Tabu Search and Machine-Learning Classification of Benign and Malignant Proliferative Breast Lesions.
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ABSTRACT:
SUBMITTER: Dhahri H
PROVIDER: S-EPMC7064857 | biostudies-literature | 2020
REPOSITORIES: biostudies-literature
Publications
Tabu Search and Machine-Learning Classification of Benign and Malignant Proliferative Breast Lesions.
Dhahri Habib H Rahmany Ines I Mahmood Awais A Al Maghayreh Eslam E Elkilani Wail W
BioMed research international 20200227
Breast cancer is the most diagnosed cancer among women around the world. The development of computer-aided diagnosis tools is essential to help pathologists to accurately interpret and discriminate between malignant and benign tumors. This paper proposes the development of an automated proliferative breast lesion diagnosis based on machine-learning algorithms. We used Tabu search to select the most significant features. The evaluation of the feature is based on the dependency degree of each attr ...[more]
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Project description:BackgroundDifferential diagnosis between benign and malignant breast lesions is of crucial importance relating to follow-up treatment. Recent development in texture analysis and machine learning may lead to a new solution to this problem.MethodThis current study enrolled a total number of 265 patients (benign breast lesions:malignant breast lesions = 71:194) diagnosed in our hospital and received magnetic resonance imaging between January 2014 and August 2017. Patients were randomly divided into the training group and validation group (4:1), and two radiologists extracted their texture features from the contrast-enhanced T1-weighted images. We performed five different feature selection methods including Distance correlation, Gradient Boosting Decision Tree (GBDT), least absolute shrinkage and selection operator (LASSO), random forest (RF), eXtreme gradient boosting (Xgboost) and five independent classification models were built based on Linear discriminant analysis (LDA) algorithm.ResultsAll five models showed promising results to discriminate malignant breast lesions from benign breast lesions, and the areas under the curve (AUCs) of receiver operating characteristic (ROC) were all above 0.830 in both training and validation groups. The model with a better discriminating ability was the combination of LDA + gradient boosting decision tree (GBDT). The sensitivity, specificity, AUC, and accuracy in the training group were 0.814, 0.883, 0.922, and 0.868, respectively; LDA + random forest (RF) also suggests promising results with the AUC of 0.906 in the training group.ConclusionThe evidence of this study, while preliminary, suggested that a combination of MRI texture analysis and LDA algorithm could discriminate benign breast lesions from malignant breast lesions. Further multicenter researches in this field would be of great help in the validation of the result.
| S-EPMC8558475 | biostudies-literature
Project description:PurposeThis study aimed to establish and evaluate the usefulness of a simple, practical, and easy-to-promote machine learning model based on ultrasound imaging features for diagnosing breast cancer (BC).Materials and methodsLogistic regression, random forest, extra trees, support vector, multilayer perceptron, and XG Boost models were developed. The modeling data set of 1345 cases was from a tertiary class A hospital in China. The external validation data set of 1965 cases were from 3 tertiary class A hospitals and 2 primary hospitals. The area under the receiver operating characteristic curve (AUC) was used as the main evaluation index, and pathological biopsy was used as the gold standard for evaluating each model. Diagnostic capability was also compared with that of clinicians.ResultsAmong the six models, the logistic model showed superior diagnostic efficiency, with an AUC of 0.771 and 0.906 and Brier scores of 0.181 and 0.165 in the test and validation sets, respectively. The AUCs of the clinician diagnosis and the logistic model were 0.913 and 0.906. Their AUCs in the tertiary class A hospitals were 0.915 and 0.915, respectively, and were 0.894 and 0.873 in primary hospitals, respectively.ConclusionThe externally validated logical model can be used to distinguish between malignant and benign breast lesions in ultrasound images. Compared with clinician diagnosis, the logistic model has better diagnostic efficiency, making it potentially useful to assist in screening, particularly in lower level medical institutions.Trial registrationhttp://www.clinicaltrials.gov. ClinicalTrials.gov ID: NCT03080623.
| S-EPMC8057795 | biostudies-literature
Project description:ObjectivesWe aimed to assess the performance of radiomics and machine learning (ML) for classification of non-cystic benign and malignant breast lesions on ultrasound images, compare ML's accuracy with that of a breast radiologist, and verify if the radiologist's performance is improved by using ML.MethodsOur retrospective study included patients from two institutions. A total of 135 lesions from Institution 1 were used to train and test the ML model with cross-validation. Radiomic features were extracted from manually annotated images and underwent a multistep feature selection process. Not reproducible, low variance, and highly intercorrelated features were removed from the dataset. Then, 66 lesions from Institution 2 were used as an external test set for ML and to assess the performance of a radiologist without and with the aid of ML, using McNemar's test.ResultsAfter feature selection, 10 of the 520 features extracted were employed to train a random forest algorithm. Its accuracy in the training set was 82% (standard deviation, SD, ± 6%), with an AUC of 0.90 (SD ± 0.06), while the performance on the test set was 82% (95% confidence intervals (CI) = 70-90%) with an AUC of 0.82 (95% CI = 0.70-0.93). It resulted in being significantly better than the baseline reference (p = 0.0098), but not different from the radiologist (79.4%, p = 0.815). The radiologist's performance improved when using ML (80.2%), but not significantly (p = 0.508).ConclusionsA radiomic analysis combined with ML showed promising results to differentiate benign from malignant breast lesions on ultrasound images.Key points• Machine learning showed good accuracy in discriminating benign from malignant breast lesions • The machine learning classifier's performance was comparable to that of a breast radiologist • The radiologist's accuracy improved with machine learning, but not significantly.
| S-EPMC8589755 | biostudies-literature
Project description:Artificial intelligence as a screening tool for eyelid lesions will be helpful for early diagnosis of eyelid malignancies and proper decision-making. This study aimed to evaluate the performance of a deep learning model in differentiating eyelid lesions using clinical eyelid photographs in comparison with human ophthalmologists. We included 4954 photographs from 928 patients in this retrospective cross-sectional study. Images were classified into three categories: malignant lesion, benign lesion, and no lesion. Two pre-trained convolutional neural network (CNN) models, DenseNet-161 and EfficientNetV2-M architectures, were fine-tuned to classify images into three or two (malignant versus benign) categories. For a ternary classification, the mean diagnostic accuracies of the CNNs were 82.1% and 83.0% using DenseNet-161 and EfficientNetV2-M, respectively, which were inferior to those of the nine clinicians (87.0-89.5%). For the binary classification, the mean accuracies were 87.5% and 92.5% using DenseNet-161 and EfficientNetV2-M models, which was similar to that of the clinicians (85.8-90.0%). The mean AUC of the two CNN models was 0.908 and 0.950, respectively. Gradient-weighted class activation map successfully highlighted the eyelid tumors on clinical photographs. Deep learning models showed a promising performance in discriminating malignant versus benign eyelid lesions on clinical photographs, reaching the level of human observers.
| S-EPMC10011394 | biostudies-literature
Project description:Benign normal (NL), premalignant (endometrial intraepithelial neoplasia, EIN) and malignant (cancer, EMCA) endometria must be precisely distinguished for optimal management. EIN was objectively defined previously as a regression model incorporating manually traced histologic variables to predict clonal growth and cancer outcomes. Results from this early computational study were used to revise subjective endometrial precancer diagnostic criteria currently in use. We here use automated feature segmentation and updated machine learning algorithms to develop a new classification algorithm. Endometrial tissue from 148 patients was randomly separated into 72-patient training and 76-patient validation cohorts encompassing all 3 diagnostic classes. We applied image analysis software to keratin stained endometrial tissues to automatically segment whole-slide digital images into epithelium, cells, and nuclei and extract corresponding variables. A total of 1413 variables were culled to 75 based on random forest classification performance in a 3-group (NL, EIN, EMCA) model. This algorithm correctly classifies cases with 3-class error rates of 0.04 (training set) and 0.058 (validation set); and 2-class (NL vs. EIN+EMCA) error rate of 0.016 (training set) and 0 (validation set). The 4 most heavily weighted variables are surrogates of those previously identified in manual-segmentation machine learning studies (stromal and epithelial area percentages, and normalized epithelial surface lengths). Lesser weighted predictors include gland and lumen axis lengths and ratios, and individual cell measures. Automated image analysis and random forest classification algorithms can classify normal, premalignant, and malignant endometrial tissues. Highest predictive variables overlap with those discovered independently in early models based on manual segmentation.
| S-EPMC6884662 | biostudies-literature
Project description:Background: Because neurofibromatosis type I (NF1) is a cancer predisposition disease, it is important to distinguish between benign and malignant lesions, especially in the craniofacial area. Purpose: The purpose of this study is to improve effectiveness in the diagnostic performance in discriminating malignant from benign craniofacial lesions based on computed tomography (CT) using a Keras-based machine-learning model. Methods: The Keras-based machine learning technique, a neural network package in the Python language, was used to train the diagnostic model on CT datasets. Fifty NF1 patients with benign craniofacial neurofibromas and six NF1 patients with malignant peripheral nerve sheath tumors (MPNSTs) were selected as the training set. Three validation cohorts were used: validation cohort 1 (random selection of 90% of the patients in the training cohort), validation cohort 2 (an independent cohort of 9 NF1 patients with benign craniofacial neurofibromas and 11 NF1 patients with MPNST), and validation cohort 3 (eight NF1 patients with MPNST, not restricted to the craniofacial area). Sensitivity and specificity were tested using validation cohorts 1 and 2, and generalizability was evaluated using validation cohort 3. Results: A total of 59 NF1 patients with benign neurofibroma and 23 NF1 patients with MPNST were included. A Keras-based machine-learning model was successfully established using the training cohort. The accuracy was 96.99 and 100% in validation cohorts 1 and 2, respectively, discriminating NF1-related benign and malignant craniofacial lesions. However, the accuracy of this model was significantly reduced to 51.72% in the identification of MPNSTs in different body regions. Conclusion: The Keras-based machine learning technique showed the potential of robust diagnostic performance in the differentiation of craniofacial MPNSTs and benign neurofibromas in NF1 patients using CT images. However, the model has limited generalizability when applied to other body areas. With more clinical data accumulating in the model, this system may support clinical doctors in the primary screening of true MPNSTs from benign lesions in NF1 patients.
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Project description:ImportanceFollowing recent US Food and Drug Administration approval, adoption of whole slide imaging in clinical settings may be imminent, and diagnostic accuracy, particularly among challenging breast biopsy specimens, may benefit from computerized diagnostic support tools.ObjectiveTo develop and evaluate computer vision methods to assist pathologists in diagnosing the full spectrum of breast biopsy samples, from benign to invasive cancer.Design, setting, and participantsIn this diagnostic study, 240 breast biopsies from Breast Cancer Surveillance Consortium registries that varied by breast density, diagnosis, patient age, and biopsy type were selected, reviewed, and categorized by 3 expert pathologists as benign, atypia, ductal carcinoma in situ (DCIS), and invasive cancer. The atypia and DCIS cases were oversampled to increase statistical power. High-resolution digital slide images were obtained, and 2 automated image features (tissue distribution feature and structure feature) were developed and evaluated according to the consensus diagnosis of the expert panel. The performance of the automated image analysis methods was compared with independent interpretations from 87 practicing US pathologists. Data analysis was performed between February 2017 and February 2019.Main outcomes and measuresDiagnostic accuracy defined by consensus reference standard of 3 experienced breast pathologists.ResultsThe accuracy of machine learning tissue distribution features, structure features, and pathologists for classification of invasive cancer vs noninvasive cancer was 0.94, 0.91, and 0.98, respectively; the accuracy of classification of atypia and DCIS vs benign tissue was 0.70, 0.70, and 0.81, respectively; and the accuracy of classification of DCIS vs atypia was 0.83, 0.85, and 0.80, respectively. The sensitivity of both machine learning features was lower than that of the pathologists for the invasive vs noninvasive classification (tissue distribution feature, 0.70; structure feature, 0.49; pathologists, 0.84) but higher for the classification of atypia and DCIS vs benign cases (tissue distribution feature, 0.79; structure feature, 0.85; pathologists, 0.72) and the classification of DCIS vs atypia (tissue distribution feature, 0.88; structure feature, 0.89; pathologists, 0.70). For the DCIS vs atypia classification, the specificity of the machine learning feature classification was similar to that of the pathologists (tissue distribution feature, 0.78; structure feature, 0.80; pathologists, 0.82).Conclusion and relevanceThe computer-based automated approach to interpreting breast pathology showed promise, especially as a diagnostic aid in differentiating DCIS from atypical hyperplasia.
| S-EPMC6692690 | biostudies-literature
Project description:BACKGROUND:Peripheral blood transcriptome profiling is a potentially important tool for disease detection. We utilize this technique in a case-control study to identify candidate transcriptomic biomarkers able to differentiate women with breast lesions from normal controls. METHODS:Whole blood samples were collected from 50 women with high-risk breast lesions, 57 with breast cancers and 44 controls (151 samples). Blood gene expression profiling was carried out using microarray hybridization. We identified blood gene expression signatures using AdaBoost, and constructed a predictive model differentiating breast lesions from controls. Model performance was then characterized by AUC sensitivity, specificity and accuracy. Biomarker biological processes and functions were analyzed for clues to the pathogenesis of breast lesions. RESULTS:Ten gene biomarkers were identified (YWHAQ, BCLAF1, WSB1, PBX2, DDIT4, LUC7L3, FKBP1A, APP, HERC2P2, FAM126B). A ten-gene panel predictive model showed discriminatory power in the test set (sensitivity: 100%, specificity: 84.2%, accuracy: 93.5%, AUC: 0.99). These biomarkers were involved in apoptosis, TGF-beta signaling, adaptive immune system regulation, gene transcription and post-transcriptional protein modification. CONCLUSION:A promising method for the detection of breast lesions is reported. This study also sheds light on breast cancer/immune system interactions, providing clues to new targets for breast cancer immune therapy.
| S-EPMC7272048 | biostudies-literature
Project description:Gastric cancer (GC) is one of the leading causes of cancer-related death worldwide. It takes some time from chronic gastritis to develop in GC. Early detection of GC will help patients obtain timely treatment. Understanding disease evolution is crucial for the prevention and treatment of GC. Here, we present a convolutional neural network (CNN)-based system to detect abnormalities in the gastric mucosa. We identified normal mucosa, chronic gastritis, and intestinal-type GC: this is the most common route of gastric carcinogenesis. We integrated digitalizing histopathology of whole-slide images (WSIs), stain normalization, a deep CNN, and a random forest classifier. The staining variability of WSIs was reduced significantly through stain normalization, and saved the cost and time of preparing new slides. Stain normalization improved the effect of the CNN model. The accuracy rate at the patch-level reached 98.4%, and 94.5% for discriminating normal → chronic gastritis → GC. The accuracy rate at the WSIs-level for discriminating normal tissue and cancerous tissue reached 96.0%, which is a state-of-the-art result. Survival analyses indicated that the features extracted from the CNN exerted a significant impact on predicting the survival of cancer patients. Our CNN model disclosed significant potential for adjuvant diagnosis of gastric diseases, especially GC, and usefulness for predicting the prognosis.
| S-EPMC7562716 | biostudies-literature
Project description:BackgroundGrading of cancer histopathology slides requires more pathologists and expert clinicians as well as it is time consuming to look manually into whole-slide images. Hence, an automated classification of histopathological breast cancer sub-type is useful for clinical diagnosis and therapeutic responses. Recent deep learning methods for medical image analysis suggest the utility of automated radiologic imaging classification for relating disease characteristics or diagnosis and patient stratification.MethodsTo develop a hybrid model using the convolutional neural network (CNN) and the long short-term memory recurrent neural network (LSTM RNN) to classify four benign and four malignant breast cancer subtypes. The proposed CNN-LSTM leveraging on ImageNet uses a transfer learning approach in classifying and predicting four subtypes of each. The proposed model was evaluated on the BreakHis dataset comprises 2480 benign and 5429 malignant cancer images acquired at magnifications of 40×, 100×, 200× and 400×.ResultsThe proposed hybrid CNN-LSTM model was compared with the existing CNN models used for breast histopathological image classification such as VGG-16, ResNet50, and Inception models. All the models were built using three different optimizers such as adaptive moment estimator (Adam), root mean square propagation (RMSProp), and stochastic gradient descent (SGD) optimizers by varying numbers of epochs. From the results, we noticed that the Adam optimizer was the best optimizer with maximum accuracy and minimum model loss for both the training and validation sets. The proposed hybrid CNN-LSTM model showed the highest overall accuracy of 99% for binary classification of benign and malignant cancer, and, whereas, 92.5% for multi-class classifier of benign and malignant cancer subtypes, respectively.ConclusionTo conclude, the proposed transfer learning approach outperformed the state-of-the-art machine and deep learning models in classifying benign and malignant cancer subtypes. The proposed method is feasible in classification of other cancers as well as diseases.
| S-EPMC9885590 | biostudies-literature