Dataset Information

A Comparative Study of Machine Learning Methods for Persistence Diagrams.

ABSTRACT: Many and varied methods currently exist for featurization, which is the process of mapping persistence diagrams to Euclidean space, with the goal of maximally preserving structure. However, and to our knowledge, there are presently no methodical comparisons of existing approaches, nor a standardized collection of test data sets. This paper provides a comparative study of several such methods. In particular, we review, evaluate, and compare the stable multi-scale kernel, persistence landscapes, persistence images, the ring of algebraic functions, template functions, and adaptive template systems. Using these approaches for feature extraction, we apply and compare popular machine learning methods on five data sets: MNIST, Shape retrieval of non-rigid 3D Human Models (SHREC14), extracts from the Protein Classification Benchmark Collection (Protein), MPEG7 shape matching, and HAM10000 skin lesion data set. These data sets are commonly used in the above methods for featurization, and we use them to evaluate predictive utility in real-world applications.

SUBMITTER: Barnes D

PROVIDER: S-EPMC8355525 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundTwitter presents a valuable and relevant social media platform to study the prevalence of information and sentiment on vaping that may be useful for public health surveillance. Machine learning classifiers that identify vaping-relevant tweets and characterize sentiments in them can underpin a Twitter-based vaping surveillance system. Compared with traditional machine learning classifiers that are reliant on annotations that are expensive to obtain, deep learning classifiers offer the advantage of requiring fewer annotated tweets by leveraging the large numbers of readily available unannotated tweets.ObjectiveThis study aims to derive and evaluate traditional and deep learning classifiers that can identify tweets relevant to vaping, tweets of a commercial nature, and tweets with provape sentiments.MethodsWe continuously collected tweets that matched vaping-related keywords over 2 months from August 2018 to October 2018. From this data set of tweets, a set of 4000 tweets was selected, and each tweet was manually annotated for relevance (vape relevant or not), commercial nature (commercial or not), and sentiment (provape or not). Using the annotated data, we derived traditional classifiers that included logistic regression, random forest, linear support vector machine, and multinomial naive Bayes. In addition, using the annotated data set and a larger unannotated data set of tweets, we derived deep learning classifiers that included a convolutional neural network (CNN), long short-term memory (LSTM) network, LSTM-CNN network, and bidirectional LSTM (BiLSTM) network. The unannotated tweet data were used to derive word vectors that deep learning classifiers can leverage to improve performance.ResultsLSTM-CNN performed the best with the highest area under the receiver operating characteristic curve (AUC) of 0.96 (95% CI 0.93-0.98) for relevance, all deep learning classifiers including LSTM-CNN performed better than the traditional classifiers with an AUC of 0.99 (95% CI 0.98-0.99) for distinguishing commercial from noncommercial tweets, and BiLSTM performed the best with an AUC of 0.83 (95% CI 0.78-0.89) for provape sentiment. Overall, LSTM-CNN performed the best across all 3 classification tasks.ConclusionsWe derived and evaluated traditional machine learning and deep learning classifiers to identify vaping-related relevant, commercial, and provape tweets. Overall, deep learning classifiers such as LSTM-CNN had superior performance and had the added advantage of requiring no preprocessing. The performance of these classifiers supports the development of a vaping surveillance system.

Project description:BackgroundNonalcoholic steatohepatitis (NASH), advanced fibrosis, and subsequent cirrhosis and hepatocellular carcinoma are becoming the most common etiology for liver failure and liver transplantation; however, they can only be diagnosed at these potentially reversible stages with a liver biopsy, which is associated with various complications and high expenses. Knowing the difference between the more benign isolated steatosis and the more severe NASH and cirrhosis informs the physician regarding the need for more aggressive management.ObjectiveWe intend to explore the feasibility of using machine learning methods for noninvasive diagnosis of NASH and advanced liver fibrosis and compare machine learning methods with existing quantitative risk scores.MethodsWe conducted a retrospective analysis of clinical data from a cohort of 492 patients with biopsy-proven nonalcoholic fatty liver disease (NAFLD), NASH, or advanced fibrosis. We systematically compared 5 widely used machine learning algorithms for the prediction of NAFLD, NASH, and fibrosis using 2 variable encoding strategies. Then, we compared the machine learning methods with 3 existing quantitative scores and identified the important features for prediction using the SHapley Additive exPlanations method.ResultsThe best machine learning method, gradient boosting (GB), achieved the best area under the curve scores of 0.9043, 0.8166, and 0.8360 for NAFLD, NASH, and advanced fibrosis, respectively. GB also outperformed 3 existing risk scores for fibrosis. Among the variables, alanine aminotransferase (ALT), triglyceride (TG), and BMI were the important risk factors for the prediction of NAFLD, whereas aspartate transaminase (AST), ALT, and TG were the important variables for the prediction of NASH, and AST, hyperglycemia (A1c), and high-density lipoprotein were the important variables for predicting advanced fibrosis.ConclusionsIt is feasible to use machine learning methods for predicting NAFLD, NASH, and advanced fibrosis using routine clinical data, which potentially can be used to better identify patients who still need liver biopsy. Additionally, understanding the relative importance and differences in predictors could lead to improved understanding of the disease process as well as support for identifying novel treatment options.

Dataset Information

A Comparative Study of Machine Learning Methods for Persistence Diagrams.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets