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A robust kernel machine regression towards biomarker selection in multi-omics datasets of osteoporosis for drug discovery

arXiv.org Machine Learning

Many statistical machine approaches could ultimately highlight novel features of the etiology of complex diseases by analyzing multi-omics data. However, they are sensitive to some deviations in distribution when the observed samples are potentially contaminated with adversarial corrupted outliers (e.g., a fictional data distribution). Likewise, statistical advances lag in supporting comprehensive data-driven analyses of complex multi-omics data integration. We propose a novel non-linear M-estimator-based approach, "robust kernel machine regression (RobKMR)," to improve the robustness of statistical machine regression and the diversity of fictional data to examine the higher-order composite effect of multi-omics datasets. We address a robust kernel-centered Gram matrix to estimate the model parameters accurately. We also propose a robust score test to assess the marginal and joint Hadamard product of features from multi-omics data. We apply our proposed approach to a multi-omics dataset of osteoporosis (OP) from Caucasian females. Experiments demonstrate that the proposed approach effectively identifies the inter-related risk factors of OP. With solid evidence (p-value = 0.00001), biological validations, network-based analysis, causal inference, and drug repurposing, the selected three triplets ((DKK1, SMTN, DRGX), (MTND5, FASTKD2, CSMD3), (MTND5, COG3, CSMD3)) are significant biomarkers and directly relate to BMD. Overall, the top three selected genes (DKK1, MTND5, FASTKD2) and one gene (SIDT1 at p-value= 0.001) significantly bond with four drugs- Tacrolimus, Ibandronate, Alendronate, and Bazedoxifene out of 30 candidates for drug repurposing in OP. Further, the proposed approach can be applied to any disease model where multi-omics datasets are available.


Active Learning-Based Multistage Sequential Decision-Making Model with Application on Common Bile Duct Stone Evaluation

arXiv.org Machine Learning

Multistage sequential decision-making scenarios are commonly seen in the healthcare diagnosis process. In this paper, an active learning-based method is developed to actively collect only the necessary patient data in a sequential manner. There are two novelties in the proposed method. First, unlike the existing ordinal logistic regression model which only models a single stage, we estimate the parameters for all stages together. Second, it is assumed that the coefficients for common features in different stages are kept consistent. The effectiveness of the proposed method is validated in both a simulation study and a real case study. Compared with the baseline method where the data is modeled individually and independently, the proposed method improves the estimation efficiency by 62\%-1838\%. For both simulation and testing cohorts, the proposed method is more effective, stable, interpretable, and computationally efficient on parameter estimation. The proposed method can be easily extended to a variety of scenarios where decision-making can be done sequentially with only necessary information.


Fighting Money Laundering with Statistics and Machine Learning: An Introduction and Review

arXiv.org Machine Learning

Money laundering is a profound, global problem. Nonetheless, there is little statistical and machine learning research on the topic. In this paper, we focus on anti-money laundering in banks. To help organize existing research in the field, we propose a unifying terminology and provide a review of the literature. This is structured around two central tasks: (i) client risk profiling and (ii) suspicious behavior flagging. We find that client risk profiling is characterized by diagnostics, i.e., efforts to find and explain risk factors. Suspicious behavior flagging, on the other hand, is characterized by non-disclosed features and hand-crafted risk indices. Finally, we discuss directions for future research. One major challenge is the lack of public data sets. This may, potentially, be addressed by synthetic data generation. Other possible research directions include semi-supervised and deep learning, interpretability and fairness of the results.


Leveraging Intrinsic Gradient Information for Further Training of Differentiable Machine Learning Models

arXiv.org Machine Learning

This work presents methods demonstrating that when the derivatives of target variables (outputs) with respect to inputs can be extracted - We introduce a novel metric that can be utilised in a from processes of interest, e.g., neural networks hyper-parameter optimisation pipeline that provides an (NN) based surrogate models, they can be leveraged indicator of an upper bound to NN model complexity to further improve the accuracy of differentiable - We propose an alternative regularisation method for linear ML models. This paper generalises the idea regression problems (using ridge regression as an and provides practical methodologies that can be example) that outperforms conventional regularisation used to leverage gradient information (GI) across over varying training sample sizes by utilising GI a variety of applications including: (1) Improving the performance of generative adversarial networks In the rest of this paper, Section 2 formulates the GI idea (GANs); (2) efficiently tuning NN model under a supervised learning setting. The proposed GI assisted complexity; (3) regularising linear regressions. Numerical methodologies are presented between Section 3 to 5, and followed results show that GI can effective enhance by a conclusion in Section 6. ML models with existing datasets, demonstrating its value for a variety of applications.


The Fairness Field Guide: Perspectives from Social and Formal Sciences

arXiv.org Artificial Intelligence

Over the past several years, a slew of different methods to measure the fairness of a machine learning model have been proposed. However, despite the growing number of publications and implementations, there is still a critical lack of literature that explains the interplay of fair machine learning with the social sciences of philosophy, sociology, and law. We hope to remedy this issue by accumulating and expounding upon the thoughts and discussions of fair machine learning produced by both social and formal (specifically machine learning and statistics) sciences in this field guide. Specifically, in addition to giving the mathematical and algorithmic backgrounds of several popular statistical and causal-based fair machine learning methods, we explain the underlying philosophical and legal thoughts that support them. Further, we explore several criticisms of the current approaches to fair machine learning from sociological and philosophical viewpoints. It is our hope that this field guide will help fair machine learning practitioners better understand how their algorithms align with important humanistic values (such as fairness) and how we can, as a field, design methods and metrics to better serve oppressed and marginalized populaces.


A Survey on Hyperdimensional Computing aka Vector Symbolic Architectures, Part II: Applications, Cognitive Models, and Challenges

arXiv.org Artificial Intelligence

This is Part II of the two-part comprehensive survey devoted to a computing framework most commonly known under the names Hyperdimensional Computing and Vector Symbolic Architectures (HDC/VSA). Both names refer to a family of computational models that use high-dimensional distributed representations and rely on the algebraic properties of their key operations to incorporate the advantages of structured symbolic representations and vector distributed representations. Holographic Reduced Representations is an influential HDC/VSA model that is well-known in the machine learning domain and often used to refer to the whole family. However, for the sake of consistency, we use HDC/VSA to refer to the area. Part I of this survey covered foundational aspects of the area, such as historical context leading to the development of HDC/VSA, key elements of any HDC/VSA model, known HDC/VSA models, and transforming input data of various types into high-dimensional vectors suitable for HDC/VSA. This second part surveys existing applications, the role of HDC/VSA in cognitive computing and architectures, as well as directions for future work. Most of the applications lie within the machine learning/artificial intelligence domain, however we also cover other applications to provide a thorough picture. The survey is written to be useful for both newcomers and practitioners.


Data transformation based optimized customer churn prediction model for the telecommunication industry

arXiv.org Artificial Intelligence

Data transformation (DT) is a process that transfers the original data into a form which supports a particular classification algorithm and helps to analyze the data for a special purpose. To improve the prediction performance we investigated various data transform methods. This study is conducted in a customer churn prediction (CCP) context in the telecommunication industry (TCI), where customer attrition is a common phenomenon. We have proposed a novel approach of combining data transformation methods with the machine learning models for the CCP problem. We conducted our experiments on publicly available TCI datasets and assessed the performance in terms of the widely used evaluation measures (e.g. AUC, precision, recall, and F-measure). In this study, we presented comprehensive comparisons to affirm the effect of the transformation methods. The comparison results and statistical test proved that most of the proposed data transformation based optimized models improve the performance of CCP significantly. Overall, an efficient and optimized CCP model for the telecommunication industry has been presented through this manuscript.


A Cross Validation Framework for Signal Denoising with Applications to Trend Filtering, Dyadic CART and Beyond

arXiv.org Machine Learning

This paper formulates a general cross validation framework for signal denoising. The general framework is then applied to nonparametric regression methods such as Trend Filtering and Dyadic CART. The resulting cross validated versions are then shown to attain nearly the same rates of convergence as are known for the optimally tuned analogues. There did not exist any previous theoretical analyses of cross validated versions of Trend Filtering or Dyadic CART. To illustrate the generality of the framework we also propose and study cross validated versions of two fundamental estimators; lasso for high dimensional linear regression and singular value thresholding for matrix estimation. Our general framework is inspired by the ideas in Chatterjee and Jafarov (2015) and is potentially applicable to a wide range of estimation methods which use tuning parameters.


Bootstrapping Informative Graph Augmentation via A Meta Learning Approach

arXiv.org Artificial Intelligence

Recent works explore learning graph representations in a self-supervised manner. In graph contrastive learning, benchmark methods apply various graph augmentation approaches. However, most of the augmentation methods are non-learnable, which causes the issue of generating unbeneficial augmented graphs. Such augmentation may degenerate the representation ability of graph contrastive learning methods. Therefore, we motivate our method to generate augmented graph by a learnable graph augmenter, called MEta Graph Augmentation (MEGA). We then clarify that a "good" graph augmentation must have uniformity at the instance-level and informativeness at the feature-level. To this end, we propose a novel approach to learning a graph augmenter that can generate an augmentation with uniformity and informativeness. The objective of the graph augmenter is to promote our feature extraction network to learn a more discriminative feature representation, which motivates us to propose a meta-learning paradigm. Empirically, the experiments across multiple benchmark datasets demonstrate that MEGA outperforms the state-of-the-art methods in graph self-supervised learning tasks. Further experimental studies prove the effectiveness of different terms of MEGA.


Cross-view Self-Supervised Learning on Heterogeneous Graph Neural Network via Bootstrapping

arXiv.org Artificial Intelligence

Heterogeneous graph neural networks can represent information of heterogeneous graphs with excellent ability. Recently, self-supervised learning manner is researched which learns the unique expression of a graph through a contrastive learning method. In the absence of labels, this learning methods show great potential. However, contrastive learning relies heavily on positive and negative pairs, and generating high-quality pairs from heterogeneous graphs is difficult. In this paper, in line with recent innovations in self-supervised learning called BYOL or bootstrapping, we introduce a that can generate good representations without generating large number of pairs. In addition, paying attention to the fact that heterogeneous graphs can be viewed from two perspectives, network schema and meta-path views, high-level expressions in the graphs are captured and expressed. The proposed model showed state-of-the-art performance than other methods in various real world datasets.