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Utilizing Semi-supervised Method in Predicting BRCA1 Pathogenicity Variants

Procedia Computer science 2023年 227卷 36-45页

作者： Alam Ahmad Hidayat Joko Pebrianto Trinugroho Rudi Nirwantono Digdo Sudigyo Bens Pardamean Department of Mathematics School of Computer Science Bina Nusantara University Indonesia 11480 Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia 11480 Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta Indonesia 11480

Quantifying the effect of mutations in the BRCA1 gene is useful for understanding their clinical consequences on breast cancer. Machine learning models can be applied to predict the landscape of protein variant effects that might not be always accessible by experiments. In this work, we propose a simple semi-supervised learning method using a Gaussian mixture model to predict ∼90% of the unlabeled missense variants of the BRCA1 gene collected from the ClinVar database. High-quality embeddings are used as a feature of the protein sequences, extracted using the latest pre-trained transformer-based language protein model. A statistical test show that the protein embeddings are effective and robust for predicting pathogenicity. Further, the lower representations of the features are then fed into the semi-supervised model. The prediction performance of the model only for the labeled testing data achieves an AUC score and an accuracy of 79.27% and 71.58%, respectively. Using our defined pathogenic probability score, we find that ∼94% of variants in our unlabeled dataset are well-separated into either benign or pathogenic classes according to that scoring. Our scores obtain a moderate Spearman rank correlation with the results of established unsupervised variant effect models. Finally, our approach can potentially be developed for more accurate and biologically reliable predictions of the variant effects.

关键词： embeddings mutation effect language model protein sequence semi-supervised learning

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Pairwise Learning for Autism Spectrum Disorder Imbalanced Classification

Pairwise Learning for Autism Spectrum Disorder Imbalanced Cl...

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IEEE Eurasia Conference on Biomedical Engineering, Healthcare and Sustainability (ECBIOS)

作者： Shu Liu Qiang Wu Xin Yang Computational and Data Science PhD Program Middle Tennessee State University Murfreesboro TN USA Department of Mathematics University of Tennessee Knoxville TN USA Department of Computer Science Middle Tennessee State University Murfreesboro TN USA

ISBN: (数字)9798350396133

ISBN: (纸本)9798350396140

This paper performs a classification task on data obtained from the Autism Brain Imaging data Exchange (ABIDE) repository. In real-world case analysis, the number of autism spectrum disorder (ASD) patients is much smaller than typically developed people. To address this issue, this paper proposes the utilization of pairwise robust support vector machine (PRSVM) algorithms to classify autism spectrum disorder (ASD) patients. In this project's experiments, the correlation matrix derived from functional magnetic resonance imaging (fMRI) data was employed as a classification feature. A comprehensive evaluation was conducted to compare the classification performance of PRSVM with various machine learning methods. The comparative analysis encompassed various aspects, including different data dimensions, imbalanced ratios, and sample sizes, providing valuable insights into the relative performance of the algorithms under different experimental conditions. The experimental results demonstrate that PRSVM can detect autistic patients more accurately when the data is imbalanced. Moreover, the results indicate that PRSVM outperforms or achieves comparable performance to other conventional classification methods in a variety of situations. Furthermore, our approach can be further improved by augmenting the training set with either exclusively normal person samples or by incorporating patient samples and normal people samples in a proportionate manner. This augmentation strategy holds promising application value, as it contributes to improving the performance and robustness of our method.

关键词： Training Support vector machines Neuroimaging Autism Machine learning algorithms Functional magnetic resonance imaging Vectors Robustness Classification algorithms Sustainable development

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A General Framework for Clustering and Distribution Matching with Bandit Feedback

arXiv

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arXiv 2024年

作者： Yavas, Recep Can Huang, Yuqi Tan, Vincent Y.F. Scarlett, Jonathan Descartes Program CNRS@CREATE 138602 Singapore Department of Information Systems and Analytics School of Computing National University of Singapore 119077 Singapore Department of Mathematics Department of Electrical and Computer Engineering National University of Singapore 119077 Singapore Department of Computer Science Department of Mathematics Institute of Data Science National University of Singapore 119077 Singapore

We develop a general framework for clustering and distribution matching problems with bandit feedback. We consider a K-armed bandit model where some subset of K arms is partitioned into M groups. Within each group, the random variable associated to each arm follows the same distribution on a finite alphabet. At each time step, the decision maker pulls an arm and observes its outcome from the random variable associated to that arm. Subsequent arm pulls depend on the history of arm pulls and their outcomes. The decision maker has no knowledge of the distributions of the arms or the underlying partitions. The task is to devise an online algorithm to learn the underlying partition of arms with the least number of arm pulls on average and with an error probability not exceeding a pre-determined value δ. Several existing problems fall under our general framework, including finding M pairs of arms, odd arm identification, and N-ary clustering of K arms belong to our general framework. We derive a non-asymptotic lower bound on the average number of arm pulls for any online algorithm with an error probability not exceeding δ. Furthermore, we develop a computationally-efficient online algorithm based on the Track-and-Stop method and Frank–Wolfe algorithm, and show that the average number of arm pulls of our algorithm asymptotically matches that of the lower bound. Our refined analysis also uncovers a novel bound on the speed at which the average number of arm pulls of our algorithm converges to the fundamental limit as δ *** Codes 68T05 Copyright © 2024, The Authors. All rights reserved.

关键词： Clustering algorithms

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Machine Learning Approach for Single Nucleotide Polymorphism Selection in Genetic Testing Results

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Procedia Computer science 2023年 227卷 46-54页

作者： Joko Pebrianto Trinugroho Alam Ahmad Hidayat Mahmud Isnan Bens Pardamean Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Department of Mathematics School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program Bina Nusantara University Jakarta 11480 Indonesia

Lactose intolerance is a type of digestive problem that may threaten the population because milk and dairy products compose of nutrients that are essential for human body. Genetic tests possess a great potential to detect lactose intolerance as it can be used in children and even infants. However, a new approach to analyze the genetic test results is needed to elucidate the Single Nucleotide Polymorphisms (SNPs) that are related to lactose intolerance. In this work, we utilized the machine learning based feature selection to select the SNPs associated with lactose tolerance trait from genotyping samples of direct-to-customer (DTCG genetic tests, obtained from the public database. Recursive Feature Elimination (RFE) with XGBoost model was used to perform feature selection. We also compared three different models, such as XGBoost, support vector machine (SVM), and random forest (RF) for training the selected features. Our findings revealed that 20 SNPs (out of 3501) were chosen, with rs4394668 as the most important variables (F-score 0.009). Furthermore, when compared to the RF and SVM models, the XGBoost model had the highest accuracy (0.87). Further studies should be undertaken to elucidate how the selected SNPs may lead to the lactose intolerance trait.

关键词： lactose intolerance SNP genetic test feature selection

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Long Short-Term Memory-based Models for Sleep Quality Prediction from Wearable Device Time Series data

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Procedia Computer science 2023年 227卷 1062-1069页

作者： Alam Ahmad Hidayat Arif Budiarto Bens Pardamean Mathematics Department School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department School of Computer Science Bina Nusantara University Jakarta 11480 Indonesia Computer Science Department BINUS Graduate Program – Master of Computer Science Program Bina Nusantara University Jakarta 11480 Indonesia

Several studies suggest that sleep quality is associated with physical activities. Moreover, deep sleep time can be used to determine the sleep quality of an individual. In this work, we aim to find the association between physical activities and deep sleep time by modeling the time series data such as heart rate and a number of steps captured from a commercial wearable device. Our previous study demonstrates that deep learning-based time series modeling is well suited for our problem since the temporal patterns in the two physical parameters need to be captured to obtain more accurate results. We first preprocess our series data to have a time-step size of 10 minutes. To improve our previous effort in this modeling, we compare four different variants of Long Short-Term Memory (LSTM)-based models, ranging from single input to dual input models. Our result shows that the simple stacked LSTM model performs better for our data because the remaining models suffer from overfitting due to a larger number of the trained parameters.

关键词： deep learning forecasting sleep quality time series wearable devices

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Detecting Foreground in Videos via Posterior Regularized Robust Bayesian Tensor Factorization

Detecting Foreground in Videos via Posterior Regularized Rob...

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IEEE International Conference on Automation science and Engineering (CASE)

作者： Shenghao Xia Yinwei Zhang Biao Zhang Jian Liu Department of Mathematics Statistics & Data Science GIDP program University of Arizona USA Department of System & Industrial Engineering University of Arizona USA ABB Inc. USA

Foreground detection is a critical step for separating the moving object from the background in video processing. Tensor factorization has been used in foreground detection due to its ability to process complex high-dimensional data, such as color images and videos. However, traditional tensor factorization often lacks the ability for uncertainty quantification. Bayesian tensor factorization can measure the uncertainty by considering the distributions of the tensor factorization model parameters. Besides, domain knowledge is commonly available and could improve the accuracy of foreground detection of the Bayesian tensor factorization model if it can be appropriately incorporated. In this work, a new Bayesian tensor factorization model, named Posterior Regularized Bayesian Robust Tensor Factorization (PR-BRTF), is proposed with incorporating characteristics of dynamic foreground, as a sparsity posterior regularization term. Furthermore, the variational Bayesian inference and $L_{1}$ norm is combined for inducing sparsity with an efficient inference. The experiments in real-world case studies have shown the performance improvement of the proposed model over state-of-art methods.

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Unbiased Parameter Estimation for Bayesian Inverse Problems

arXiv

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arXiv 2025年

作者： Chada, Neil K. Jasra, Ajay Maama, Mohamed Tempone, Raul Department of Mathematics City University of Hong Kong China School of Data Science The Chinese University of Hong Kong Shenzhen CN Shenzhen China Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this paper we consider the estimation of unknown parameters in Bayesian inverse problems. In most cases of practical interest, there are several barriers to performing such estimation, This includes a numerical approximation of a solution of a differential equation and, even if exact solutions are available, an analytical intractability of the marginal likelihood and its associated gradient, which is used for parameter estimation. The focus of this article is to deliver unbiased estimates of the unknown parameters, that is, stochastic estimators that, in expectation, are equal to the maximizer of the marginal likelihood, and possess no numerical approximation error. Based upon the ideas of [4] we develop a new approach for unbiased parameter estimation for Bayesian inverse problems. We prove unbiasedness and establish numerically that the associated estimation procedure is faster than the current state-of-the-art methodology for this problem. We demonstrate the performance of our methodology on a range of problems which include a PDE and ODE. Copyright © 2025, The Authors. All rights reserved.

关键词： Markov processes

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Aggregating Structural Features for Computational Analysis of Mutations in BRCT Domains of BRCA1 Protein

Aggregating Structural Features for Computational Analysis o...

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International Conference on Informatics, Multimedia, Cyber and Information System (ICIMCIS)

作者： Alam Ahmad Hidayat Rudi Nirwantono Mahmud Isnan Joko Pebrianto Trinugroho Bens Pardamean Mathematics Department School of Computer Science Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Biotechnology Department Faculty of Engineering Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Bioinformatics and Data Science Research Center Bina Nusantara University Jakarta Indonesia Computer Science Department Bioinformatics and Data Science Research Center BINUS Graduate Program Jakarta Indonesia

Understanding the mechanistic interpretability of mutation effects in a protein can help predict the clinical implications of the genetic variants. Hence, computational variant effect predictions that involve protein structural features of the protein mutations might be suitable in this case. In this work, we focus on BRCT domains of BRCA1 gene that is widely studied in breast cancer studies. We retrieved 88 selected missense variants found in BRCT domains annotated in both ClinVar and gnomAD databases. To computationally characterize the pathogenic property of the mutations we used two types of features extracted from protein structures: a change in free Gibbs energy and a set of features derived from molecular dynamics simulations of each mutant. Using a dimensional reduction and Gaussian mixture model (GMM)-based clustering we demonstrate that the variants are segregated into two regions that may correspond to their pathogenic status. This method can be a potential computational pipeline for providing the preliminary mechanistic interpretation of mutation effects in terms of their thermodynamic and structural features.

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Unbiased Approximations for Stationary Distributions of McKean-Vlasov SDEs

arXiv

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arXiv 2024年

作者： Awadelkarim, Elsiddig Chada, Neil K. Jasra, Ajay Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Mathematics City University of Hong Kong Hong Kong School of Data Science The Chinese University of Hong Kong Shenzhen Shenzhen China

We consider the development of unbiased estimators, to approximate the stationary distribution of Mckean-Vlasov stochastic differential equations (MVSDEs). These are an important class of processes, which frequently appear in applications such as mathematical finance, biology and opinion dynamics. Typically the stationary distribution is unknown and indeed one cannot simulate such processes exactly. As a result one commonly requires a time-discretization scheme which results in a discretization bias and a bias from not being able to simulate the associated stationary distribution. To overcome this bias, we present a new unbiased estimator taking motivation from the literature on unbiased Monte Carlo. We prove the unbiasedness of our estimator, under assumptions. In order to prove this we require developing ergodicity results of various discrete time processes, through an appropriate discretization scheme, towards the invariant measure. Numerous numerical experiments are provided, on a range of MVSDEs, to demonstrate the effectiveness of our unbiased estimator. Such examples include the Currie-Weiss model, a 3D neuroscience model and a parameter estimation problem. © 2024, CC BY-NC-SA.

关键词： Stochastic systems

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Discrete null field equation methods for solving Laplace's equation: Boundary layer computations

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Numerical Methods for Partial Differential Equations 2024年第4期40卷 e23092-e23092页

作者： Zhang, Li-Ping Li, Zi-Cai Lee, Ming-Gong Huang, Hung-Tsai School of Mathematical Sciences Qufu Normal University Shandong Qufu China Department of Applied Mathematics National Sun Yat-sen University Kaohsiung Taiwan Department of Tourism and Leisure/Ph.D. Program in Engineering Science Chung Hua University Hsinchu Taiwan Department of Data Science and Analytics I-Shou University Kaohsiung Taiwan

Consider Dirichlet problems of Laplace's equation in a bounded simply-connected domain (Formula presented.), and use the null field equation (NFE) of Green's representation formulation, where the source nodes (Formula presented.) are located on a pseudo-boundary (Formula presented.) outside (Formula presented.) but not close to its boundary (Formula presented.). Simple algorithms are proposed in this article by using the central rule for the NFE, and the normal derivatives (Formula presented.) of the solutions on the boundary (Formula presented.) can be easily obtained. These algorithms are called the discrete null field equation method (DNFEM) because the collocation equations are, indeed, the direct discrete form of the NFE. The bounds of the condition number are like those by the method of fundamental solutions (MFS) yielding the exponential growth as the number of unknowns increases. One trouble of the DNFEM is the near singularity of integrations for the solutions in boundary layers in Green's representation formulation. The traditional BEM also suffers from the same trouble. To deal with the near singularity, quadrature by expansions and the sinh transformation are often used. To handle this trouble, however, we develop two kinds of new techniques: (I) the interpolation techniques by Taylor's formulas with piecewise (Formula presented.) -degree polynomials and the Fourier series, and (II) the mini-rules of integrals, such as the mini-Simpson's and the mini-Gaussian rules. Error analysis is made for technique I to achieve optimal convergence rates. Numerical experiments are carried out for disk domains to support the theoretical analysis made. The numerical performance of the DNFEM is excellent for disk domains to compete with the MFS. The errors with (Formula presented.) can be obtained by combination algorithms, which are satisfactory for most engineering problems. In summary, the new simple DNFEM is based on the NFE, which is different from the boundary elem

关键词： Fourier series

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