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Reyes, Kristofer G.

Publications and source records attributed to Reyes, Kristofer G..

6 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Identifying Bayesian optimal experiments for uncertain biochemical pathway models

Abstract Pharmacodynamic (PD) models are mathematical models of cellular reaction networks that include drug mechanisms of action. These models are useful for studying predictive therapeutic outcomes of novel drug therapies in silico. However, PD models are known to possess significant uncertainty with respect to constituent parameter data, leading to uncertainty in the model predictions. Furthermore, experimental data to calibrate these models is often limited or unavailable for novel pathways. In this study, we present a Bayesian optimal experimental design approach for improving PD model prediction accuracy. We then apply our method using simulated experimental data to account for uncertainty in hypothetical laboratory measurements. This leads to a probabilistic prediction of drug performance and a quantitative measure of which prospective laboratory experiment will optimally reduce prediction uncertainty in the PD model. The methods proposed here provide a way forward for uncertainty quantification and guided experimental design for models of novel biological pathways.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Exact Gaussian processes for massive datasets via non-stationary sparsity-discovering kernels

Abstract A Gaussian Process (GP) is a prominent mathematical framework for stochastic function approximation in science and engineering applications. Its success is largely attributed to the GP’s analytical tractability, robustness, and natural inclusion of uncertainty quantification. Unfortunately, the use of exact GPs is prohibitively expensive for large datasets due to their unfavorable numerical complexity of $$O(N^3)$$ O ( N 3 ) in computation and $$O(N^2)$$ O ( N 2 ) in storage. All existing methods addressing this issue utilize some form of approximation—usually considering subsets of the full dataset or finding representative pseudo-points that render the covariance matrix well-structured and sparse. These approximate methods can lead to inaccuracies in function approximations and often limit the user’s flexibility in designing expressive kernels. Instead of inducing sparsity via data-point geometry and structure, we propose to take advantage of naturally-occurring sparsity by allowing the kernel to discover—instead of induce—sparse structure. The premise of this paper is that the data sets and physical processes modeled by GPs often exhibit natural or implicit sparsities, but commonly-used kernels do not allow us to exploit such sparsity. The core concept of exact, and at the same time sparse GPs relies on kernel definitions that provide enough flexibility to learn and encode not only non-zero but also zero covariances. This principle of ultra-flexible, compactly-supported, and non-stationary kernels, combined with HPC and constrained optimization, lets us scale exact GPs well beyond 5 million data points.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2023

Mathematical nuances of Gaussian process-driven autonomous experimentation

Abstract The fields of machine learning (ML) and artificial intelligence (AI) have transformed almost every aspect of science and engineering. The excitement for AI/ML methods is in large part due to their perceived novelty, as compared to traditional methods of statistics, computation, and applied mathematics. But clearly, all methods in ML have their foundations in mathematical theories, such as function approximation, uncertainty quantification, and function optimization. Autonomous experimentation is no exception; it is often formulated as a chain of off-the-shelf tools, organized in a closed loop, without emphasis on the intricacies of each algorithm involved. The uncomfortable truth is that the success of any ML endeavor, and this includes autonomous experimentation, strongly depends on the sophistication of the underlying mathematical methods and software that have to allow for enough flexibility to consider functions that are in agreement with particular physical theories. We have observed that standard off-the-shelf tools, used by many in the applied ML community, often hide the underlying complexities and therefore perform poorly. In this paper, we want to give a perspective on the intricate connections between mathematics and ML, with a focus on Gaussian process-driven autonomous experimentation. Although the Gaussian process is a powerful mathematical concept, it has to be implemented and customized correctly for optimal performance. We present several simple toy problems to explore these nuances and highlight the importance of mathematical and statistical rigor in autonomous experimentation and ML. One key takeaway is that ML is not, as many had hoped, a set of agnostic plug-and-play solvers for everyday scientific problems, but instead needs expertise and mastery to be applied successfully. Graphical abstract

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Autonomous experimentation systems for materials development: A community perspective

Solutions to many of the world's problems depend upon materials research and development. However, advanced materials can take decades to discover and decades more to fully deploy. Humans and robots have begun to partner to advance science and technology orders of magnitude faster than humans do today through the development and exploitation of closed-loop, autonomous experimentation systems. This review discusses the specific challenges and opportunities related to materials discovery and development that will emerge from this new paradigm. Our perspective incorporates input from stakeholders in academia, industry, government laboratories, and funding agencies. We outline the current status, barriers, and needed investments, culminating with a vision for the path forward. We intend the article to spark interest in this emerging research area and to motivate potential practitioners by illustrating early successes. We also aspire to encourage a creative reimagining of the next generation of materials science infrastructure. To this end, we frame future investments in materials science and technology, hardware and software infrastructure, artificial intelligence and autonomy methods, and critical workforce development for autonomous research.

36 MATERIALS SCIENCE↗