Prediction model of the response to neoadjuvant chemotherapy in breast cancers by a Naive Bayes algorithm

Public health implications of computer-aided diagnosis and treatment technologies in breast cancer care

Breast cancer remains a significant public health issue, being a leading cause of cancer-related mortality among women globally. Timely diagnosis and efficient treatment are crucial for enhancing patient outcomes, reducing healthcare burdens and advancing community health. This systematic review, following the PRISMA guidelines, aims to comprehensively synthesize the recent advancements in computer-aided diagnosis and treatment for breast cancer. The study covers the latest developments in image analysis and processing, machine learning and deep learning algorithms, multimodal fusion techniques and radiation therapy planning and simulation. The results of the review suggest that machine learning, augmented and virtual reality and data mining are the three major research hotspots in breast cancer management. Moreover, this paper discusses the challenges and opportunities for future research in this field. The conclusion highlights the importance of computer-aided techniques in the management of breast cancer and summarizes the key findings of the review.

Psychological Distress, Coping Strategies, and Quality of Life in Breast Cancer Patients Under Neoadjuvant Therapy: Protocol of a Systematic Review

Introduction

Women with breast cancer eligible for neoadjuvant therapy (NAT) present a disorder of biopsychosocial variables and alteration of their quality of life. They cope with this changing by adopting psychological adjustment strategies, either passive or active. This systematic review aims to investigate the psychological distress, coping strategies, and quality of life in breast cancer patients under neoadjuvant therapy.

Methods

Cochrane Library, PubMed, ScienceDirect, Scopus, Web of Science, and Wiley Online library represent the databases that were searched to identify relevant published articles until September 27, 2021. Full-text published articles, written in English and assessing the main outcomes (namely: psychological distress, coping strategies, and quality of life) in women with breast cancer under NAT will be included. Also, we will integrate papers dealing with the related bio psychosocial variables to the main variables. The paper selection, data extraction, and quality assessment of selected studies will be performed independently by two researchers, and disagreements will be resolved through discussions. We will bring together the results of all of the included studies to draw conclusions based on the body of evidence. The narrative approach will be adopted to analyze the results and conclusions extracted and we would perform quantitative groupings if we have similar data.

Ethics and dissemination

Ethical approval is not required as the proposed systematic review will not use primary data. The results of this review will be disseminated through publication in a peer-reviewed journal and conference presentation(s). PROSPERO registration number: CRD42021230300.

FeCO3, constructing the network biomarkers using the inter-feature correlation coefficients and its application in detecting high-order breast cancer biomarkers

Aims:

This study aims to formulate the inter-feature correlation as the engineered features.

Background:

Modern biotechnologies tend to generate a huge number of characteristics of a sample, while an OMIC dataset usually has a few dozens or hundreds of samples due to the high costs of generating the OMIC data. So many bio-OMIC studies assumed the inter-feature independence and selected a feature with a high phenotype-association.

Objective:

However, many features are closely associated with each other due to their physical or functional interactions, which may be utilized as a new view of features.

Method:

This study proposed a feature engineering algorithm based on the correlation coefficients (FeCO3) by utilizing the correlations between a given sample and a few reference samples. A comprehensive evaluation was carried out for the proposed FeCO3 network features using 24 bio-OMIC datasets.

Result:

The experimental data suggested that the newly calculated FeCO3 network features tended to achieve better classification performances than the original features, using the same popular feature selection and classification algorithms. The FeCO3 network features were also consistently supported by the literature. FeCO3 was utilized to investigate the high-order engineered biomarkers of breast cancer, and detected the PBX2 gene (Pre-B-Cell Leukemia Transcription Factor 2) as one of the candidate breast cancer biomarkers. Although the two methylated residues cg14851325 (Pvalue=8.06e-2) and cg16602460 (Pvalue=1.19e-1) within PBX2 did not have statistically significant association with breast cancers, the high-order inter-feature correlations showed a significant association with breast cancers.

Conclusion:

The proposed FeCO3 network features calculated the high-order inter-feature correlations as novel features, and may facilitate the investigations of complex diseases from this new perspective. The source code is available in FigShare at 10.6084/m9.figshare.13550051 or the web site http://www.healthinformaticslab.org/supp/ .

Application of Machine Learning for the Prediction of Etiological Types of Classic Fever of Unknown Origin

Background: The etiology of fever of unknown origin (FUO) is complex and remains a major challenge for clinicians. This study aims to investigate the distribution of the etiology of classic FUO and the differences in clinical indicators in patients with different etiologies of classic FUO and to establish a machine learning (ML) model based on clinical data. Methods: The clinical data and final diagnosis results of 527 patients with classic FUO admitted to 7 medical institutions in Chongqing from January 2012 to August 2021 and who met the classic FUO diagnostic criteria were collected. Three hundred seventy-three patients with final diagnosis were divided into 4 groups according to 4 different etiological types of classical FUO, and statistical analysis was carried out to screen out the indicators with statistical differences under different etiological types. On the basis of these indicators, five kinds of ML models, i.e., random forest (RF), support vector machine (SVM), Light Gradient Boosting Machine (LightGBM), artificial neural network (ANN), and naive Bayes (NB) models, were used to evaluate all datasets using 5-fold cross-validation, and the performance of the models were evaluated using micro-F1 scores. Results: The 373 patients were divided into the infectious disease group (n = 277), non-infectious inflammatory disease group (n = 51), neoplastic disease group (n = 31), and other diseases group (n = 14) according to 4 different etiological types. Another 154 patients were classified as undetermined group because the cause of fever was still unclear at discharge. There were significant differences in gender, age, and 18 other indicators among the four groups of patients with classic FUO with different etiological types (P < 0.05). The micro-F1 score for LightGBM was 75.8%, which was higher than that for the other four ML models, and the LightGBM prediction model had the best performance. Conclusions: Infectious diseases are still the main etiological type of classic FUO. Based on 18 statistically significant clinical indicators such as gender and age, we constructed and evaluated five ML models. LightGBM model has a good effect on predicting the etiological type of classic FUO, which will play a good auxiliary decision-making function.

Artificial intelligence, machine learning, and deep learning for clinical outcome prediction

AI is a broad concept, grouping initiatives that use a computer to perform tasks that would usually require a human to complete. AI methods are well suited to predict clinical outcomes. In practice, AI methods can be thought of as functions that learn the outcomes accompanying standardized input data to produce accurate outcome predictions when trialed with new data. Current methods for cleaning, creating, accessing, extracting, augmenting, and representing data for training AI clinical prediction models are well defined. The use of AI to predict clinical outcomes is a dynamic and rapidly evolving arena, with new methods and applications emerging. Extraction or accession of electronic health care records and combining these with patient genetic data is an area of present attention, with tremendous potential for future growth. Machine learning approaches, including decision tree methods of Random Forest and XGBoost, and deep learning techniques including deep multi-layer and recurrent neural networks, afford unique capabilities to accurately create predictions from high dimensional, multimodal data. Furthermore, AI methods are increasing our ability to accurately predict clinical outcomes that previously were difficult to model, including time-dependent and multi-class outcomes. Barriers to robust AI-based clinical outcome model deployment include changing AI product development interfaces, the specificity of regulation requirements, and limitations in ensuring model interpretability, generalizability, and adaptability over time.

RIFS2D: A two-dimensional version of a randomly restarted incremental feature selection algorithm with an application for detecting low-ranked biomarkers

The era of big data introduces both opportunities and challenges for biomedical researchers. One of the inherent difficulties in the biomedical research field is to recruit large cohorts of samples, while high-throughput biotechnologies may produce thousands or even millions of features for each sample. Researchers tend to evaluate the individual correlation of each feature with the class label and use the incremental feature selection (IFS) strategy to select the top-ranked features with the best prediction performance. Recent experimental data showed that a subset of continuously ranked features randomly restarted from a low-ranked feature (an RIFS block) may outperform the subset of top-ranked features. This study proposed a feature selection Algorithm RIFS2D by integrating multiple RIFS blocks. A comprehensive comparative experiment was conducted with the IFS, RIFS and existing feature selection algorithms and demonstrated that a subset of low-ranked features may also achieve promising prediction performance. This study suggested that a prediction model with promising performance may be trained by low-ranked features, even when top-ranked features did not achieve satisfying prediction performance. Further comparative experiments were conducted between RIFS2D and t-tests for the detection of early-stage breast cancer. The data showed that the RIFS2D-recommended features achieved better prediction accuracy and were targeted by more drugs than the t-test top-ranked features.

Predicting breast cancer 5-year survival using machine learning: A systematic review

BACKGROUND

Accurately predicting the survival rate of breast cancer patients is a major issue for cancer researchers. Machine learning (ML) has attracted much attention with the hope that it could provide accurate results, but its modeling methods and prediction performance remain controversial. The aim of this systematic review is to identify and critically appraise current studies regarding the application of ML in predicting the 5-year survival rate of breast cancer.

METHODS

In accordance with the PRISMA guidelines, two researchers independently searched the PubMed (including MEDLINE), Embase, and Web of Science Core databases from inception to November 30, 2020. The search terms included breast neoplasms, survival, machine learning, and specific algorithm names. The included studies related to the use of ML to build a breast cancer survival prediction model and model performance that can be measured with the value of said verification results. The excluded studies in which the modeling process were not explained clearly and had incomplete information. The extracted information included literature information, database information, data preparation and modeling process information, model construction and performance evaluation information, and candidate predictor information.

RESULTS

Thirty-one studies that met the inclusion criteria were included, most of which were published after 2013. The most frequently used ML methods were decision trees (19 studies, 61.3%), artificial neural networks (18 studies, 58.1%), support vector machines (16 studies, 51.6%), and ensemble learning (10 studies, 32.3%). The median sample size was 37256 (range 200 to 659820) patients, and the median predictor was 16 (range 3 to 625). The accuracy of 29 studies ranged from 0.510 to 0.971. The sensitivity of 25 studies ranged from 0.037 to 1. The specificity of 24 studies ranged from 0.008 to 0.993. The AUC of 20 studies ranged from 0.500 to 0.972. The precision of 6 studies ranged from 0.549 to 1. All of the models were internally validated, and only one was externally validated.

CONCLUSIONS

Overall, compared with traditional statistical methods, the performance of ML models does not necessarily show any improvement, and this area of research still faces limitations related to a lack of data preprocessing steps, the excessive differences of sample feature selection, and issues related to validation. Further optimization of the performance of the proposed model is also needed in the future, which requires more standardization and subsequent validation.

A dynamic recursive feature elimination framework (dRFE) to further refine a set of OMIC biomarkers

MOTIVATION

A feature selection algorithm may select the subset of features with the best associations with the class labels. The recursive feature elimination (RFE) is a heuristic feature screening framework and has been widely used to select the biological OMIC biomarkers. This study proposed a dynamic recursive feature elimination (dRFE) framework with more flexible feature elimination operations. The proposed dRFE was comprehensively compared with 11 existing feature selection algorithms and five classifiers on the eight difficult transcriptome datasets from a previous study, the ten newly collected transcriptome datasets and the five methylome datasets.

RESULTS

The experimental data suggested that the regular RFE framework did not perform well, and dRFE outperformed the existing feature selection algorithms in most cases. The dRFE-detected features achieved Acc=1.0000 for the two methylome datasets GSE53045 and GSE66695. The best prediction accuracies of the dRFE-detected features were 0.9259, 0.9424, and 0.8601 for the other three methylome datasets GSE74845, GSE103186, and GSE80970, respectively. Four transcriptome datasets received Acc=1.0000 using the dRFE-detected features, and the prediction accuracies for the other six newly collected transcriptome datasets were between 0.6301 and 0.9917.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.