Regression
Linear Regression in Python for Data Scientists
Linear Regression is a statistical method used for modelling the dependence or relationship between two or more quantities. The aim of this is to be able to either better understand the existing relationships or to be able to predict the behaviour at points for which we currently don't have data. By using the method of linear regression (also called least squares fitting), we can calculate the values for the two parameters and plot the line of best fit to achieve our aims of better understanding the relationship or finding the estimated values of unknown points. For this, we have to be able to calculate the slope (m) and intercept (c) to give us the line of best fit for the data. This is made simple however by libraries that have already been implemented such as Scikit-Learn and Statsmodels Api that have linear regression functionality built in.
A robust kernel machine regression towards biomarker selection in multi-omics datasets of osteoporosis for drug discovery
Alam, Md Ashad, Shen, Hui, Deng, Hong-Wen
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
Tian, Hongzhen, Cohen, Reuven Zev, Zhang, Chuck, Mei, Yajun
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.
Leveraging Intrinsic Gradient Information for Further Training of Differentiable Machine Learning Models
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.
Generalized Shape Metrics on Neural Representations
Williams, Alex H., Kunz, Erin, Kornblith, Simon, Linderman, Scott W.
Understanding the operation of biological and artificial networks remains a difficult and important challenge. To identify general principles, researchers are increasingly interested in surveying large collections of networks that are trained on, or biologically adapted to, similar tasks. A standardized set of analysis tools is now needed to identify how network-level covariates -- such as architecture, anatomical brain region, and model organism -- impact neural representations (hidden layer activations). Here, we provide a rigorous foundation for these analyses by defining a broad family of metric spaces that quantify representational dissimilarity. Using this framework we modify existing representational similarity measures based on canonical correlation analysis to satisfy the triangle inequality, formulate a novel metric that respects the inductive biases in convolutional layers, and identify approximate Euclidean embeddings that enable network representations to be incorporated into essentially any off-the-shelf machine learning method. We demonstrate these methods on large-scale datasets from biology (Allen Institute Brain Observatory) and deep learning (NAS-Bench-101). In doing so, we identify relationships between neural representations that are interpretable in terms of anatomical features and model performance.
SLISEMAP: Explainable Dimensionality Reduction
Bjรถrklund, Anton, Mรคkelรค, Jarmo, Puolamรคki, Kai
Existing explanation methods for black-box supervised learning models generally work by building local models that explain the models behaviour for a particular data item. It is possible to make global explanations, but the explanations may have low fidelity for complex models. Most of the prior work on explainable models has been focused on classification problems, with less attention on regression. We propose a new manifold visualization method, SLISEMAP, that at the same time finds local explanations for all of the data items and builds a two-dimensional visualization of model space such that the data items explained by the same model are projected nearby. We provide an open source implementation of our methods, implemented by using GPU-optimized PyTorch library. SLISEMAP works both on classification and regression models. We compare SLISEMAP to most popular dimensionality reduction methods and some local explanation methods. We provide mathematical derivation of our problem and show that SLISEMAP provides fast and stable visualizations that can be used to explain and understand black box regression and classification models.
A Cross Validation Framework for Signal Denoising with Applications to Trend Filtering, Dyadic CART and Beyond
Chaudhuri, Anamitra, Chatterjee, Sabyasachi
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.
Machine Learning Regression Masterclass in Python
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A novel interpretable machine learning system to generate clinical risk scores: An application for predicting early mortality or unplanned readmission in a retrospective cohort study
Ning, Yilin, Li, Siqi, Ong, Marcus Eng Hock, Xie, Feng, Chakraborty, Bibhas, Ting, Daniel Shu Wei, Liu, Nan
Risk scores are widely used for clinical decision making and commonly generated from logistic regression models. Machine-learning-based methods may work well for identifying important predictors, but such 'black box' variable selection limits interpretability, and variable importance evaluated from a single model can be biased. We propose a robust and interpretable variable selection approach using the recently developed Shapley variable importance cloud (ShapleyVIC) that accounts for variability across models. Our approach evaluates and visualizes overall variable contributions for in-depth inference and transparent variable selection, and filters out non-significant contributors to simplify model building steps. We derive an ensemble variable ranking from variable contributions, which is easily integrated with an automated and modularized risk score generator, AutoScore, for convenient implementation. In a study of early death or unplanned readmission, ShapleyVIC selected 6 of 41 candidate variables to create a well-performing model, which had similar performance to a 16-variable model from machine-learning-based ranking.
Permuted and Unlinked Monotone Regression in $\mathbb{R}^d$: an approach based on mixture modeling and optimal transport
Slawski, Martin, Sen, Bodhisattva
Suppose that we have a regression problem with response variable Y in $\mathbb{R}^d$ and predictor X in $\mathbb{R}^d$, for $d \geq 1$. In permuted or unlinked regression we have access to separate unordered data on X and Y, as opposed to data on (X,Y)-pairs in usual regression. So far in the literature the case $d=1$ has received attention, see e.g., the recent papers by Rigollet and Weed [Information & Inference, 8, 619--717] and Balabdaoui et al. [J. Mach. Learn. Res., 22(172), 1--60]. In this paper, we consider the general multivariate setting with $d \geq 1$. We show that the notion of cyclical monotonicity of the regression function is sufficient for identification and estimation in the permuted/unlinked regression model. We study permutation recovery in the permuted regression setting and develop a computationally efficient and easy-to-use algorithm for denoising based on the Kiefer-Wolfowitz [Ann. Math. Statist., 27, 887--906] nonparametric maximum likelihood estimator and techniques from the theory of optimal transport. We provide explicit upper bounds on the associated mean squared denoising error for Gaussian noise. As in previous work on the case $d = 1$, the permuted/unlinked setting involves slow (logarithmic) rates of convergence rooting in the underlying deconvolution problem. Numerical studies corroborate our theoretical analysis and show that the proposed approach performs at least on par with the methods in the aforementioned prior work in the case $d = 1$ while achieving substantial reductions in terms of computational complexity.