A reciprocal LASSO (rLASSO) regularization employs a decreasing penalty function as opposed to conventional penalization approaches that use increasing penalties on the coefficients, leading to stronger parsimony and superior model selection relative to traditional shrinkage methods. Here we consider a fully Bayesian formulation of the rLASSO problem, which is based on the observation that the rLASSO estimate for linear regression parameters can be interpreted as a Bayesian posterior mode estimate when the regression parameters are assigned independent inverse Laplace priors. Bayesian inference from this posterior is possible using an expanded hierarchy motivated by a scale mixture of double Pareto or truncated normal distributions. On simulated and real datasets, we show that the Bayesian formulation outperforms its classical cousin in estimation, prediction, and variable selection across a wide range of scenarios while offering the advantage of posterior inference. Finally, we discuss other variants of this new approach and provide a unified framework for variable selection using flexible reciprocal penalties. All methods described in this paper are publicly available as an R package at: //github.com/himelmallick/BayesRecipe.
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Dimensionality reduction (DR) techniques help analysts to understand patterns in high-dimensional spaces. These techniques, often represented by scatter plots, are employed in diverse science domains and facilitate similarity analysis among clusters and data samples. For datasets containing many granularities or when analysis follows the information visualization mantra, hierarchical DR techniques are the most suitable approach since they present major structures beforehand and details on demand. However, current hierarchical DR techniques are not fully capable of addressing literature problems because they do not preserve the projection mental map across hierarchical levels or are not suitable for most data types. This work presents HUMAP, a novel hierarchical dimensionality reduction technique designed to be flexible on preserving local and global structures and preserve the mental map throughout hierarchical exploration. We provide empirical evidence of our technique's superiority compared with current hierarchical approaches and show two case studies to demonstrate its strengths.
Current treatment planning of patients diagnosed with brain tumor could significantly benefit by accessing the spatial distribution of tumor cell concentration. Existing diagnostic modalities, such as magnetic-resonance imaging (MRI), contrast sufficiently well areas of high cell density. However, they do not portray areas of low concentration, which can often serve as a source for the secondary appearance of the tumor after treatment. Numerical simulations of tumor growth could complement imaging information by providing estimates of full spatial distributions of tumor cells. Over recent years a corpus of literature on medical image-based tumor modeling was published. It includes different mathematical formalisms describing the forward tumor growth model. Alongside, various parametric inference schemes were developed to perform an efficient tumor model personalization, i.e. solving the inverse problem. However, the unifying drawback of all existing approaches is the time complexity of the model personalization that prohibits a potential integration of the modeling into clinical settings. In this work, we introduce a methodology for inferring patient-specific spatial distribution of brain tumor from T1Gd and FLAIR MRI medical scans. Coined as \textit{Learn-Morph-Infer} the method achieves real-time performance in the order of minutes on widely available hardware and the compute time is stable across tumor models of different complexity, such as reaction-diffusion and reaction-advection-diffusion models. We believe the proposed inverse solution approach not only bridges the way for clinical translation of brain tumor personalization but can also be adopted to other scientific and engineering domains.
We present Bayesian techniques for solving inverse problems which involve mean-square convergent random approximations of the forward map. Noisy approximations of the forward map arise in several fields, such as multiscale problems and probabilistic numerical methods. In these fields, a random approximation can enhance the quality or the efficiency of the inference procedure, but entails additional theoretical and computational difficulties due to the randomness of the forward map. A standard technique to address this issue is to combine Monte Carlo averaging with Markov chain Monte Carlo samplers, as for example in the pseudo-marginal Metropolis--Hastings methods. In this paper, we consider mean-square convergent random approximations, and quantify how Monte Carlo errors propagate from the forward map to the solution of the inverse problems. Moreover, we review and describe simple techniques to solve such inverse problems, and compare performances with a series of numerical experiments.
We describe a new approach to derive numerical approximations of boundary conditions for high-order accurate finite-difference approximations. The approach, called the Local Compatibility Boundary Condition (LCBC) method, uses boundary conditions and compatibility boundary conditions derived from the governing equations, as well as interior and boundary grid values, to construct a local polynomial, whose degree matches the order of accuracy of the interior scheme, centered at each boundary point. The local polynomial is then used to derive a discrete formula for each ghost point in terms of the data. This approach leads to centered approximations that are generally more accurate and stable than one-sided approximations. Moreover, the stencil approximations are local since they do not couple to neighboring ghost-point values which can occur with traditional compatibility conditions. The local polynomial is derived using continuous operators and derivatives which enables the automatic construction of stencil approximations at different orders of accuracy. The LCBC method is developed here for problems governed by second-order partial differential equations, and it is verified for a wide range of sample problems, both time-dependent and time-independent, in two space dimensions and for schemes up to sixth-order accuracy.
Even though Weighted Lasso regression has appealing statistical guarantees, it is typically avoided due to its complex search space described with thousands of hyperparameters. On the other hand, the latest progress with high-dimensional HPO methods for black-box functions demonstrates that high-dimensional applications can indeed be efficiently optimized. Despite this initial success, the high-dimensional HPO approaches are typically applied to synthetic problems with a moderate number of dimensions which limits its impact in scientific and engineering applications. To address this limitation, we propose LassoBench, a new benchmark suite tailored for an important open research topic in the Lasso community that is Weighted Lasso regression. LassoBench consists of benchmarks on both well-controlled synthetic setups (number of samples, SNR, ambient and effective dimensionalities, and multiple fidelities) and real-world datasets, which enable the use of many flavors of HPO algorithms to be improved and extended to the high-dimensional setting. We evaluate 5 state-of-the-art HPO methods and 3 baselines, and demonstrate that Bayesian optimization, in particular, can improve over the methods commonly used for sparse regression while highlighting limitations of these frameworks in very high-dimensions. Remarkably, Bayesian optimization improve the Lasso baselines on 60, 100, 300, and 1000 dimensional problems by 45.7%, 19.2%, 19.7% and 15.5%, respectively.
In this paper, we investigate the imaging inverse problem by employing an infinite-dimensional Bayesian inference method with a general fractional total variation-Gaussian (GFTG) prior. This novel hybrid prior is a development for the total variation-Gaussian (TG) prior and the non-local total variation-Gaussian (NLTG) prior, which is a combination of the Gaussian prior and a general fractional total variation regularization term, which contains a wide class of fractional derivative. Compared to the TG prior, the GFTG prior can effectively reduce the staircase effect, enhance the texture details of the images and also provide a complete theoretical analysis in the infinite-dimensional limit similarly to TG prior. The separability of the state space in Bayesian inference is essential for developments of probability and integration theory in infinite-dimensional setting, thus we first introduce the corresponding general fractional Sobolev space and prove that the space is a separable Banach space. Thereafter, we give the well-posedness and finite-dimensional approximation of the posterior measure of the Bayesian inverse problem based on the GFTG prior, and then the samples are extracted from the posterior distribution by using the preconditioned Crank-Nicolson (pCN) algorithm. Finally, we give several numerical examples of image reconstruction under liner and nonlinear models to illustrate the advantages of the proposed improved prior.
The Bayesian paradigm has the potential to solve core issues of deep neural networks such as poor calibration and data inefficiency. Alas, scaling Bayesian inference to large weight spaces often requires restrictive approximations. In this work, we show that it suffices to perform inference over a small subset of model weights in order to obtain accurate predictive posteriors. The other weights are kept as point estimates. This subnetwork inference framework enables us to use expressive, otherwise intractable, posterior approximations over such subsets. In particular, we implement subnetwork linearized Laplace: We first obtain a MAP estimate of all weights and then infer a full-covariance Gaussian posterior over a subnetwork. We propose a subnetwork selection strategy that aims to maximally preserve the model's predictive uncertainty. Empirically, our approach is effective compared to ensembles and less expressive posterior approximations over full networks.
This paper aims to explore models based on the extreme gradient boosting (XGBoost) approach for business risk classification. Feature selection (FS) algorithms and hyper-parameter optimizations are simultaneously considered during model training. The five most commonly used FS methods including weight by Gini, weight by Chi-square, hierarchical variable clustering, weight by correlation, and weight by information are applied to alleviate the effect of redundant features. Two hyper-parameter optimization approaches, random search (RS) and Bayesian tree-structured Parzen Estimator (TPE), are applied in XGBoost. The effect of different FS and hyper-parameter optimization methods on the model performance are investigated by the Wilcoxon Signed Rank Test. The performance of XGBoost is compared to the traditionally utilized logistic regression (LR) model in terms of classification accuracy, area under the curve (AUC), recall, and F1 score obtained from the 10-fold cross validation. Results show that hierarchical clustering is the optimal FS method for LR while weight by Chi-square achieves the best performance in XG-Boost. Both TPE and RS optimization in XGBoost outperform LR significantly. TPE optimization shows a superiority over RS since it results in a significantly higher accuracy and a marginally higher AUC, recall and F1 score. Furthermore, XGBoost with TPE tuning shows a lower variability than the RS method. Finally, the ranking of feature importance based on XGBoost enhances the model interpretation. Therefore, XGBoost with Bayesian TPE hyper-parameter optimization serves as an operative while powerful approach for business risk modeling.
Combining Bayesian nonparametrics and a forward model selection strategy, we construct parsimonious Bayesian deep networks (PBDNs) that infer capacity-regularized network architectures from the data and require neither cross-validation nor fine-tuning when training the model. One of the two essential components of a PBDN is the development of a special infinite-wide single-hidden-layer neural network, whose number of active hidden units can be inferred from the data. The other one is the construction of a greedy layer-wise learning algorithm that uses a forward model selection criterion to determine when to stop adding another hidden layer. We develop both Gibbs sampling and stochastic gradient descent based maximum a posteriori inference for PBDNs, providing state-of-the-art classification accuracy and interpretable data subtypes near the decision boundaries, while maintaining low computational complexity for out-of-sample prediction.
We propose a Bayesian convolutional neural network built upon Bayes by Backprop and elaborate how this known method can serve as the fundamental construct of our novel, reliable variational inference method for convolutional neural networks. First, we show how Bayes by Backprop can be applied to convolutional layers where weights in filters have probability distributions instead of point-estimates; and second, how our proposed framework leads with various network architectures to performances comparable to convolutional neural networks with point-estimates weights. In the past, Bayes by Backprop has been successfully utilised in feedforward and recurrent neural networks, but not in convolutional ones. This work symbolises the extension of the group of Bayesian neural networks which encompasses all three aforementioned types of network architectures now.
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