We review our recent work in the area of autonomous materials research, highlighting the coupling of machine learning methods and models and more problem-aware modeling. We review the general Bayesian framework for closed-loop design employed by many autonomous materials platforms. We then provide examples of our work on such platforms. We finally review our approaches to extend current statistical and ML models to better reflect problem-specific structure including the use of physics-based models and incorporation of operational considerations into the decision-making procedure.

Feature selection is an important problem in machine learning, which aims to select variables that lead to an optimal predictive model. In this paper, we focus on feature selection for post-intervention outcome prediction from pre-intervention variables. We are motivated by healthcare settings, where the goal is often to select the treatment that will maximize a specific patient's outcome; however, we often do not have sufficient randomized control trial data to identify well the conditional treatment effect. We show how we can use observational data to improve feature selection and effect estimation in two cases: (a) using observational data when we know the causal graph, and (b) when we do not know the causal graph but have observational and limited experimental data. Our paper extends the notion of Markov boundary to treatment-outcome pairs. We provide theoretical guarantees for the methods we introduce. In simulated data, we show that combining observational and experimental data improves feature selection and effect estimation.

With the worldwide population booming, the healthcare industry must adapt and develop the most innovative technologies to gather and analyze such massive clinical data and information about patients. It's about bringing in machine learning (ML) and artificial intelligence (AI) to make the real-world healthcare system high-powered and error-free. In 2017, Google developed an algorithm that can detect diseases, such as cancer, with 89% accuracy. Three years later, in 2020, smartphone-based mental healthcare apps are becoming the biggest buzzword, thanks to digital behavioral solutions, and machine learning in healthcare has just started. The purpose of ML in healthcare is to minimize human error without limiting the human factor.

Thanks to my CS7641 class at Georgia Tech in my MS Analytics program, where I discovered this concept and was inspired to write about it. It is somewhat surprising that among all the high-flying buzzwords of machine learning, we don't hear much about the one phrase which fuses some of the core concepts of statistical learning, information theory, and natural philosophy into a single three-word-combo. Moreover, it is not just an obscure and pedantic phrase meant for machine learning (ML) Ph. It has a precise and easily accessible meaning for anyone interested to explore, and a practical pay-off for the practitioners of ML and data science. I am talking about the Minimum Description Length.

Canonical Correlation Analysis (CCA) and its regularised versions have been widely used in the neuroimaging community to uncover multivariate associations between two data modalities (e.g., brain imaging and behaviour). However, these methods have inherent limitations: (1) statistical inferences about the associations are often not robust; (2) the associations within each data modality are not modelled; (3) missing values need to be imputed or removed. Group Factor Analysis (GFA) is a hierarchical model that addresses the first two limitations by providing Bayesian inference and modelling modality-specific associations. Here, we propose an extension of GFA that handles missing data, and highlight that GFA can be used as a predictive model. We applied GFA to synthetic and real data consisting of brain connectivity and non-imaging measures from the Human Connectome Project (HCP). In synthetic data, GFA uncovered the underlying shared and specific factors and predicted correctly the non-observed data modalities in complete and incomplete data sets. In the HCP data, we identified four relevant shared factors, capturing associations between mood, alcohol and drug use, cognition, demographics and psychopathological measures and the default mode, frontoparietal control, dorsal and ventral networks and insula, as well as two factors describing associations within brain connectivity. In addition, GFA predicted a set of non-imaging measures from brain connectivity. These findings were consistent in complete and incomplete data sets, and replicated previous findings in the literature. GFA is a promising tool that can be used to uncover associations between and within multiple data modalities in benchmark datasets (such as, HCP), and easily extended to more complex models to solve more challenging tasks.

Trustworthy deployment of ML models requires a proper measure of uncertainty, especially in safety-critical applications. We focus on uncertainty quantification (UQ) for classification problems via two avenues -- prediction sets using conformal prediction and calibration of probabilistic predictors by post-hoc binning -- since these possess distribution-free guarantees for i.i.d. data. Two common ways of generalizing beyond the i.i.d. setting include handling covariate and label shift. Within the context of distribution-free UQ, the former has already received attention, but not the latter. It is known that label shift hurts prediction, and we first argue that it also hurts UQ, by showing degradation in coverage and calibration. Piggybacking on recent progress in addressing label shift (for better prediction), we examine the right way to achieve UQ by reweighting the aforementioned conformal and calibration procedures whenever some unlabeled data from the target distribution is available. We examine these techniques theoretically in a distribution-free framework and demonstrate their excellent practical performance.

Causal Learner is a toolbox for learning causal structure and Markov blanket (MB) from data. It integrates functions for generating simulated Bayesian network data, a set of state-of-the-art global causal structure learning algorithms, a set of state-of-the-art local causal structure learning algorithms, a set of state-of-the-art MB learning algorithms, and functions for evaluating algorithms. The data generation part of Causal Learner is written in R, and the rest of Causal Learner is written in MATLAB. Causal Learner aims to provide researchers and practitioners with an open-source platform for causal learning from data and for the development and evaluation of new causal learning algorithms. The Causal Learner project is available at http://bigdata.ahu.edu.cn/causal-learner.

For many psychiatric disorders, neuroimaging offers a potential for revolutionizing diagnosis and treatment by providing access to preverbal mental processes. In their study "Machine learning of neural representations of suicide and emotion concepts identifies suicidal youth."1, Just and colleagues report that a Naive Bayes classifier, trained on voxelwise fMRI responses in human participants during the presentation of words and concepts related to mortality, can predict whether an individual had reported having suicidal ideations with a classification accuracy of 91%. Here we report a reappraisal of the methods employed by the authors, including re-analysis of the same data set, that calls into question the accuracy of the authors findings.

We present a framework for fitting inverse problem models via variational Bayes approximations. This methodology guarantees flexibility to statistical model specification for a broad range of applications, good accuracy performances and reduced model fitting times, when compared with standard Markov chain Monte Carlo methods. The message passing and factor graph fragment approach to variational Bayes we describe facilitates streamlined implementation of approximate inference algorithms and forms the basis to software development. Such approach allows for supple inclusion of numerous response distributions and penalizations into the inverse problem model. Albeit our analysis is circumscribed to one- and two-dimensional response variables, we lay down an infrastructure where streamlining algorithmic steps based on nullifying weak interactions between variables are extendible to inverse problems in higher dimensions. Image processing applications motivated by biomedical and archaeological problems are included as illustrations.

This paper proposes a hierarchical Bayesian model based on spatial concepts that enables a robot to transfer the knowledge of places from experienced environments to a new environment. The transfer of knowledge based on spatial concepts is modeled as the calculation process of the posterior distribution based on the observations obtained in each environment with the parameters of spatial concepts generalized to environments as prior knowledge. We conducted experiments to evaluate the generalization performance of spatial knowledge for general places such as kitchens and the adaptive performance of spatial knowledge for unique places such as `Emma's room' in a new environment. In the experiments, the accuracies of the proposed method and conventional methods were compared in the prediction task of location names from an image and a position, and the prediction task of positions from a location name. The experimental results demonstrated that the proposed method has a higher prediction accuracy of location names and positions than the conventional method owing to the transfer of knowledge.