A review of Topological Data Analysis and Machine Learning

The last decade saw an enormous boost in the field of computational topology: methods and concepts from algebraic and differential topology, formerly confined to the realm of pure mathematics, have demonstrated their utility in numerous areas such as computational biology personalised medicine, and time-dependent data analysis, to name a few. The newly-emerging domain comprising topology-based techniques is often referred to as topological data analysis (TDA). Next to their applications in the aforementioned areas, TDA methods have also proven to be effective in supporting, enhancing, and augmenting both classical machine learning and deep learning models. In this paper, we review the state of the art of a nascent field we refer to as “topological machine learning,” i.e., the successful symbiosis of topology-based methods and machine learning algorithms, such as deep neural networks. We identify common threads, current applications, and future challenges.

Summary A meticulous interpretation of steady-state or unsteady-state relative permeability (Kr) experimental data is required to determine a complete set of Kr curves. In this work, different machine learning (ML) models were developed to assist in a faster estimation of these curves from steady-state drainage coreflooding experimental runs. These ML algorithms include gradient boosting (GB), random forest (RF), extreme gradient boosting (XGB), and deep neural network (DNN) with a main focus on and comparison of the two latter algorithms (XGB and DNN). Based on existing mathematical models, a leading-edge framework was developed where a large database of Kr and capillary pressure (Pc) curves were generated. This database was used to perform thousands of coreflood simulation runs representing oil-water drainage steady-state experiments. The results obtained from these simulation runs, mainly pressure drop along with other conventional core analysis data, were used to estimate analytical Kr curves based on Darcy’s law. These analytically estimated Kr curves along with the previously generated Pc curves were fed as features into the ML model. The entire data set was split into 80% for training and 20% for testing. The k-fold cross-validation technique was applied to increase the model’s accuracy by splitting 80% of the training data into 10 folds. In this manner, for each of the 10 experiments, nine folds were used for training and the remaining fold was used for model validation. Once the model was trained and validated, it was subjected to blind testing on the remaining 20% of the data set. The ML model learns to capture fluid flow behavior inside the core from the training data set. In terms of applicability of these ML models, two sets of experimental data were needed as input; the first was the analytically estimated Kr curves from the steady-state drainage coreflooding experiments, while the other was the Pc curves estimated from centrifuge or mercury injection capillary pressure (MICP) measurements. The trained/tested model was then able to estimate Kr curves based on the experimental results fed as input. Furthermore, to test the performance of the ML model when only one set of experimental data is available to an end user, a recurrent neural network (RNN) algorithm was trained/tested to predict Kr curves in the absence of Pc curves as an input. The performance of the three developed models (XGB, DNN, and RNN) was assessed using the values of the coefficient of determination (R2) along with the loss calculated during training/validation of the model. The respective crossplots along with comparisons of ground truth vs. artificial intelligence (AI)-predicted curves indicated that the model is capable of making accurate predictions with an error percentage between 0.2% and 0.6% on history-matching experimental data for all three tested ML techniques. This implies that the AI-based model exhibits better efficiency and reliability in determining Kr curves when compared to conventional methods. The developed ML models by no means replace the need to conduct drainage coreflooding or centrifuge experiments but act as an alternative to existing commercial platforms that are used to interpret experimental data to predict Kr curves. The two main advantages of the developed ML models are their capability of predicting Kr curves within a matter of a few minutes as well as with limited intervention from the end user. The results also include a comparison between classical ML approaches, shallow neural networks, and DNNs in terms of accuracy in predicting the final Kr curves. The research presented here is an extension of the state-of-the-art framework proposed by Mathew et al. (2021). However, the two main aspects of the current study are the application of deep learning for the prediction of Kr curves and the application of feature engineering. The latter not only reduces the training/testing time for the ML models but also enables the end user to obtain the final predictions with the least set of experimental data. The various models discussed in this research work currently focus on the prediction of Kr curves for drainage steady-state experiments; however, the work can be extended to capture the imbibition cycle as well.

An Artificial Intelligence Ultrasound Platform for Screening and Staging of Thyroid Cancer

Machine learning has achieved remarkable success across diverse domains. Nevertheless, concerns about interpretability in black-box models, especially within Deep Neural Networks (DNNs), have become pronounced in safety-critical fields like healthcare and finance. Classical machine learning (ML) classifiers, known for their higher interpretability, are preferred in these domains. Similar to DNNs, classical ML classifiers can exhibit bugs that could lead to severe consequences in practice. Test input prioritization has emerged as a promising approach to ensure the quality of an ML system, which prioritizes potentially misclassified tests so that such tests can be identified earlier with limited manual labeling costs. However, when applying to classical ML classifiers, existing DNN test prioritization methods are constrained from three perspectives: 1) Coverage-based methods are inefficient and time-consuming; 2) Mutation-based methods cannot be adapted to classical ML models due to mismatched model mutation rules; 3) Confidence-based methods are restricted to a single dimension when applying to binary ML classifiers, solely depending on the model’s prediction probability for one class. To overcome the challenges, we propose MLPrior, a test prioritization approach specifically tailored for classical ML models. MLPrior leverages the characteristics of classical ML classifiers (i.e., interpretable models and carefully engineered attribute features) to prioritize test inputs. The foundational principles are: 1) tests more sensitive to mutations are more likely to be misclassified, and 2) tests closer to the model’s decision boundary are more likely to be misclassified. Building on the first concept, we design mutation rules to generate two types of mutation features (i.e., <bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">model mutation features</b> and <bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">input mutation features</b> ) for each test. Drawing from the second notion, MLPrior generates <bold xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">attribute features</b> of each test based on its attribute values, which can indirectly reveal the proximity between the test and the decision boundary. For each test, MLPrior combines all three types of features of it into a final vector. Subsequently, MLPrior employs a pre-trained ranking model to predict the misclassification probability of each test based on its final vector and ranks tests accordingly. We conducted an extensive study to evaluate MLPrior based on 185 subjects, encompassing natural datasets, mixed noisy datasets, and fairness datasets. The results demonstrate that MLPrior outperforms all the compared test prioritization approaches, with an average improvement of 14.74%∼66.93% on natural datasets, 18.55%∼67.73% on mixed noisy datasets, and 15.34%∼62.72% on fairness datasets.

Objective: Congestive heart failure is a problem affecting millions of Americans. A continuous, non-invasive, telemonitoring device that can accurately monitor cardiac metrics could greatly help this population, reducing unnecessary hospitalizations and cost. Approach: Machine learning (ML) algorithms trained on electrical-impedance tomography (EIT) data are presented for portable cardiac monitoring. The approach was validated on a simulated thorax and a measured tank experiment. A highly detailed 4D chest model (finite element method mesh and conductivity profiles) was developed utilizing the 4D XCAT phantom to provide realistic data. The ML algorithms were trained using databases that assumed the presence of poorly contacting electrodes without any assumptions of knowing which electrodes would be bad in the experiment. The trained ML algorithms were compared to EIT evaluated with and without removing bad electrodes. Main results: A regression support vector machine and a deep neural network (DNN) were found to be the most accurate and robust to poorly contacting electrodes while not needing to know which electrodes were in poor contact in the simulated and measured experiments, respectively. Significance: Although the ML algorithms are not always better than EIT (with bad electrodes removed), the comparable results without needing a priori knowledge of which electrodes are bad is seen as a very promising feature. An evaluation of computational costs showed that the DNN required comparable computational power to the other methods while requiring less memory, which could make the DNNs an attractive algorithm for a low-power, portable system. This work represents an important validation of the method using measured data, and model development, which is needed to apply this method on real clinical data. Additionally, the developed 4D simulated thorax model could be an important tool within the EIT community.

Despite the promise for performance and accuracy improvements of quantum inspired (QI) algorithms over classical machine learning (ML) algorithms, such gains have not been realized in practice. The quantum inspired algorithms can theoretically achieve significant speed up based on sampling assumptions and have thus far failed to outperform the existing classical ML models in practical applications. The speedup of quantum machine learning (QML) algorithms assume the access to data in quantum random access memory (QRAM) which is a strong assumption with current quantum architectures. QI algorithms assume sample and query (SQ) access to input vector and norms of matrices using a dynamic data structure. We explore the components of these models and the assumptions in this paper by surveying the recent works in QML and QI Machine learning (QIML) algorithms. We limit our study to QML and QIML models on achieving a speed up over classical ML techniques rather than individual proofs of these algorithms. This study highlights the assumptions being made that are currently not practical for QML and QIML algorithms in achieving performance advantage over classical ML algorithms.

The aging and multimorbid population and health personnel shortages pose a substantial burden on primary health care. While predictive machine learning (ML) algorithms have the potential to address these challenges, concerns include transparency and insufficient reporting of model validation and effectiveness of the implementation in the clinical workflow. To systematically identify predictive ML algorithms implemented in primary care from peer-reviewed literature and US Food and Drug Administration (FDA) and Conformité Européene (CE) registration databases and to ascertain the public availability of evidence, including peer-reviewed literature, gray literature, and technical reports across the artificial intelligence (AI) life cycle. PubMed, Embase, Web of Science, Cochrane Library, Emcare, Academic Search Premier, IEEE Xplore, ACM Digital Library, MathSciNet, AAAI.org (Association for the Advancement of Artificial Intelligence), arXiv, Epistemonikos, PsycINFO, and Google Scholar were searched for studies published between January 2000 and July 2023, with search terms that were related to AI, primary care, and implementation. The search extended to CE-marked or FDA-approved predictive ML algorithms obtained from relevant registration databases. Three reviewers gathered subsequent evidence involving strategies such as product searches, exploration of references, manufacturer website visits, and direct inquiries to authors and product owners. The extent to which the evidence for each predictive ML algorithm aligned with the Dutch AI predictive algorithm (AIPA) guideline requirements was assessed per AI life cycle phase, producing evidence availability scores. The systematic search identified 43 predictive ML algorithms, of which 25 were commercially available and CE-marked or FDA-approved. The predictive ML algorithms spanned multiple clinical domains, but most (27 [63%]) focused on cardiovascular diseases and diabetes. Most (35 [81%]) were published within the past 5 years. The availability of evidence varied across different phases of the predictive ML algorithm life cycle, with evidence being reported the least for phase 1 (preparation) and phase 5 (impact assessment) (19% and 30%, respectively). Twelve (28%) predictive ML algorithms achieved approximately half of their maximum individual evidence availability score. Overall, predictive ML algorithms from peer-reviewed literature showed higher evidence availability compared with those from FDA-approved or CE-marked databases (45% vs 29%). The findings indicate an urgent need to improve the availability of evidence regarding the predictive ML algorithms' quality criteria. Adopting the Dutch AIPA guideline could facilitate transparent and consistent reporting of the quality criteria that could foster trust among end users and facilitating large-scale implementation.

P125. Development of a novel ensemble machine learning algorithm for prediction of complications and readmission after anterior cervical spinal fusion

In the realm of software development, detecting code smells is a critical task for ensuring good code quality. God class code smell specifically has a specific nature associated with a great deal of subjectivity due to the levels of coupling and cohesion associated to it. Automated techniques for code smell detection aim to resolve this subjectivity. Machine learning techniques have shown promising results that tend to improve accuracy and reduce the bias associated with other techniques for God class identification. This is due to their pattern recognition capabilities making them more objective in identifying patterns that indicate code smells. However, current results need to be further improved in terms of both accuracy and generalizability. The challenge in the use of machine learning is not only in selecting the most appropriate technique but also lies in effectively representing source code as input patterns fed to Machine Learning (ML) classifier(s). Code representation plays a pivotal role in encoding source code for ML algorithms. This study aims improving the accuracy and generalizability of God class code smell detection via exploring the effect of using various code representation techniques, namely, tree-based, metric-based, code embedding, and token-based code representation techniques on the ML detection results. The study is conducted on the MLCQ dataset, and applies various ML algorithms (specifically: Logistic Regression, Random Forest, SVM, Decision Tree, Naive Bayes, Gradient Boosting, XGBoost). The evaluation results show how different code representation techniques influence ML detection outcomes and the comparative performance of ML algorithms. The study findings reveal that the F1-score achieved outperforms prior studies on the MLCQ dataset, indicating the effectiveness of the proposed approach. The presented results reveal how the code representation technique used makes a significant impact on the ML classifier results. This paves the way for developing intelligent IDE plugins for just in time God Class code smell detection among other code smells.

Discovery of new antibiotics is the need of the hour to treat infectious diseases. An ever-increasing repertoire of multidrug-resistant pathogens poses an imminent threat to human lives across the globe. However, the low success rate of the existing approaches and technologies for antibiotic discovery remains a major bottleneck. In silico methods like machine learning (ML) deem more promising to meet the above challenges compared with the conventional experimental approaches. The goal of this study was to create ML models that may be used to successfully predict new antimicrobial compounds. In this article, we employed eight different ML algorithms namely, extreme gradient boosting, random forest, gradient boosting classifier, deep neural network, support vector machine, multilayer perceptron, decision tree, and logistic regression. These models were trained using a dataset comprising 312 antibiotic drugs and a negative set of 936 non-antibiotic drugs in a five-fold cross validation approach. The top four ML classifiers (extreme gradient boosting, random forest, gradient boosting classifier and deep neural network) were able to achieve an accuracy of 80 per cent and above during the evaluation of testing and blind datasets. We aggregated the top performing four models through a soft-voting technique to develop an ensemble-based ML method and incorporated it into a freely accessible online prediction server named ABDpred ( http://clinicalmedicinessd.com.in/abdpred/ ).

The purpose of this analysis is to assess the use of machine learning (ML) algorithms in the prediction of postoperative outcomes, including complications, recurrence, and death in transsphenoidal surgery. Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we systematically reviewed all papers that used at least one ML algorithm to predict outcomes after transsphenoidal surgery. We searched Scopus, PubMed, and Web of Science databases for studies published prior to May 12, 2021. We identified 13 studies enrolling 5,048 patients. We extracted the general characteristics of each study; the sensitivity, specificity, area under the curve (AUC) of the ML models developed as well as the features identified as important by the ML models. We identified 12 studies with 5,048 patients that included ML algorithms for adenomas, three with 1807 patients specifically for acromegaly, and five with 2105 patients specifically for Cushing's disease. Nearly all were single-institution studies. The studies used a heterogeneous mix of ML algorithms and features to build predictive models. All papers reported an AUC greater than 0.7, which indicates clinical utility. ML algorithms have the potential to predict postoperative outcomes of transsphenoidal surgery and can improve patient care. Ensemble algorithms and neural networks were often top performers when compared with other ML algorithms. Biochemical and preoperative features were most likely to be selected as important by ML models. Inexplicability remains a challenge, but algorithms such as local interpretable model–agnostic explanation or Shapley value can increase explainability of ML algorithms. Our analysis shows that ML algorithms have the potential to greatly assist surgeons in clinical decision making.

6 - Machine learning and deep learning algorithms for fault diagnosis of photovoltaic systems

The aim of this paper is to review machine learning (ML) algorithms and techniques for hate speech detection in social media (SM). Hate speech problem is normally model as a text classification task. In this study, we examined the basic baseline components of hate speech classification using ML algorithms. There are five basic baseline components &#x2013; data collection and exploration, feature extraction, dimensionality reduction, classifier selection and training, and model evaluation, were reviewed. There have been improvements in ML algorithms that were employed for hate speech detection over time. New datasets and different performance metrics have been proposed in the literature. To keep the researchers informed regarding these trends in the automatic detection of hate speech, it calls for a comprehensive and an updated state-of-the-art. The contributions of this study are three-fold. First to equip the readers with the necessary information on the critical steps involved in hate speech detection using ML algorithms. Secondly, the weaknesses and strengths of each method is critically evaluated to guide researchers in the algorithm choice dilemma. Lastly, some research gaps and open challenges were identified. The different variants of ML techniques were reviewed which include classical ML, ensemble approach and deep learning methods. Researchers and professionals alike will benefit immensely from this study.

BackgroundDespite the interest in machine learning (ML) algorithms for analyzing real-world data (RWD) in healthcare, the use of ML in predicting time-to-event data, a common scenario in clinical practice, is less explored. ML models are capable of algorithmically learning from large, complex datasets and can offer advantages in predicting time-to-event data. We reviewed the recent applications of ML for survival analysis using RWD in healthcare.MethodsPUBMED and EMBASE were searched from database inception through March 2023 to identify peer-reviewed English-language studies of ML models for predicting time-to-event outcomes using the RWD. Two reviewers extracted information on the data source, patient population, survival outcome, ML algorithms, and the Area Under the Curve (AUC).ResultsOf 257 citations, 28 publications were included. Random survival forests (N = 16, 57%) and neural networks (N = 11, 39%) were the most popular ML algorithms. There was variability across AUC for these ML models (median 0.789, range 0.6–0.950). ML algorithms were predominately considered for predicting overall survival in oncology (N = 12, 43%). ML survival models were often used to predict disease prognosis or clinical events (N = 27, 96%) in the oncology, while less were used for treatment outcomes (N = 1, 4%).ConclusionsThe ML algorithms, random survival forests and neural networks, are mainly used for RWD to predict survival outcomes such as disease prognosis or clinical events in the oncology. This review shows that more opportunities remain to apply these ML algorithms to inform treatment decision-making in clinical practice. More methodological work is also needed to ensure the utility and applicability of ML models in survival outcomes.

This study presents a comparative analysis of the classification performance of facial and emotion recognition systems using Machine Learning (ML) and Deep Learning (DL) algorithms. The primary objective of this work is to evaluate the applicability of emotion recognition in fields such as psychotherapy and crime analysis, using the FER-2013 dataset.The study was conducted with ML algorithms such as Support Vector Machines (SVM), Random Forest (RF), K-Nearest Neighbor (KNN), Decision Trees, and Gradient Boosting, as well as the DL algorithm, Convolutional Neural Network (CNN). Supported by the application of feature selection, preprocessing, and feature extraction techniques, the model’s performance was measured using standard metrics such as accuracy, precision, F1-score, and AUC-ROC.The experimental results showed that the highest classification accuracy (46.61%) was achieved with the CNN model. While the ML models generally offered lower accuracy, they provided advantages in terms of computational efficiency in specific scenarios.This study aims to contribute to the literature by providing a comparative analysis of ML and DL algorithms and by highlighting the effect of data preprocessing on performance. The findings set targets for future work, such as real-time system integration and hybrid model development.