A Roadmap towards Breast Cancer Therapies Supported by Explainable Artificial Intelligence

Developing an ensemble machine learning study: Insights from a multi-center proof-of-concept study

BACKGROUND

To address the numerous unmeet clinical needs, in recent years several Machine Learning models applied to medical images and clinical data have been introduced and developed. Even when they achieve encouraging results, they lack evolutionary progression, thus perpetuating their status as autonomous entities. We postulated that different algorithms which have been proposed in the literature to address the same diagnostic task, can be aggregated to enhance classification performance. We suggested a proof of concept to define an ensemble approach useful for integrating different algorithms proposed to solve the same clinical task.

METHODS

The proposed approach was developed starting from a public database consisting of radiomic features extracted from CT images relating to 535 patients suffering from lung cancer. Seven algorithms were trained independently by participants in the AI4MP working group on Artificial Intelligence of the Italian Association of Physics in Medicine to discriminate metastatic from non-metastatic patients. The classification scores generated by these algorithms are used to train SVM classifier. The Explainable Artificial Intelligence approach is applied to the final model. The ensemble model was validated following an 80-20 hold-out and leave-one-out scheme on the training set.

RESULTS

Compared to individual algorithms, a more accurate result was achieved. On the independent test the ensemble model achieved an accuracy of 0.78, a F1-score of 0.57 and a log-loss of 0.49. Shapley values representing the contribution of each algorithm to the final classification result of the ensemble model were calculated. This information represents an added value for the end user useful for evaluating the appropriateness of the classification result on a particular case. It also allows us to evaluate on a global level which methodological approaches of the individual algorithms are likely to have the most impact.

CONCLUSION

Our proposal represents an innovative approach useful for integrating different algorithms that populate the literature and which lays the foundations for future evaluations in broader application scenarios.

A prediction model based on digital breast pathology image information

BACKGROUND

The workload of breast cancer pathological diagnosis is very heavy. The purpose of this study is to establish a nomogram model based on pathological images to predict the benign and malignant nature of breast diseases and to validate its predictive performance.

METHODS

In retrospect, a total of 2,723 H&E-stained pathological images were collected from 1,474 patients at Qingdao Central Hospital between 2019 and 2022. The dataset consisted of 509 benign tumor images (adenosis and fibroadenoma) and 2,214 malignant tumor images (infiltrating ductal carcinoma). The images were divided into a training set (1,907) and a validation set (816). Python3.7 was used to extract the values of the R channel, G channel, B channel, and one-dimensional information entropy from all images. Multivariable logistic regression was used to select variables and establish the breast tissue pathological image prediction model.

RESULTS

The R channel value, B channel value, and one-dimensional information entropy of the images were identified as independent predictive factors for the classification of benign and malignant pathological images (P < 0.05). The area under the curve (AUC) of the nomogram model in the training set was 0.889 (95% CI: 0.869, 0.909), and the AUC in the validation set was 0.838 (95% CI: 0.7980.877). The calibration curve results showed that the calibration curve of this nomogram model was close to the ideal curve. The decision curve results indicated that the predictive model curve had a high value for auxiliary diagnosis.

CONCLUSION

The nomogram model for the prediction of benign and malignant breast diseases based on pathological images demonstrates good predictive performance. This model can assist in the diagnosis of breast tissue pathological images.

Radiomic model based on magnetic resonance imaging for predicting pathological complete response after neoadjuvant chemotherapy in breast cancer patients

Purpose

To establish a model combining radiomic and clinicopathological factors based on magnetic resonance imaging to predict pathological complete response (pCR) after neoadjuvant chemotherapy in breast cancer patients.

Method

MRI images and clinicopathologic data of 329 eligible breast cancer patients from the Affiliated Hospital of Qingdao University from August 2018 to August 2022 were included in this study. All patients received neoadjuvant chemotherapy (NAC), and imaging examinations were performed before and after NAC. A total of 329 patients were randomly allocated to a training set and a test set at a ratio of 7:3. We mainly studied the following three types of prediction models: radiomic models, clinical models, and clinical-radiomic models. All models were evaluated using subject operating characteristic curve analysis and area under the curve (AUC), decision curve analysis (DCA) and calibration curves.

Results

The AUCs of the clinical prediction model, independent imaging model and clinical combined imaging model in the training set were 0.864 0.968 and 0.984, and those in the test set were 0.724, 0.754 and 0.877, respectively. According to DCA and calibration curves, the clinical-radiomic model showed good predictive performance in both the training set and the test set, and we found that we had developed a more concise clinical-radiomic nomogram.

Conclusion

We have developed a clinical-radiomic model by integrating radiomic features and clinical factors to predict pCR after NAC in breast cancer patients, thereby contributing to the personalized treatment of patients.

Comparison between vision transformers and convolutional neural networks to predict non-small lung cancer recurrence

Non-Small cell lung cancer (NSCLC) is one of the most dangerous cancers, with 85% of all new lung cancer diagnoses and a 30-55% of recurrence rate after surgery. Thus, an accurate prediction of recurrence risk in NSCLC patients during diagnosis could be essential to drive targeted therapies preventing either overtreatment or undertreatment of cancer patients. The radiomic analysis of CT images has already shown great potential in solving this task; specifically, Convolutional Neural Networks (CNNs) have already been proposed providing good performances. Recently, Vision Transformers (ViTs) have been introduced, reaching comparable and even better performances than traditional CNNs in image classification. The aim of the proposed paper was to compare the performances of different state-of-the-art deep learning algorithms to predict cancer recurrence in NSCLC patients. In this work, using a public database of 144 patients, we implemented a transfer learning approach, involving different Transformers architectures like pre-trained ViTs, pre-trained Pyramid Vision Transformers, and pre-trained Swin Transformers to predict the recurrence of NSCLC patients from CT images, comparing their performances with state-of-the-art CNNs. Although, the best performances in this study are reached via CNNs with AUC, Accuracy, Sensitivity, Specificity, and Precision equal to 0.91, 0.89, 0.85, 0.90, and 0.78, respectively, Transformer architectures reach comparable ones with AUC, Accuracy, Sensitivity, Specificity, and Precision equal to 0.90, 0.86, 0.81, 0.89, and 0.75, respectively. Based on our preliminary experimental results, it appears that Transformers architectures do not add improvements in terms of predictive performance to the addressed problem.

Profiling of patients with type 2 diabetes based on medication adherence data

Introduction

Type 2 diabetes mellitus (T2DM) is a complex, chronic disease affecting multiple organs with varying symptoms and comorbidities. Profiling patients helps identify those with unfavorable disease progression, allowing for tailored therapy and addressing special needs. This study aims to uncover different T2DM profiles based on medication intake records and laboratory measurements, with a focus on how individuals with diabetes move through disease phases.

Methods

We use medical records from databases of the last 20 years from the Department of Endocrinology and Diabetology of the University Medical Center in Maribor. Using the standard ATC medication classification system, we created a patient-specific drug profile, created using advanced natural language processing methods combined with data mining and hierarchical clustering.

Results

Our results show a well-structured profile distribution characterizing different age groups of individuals with diabetes. Interestingly, only two main profiles characterize the early 40-50 age group, and the same is true for the last 80+ age group. One of these profiles includes individuals with diabetes with very low use of various medications, while the other profile includes individuals with diabetes with much higher use. The number in both groups is reciprocal. Conversely, the middle-aged groups are characterized by several distinct profiles with a wide range of medications that are associated with the distinct concomitant complications of T2DM. It is intuitive that the number of profiles increases in the later age groups, but it is not obvious why it is reduced later in the 80+ age group. In this context, further studies are needed to evaluate the contributions of a range of factors, such as drug development, drug adoption, and the impact of mortality associated with all T2DM-related diseases, which characterize these middle-aged groups, particularly those aged 55-75.

Conclusion

Our approach aligns with existing studies and can be widely implemented without complex or expensive analyses. Treatment and drug use data are readily available in healthcare facilities worldwide, allowing for profiling insights into individuals with diabetes. Integrating data from other departments, such as cardiology and renal disease, may provide a more sophisticated understanding of T2DM patient profiles.

Adaptive Aquila Optimizer with Explainable Artificial Intelligence-Enabled Cancer Diagnosis on Medical Imaging

Explainable Artificial Intelligence (XAI) is a branch of AI that mainly focuses on developing systems that provide understandable and clear explanations for their decisions. In the context of cancer diagnoses on medical imaging, an XAI technology uses advanced image analysis methods like deep learning (DL) to make a diagnosis and analyze medical images, as well as provide a clear explanation for how it arrived at its diagnoses. This includes highlighting specific areas of the image that the system recognized as indicative of cancer while also providing data on the fundamental AI algorithm and decision-making process used. The objective of XAI is to provide patients and doctors with a better understanding of the system's decision-making process and to increase transparency and trust in the diagnosis method. Therefore, this study develops an Adaptive Aquila Optimizer with Explainable Artificial Intelligence Enabled Cancer Diagnosis (AAOXAI-CD) technique on Medical Imaging. The proposed AAOXAI-CD technique intends to accomplish the effectual colorectal and osteosarcoma cancer classification process. To achieve this, the AAOXAI-CD technique initially employs the Faster SqueezeNet model for feature vector generation. As well, the hyperparameter tuning of the Faster SqueezeNet model takes place with the use of the AAO algorithm. For cancer classification, the majority weighted voting ensemble model with three DL classifiers, namely recurrent neural network (RNN), gated recurrent unit (GRU), and bidirectional long short-term memory (BiLSTM). Furthermore, the AAOXAI-CD technique combines the XAI approach LIME for better understanding and explainability of the black-box method for accurate cancer detection. The simulation evaluation of the AAOXAI-CD methodology can be tested on medical cancer imaging databases, and the outcomes ensured the auspicious outcome of the AAOXAI-CD methodology than other current approaches.

Analyzing breast cancer invasive disease event classification through explainable artificial intelligence

Introduction

Recently, accurate machine learning and deep learning approaches have been dedicated to the investigation of breast cancer invasive disease events (IDEs), such as recurrence, contralateral and second cancers. However, such approaches are poorly interpretable.

Methods

Thus, we designed an Explainable Artificial Intelligence (XAI) framework to investigate IDEs within a cohort of 486 breast cancer patients enrolled at IRCCS Istituto Tumori "Giovanni Paolo II" in Bari, Italy. Using Shapley values, we determined the IDE driving features according to two periods, often adopted in clinical practice, of 5 and 10 years from the first tumor diagnosis.

Results

Age, tumor diameter, surgery type, and multiplicity are predominant within the 5-year frame, while therapy-related features, including hormone, chemotherapy schemes and lymphovascular invasion, dominate the 10-year IDE prediction. Estrogen Receptor (ER), proliferation marker Ki67 and metastatic lymph nodes affect both frames.

Discussion

Thus, our framework aims at shortening the distance between AI and clinical practice.

Expression of the Immunohistochemical Markers CK5, CD117, and EGFR in Molecular Subtypes of Breast Cancer Correlated with Prognosis

Molecular-based subclassifications of breast cancer are important for identifying treatment options and stratifying the prognosis in breast cancer. This study aimed to assess the prognosis relative to disease-free survival (DFS) and overall survival (OS) in patients with triple-negative breast cancer (TNBC) and other subtypes, using a biomarker panel including cytokeratin 5 (CK5), cluster of differentiation 117 (CD117), and epidermal growth factor receptor (EGFR). This cohort-case study included histologically confirmed breast carcinomas as cohort arm. From a total of 894 patients, 572 patients with early breast cancer, sufficient clinical data, and archived tumor tissue were included. Using the immunohistochemical markers CK5, CD117, and EGFR, two subgroups were formed: one with all three biomarkers negative (TBN) and one with at least one of those three biomarkers positive (non-TBN). There were significant differences between the two biomarker subgroups (TBN versus non-TBN) in TNBC for DFS (p = 0.04) and OS (p = 0.02), with higher survival rates (DFS and OS) in the non-TBN subgroup. In this study, we found the non-TBN subgroup of TNBC lesions with at least one positive biomarker of CK5, CD117, and/or EGFR, to be associated with longer DFS and OS.

Explainable artificial intelligence (XAI) detects wildfire occurrence in the Mediterranean countries of Southern Europe

The impacts and threats posed by wildfires are dramatically increasing due to climate change. In recent years, the wildfire community has attempted to estimate wildfire occurrence with machine learning models. However, to fully exploit the potential of these models, it is of paramount importance to make their predictions interpretable and intelligible. This study is a first attempt to provide an eXplainable artificial intelligence (XAI) framework for estimating wildfire occurrence using a Random Forest model with Shapley values for interpretation. Our findings accurately detected regions with a high presence of wildfires (area under the curve 81.3%) and outlined the drivers empowering occurrence, such as the Fire Weather Index and Normalized Difference Vegetation Index. Furthermore, our analysis suggests the presence of anomalous hotspots. In contexts where human and natural spheres constantly intermingle and interact, the XAI framework, suitably integrated into decision support systems, could support forest managers to prevent and mitigate future wildfire disasters and develop strategies for effective fire management, response, recovery, and resilience.

Federated learning-based AI approaches in smart healthcare: concepts, taxonomies, challenges and open issues

Federated Learning (FL), Artificial Intelligence (AI), and Explainable Artificial Intelligence (XAI) are the most trending and exciting technology in the intelligent healthcare field. Traditionally, the healthcare system works based on centralized agents sharing their raw data. Therefore, huge vulnerabilities and challenges are still existing in this system. However, integrating with AI, the system would be multiple agent collaborators who are capable of communicating with their desired host efficiently. Again, FL is another interesting feature, which works decentralized manner; it maintains the communication based on a model in the preferred system without transferring the raw data. The combination of FL, AI, and XAI techniques can be capable of minimizing several limitations and challenges in the healthcare system. This paper presents a complete analysis of FL using AI for smart healthcare applications. Initially, we discuss contemporary concepts of emerging technologies such as FL, AI, XAI, and the healthcare system. We integrate and classify the FL-AI with healthcare technologies in different domains. Further, we address the existing problems, including security, privacy, stability, and reliability in the healthcare field. In addition, we guide the readers to solving strategies of healthcare using FL and AI. Finally, we address extensive research areas as well as future potential prospects regarding FL-based AI research in the healthcare management system.

Considerations for the Use of Machine Learning Extracted Real-World Data to Support Evidence Generation: A Research-Centric Evaluation Framework

A vast amount of real-world data, such as pathology reports and clinical notes, are captured as unstructured text in electronic health records (EHRs). However, this information is both difficult and costly to extract through human abstraction, especially when scaling to large datasets is needed. Fortunately, Natural Language Processing (NLP) and Machine Learning (ML) techniques provide promising solutions for a variety of information extraction tasks such as identifying a group of patients who have a specific diagnosis, share common characteristics, or show progression of a disease. However, using these ML-extracted data for research still introduces unique challenges in assessing validity and generalizability to different cohorts of interest. In order to enable effective and accurate use of ML-extracted real-world data (RWD) to support research and real-world evidence generation, we propose a research-centric evaluation framework for model developers, ML-extracted data users and other RWD stakeholders. This framework covers the fundamentals of evaluating RWD produced using ML methods to maximize the use of EHR data for research purposes.

Applications of Explainable Artificial Intelligence in Diagnosis and Surgery

In recent years, artificial intelligence (AI) has shown great promise in medicine. However, explainability issues make AI applications in clinical usages difficult. Some research has been conducted into explainable artificial intelligence (XAI) to overcome the limitation of the black-box nature of AI methods. Compared with AI techniques such as deep learning, XAI can provide both decision-making and explanations of the model. In this review, we conducted a survey of the recent trends in medical diagnosis and surgical applications using XAI. We have searched articles published between 2019 and 2021 from PubMed, IEEE Xplore, Association for Computing Machinery, and Google Scholar. We included articles which met the selection criteria in the review and then extracted and analyzed relevant information from the studies. Additionally, we provide an experimental showcase on breast cancer diagnosis, and illustrate how XAI can be applied in medical XAI applications. Finally, we summarize the XAI methods utilized in the medical XAI applications, the challenges that the researchers have met, and discuss the future research directions. The survey result indicates that medical XAI is a promising research direction, and this study aims to serve as a reference to medical experts and AI scientists when designing medical XAI applications.

A Cascade Flexible Neural Forest Model for Cancer Subtypes Classification on Gene Expression Data

The correct classification of cancer subtypes is of great significance for the in-depth study of cancer pathogenesis and the realization of accurate treatment for cancer patients. In recent years, the classification of cancer subtypes using deep neural networks and gene expression data has become a hot topic. However, most classifiers may face the challenges of overfitting and low classification accuracy when dealing with small sample size and high-dimensional biological data. In this paper, the Cascade Flexible Neural Forest (CFNForest) Model was proposed to accomplish cancer subtype classification. CFNForest extended the traditional flexible neural tree structure to FNT Group Forest exploiting a bagging ensemble strategy and could automatically generate the model's structure and parameters. In order to deepen the FNT Group Forest without introducing new hyperparameters, the multilayer cascade framework was exploited to design the FNT Group Forest model, which transformed features between levels and improved the performance of the model. The proposed CFNForest model also improved the operational efficiency and the robustness of the model by sample selection mechanism between layers and setting different weights for the output of each layer. To accomplish cancer subtype classification, FNT Group Forest with different feature sets was used to enrich the structural diversity of the model, which make it more suitable for processing small sample size datasets. The experiments on RNA-seq gene expression data showed that CFNForest effectively improves the accuracy of cancer subtype classification. The classification results have good robustness.

Reinforcement Learning for Precision Oncology

Precision oncology is grounded in the increasing understanding of genetic and molecular mechanisms that underly malignant disease and offer different treatment pathways for the individual patient. The growing complexity of medical data has led to the implementation of machine learning techniques that are vastly applied for risk assessment and outcome prediction using either supervised or unsupervised learning. Still largely overlooked is reinforcement learning (RL) that addresses sequential tasks by exploring the underlying dynamics of an environment and shaping it by taking actions in order to maximize cumulative rewards over time, thereby achieving optimal long-term outcomes. Recent breakthroughs in RL demonstrated remarkable results in gameplay and autonomous driving, often achieving human-like or even superhuman performance. While this type of machine learning holds the potential to become a helpful decision support tool, it comes with a set of distinctive challenges that need to be addressed to ensure applicability, validity and safety. In this review, we highlight recent advances of RL focusing on studies in oncology and point out current challenges and pitfalls that need to be accounted for in future studies in order to successfully develop RL-based decision support systems for precision oncology.

The Multiple Dimensions of Networks in Cancer: A Perspective

This perspective article gathers the latest developments in mathematical and computational oncology tools that exploit network approaches for the mathematical modelling, analysis, and simulation of cancer development and therapy design. It instigates the community to explore new paths and synergies under the umbrella of the Special Issue “Networks in Cancer: From Symmetry Breaking to Targeted Therapy”. The focus of the perspective is to demonstrate how networks can model the physics, analyse the interactions, and predict the evolution of the multiple processes behind tumour-host encounters across multiple scales. From agent-based modelling and mechano-biology to machine learning and predictive modelling, the perspective motivates a methodology well suited to mathematical and computational oncology and suggests approaches that mark a viable path towards adoption in the clinic.