several methodologies are emerging to derive novel biomarkers to be incorporated in the risk assessment. We realized a pipeline that relies on autoencoders (AE) and Explainable Artificial Intelligence (XAI) to stratify prognosis and derive a gene-based signature.

METHODS

AE was exploited to learn an unsupervised representation of the gene expression (GE) from three publicly available datasets, each with its own technology. Multi-layer perceptron (MLP) was used to classify prognosis from latent representation. GE data were preprocessed as normalized, scaled, and standardized. Four different AE architectures (Large, Medium, Small and Extra Small) were compared to find the most suitable for GE data. The joint AE-MLP classified patients on six different outcomes: overall survival at 12, 36, 60 months and progression-free survival (PFS) at 12, 36, 60 months. XAI techniques were used to derive a gene-based signature aimed at refining the Revised International Prognostic Index (R-IPI) risk, which was validated in a fourth independent publicly available dataset. We named our tool SurvIAE: Survival prediction with Interpretable AE.

RESULTS

From the latent space of AEs, we observed that scaled and standardized data reduced the batch effect. SurvIAE models outperformed R-IPI with Matthews Correlation Coefficient up to 0.42 vs. 0.18 for the validation-set (PFS36) and to 0.30 vs. 0.19 for the test-set (PFS60). We selected the SurvIAE-Small-PFS36 as the best model and, from its gene signature, we stratified patients in three risk groups: R-IPI Poor patients with High levels of GAB1, R-IPI Poor patients with Low levels of GAB1 or R-IPI Good/Very Good patients with Low levels of GPR132, and R-IPI Good/Very Good patients with High levels of GPR132.

CONCLUSIONS

SurvIAE showed the potential to derive a gene signature with translational purpose in DLBCL. The pipeline was made publicly available and can be reused for other pathologies.

The enlightening role of explainable artificial intelligence in medical & healthcare domains: A systematic literature review

In domains such as medical and healthcare, the interpretability and explainability of machine learning and artificial intelligence systems are crucial for building trust in their results. Errors caused by these systems, such as incorrect diagnoses or treatments, can have severe and even life-threatening consequences for patients. To address this issue, Explainable Artificial Intelligence (XAI) has emerged as a popular area of research, focused on understanding the black-box nature of complex and hard-to-interpret machine learning models. While humans can increase the accuracy of these models through technical expertise, understanding how these models actually function during training can be difficult or even impossible. XAI algorithms such as Local Interpretable Model-Agnostic Explanations (LIME) and SHapley Additive exPlanations (SHAP) can provide explanations for these models, improving trust in their predictions by providing feature importance and increasing confidence in the systems. Many articles have been published that propose solutions to medical problems by using machine learning models alongside XAI algorithms to provide interpretability and explainability. In our study, we identified 454 articles published from 2018-2022 and analyzed 93 of them to explore the use of these techniques in the medical 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.

ResRandSVM: Hybrid Approach for Acute Lymphocytic Leukemia Classification in Blood Smear Images

Acute Lymphocytic Leukemia is a type of cancer that occurs when abnormal white blood cells are produced in the bone marrow which do not function properly, crowding out healthy cells and weakening the immunity of the body and thus its ability to resist infections. It spreads quickly in children's bodies, and if not treated promptly it may lead to death. The manual detection of this disease is a tedious and slow task. Machine learning and deep learning techniques are faster than manual detection and more accurate. In this paper, a deep feature selection-based approach ResRandSVM is proposed for the detection of Acute Lymphocytic Leukemia in blood smear images. The proposed approach uses seven deep-learning models: ResNet152, VGG16, DenseNet121, MobileNetV2, InceptionV3, EfficientNetB0 and ResNet50 for deep feature extraction from blood smear images. After that, three feature selection methods are used to extract valuable and important features: analysis of variance (ANOVA), principal component analysis (PCA), and Random Forest. Then the selected feature map is fed to four different classifiers, Adaboost, Support Vector Machine, Artificial Neural Network and Naïve Bayes models, to classify the images into leukemia and normal images. The model performs best with a combination of ResNet50 as a feature extractor, Random Forest as feature selection and Support Vector Machine as a classifier with an accuracy of 0.900, precision of 0.902, recall of 0.957 and F1-score of 0.929.

One-stage and lightweight CNN detection approach with attention: Application to WBC detection of microscopic images

White blood cell (WBC) detection in microscopic images is indispensable in medical diagnostics; however, this work, based on manual checking, is time-consuming, labor-intensive, and easily results in errors. Using object detectors for WBCs with deep convolutional neural networks can be regarded as a feasible solution. In this paper, to improve the examination precision and efficiency, a one-stage and lightweight CNN detector with an attention mechanism for detecting microscopic WBC images, and a white blood cell detection vision system are proposed. The method integrates different optimizing strategies to strengthen the feature extraction capability through the combination of an improved residual convolution module, hybrid spatial pyramid pooling module, improved coordinate attention mechanism, efficient intersection over union (EIOU) loss and Mish activation function. Extensive ablation and contrast experiments on the latest public Raabin-WBC dataset verify the effectiveness and robustness of the proposed detector for achieving a better overall detection performance. It is also more efficient than other existing studies for blood cell detection on two additional classic public BCCD and LISC datasets. The novel detection approach is significant and flexible for medical technicians to use for blood cell microscopic examination in clinical practice.

Computer-Aided Diagnosis System for Blood Diseases Using EfficientNet-B3 Based on a Dynamic Learning Algorithm

The immune system's overproduction of white blood cells (WBCs) results in the most common blood cancer, leukemia. It accounts for about 25% of childhood cancers and is one of the primary causes of death worldwide. The most well-known type of leukemia found in the human bone marrow is acute lymphoblastic leukemia (ALL). It is a disease that affects the bone marrow and kills white blood cells. Better treatment and a higher likelihood of survival can be helped by early and precise cancer detection. As a result, doctors can use computer-aided diagnostic (CAD) models to detect early leukemia effectively. In this research, we proposed a classification model based on the EfficientNet-B3 convolutional neural network (CNN) model to distinguish ALL as an automated model that automatically changes the learning rate (LR). We set up a custom LR that compared the loss value and training accuracy at the beginning of each epoch. We evaluated the proposed model on the C-NMC_Leukemia dataset. The dataset was pre-processed with normalization and balancing. The proposed model was evaluated and compared with recent classifiers. The proposed model's average precision, recall, specificity, accuracy, and Disc similarity coefficient (DSC) were 98.29%, 97.83%, 97.82%, 98.31%, and 98.05%, respectively. Moreover, the proposed model was used to examine microscopic images of the blood to identify the malaria parasite. Our proposed model's average precision, recall, specificity, accuracy, and DSC were 97.69%, 97.68%, 97.67%, 97.68%, and 97.68%, respectively. Therefore, the evaluation of the proposed model showed that it is an unrivaled perceptive outcome with tuning as opposed to other ongoing existing models.

An efficient computer vision-based approach for acute lymphoblastic leukemia prediction

Leukemia (blood cancer) diseases arise when the number of White blood cells (WBCs) is imbalanced in the human body. When the bone marrow produces many immature WBCs that kill healthy cells, acute lymphocytic leukemia (ALL) impacts people of all ages. Thus, timely predicting this disease can increase the chance of survival, and the patient can get his therapy early. Manual prediction is very expensive and time-consuming. Therefore, automated prediction techniques are essential. In this research, we propose an ensemble automated prediction approach that uses four machine learning algorithms K-Nearest Neighbor (KNN), Support Vector Machine (SVM), Random Forest (RF), and Naive Bayes (NB). The C-NMC leukemia dataset is used from the Kaggle repository to predict leukemia. Dataset is divided into two classes cancer and healthy cells. We perform data preprocessing steps, such as the first images being cropped using minimum and maximum points. Feature extraction is performed to extract the feature using pre-trained Convolutional Neural Network-based Deep Neural Network (DNN) architectures (VGG19, ResNet50, or ResNet101). Data scaling is performed by using the MinMaxScaler normalization technique. Analysis of Variance (ANOVA), Recursive Feature Elimination (RFE), and Random Forest (RF) as feature Selection techniques. Classification machine learning algorithms and ensemble voting are applied to selected features. Results reveal that SVM with 90.0% accuracy outperforms compared to other algorithms.

Utilization of model-agnostic explainable artificial intelligence frameworks in oncology: a narrative review

Background and Objective

Machine learning (ML) models are increasingly being utilized in oncology research for use in the clinic. However, while more complicated models may provide improvements in predictive or prognostic power, a hurdle to their adoption are limits of model interpretability, wherein the inner workings can be perceived as a "black box". Explainable artificial intelligence (XAI) frameworks including Local Interpretable Model-agnostic Explanations (LIME) and SHapley Additive exPlanations (SHAP) are novel, model-agnostic approaches that aim to provide insight into the inner workings of the "black box" by producing quantitative visualizations of how model predictions are calculated. In doing so, XAI can transform complicated ML models into easily understandable charts and interpretable sets of rules, which can give providers with an intuitive understanding of the knowledge generated, thus facilitating the deployment of such models in routine clinical workflows.

Methods

We performed a comprehensive, non-systematic review of the latest literature to define use cases of model-agnostic XAI frameworks in oncologic research. The examined database was PubMed/MEDLINE. The last search was run on May 1, 2022.

Key Content and Findings

In this review, we identified several fields in oncology research where ML models and XAI were utilized to improve interpretability, including prognostication, diagnosis, radiomics, pathology, treatment selection, radiation treatment workflows, and epidemiology. Within these fields, XAI facilitates determination of feature importance in the overall model, visualization of relationships and/or interactions, evaluation of how individual predictions are produced, feature selection, identification of prognostic and/or predictive thresholds, and overall confidence in the models, among other benefits. These examples provide a basis for future work to expand on, which can facilitate adoption in the clinic when the complexity of such modeling would otherwise be prohibitive.

Conclusions

Model-agnostic XAI frameworks offer an intuitive and effective means of describing oncology ML models, with applications including prognostication and determination of optimal treatment regimens. Using such frameworks presents an opportunity to improve understanding of ML models, which is a critical step to their adoption in the clinic.