O-203 Application of machine learning to predict aneuploidy and mosaicism in embryos from in vitro fertilization (IVF) cycles

Abstract Study question Is it possible to predict the likelihood of an IVF embryo being aneuploid and/or mosaic using a machine learning algorithm? Summary answer There are paternal, maternal, embryonic and IVF-cycle factors that are associated with embryonic chromosomal status that can be used as predictors in machine learning models. What is known already The factors associated with embryonic aneuploidy have been extensively studied. Mostly maternal age and to a lesser extent male factor and ovarian stimulation have been related to the occurrence of chromosomal alterations in the embryo. On the other hand, the main factors that may increase the incidence of embryo mosaicism have not yet been established. The models obtained using classical statistical methods to predict embryonic aneuploidy and mosaicism are not of high reliability. As an alternative to traditional methods, different machine and deep learning algorithms are being used to generate predictive models in different areas of medicine, including human reproduction. Study design, size, duration The study design is observational and retrospective. A total of 4654 embryos from 1558 PGT-A cycles were included (January-2017 to December-2020). The trophoectoderm biopsies on D5, D6 or D7 blastocysts were analysed by NGS. Embryos with ≤25% aneuploid cells were considered euploid, between 25-50% were classified as mosaic and aneuploid with >50%. The variables of the PGT-A were recorded in a database from which predictive models of embryonic aneuploidy and mosaicism were developed. Participants/materials, setting, methods The main indications for PGT-A were advanced maternal age, abnormal sperm FISH and recurrent miscarriage or implantation failure. Embryo analysis were performed using Veriseq-NGS (Illumina). The software used to carry out all the analysis was R (RStudio). The library used to implement the different algorithms was caret. In the machine learning models, 22 predictor variables were introduced, which can be classified into 4 categories: maternal, paternal, embryonic and those specific to the IVF cycle. Main results and the role of chance The different couple, embryo and stimulation cycle variables were recorded in a database (22 predictor variables). Two different predictive models were performed, one for aneuploidy and the other for mosaicism. The predictor variable was of multi-class type since it included the segmental and whole chromosome alteration categories. The dataframe were first preprocessed and the different classes to be predicted were balanced. A 80% of the data were used for training the model and 20% were reserved for further testing. The classification algorithms applied include multinomial regression, neural networks, support vector machines, neighborhood-based methods, classification trees, gradient boosting, ensemble methods, Bayesian and discriminant analysis-based methods. The algorithms were optimized by minimizing the Log_Loss that measures accuracy but penalizing misclassifications. The best predictive models were achieved with the XG-Boost and random forest algorithms. The AUC of the predictive model for aneuploidy was 80.8% (Log_Loss 1.028) and for mosaicism 84.1% (Log_Loss: 0.929). The best predictor variables of the models were maternal age, embryo quality, day of biopsy and whether or not the couple had a history of pregnancies with chromosomopathies. The male factor only played a relevant role in the mosaicism model but not in the aneuploidy model. Limitations, reasons for caution Although the predictive models obtained can be very useful to know the probabilities of achieving euploid embryos in an IVF cycle, increasing the sample size and including additional variables could improve the models and thus increase their predictive capacity. Wider implications of the findings Machine learning can be a very useful tool in reproductive medicine since it can allow the determination of factors associated with embryonic aneuploidies and mosaicism in order to establish a predictive model for both. To identify couples at risk of embryo aneuploidy/mosaicism could benefit them of the use of PGT-A. Trial registration number Not Applicable

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A Protocol for a Market of Machine Learning Models

10.21203/rs.3.rs-1030456/v1 ◽

2021 ◽

Author(s):

Claudiu Marius Popescu

Keyword(s):

Machine Learning ◽

Computational Complexity ◽

Predictive Model ◽

Predictive Models ◽

Market Mechanism ◽

Learning Models ◽

Economic Interaction ◽

Reference Implementation ◽

Direct Market ◽

Machine Learning Models

Abstract This paper describes a protocol for a market of machine learning models. The economic interaction involves two types of agents: data providers- agents that have some data and want to use it to get a predictive model, and model providers- agents able to use the data to generate predictive models. First, we will show that the process is informationally asymmetric, therefore a standard direct market can not function. Then, we design a protocol with the aim of creating a viable and efficient market mechanism for these particular services, under the specific challenges of information asymmetries. The protocol is theoretically analysed, to establish it’s correctness and computational complexity. We also propose a simple reference implementation based on a HTTP API. The implementation is then used in a few case studies, and analysed empirically.

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Marine Data Prediction: An Evaluation of Machine Learning, Deep Learning, and Statistical Predictive Models

Computational Intelligence and Neuroscience ◽

10.1155/2021/8551167 ◽

2021 ◽

Vol 2021 ◽

pp. 1-13

Author(s):

Ahmed Ali ◽

Ahmed Fathalla ◽

Ahmad Salah ◽

Mahmoud Bekhit ◽

Esraa Eldesouky

Keyword(s):

Machine Learning ◽

Deep Learning ◽

Predictive Model ◽

Predictive Models ◽

Marine Biodiversity ◽

Learning Models ◽

Real Dataset ◽

Marine Data ◽

Predictive Approaches ◽

Machine Learning Models

Nowadays, ocean observation technology continues to progress, resulting in a huge increase in marine data volume and dimensionality. This volume of data provides a golden opportunity to train predictive models, as the more the data is, the better the predictive model is. Predicting marine data such as sea surface temperature (SST) and Significant Wave Height (SWH) is a vital task in a variety of disciplines, including marine activities, deep-sea, and marine biodiversity monitoring. The literature has efforts to forecast such marine data; these efforts can be classified into three classes: machine learning, deep learning, and statistical predictive models. To the best of the authors’ knowledge, no study compared the performance of these three approaches on a real dataset. This paper focuses on the prediction of two critical marine features: the SST and SWH. In this work, we proposed implementing statistical, deep learning, and machine learning models for predicting the SST and SWH on a real dataset obtained from the Korea Hydrographic and Oceanographic Agency. Then, we proposed comparing these three predictive approaches on four different evaluation metrics. Experimental results have revealed that the deep learning model slightly outperformed the machine learning models for overall performance, and both of these approaches greatly outperformed the statistical predictive model.

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Epigenetic Target Prediction with Accurate Machine Learning Models

10.26434/chemrxiv.13522313 ◽

2021 ◽

Author(s):

Norberto Sánchez-Cruz ◽

Jose L. Medina-Franco

Keyword(s):

Machine Learning ◽

Small Molecules ◽

Predictive Models ◽

Large Scale ◽

Target Prediction ◽

Quantitative Measure ◽

Learning Models ◽

Discovery Research ◽

Drug Discovery Research ◽

Machine Learning Models

Epigenetic targets are a significant focus for drug discovery research, as demonstrated by the eight approved epigenetic drugs for treatment of cancer and the increasing availability of chemogenomic data related to epigenetics. This data represents a large amount of structure-activity relationships that has not been exploited thus far for the development of predictive models to support medicinal chemistry efforts. Herein, we report the first large-scale study of 26318 compounds with a quantitative measure of biological activity for 55 protein targets with epigenetic activity. Through a systematic comparison of machine learning models trained on molecular fingerprints of different design, we built predictive models with high accuracy for the epigenetic target profiling of small molecules. The models were thoroughly validated showing mean precisions up to 0.952 for the epigenetic target prediction task. Our results indicate that the herein reported models have considerable potential to identify small molecules with epigenetic activity. Therefore, our results were implemented as freely accessible and easy-to-use web application.

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Prediction of Head Movement in 360-Degree Videos Using Attention Model

Sensors ◽

10.3390/s21113678 ◽

2021 ◽

Vol 21 (11) ◽

pp. 3678

Author(s):

Dongwon Lee ◽

Minji Choi ◽

Joohyun Lee

Keyword(s):

Machine Learning ◽

Short Term Memory ◽

Moving Average ◽

The Other ◽

Learning Models ◽

Short Term ◽

Term Memory ◽

Attention Model ◽

Long Short Term Memory ◽

Machine Learning Models

In this paper, we propose a prediction algorithm, the combination of Long Short-Term Memory (LSTM) and attention model, based on machine learning models to predict the vision coordinates when watching 360-degree videos in a Virtual Reality (VR) or Augmented Reality (AR) system. Predicting the vision coordinates while video streaming is important when the network condition is degraded. However, the traditional prediction models such as Moving Average (MA) and Autoregression Moving Average (ARMA) are linear so they cannot consider the nonlinear relationship. Therefore, machine learning models based on deep learning are recently used for nonlinear predictions. We use the Long Short-Term Memory (LSTM) and Gated Recurrent Unit (GRU) neural network methods, originated in Recurrent Neural Networks (RNN), and predict the head position in the 360-degree videos. Therefore, we adopt the attention model to LSTM to make more accurate results. We also compare the performance of the proposed model with the other machine learning models such as Multi-Layer Perceptron (MLP) and RNN using the root mean squared error (RMSE) of predicted and real coordinates. We demonstrate that our model can predict the vision coordinates more accurately than the other models in various videos.

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Machine Learning Predictive Models to Estimate the Minimum Miscibility Pressure of CO2-Oil System

10.2118/207865-ms ◽

2021 ◽

Author(s):

Abderraouf Chemmakh ◽

Ahmed Merzoug ◽

Habib Ouadi ◽

Abdelhak Ladmia ◽

Vamegh Rasouli

Keyword(s):

Machine Learning ◽

Predictive Models ◽

Critical Parameters ◽

Co2 Injection ◽

Learning Models ◽

Minimum Miscibility Pressure ◽

Reservoir Conditions ◽

Important Amount ◽

Machine Learning Models

Abstract One of the most critical parameters of the CO2 injection (for EOR purposes) is the Minimum Miscibility Pressure MMP. The determination of this parameter is crucial for the success of the operation. Different experimental, analytical, and statistical technics are used to predict the MMP. Nevertheless, experimental technics are costly and tedious, while correlations are used for specific reservoir conditions. Based on that, the purpose of this paper is to build machine learning models aiming to predict the MMP efficiently and in broad-based reservoir conditions. Two ML models are proposed for both pure CO2 and non-pure CO2 injection. An important amount of data collected from literature is used in this work. The ANN and SVR-GA models have shown enhanced performance comparing to existing correlations in literature for both the pure and non-pure models, with a coefficient of R2 0.98, 0.93 and 0.96, 0.93 respectively, which confirms that the proposed models are reliable and ready to use.

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Implementing clinical decision support for oncology advanced care planning: A systems engineering framework to optimize the usability and utility of a machine learning predictive model in clinical practice.

Journal of Clinical Oncology ◽

10.1200/jco.2020.39.28_suppl.330 ◽

2021 ◽

Vol 39 (28_suppl) ◽

pp. 330-330

Author(s):

Teja Ganta ◽

Stephanie Lehrman ◽

Rachel Pappalardo ◽

Madalene Crow ◽

Meagan Will ◽

...

Keyword(s):

Machine Learning ◽

High Risk ◽

Predictive Model ◽

Systems Engineering ◽

Care Planning ◽

Learning Models ◽

Predictive Tool ◽

Risk Of Death ◽

The Impact ◽

Machine Learning Models

330 Background: Machine learning models are well-positioned to transform cancer care delivery by providing oncologists with more accurate or accessible information to augment clinical decisions. Many machine learning projects, however, focus on model accuracy without considering the impact of using the model in real-world settings and rarely carry forward to clinical implementation. We present a human-centered systems engineering approach to address clinical problems with workflow interventions utilizing machine learning algorithms. Methods: We aimed to develop a mortality predictive tool, using a Random Forest algorithm, to identify oncology patients at high risk of death within 30 days to move advance care planning (ACP) discussions earlier in the illness trajectory. First, a project sponsor defined the clinical need and requirements of an intervention. The data scientists developed the predictive algorithm using data available in the electronic health record (EHR). A multidisciplinary workgroup was assembled including oncology physicians, advanced practice providers, nurses, social workers, chaplain, clinical informaticists, and data scientists. Meeting bi-monthly, the group utilized human-centered design (HCD) methods to understand clinical workflows and identify points of intervention. The workgroup completed a workflow redesign workshop, a 90-minute facilitated group discussion, to integrate the model in a future state workflow. An EHR (Epic) analyst built the user interface to support the intervention per the group’s requirements. The workflow was piloted in thoracic oncology and bone marrow transplant with plans to scale to other cancer clinics. Results: Our predictive model performance on test data was acceptable (sensitivity 75%, specificity 75%, F-1 score 0.71, AUC 0.82). The workgroup identified a “quality of life coordinator” who: reviews an EHR report of patients scheduled in the upcoming 7 days who have a high risk of 30-day mortality; works with the oncology team to determine ACP clinical appropriateness; documents the need for ACP; identifies potential referrals to supportive oncology, social work, or chaplain; and coordinates the oncology appointment. The oncologist receives a reminder on the day of the patient’s scheduled visit. Conclusions: This workgroup is a viable approach that can be replicated at institutions to address clinical needs and realize the full potential of machine learning models in healthcare. The next steps for this project are to address end-user feedback from the pilot, expand the intervention to other cancer disease groups, and track clinical metrics.

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A machine learning approach to inform developmental milestone achievement for children with autism (Preprint)

10.2196/preprints.29242 ◽

2021 ◽

Author(s):

Munirul M. Haque ◽

Masud Rabbani ◽

Dipranjan Das Dipal ◽

Md Ishrak Islam Zarif ◽

Anik Iqbal ◽

...

Keyword(s):

Machine Learning ◽

Autism Spectrum Disorder ◽

Children With Autism ◽

Autism Spectrum ◽

The Other ◽

Supervised Machine Learning ◽

Learning Models ◽

Children With Asd ◽

Socio Demographic Factors ◽

Machine Learning Models

BACKGROUND Care for children with autism spectrum disorder (ASD) can be challenging for families and medical care systems. This is especially true in Low-and-Middle-Income-countries (LMIC) like Bangladesh. To improve family-practitioner communication and developmental monitoring of children with ASD, [spell out] (mCARE) was developed. Within this study, mCARE was used to track child milestone achievement and family socio-demographic assets to inform mCARE feasibility/scalability and family-asset informed practitioner recommendations. OBJECTIVE The objectives of this paper are three-fold. First, document how mCARE can be used to monitor child milestone achievement. Second, demonstrate how advanced machine learning models can inform our understanding of milestone achievement in children with ASD. Third, describe family/child socio-demographic factors that are associated with earlier milestone achievement in children with ASD (across five machine learning models). METHODS Using mCARE collected data, this study assessed milestone achievement in 300 children with ASD from Bangladesh. In this study, we used four supervised machine learning (ML) algorithms (Decision Tree, Logistic Regression, k-Nearest Neighbors, Artificial Neural Network) and one unsupervised machine learning (K-means Clustering) to build models of milestone achievement based on family/child socio-demographic details. For analyses, the sample was randomly divided in half to train the ML models and then their accuracy was estimated based on the other half of the sample. Each model was specified for the following milestones: Brushes teeth, Asks to use the toilet, Urinates in the toilet or potty, and Buttons large buttons. RESULTS This study aimed to find a suitable machine learning algorithm for milestone prediction/achievement for children with ASD using family/child socio-demographic characteristics. For, Brushes teeth, the three supervised machine learning models met or exceeded an accuracy of 95% with Logistic Regression, KNN, and ANN as the most robust socio-demographic predictors. For Asks to use toilet, 84.00% accuracy was achieved with the KNN and ANN models. For these models, the family socio-demographic predictors of “family expenditure” and “parents’ age” accounted for most of the model variability. The last two parameters, Urinates in toilet or potty and Buttons large buttons had an accuracy of 91.00% and 76.00%, respectively, in ANN. Overall, the ANN had a higher accuracy (Above ~80% on average) among the other algorithms for all the parameters. Across the models and milestones, “family expenditure”, “family size/ type”, “living places” and “parent’s age and occupation” were the most influential family/child socio-demographic factors. CONCLUSIONS mCARE was successfully deployed in an LMIC (i.e., Bangladesh), allowing parents and care-practitioners a mechanism to share detailed information on child milestones achievement. Using advanced modeling techniques this study demonstrates how family/child socio-demographic elements can inform child milestone achievement. Specifically, families with fewer socio-demographic resources reported later milestone attainment. Developmental science theories highlight how family/systems can directly influence child development and this study provides a clear link between family resources and child developmental progress. Clinical implications for this work could include supporting the larger family system to improve child milestone achievement. CLINICALTRIAL We took the IRB from Marquette University Institutional Review Board on July 9, 2020, with the protocol number HR-1803022959, and titled “MOBILE-BASED CARE FOR CHILDREN WITH AUTISM SPECTRUM DISORDER USING REMOTE EXPERIENCE SAMPLING METHOD (MCARE)” for recruiting a total of 316 subjects, of which we recruited 300. (Details description of participants in Methods section)

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Comparison of Resampling Algorithms to Address Class Imbalance when Developing Machine Learning Models to Predict Foodborne Pathogen Presence in Agricultural Water

Frontiers in Environmental Science ◽

10.3389/fenvs.2021.701288 ◽

2021 ◽

Vol 9 ◽

Author(s):

Daniel Lowell Weller ◽

Tanzy M. T. Love ◽

Martin Wiedmann

Keyword(s):

Machine Learning ◽

Random Forest ◽

Predictive Models ◽

Training Data ◽

Agricultural Water ◽

Learning Models ◽

Safety Hazards ◽

E Coli ◽

Resampling Method ◽

Machine Learning Models

Recent studies have shown that predictive models can supplement or provide alternatives to E. coli-testing for assessing the potential presence of food safety hazards in water used for produce production. However, these studies used balanced training data and focused on enteric pathogens. As such, research is needed to determine 1) if predictive models can be used to assess Listeria contamination of agricultural water, and 2) how resampling (to deal with imbalanced data) affects performance of these models. To address these knowledge gaps, this study developed models that predict nonpathogenic Listeria spp. (excluding L. monocytogenes) and L. monocytogenes presence in agricultural water using various combinations of learner (e.g., random forest, regression), feature type, and resampling method (none, oversampling, SMOTE). Four feature types were used in model training: microbial, physicochemical, spatial, and weather. “Full models” were trained using all four feature types, while “nested models” used between one and three types. In total, 45 full (15 learners*3 resampling approaches) and 108 nested (5 learners*9 feature sets*3 resampling approaches) models were trained per outcome. Model performance was compared against baseline models where E. coli concentration was the sole predictor. Overall, the machine learning models outperformed the baseline E. coli models, with random forests outperforming models built using other learners (e.g., rule-based learners). Resampling produced more accurate models than not resampling, with SMOTE models outperforming, on average, oversampling models. Regardless of resampling method, spatial and physicochemical water quality features drove accurate predictions for the nonpathogenic Listeria spp. and L. monocytogenes models, respectively. Overall, these findings 1) illustrate the need for alternatives to existing E. coli-based monitoring programs for assessing agricultural water for the presence of potential food safety hazards, and 2) suggest that predictive models may be one such alternative. Moreover, these findings provide a conceptual framework for how such models can be developed in the future with the ultimate aim of developing models that can be integrated into on-farm risk management programs. For example, future studies should consider using random forest learners, SMOTE resampling, and spatial features to develop models to predict the presence of foodborne pathogens, such as L. monocytogenes, in agricultural water when the training data is imbalanced.

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Kernel-Based Machine Learning Models to Predict Mitigation Time During Cloud Security Attacks

International Journal of e-Collaboration ◽

10.4018/ijec.2021100106 ◽

2021 ◽

Vol 17 (4) ◽

pp. 75-88

Author(s):

Padmaja Kadiri ◽

Seshadri Ravala

Keyword(s):

Machine Learning ◽

Service Provider ◽

Predictive Models ◽

Cloud Service ◽

Cloud Services ◽

Security Threats ◽

Learning Models ◽

Security Attacks ◽

Cloud Service Provider ◽

Machine Learning Models

Security threats are unforeseen attacks to the services provided by the cloud service provider. Depending on the type of attack, the cloud service and its associated features will be unavailable. The mitigation time is an integral part of attack recovery. This research paper explores the different parameters that will aid in predicting the mitigation time after an attack on cloud services. Further, the paper presents machine learning models that can predict the mitigation time. The paper presents the kernel-based machine learning models that can predict the average mitigation time during security attacks. The analysis of the results shows that the kernel-based models show 87% accuracy in predicting the mitigation time. Furthermore, the paper explores the performance of the kernel-based machine learning models based on the regression-based predictive models. The regression model is used as a benchmark model to analyze the performance of the machine learning-based predictive models in the prediction of mitigation time in the wake of an attack.

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Intra-domain and cross-domain transfer learning for time series

10.5194/egusphere-egu21-12142 ◽

2021 ◽

Author(s):

Erik Otović ◽

Marko Njirjak ◽

Dario Jozinović ◽

Goran Mauša ◽

Alberto Michelini ◽

...

Keyword(s):

Machine Learning ◽

Time Series ◽

Transfer Learning ◽

Time Series Data ◽

The Other ◽

Series Data ◽

Sound Recognition ◽

Transfer Of Knowledge ◽

Learning Models ◽

Machine Learning Models

In this study, we compared the performance of machine learning models trained using transfer learning and those that were trained from scratch - on time series data. Four machine learning models were used for the experiment. Two models were taken from the field of seismology, and the other two are general-purpose models for working with time series data. The accuracy of selected models was systematically observed and analyzed when switching within the same domain of application (seismology), as well as between mutually different domains of application (seismology, speech, medicine, finance). In seismology, we used two databases of local earthquakes (one in counts, and the other with the instrument response removed) and a database of global earthquakes for predicting earthquake magnitude; other datasets targeted classifying spoken words (speech), predicting stock prices (finance) and classifying muscle movement from EMG signals (medicine). In practice, it is very demanding and sometimes impossible to collect datasets of tagged data large enough to successfully train a machine learning model. Therefore, in our experiment, we use reduced data sets of 1,500 and 9,000 data instances to mimic such conditions. Using the same scaled-down datasets, we trained two sets of machine learning models: those that used transfer learning for training and those that were trained from scratch. We compared the performances between pairs of models in order to draw conclusions about the utility of transfer learning. In order to confirm the validity of the obtained results, we repeated the experiments several times and applied statistical tests to confirm the significance of the results. The study shows when, within the set experimental framework, the transfer of knowledge brought improvements in terms of model accuracy and in terms of model convergence rate. Our results show that it is possible to achieve better performance and faster convergence by transferring knowledge from the domain of global earthquakes to the domain of local earthquakes; sometimes also vice versa. However, improvements in seismology can sometimes also be achieved by transferring knowledge from medical and audio domains. The results show that the transfer of knowledge between other domains brought even more significant improvements, compared to those within the field of seismology. For example, it has been shown that models in the field of sound recognition have achieved much better performance compared to classical models and that the domain of sound recognition is very compatible with knowledge from other domains. We came to similar conclusions for the domains of medicine and finance. Ultimately, the paper offers suggestions when transfer learning is useful, and the explanations offered can provide a good starting point for knowledge transfer using time series data.

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