Classification and diagnostic prediction of breast cancer metastasis on clinical data using machine learning algorithms

Identification of phytoestrogens as sirtuin inhibitor against breast cancer: Multitargeted approach

Despite progress in diagnosis and treatment strategies, breast cancer remains a primary risk to female health as indicated by second most cancer-deaths globally caused by this cancer. High risk mutation is linked to prognosis of breast cancer. Due to high resistance of breast cancer against current therapies, there is necessity of novel treatment strategies. Sirtuins are signaling proteins belonging to histone deacetylase class III family, known to control several cellular processes. Therefore, targeting sirtuins could be one of the approaches to treat breast cancer. Several plants synthesize phytoestrogens which exhibit structural and physiological similarities to estrogens and have been recognized to possess anticancer activity. In our study, we investigated several phytoestrogens for sirtuin inhibition by conducting molecular docking studies, and in-vitro studies against breast cancer cell lines. In molecular docking studies, we identified coumestrol possessing high binding energy with sirtuin proteins 1-3 as compared to other phytoestrogens. The molecular dynamic studies showed stable interaction of ligand and protein with higher affinity at sirtuin proteins 1-3 binding sites. In cell proliferation assay and colony formation assay using breast cancer cell lines (MCF-7 and MDAMB-231) coumestrol caused significant reduction in cell proliferation and number of colonies formed. Further, the flow cytometric analysis showed that coumestrol induces intracellular reactive oxygen species and the western blot analysis revealed reduction in the level of SIRT-1 expression in breast cancer cell lines. In conclusion, in-silico data and in-vitro studies suggest that the phytoestrogen coumestrol has sirtuin inhibitory activity against breast cancer.

A BERT-GNN Approach for Metastatic Breast Cancer Prediction Using Histopathology Reports

Metastatic breast cancer (MBC) continues to be a leading cause of cancer-related deaths among women. This work introduces an innovative non-invasive breast cancer classification model designed to improve the identification of cancer metastases. While this study marks the initial exploration into predicting MBC, additional investigations are essential to validate the occurrence of MBC. Our approach combines the strengths of large language models (LLMs), specifically the bidirectional encoder representations from transformers (BERT) model, with the powerful capabilities of graph neural networks (GNNs) to predict MBC patients based on their histopathology reports. This paper introduces a BERT-GNN approach for metastatic breast cancer prediction (BG-MBC) that integrates graph information derived from the BERT model. In this model, nodes are constructed from patient medical records, while BERT embeddings are employed to vectorise representations of the words in histopathology reports, thereby capturing semantic information crucial for classification by employing three distinct approaches (namely univariate selection, extra trees classifier for feature importance, and Shapley values to identify the features that have the most significant impact). Identifying the most crucial 30 features out of 676 generated as embeddings during model training, our model further enhances its predictive capabilities. The BG-MBC model achieves outstanding accuracy, with a detection rate of 0.98 and an area under curve (AUC) of 0.98, in identifying MBC patients. This remarkable performance is credited to the model's utilisation of attention scores generated by the LLM from histopathology reports, effectively capturing pertinent features for classification.

A contemporary review of breast cancer risk factors and the role of artificial intelligence

Background

Breast cancer continues to be a significant global health issue, necessitating advancements in prevention and early detection strategies. This review aims to assess and synthesize research conducted from 2020 to the present, focusing on breast cancer risk factors, including genetic, lifestyle, and environmental aspects, as well as the innovative role of artificial intelligence (AI) in prediction and diagnostics.

Methods

A comprehensive literature search, covering studies from 2020 to the present, was conducted to evaluate the diversity of breast cancer risk factors and the latest advances in Artificial Intelligence (AI) in this field. The review prioritized high-quality peer-reviewed research articles and meta-analyses.

Results

Our analysis reveals a complex interplay of genetic, lifestyle, and environmental risk factors for breast cancer, with significant variability across different populations. Furthermore, AI has emerged as a promising tool in enhancing the accuracy of breast cancer risk prediction and the personalization of prevention strategies.

Conclusion

The review highlights the necessity for personalized breast cancer prevention and detection approaches that account for individual risk factor profiles. It underscores the potential of AI to revolutionize these strategies, offering clear recommendations for future research directions and clinical practice improvements.

Machine learning pipeline to analyze clinical and proteomics data: experiences on a prostate cancer case

Proteomic-based analysis is used to identify biomarkers in blood samples and tissues. Data produced by devices such as mass spectrometry requires platforms to identify and quantify proteins (or peptides). Clinical information can be related to mass spectrometry data to identify diseases at an early stage. Machine learning techniques can be used to support physicians and biologists in studying and classifying pathologies. We present the application of machine learning techniques to define a pipeline aimed at studying and classifying proteomics data enriched using clinical information. The pipeline allows users to relate established blood biomarkers with clinical parameters and proteomics data. The proposed pipeline entails three main phases: (i) feature selection, (ii) models training, and (iii) models ensembling. We report the experience of applying such a pipeline to prostate-related diseases. Models have been trained on several biological datasets. We report experimental results about two datasets that result from the integration of clinical and mass spectrometry-based data in the contexts of serum and urine analysis. The pipeline receives input data from blood analytes, tissue samples, proteomic analysis, and urine biomarkers. It then trains different models for feature selection, classification and voting. The presented pipeline has been applied on two datasets obtained in a 2 years research project which aimed to extract hidden information from mass spectrometry, serum, and urine samples from hundreds of patients. We report results on analyzing prostate datasets serum with 143 samples, including 79 PCa and 84 BPH patients, and an urine dataset with 121 samples, including 67 PCa and 54 BPH patients. As results pipeline allowed to identify interesting peptides in the two datasets, 6 for the first one and 2 for the second one. The best model for both serum (AUC=0.87, Accuracy=0.83, F1=0.81, Sensitivity=0.84, Specificity=0.81) and urine (AUC=0.88, Accuracy=0.83, F1=0.83, Sensitivity=0.85, Specificity=0.80) datasets showed good predictive performances. We made the pipeline code available on GitHub and we are confident that it will be successfully adopted in similar clinical setups.

Photodegradation of polycyclic aromatic hydrocarbons on soil surface: Kinetics and quantitative structure-activity relationship (QSAR) model development

Polycyclic aromatic hydrocarbons (PAHs) have attracted much attention because of their widespread existence and toxicity. Photodegradation is the main natural decay process of PAHs in soil. The photodegradation kinetics of benzopyrene (BaP) on 16 kinds of soils and 10 kinds of PAHs on Hebei (HE) soil were studied. The results showed that BaP had the highest degradation rate in Shaanxi (SN) soil (kobs = 0.11 min-1), and anthracene (Ant) was almost completely degraded after 16 h of irradiation in HE soil. Two quantitative structure-activity relationship (QSAR) models were established by the multiple linear regression (MLR) method. The developed QSAR models have good stability, robustness and predictability. The model revealed that the main factors affecting the photodegradation of PAHs are soil organic matter (SOM) and the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital (Egap). SOM can function as a photosensitizer to induce the production of active species for photodegradation, thus favoring the photodegradation of PAHs. In addition, compounds with lower Egap are less stable and more reactive, and thus are more prone to photodegradation. Finally, the QSAR model was optimized using machine learning approach. The results of this study provide basic information on the photodegradation of PAHs and have important significance for predicting the environmental behavior of PAHs in soil.

Opportunities and challenges of artificial intelligence and distributed systems to improve the quality of healthcare service

The healthcare sector, characterized by vast datasets and many diseases, is pivotal in shaping community health and overall quality of life. Traditional healthcare methods, often characterized by limitations in disease prevention, predominantly react to illnesses after their onset rather than proactively averting them. The advent of Artificial Intelligence (AI) has ushered in a wave of transformative applications designed to enhance healthcare services, with Machine Learning (ML) as a noteworthy subset of AI. ML empowers computers to analyze extensive datasets, while Deep Learning (DL), a specific ML methodology, excels at extracting meaningful patterns from these data troves. Despite notable technological advancements in recent years, the full potential of these applications within medical contexts remains largely untapped, primarily due to the medical community's cautious stance toward novel technologies. The motivation of this paper lies in recognizing the pivotal role of the healthcare sector in community well-being and the necessity for a shift toward proactive healthcare approaches. To our knowledge, there is a notable absence of a comprehensive published review that delves into ML, DL and distributed systems, all aimed at elevating the Quality of Service (QoS) in healthcare. This study seeks to bridge this gap by presenting a systematic and organized review of prevailing ML, DL, and distributed system algorithms as applied in healthcare settings. Within our work, we outline key challenges that both current and future developers may encounter, with a particular focus on aspects such as approach, data utilization, strategy, and development processes. Our study findings reveal that the Internet of Things (IoT) stands out as the most frequently utilized platform (44.3 %), with disease diagnosis emerging as the predominant healthcare application (47.8 %). Notably, discussions center significantly on the prevention and identification of cardiovascular diseases (29.2 %). The studies under examination employ a diverse range of ML and DL methods, along with distributed systems, with Convolutional Neural Networks (CNNs) being the most commonly used (16.7 %), followed by Long Short-Term Memory (LSTM) networks (14.6 %) and shallow learning networks (12.5 %). In evaluating QoS, the predominant emphasis revolves around the accuracy parameter (80 %). This study highlights how ML, DL, and distributed systems reshape healthcare. It contributes to advancing healthcare quality, bridging the gap between technology and medical adoption, and benefiting practitioners and patients.

Machine learning-based prediction model for distant metastasis of breast cancer

BACKGROUND

Breast cancer is the most prevalent malignancy in women. Advanced breast cancer can develop distant metastases, posing a severe threat to the life of patients. Because the clinical warning signs of distant metastasis are manifested in the late stage of the disease, there is a need for better methods of predicting metastasis.

METHODS

First, we screened breast cancer distant metastasis target genes by performing difference analysis and weighted gene co-expression network analysis (WGCNA) on the selected datasets, and performed analyses such as GO enrichment analysis on these target genes. Secondly, we screened breast cancer distant metastasis target genes by LASSO regression analysis and performed correlation analysis and other analyses on these biomarkers. Finally, we constructed several breast cancer distant metastasis prediction models based on Logistic Regression (LR) model, Random Forest (RF) model, Support Vector Machine (SVM) model, Gradient Boosting Decision Tree (GBDT) model and eXtreme Gradient Boosting (XGBoost) model, and selected the optimal model from them.

RESULTS

Several 21-gene breast cancer distant metastasis prediction models were constructed, with the best performance of the model constructed based on the random forest model. This model accurately predicted the emergence of distant metastases from breast cancer, with an accuracy of 93.6 %, an F1-score of 88.9 % and an AUC value of 91.3 % on the validation set.

CONCLUSION

Our findings have the potential to be translated into a point-of-care prognostic analysis to reduce breast cancer mortality.

Subcutaneous fat predicts bone metastasis in breast cancer: A novel multimodality-based deep learning model

OBJECTIVES

This study explores a deep learning (DL) approach to predicting bone metastases in breast cancer (BC) patients using clinical information, such as the fat index, and features like Computed Tomography (CT) images.

METHODS

CT imaging data and clinical information were collected from 431 BC patients who underwent radical surgical resection at Harbin Medical University Cancer Hospital. The area of muscle and adipose tissue was obtained from CT images at the level of the eleventh thoracic vertebra. The corresponding histograms of oriented gradients (HOG) and local binary pattern (LBP) features were extracted from the CT images, and the network features were derived from the LBP and HOG features as well as the CT images through deep learning (DL). The combination of network features with clinical information was utilized to predict bone metastases in BC patients using the Gradient Boosting Decision Tree (GBDT) algorithm. Regularized Cox regression models were employed to identify independent prognostic factors for bone metastasis.

RESULTS

The combination of clinical information and network features extracted from LBP features, HOG features, and CT images using a convolutional neural network (CNN) yielded the best performance, achieving an AUC of 0.922 (95% confidence interval [CI]: 0.843-0.964, P< 0.01). Regularized Cox regression results indicated that the subcutaneous fat index was an independent prognostic factor for bone metastasis in breast cancer (BC).

CONCLUSION

Subcutaneous fat index could predict bone metastasis in BC patients. Deep learning multimodal algorithm demonstrates superior performance in assessing bone metastases in BC patients.

An ensemble-based serial cascaded attention network and improved variational auto encoder for breast cancer prognosis prediction using data

Breast cancer is one of the most common types of cancer in women and it produces a huge amount of death rate in the world. Early recognition is lessening its impact. The early recognition of breast cancer could convince patients to receive surgical therapy, which will significantly improve the chance of restoration. This information is used by the machine learning technique to find links between them and appraise our forecasts of fresh occurrences. Later recognition of breast cancer can lead to death. An accurate prescient framework for breast cancer prediction is urgently needed in the current era. In order to accomplish the objective, an adaptive ensemble model is proposed for breast cancer prognosis prediction using data. At the initial stage, the raw data are fetched from benchmark datasets. It is then followed by data cleaning and preprocessing. Subsequently, the pre-processed data is fed into the Improved Variational Autoencoder (IVAE), where the deep features are extracted. Finally, the resultant features are given as input to the Ensemble-based Serial Cascaded Attention Network (ESCANet), which is built with Deep Temporal Convolution Network (DTCN), Bi-directional Long Short-Term Memory (BiLSTM), and Recurrent Neural Network (RNN). The effectiveness of the model is validated and compared with conventional methodologies. Therefore, the results elucidate that the proposed methodology achieves extensive results; thus, it increases the system's efficiency.

Ent-16β,17-dihydroxy-kauran-19-oic acid (DKA), a kaurane diterpenoid from Sigesbeckia pubescens(Makino) Makino, inhibits the migration of MDA-MB-231 breast cancer

Ent-kaurane diterpenoids were studied as a biologically active ingredient group of Sigesbeckia pubescens (Makino) Makino. Here, five known ent-kaurane diterpenoids were isolated and identified, named ent-16β,17-dihydroxy-kauran-19-oic acid (1), ent-16β,17-dihydroxy-kauran-19-oate (2), ent-18-acetoxy-17-hydroxykauran-19-oic acid (3), ent-16β,17,18-trihydroxy-kauran-19 -oic acid (4), and ent-17-hydroxy-kauran-16βH-19-oic acid (5). Their inhibitory effects of these compounds on MDA-MB-231 breast cancer migration were firstly tested in a chemotaxis invasion assay. Among them, compound 1 (DKA) showed superior inhibitory activities with IC50 value of 1.96 µM. Then, a wound healing assay and BALB/c nude mice were used for further studying the inhibitory activity of DKA on MDA-MB-231 breast cancer migration in vitro and in vivo, respectively. The wound healing assay showed that DKA (1, 5, and 25 μM) can significantly inhibit cell migration and the mouse model of lung metastasis showed that DKA (2.5, 5, and 10 mg/kg) could strongly suppress the lung metastasis of MDA-MB-231 breast cancer cells.

Enhanced Pelican Optimization Algorithm with Deep Learning-Driven Mitotic Nuclei Classification on Breast Histopathology Images

Breast cancer (BC) is a prevalent disease worldwide, and accurate diagnoses are vital for successful treatment. Histopathological (HI) inspection, particularly the detection of mitotic nuclei, has played a pivotal function in the prognosis and diagnosis of BC. It includes the detection and classification of mitotic nuclei within breast tissue samples. Conventionally, the detection of mitotic nuclei has been a subjective task and is time-consuming for pathologists to perform manually. Automatic classification using computer algorithms, especially deep learning (DL) algorithms, has been developed as a beneficial alternative. DL and CNNs particularly have shown outstanding performance in different image classification tasks, including mitotic nuclei classification. CNNs can learn intricate hierarchical features from HI images, making them suitable for detecting subtle patterns related to the mitotic nuclei. In this article, we present an Enhanced Pelican Optimization Algorithm with a Deep Learning-Driven Mitotic Nuclei Classification (EPOADL-MNC) technique on Breast HI. This developed EPOADL-MNC system examines the histopathology images for the classification of mitotic and non-mitotic cells. In this presented EPOADL-MNC technique, the ShuffleNet model can be employed for the feature extraction method. In the hyperparameter tuning procedure, the EPOADL-MNC algorithm makes use of the EPOA system to alter the hyperparameters of the ShuffleNet model. Finally, we used an adaptive neuro-fuzzy inference system (ANFIS) for the classification and detection of mitotic cell nuclei on histopathology images. A series of simulations took place to validate the improved detection performance of the EPOADL-MNC technique. The comprehensive outcomes highlighted the better outcomes of the EPOADL-MNC algorithm compared to existing DL techniques with a maximum accuracy of 97.83%.

Applying dual models on optimized LSTM with U-net segmentation for breast cancer diagnosis using mammogram images

BACKGROUND OF THE STUDY

Breast cancer is the most fatal disease that widely affects women. When the cancerous lumps grow from the cells of the breast, it causes breast cancer. Self-analysis and regular medical check-ups help for detecting the disease earlier and enhance the survival rate. Hence, an automated breast cancer detection system in mammograms can assist clinicians in the patient's treatment. In medical techniques, the categorization of breast cancer becomes challenging for investigators and researchers. The advancement in deep learning approaches has established more attention to their advantages to medical imaging issues, especially for breast cancer detection.

AIM

The research work plans to develop a novel hybrid model for breast cancer diagnosis with the support of optimized deep-learning architecture.

METHODS

The required images are gathered from the benchmark datasets. These collected datasets are used in three pre-processing approaches like "Median Filtering, Histogram Equalization, and morphological operation", which helps to remove unwanted regions from the images. Then, the pre-processed images are applied to the Optimized U-net-based tumor segmentation phase for obtaining accurate segmented results along with the optimization of certain parameters in U-Net by employing "Adapted-Black Widow Optimization (A-BWO)". Further, the detection is performed in two different ways that is given as model 1 and model 2. In model 1, the segmented tumors are used to extract the significant patterns with the help of the "Gray-Level Co-occurrence Matrix (GLCM) and Local Gradient pattern (LGP)". Further, these extracted patterns are utilized in the "Dual Model accessed Optimized Long Short-Term Memory (DM-OLSTM)" for performing breast cancer detection and the detected score 1 is obtained. In model 2, the same segmented tumors are given into the different variants of CNN, such as "VGG19, Resnet150, and Inception". The extracted deep features from three CNN-based approaches are fused to form a single set of deep features. These fused deep features are inserted into the developed DM-OLSTM for getting the detected score 2 for breast cancer diagnosis. In the final phase of the hybrid model, the score 1 and score 2 obtained from model 1 and model 2 are averaged to get the final detection output.

RESULTS

The accuracy and F1-score of the offered DM-OLSTM model are achieved at 96 % and 95 %.

CONCLUSION

Experimental analysis proves that the recommended methodology achieves better performance by analyzing with the benchmark dataset. Hence, the designed model is helpful for detecting breast cancer in real-time applications.

Robust Classification and Detection of Big Medical Data Using Advanced Parallel K-Means Clustering, YOLOv4, and Logistic Regression

Big-medical-data classification and image detection are crucial tasks in the field of healthcare, as they can assist with diagnosis, treatment planning, and disease monitoring. Logistic regression and YOLOv4 are popular algorithms that can be used for these tasks. However, these techniques have limitations and performance issue with big medical data. In this study, we presented a robust approach for big-medical-data classification and image detection using logistic regression and YOLOv4, respectively. To improve the performance of these algorithms, we proposed the use of advanced parallel k-means pre-processing, a clustering technique that identified patterns and structures in the data. Additionally, we leveraged the acceleration capabilities of a neural engine processor to further enhance the speed and efficiency of our approach. We evaluated our approach on several large medical datasets and showed that it could accurately classify large amounts of medical data and detect medical images. Our results demonstrated that the combination of advanced parallel k-means pre-processing, and the neural engine processor resulted in a significant improvement in the performance of logistic regression and YOLOv4, making them more reliable for use in medical applications. This new approach offers a promising solution for medical data classification and image detection and may have significant implications for the field of healthcare.