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General General

AutoML for Multi-Label Classification: Overview and Empirical Evaluation.

In IEEE transactions on pattern analysis and machine intelligence ; h5-index 127.0

Automated machine learning (AutoML) supports the algorithmic construction and data-specific customization of machine learning pipelines, including the selection, combination, and parametrization of machine learning algorithms as main constituents. Generally speaking, AutoML approaches comprise two major components: a search space model and an optimizer for traversing the space. Recent approaches have shown impressive results in the realm of supervised learning, most notably (single-label) classification (SLC). Moreover, first attempts at extending these approaches towards multi-label classification (MLC) have been made. While the space of candidate pipelines is already huge in SLC, the complexity of the search space is raised to an even higher power in MLC. One may wonder, therefore, whether and to what extent optimizers established for SLC can scale to this increased complexity, and how they compare to each other. This paper makes the following contributions: First, we survey existing approaches to AutoML for MLC. Second, we augment these approaches with optimizers not previously tried for MLC. Third, we propose a benchmarking framework that supports a fair and systematic comparison. Fourth, we conduct an extensive experimental study, evaluating the methods on a suite of MLC problems. We find a grammar-based best-first search to compare favorably to other optimizers.

Wever Marcel, Tornede Alexander, Mohr Felix, Hullermeier Eyke

2021-Jan-13

General General

A Novel Multi-Ensemble Method for Identifying Essential Proteins.

In Journal of computational biology : a journal of computational molecular cell biology

Essential proteins possess critical functions for cell survival. Identifying essential proteins improves our understanding of how a cell works and also plays a vital role in the research fields of disease treatment and drug development. Recently, some machine-learning methods and ensemble learning methods have been proposed to identify essential proteins by introducing effective protein features. However, the ensemble learning method only used to focus on the choice of base classifiers. In this article, we propose a novel ensemble learning framework called multi-ensemble to integrate different base classifiers. The multi-ensemble method adopts the idea of multi-view learning and selects multiple base classifiers and trains those classifiers by continually adding the samples that are predicted correctly by the other base classifiers. We applied multi-ensemble to Yeast data and Escherichia coli data. The results show that our approach achieved better performance than both individual classifiers and the other ensemble learning methods.

Dai Wei, Chen Bingxi, Peng Wei, Li Xia, Zhong Jiancheng, Wang Jianxin

2021-Jan-13

ensemble learning, essential proteins, multi-ensemble, multi-view learning

oncology Oncology

Machine Learning Frameworks to Predict Neoadjuvant Chemotherapy Response in Breast Cancer Using Clinical and Pathological Features.

In JCO clinical cancer informatics

PURPOSE : Neoadjuvant chemotherapy (NAC) is used to treat locally advanced breast cancer (LABC) and high-risk early breast cancer (BC). Pathological complete response (pCR) has prognostic value depending on BC subtype. Rates of pCR, however, can be variable. Predictive modeling is desirable to help identify patients early who may have suboptimal NAC response. Here, we test and compare the predictive performances of machine learning (ML) prediction models to a standard statistical model, using clinical and pathological data.

METHODS : Clinical and pathological variables were collected in 431 patients, including tumor size, patient demographics, histological characteristics, molecular status, and staging information. A standard multivariable logistic regression (MLR) was developed and compared with five ML models: k-nearest neighbor classifier, random forest (RF) classifier, naive Bayes algorithm, support vector machine, and multilayer perceptron model. Model performances were measured using a receiver operating characteristic (ROC) analysis and statistically compared.

RESULTS : MLR predictors of NAC response included: estrogen receptor (ER) status, human epidermal growth factor-2 (HER2) status, tumor size, and Nottingham grade. The strongest MLR predictors of pCR included HER2+ versus HER2- BC (odds ratio [OR], 0.13; 95% CI, 0.07 to 0.23; P < .001) and Nottingham grade G3 versus G1-2 (G1-2: OR, 0.36; 95% CI, 0.20 to 0.65; P < .001). The area under the curve (AUC) for the MLR was AUC = 0.64. Among the various ML models, an RF classifier performed best, with an AUC = 0.88, sensitivity of 70.7%, and specificity of 84.6%, and included the following variables: menopausal status, ER status, HER2 status, Nottingham grade, tumor size, nodal status, and presence of inflammatory BC.

CONCLUSION : Modeling performances varied between standard versus ML classification methods. RF ML classifiers demonstrated the best predictive performance among all models.

Meti Nicholas, Saednia Khadijeh, Lagree Andrew, Tabbarah Sami, Mohebpour Majid, Kiss Alex, Lu Fang-I, Slodkowska Elzbieta, Gandhi Sonal, Jerzak Katarzyna Joanna, Fleshner Lauren, Law Ethan, Sadeghi-Naini Ali, Tran William T

2021-Jan

oncology Oncology

Artificial Intelligence Clinical Evidence Engine for Automatic Identification, Prioritization, and Extraction of Relevant Clinical Oncology Research.

In JCO clinical cancer informatics

PURPOSE : We developed a system to automate analysis of the clinical oncology scientific literature from bibliographic databases and match articles to specific patient cohorts to answer specific questions regarding the efficacy of a treatment. The approach attempts to replicate a clinician's mental processes when reviewing published literature in the context of a patient case. We describe the system and evaluate its performance.

METHODS : We developed separate ground truth data sets for each of the tasks described in the paper. The first ground truth was used to measure the natural language processing (NLP) accuracy from approximately 1,300 papers covering approximately 3,100 statements and approximately 25 concepts; performance was evaluated using a standard F1 score. The ground truth for the expert classifier model was generated by dividing papers cited in clinical guidelines into a training set and a test set in an 80:20 ratio, and performance was evaluated for accuracy, sensitivity, and specificity.

RESULTS : The NLP models were able to identify individual attributes with a 0.7-0.9 F1 score, depending on the attribute of interest. The expert classifier machine learning model was able to classify the individual records with a 0.93 accuracy (95% CI, 0.9 to 0.96, P < .0001), and sensitivity and specificity of 0.95 and 0.91, respectively. Using a decision boundary of 0.5 for the positive (expert) label, the classifier demonstrated an F1 score of 0.92.

CONCLUSION : The system identified and extracted evidence from the oncology literature with a high degree of accuracy, sensitivity, and specificity. This tool enables timely access to the most relevant biomedical literature, providing critical support to evidence-based practice in areas of rapidly evolving science.

Saiz Fernando Suarez, Sanders Corey, Stevens Rick, Nielsen Robert, Britt Michael, Yuravlivker Leemor, Preininger Anita M, Jackson Gretchen P

2021-Jan

General General

An enhanced deep image model for glaucoma diagnosis using feature-based detection in retinal fundus.

In Medical & biological engineering & computing ; h5-index 32.0

This paper proposes a deep image analysis-based model for glaucoma diagnosis that uses several features to detect the formation of glaucoma in retinal fundus. These features are combined with most extracted parameters like inferior, superior, nasal, and temporal region area, and cup-to-disc ratio that overall forms a deep image analysis. This proposed model is exercised to investigate the various aspects related to the prediction of glaucoma in retinal fundus images that help the ophthalmologist in making better decisions for the human eye. The proposed model is presented with the combination of four machine learning algorithms that provide the classification accuracy of 98.60% while other existing models like support vector machine (SVM), K-nearest neighbors (KNN), and Naïve Bayes provide individually with accuracies of 97.61%, 90.47%, and 95.23% respectively. These results clearly demonstrate that this proposed model offers the best methodology to an early diagnosis of glaucoma in retinal fundus.

Singh Law Kumar, Pooja Garg, Hitendra Khanna, Munish Bhadoria

2021-Jan-13

Cup-to-disc ratio, Glaucoma diagnosis, Inferior superior nasal temporal (ISNT) regions, Machine learning, Retinal fundus image

Radiology Radiology

Automated segmentation of kidney and renal mass and automated detection of renal mass in CT urography using 3D U-Net-based deep convolutional neural network.

In European radiology ; h5-index 62.0

OBJECTIVES : To develop a 3D U-Net-based deep learning model for automated segmentation of kidney and renal mass, and detection of renal mass in corticomedullary phase of computed tomography urography (CTU).

METHODS : Data on 882 kidneys obtained from CTU data of 441 patients with renal mass were used to learn and evaluate the deep learning model. The CTU data of 35 patients with small renal tumors (diameter ≤ 1.5 cm) were used for additional testing. The ground truth data for the kidney, renal tumor, and cyst were manually annotated on corticomedullary phase images of CTU. The proposed segmentation model for kidney and renal mass was constructed based on a 3D U-Net. The segmentation accuracy was evaluated through the Dice similarity coefficient (DSC). The volume of the maximum 3D volume of interest of renal tumor and cyst in the predicted segmentation by the model was used as an identification indicator, while the detection performance of the model was evaluated by the area under the receiver operation characteristic curve.

RESULTS : The proposed model showed a high accuracy in segmentation of kidney and renal tumor, with average DSC of 0.973 and 0.844, respectively. It performed moderately in the renal cyst segmentation, with an average DSC of 0.536 in the test set. Also, this model showed good performance in detecting renal tumor and cyst.

CONCLUSIONS : The proposed automated segmentation and detection model based on 3D U-Net shows promising results for the segmentation of kidney and renal tumor, and the detection of renal tumor and cyst.

KEY POINTS : • The segmentation model based on 3D U-Net showed high accuracy in segmentation of kidney and renal neoplasm, and good detection performance of renal neoplasm and cyst in corticomedullary phase of CTU. • The segmentation model based on 3D U-Net is a fully automated aided diagnostic tool that could be used to reduce the workload of radiologists and improve the accuracy of diagnosis. • The segmentation model based on 3D U-Net would be helpful to provide quantitative information for diagnosis, treatment, surgical planning, etc.

Lin Zhiyong, Cui Yingpu, Liu Jia, Sun Zhaonan, Ma Shuai, Zhang Xiaodong, Wang Xiaoying

2021-Jan-13

Computer-assisted diagnosis, Deep learning, Kidney, Renal neoplasm, Tomography, X-ray computed