Accelerated model-based T1, T2* and proton density mapping using a Bayesian approach with automatic hyperparameter estimation.

PURPOSE: To achieve automatic hyperparameter estimation for the model-based recovery of quantitative MR maps from undersampled data, we propose a Bayesian formulation that incorporates the signal model and sparse priors among multiple image contrasts. THEORY: We introduce a novel approximate message passing framework "AMP-PE" that enables the automatic and simultaneous recovery of hyperparameters and quantitative maps. METHODS: We employed the variable-flip-angle method to acquire multi-echo measurements using gradient echo sequence. We explored undersampling schemes to incorporate complementary sampling patterns across different flip angles and echo times. We further compared AMP-PE with conventional compressed sensing approaches such as the l 1 $$ {l}_1 $$ -norm minimization, PICS and other model-based approaches such as GraSP, MOBA. RESULTS: Compared to conventional compressed sensing approaches such as the l 1 $$ {l}_1 $$ -norm minimization and PICS, AMP-PE achieved superior reconstruction performance with lower errors in T 2 ∗ $$ {\mathrm{T}}_2^{\ast } $$ mapping and comparable performance in T 1 $$ {\mathrm{T}}_1 $$ and proton density mappings. When compared to other model-based approaches including GraSP and MOBA, AMP-PE exhibited greater robustness and outperformed GraSP in reconstruction error. AMP-PE offers faster speed than MOBA. AMP-PE performed better than MOBA at higher sampling rates and worse than MOBA at a lower sampling rate. Notably, AMP-PE eliminates the need for hyperparameter tuning, which is a requisite for all the other approaches. CONCLUSION: AMP-PE offers the benefits of model-based recovery with the additional key advantage of automatic hyperparameter estimation. It works adeptly in situations where ground-truth is difficult to obtain and in clinical environments where it is desirable to automatically adapt hyperparameters to individual protocol, scanner and patient.

Supervised Methods for Biomarker Detection from Microarray Experiments.

Biomarkers are valuable indicators of the state of a biological system. Microarray technology has been extensively used to identify biomarkers and build computational predictive models for disease prognosis, drug sensitivity and toxicity evaluations. Activation biomarkers can be used to understand the underlying signaling cascades, mechanisms of action and biological cross talk. Biomarker detection from microarray data requires several considerations both from the biological and computational points of view. In this chapter, we describe the main methodology used in biomarkers discovery and predictive modeling and we address some of the related challenges. Moreover, we discuss biomarker validation and give some insights into multiomics strategies for biomarker detection.

Learning gene regulatory networks using gaussian process emulator and graphical LASSO.

Large amounts of research efforts have been focused on learning gene regulatory networks (GRNs) based on gene expression data to understand the functional basis of a living organism. Under the assumption that the joint distribution of the gene expressions of interest is a multivariate normal distribution, such networks can be constructed by assessing the nonzero elements of the inverse covariance matrix, the so-called precision matrix or concentration matrix. This may not reflect the true connectivity between genes by considering just pairwise linear correlations. To relax this limitative constraint, we employ Gaussian process (GP) model which is well known as computationally efficient non-parametric Bayesian machine learning technique. GPs are among a class of methods known as kernel machines which can be used to approximate complex problems by tuning their hyperparameters. In fact, GP creates the ability to use the capacity and potential of different kernels in constructing precision matrix and GRNs. In this paper, in the first step, we choose the GP with appropriate kernel to learn the considered GRNs from the observed genetic data, and then we estimate kernel hyperparameters using rule-of-thumb technique. Using these hyperparameters, we can also control the degree of sparseness in the precision matrix. Then we obtain kernel-based precision matrix similar to GLASSO to construct kernel-based GRN. The findings of our research are used to construct GRNs with high performance, for different species of Drosophila fly rather than simply using the assumption of multivariate normal distribution, and the GPs, despite the use of the kernels capacity, have a much better performance than the multivariate Gaussian distribution assumption.

EO-MTRNN: evolutionary optimization of hyperparameters for a neuro-inspired computational model of spatiotemporal learning.

For spatiotemporal learning with neural networks, hyperparameters are often set manually by a human expert. This is especially the case with multiple timescale networks that require a careful setting of the values of timescales in order to learn spatiotemporal data. However, this implies a cumbersome trial-and-error process until suitable parameters are found and it reduces the long-term autonomy of artificial agents, such as robots that are controlled by multiple timescale networks. To solve the problem, we propose the evolutionary optimized multiple timescale recurrent neural network (EO-MTRNN) that is inspired by the neural plasticity of the human cortex. Our proposed network uses a method of evolutionary optimization to adjust its timescales and to rewire itself in terms of number of neurons and synapses. Moreover, it does not require additional neural networks for pre- and postprocessing input-output data. We validate our EO-MTRNN by applying it to a proposed benchmark training dataset with single and multiple sequence training cases, as well as by applying it to sensory-motor data from a robot. We compare different configuration modes of the network, and we compare the learning performance between a network configuration with manually set hyperparameters and a configuration with automatically estimated hyperparameters. The results show that automatically estimated hyperparameters yield approximately 43% better performance than manually estimated ones, without overfitting the given teaching data. We also validate the generalization ability by successfully learning data that were not included in the hyperparameter estimation process.

Exploratory-Phase-Free Estimation of GP Hyperparameters in Sequential Design Methods-At the Example of Bayesian Inverse Problems.

Methods for sequential design of computer experiments typically consist of two phases. In the first phase, the exploratory phase, a space-filling initial design is used to estimate hyperparameters of a Gaussian process emulator (GPE) and to provide some initial global exploration of the model function. In the second phase, more design points are added one by one to improve the GPE and to solve the actual problem at hand (e.g., Bayesian optimization, estimation of failure probabilities, solving Bayesian inverse problems). In this article, we investigate whether hyperparameters can be estimated without a separate exploratory phase. Such an approach will leave hyperparameters uncertain in the first iterations, so the acquisition function (which tells where to evaluate the model function next) and the GPE-based estimator need to be adapted to non-Gaussian random fields. Numerical experiments are performed exemplarily on a sequential method for solving Bayesian inverse problems. These experiments show that hyperparameters can indeed be estimated without an exploratory phase and the resulting method works almost as efficient as if the hyperparameters had been known beforehand. This means that the estimation of hyperparameters should not be the reason for including an exploratory phase. Furthermore, we show numerical examples, where these results allow us to eliminate the exploratory phase to make the sequential design method both faster (requiring fewer model evaluations) and easier to use (requiring fewer choices by the user).