arXiv subjects

Byung-Jun Yoon

Publications and source records attributed to Byung-Jun Yoon.

44 records · Page 3Linked to original sources

arXiv2022

Optimal Decision Making in High-Throughput Virtual Screening Pipelines

The need for efficient computational screening of molecular candidates that possess desired properties frequently arises in various scientific and engineering problems, including drug discovery and materials design. However, the large size of the search space containing the candidates and the substantial computational cost of high-fidelity property prediction models makes screening practically challenging. In this work, we propose a general framework for constructing and optimizing a virtual screening (HTVS) pipeline that consists of multi-fidelity models. The central idea is to optimally allocate the computational resources to models with varying costs and accuracy to optimize the return-on-computational-investment (ROCI). Based on both simulated as well as real data, we demonstrate that the proposed optimal HTVS framework can significantly accelerate screening virtually without any degradation in terms of accuracy. Furthermore, it enables an adaptive operational strategy for HTVS, where one can trade accuracy for efficiency.

math.OC↗

arXiv2022

Autism spectrum disorder: a neuro-immunometabolic hypothesis of the developmental origins

Fetal neuroinflammation and prenatal stress (PS) may contribute to lifelong neurological disabilities. Astrocytes and microglia, among the brain's non-neuronal glia cell populations, play a pivotal role in neurodevelopment, predisposition to and initiation of disease throughout lifespan. One of the most common neurodevelopmental disorders manifesting between 1-4 years of age is autism spectrum disorder (ASD). A pathological glial-neuronal interplay is thought to increase the risk for clinical manifestation of ASD in at-risk children, but the mechanisms remain poorly understood and integrative, multi-scale models are needed. We propose a model that integrates the data across the scales of physiological organization, from genome to phenotype, and provides a foundation to explain the disparate findings on the genomic level. We hypothesize that via gene-environment interactions, fetal neuroinflammation and PS may reprogram glial immunometabolic phenotypes that impact neurodevelopment and neurobehavior. Drawing on genomic data from the recently published series of ovine and rodent glial transcriptome analyses with fetuses exposed to neuroinflammation or PS, we conduct an analysis on the Simons Foundation Autism Research Initiative (SFARI) Gene database. We confirm 21 gene hits. Using unsupervised statistical network analysis, we then identify six clusters of probable protein-protein interactions mapping onto the immunometabolic and stress response networks and epigenetic memory. These findings support our hypothesis. We discuss the implications for ASD etiology, early detection, and novel therapeutic approaches. We conclude with delineation of the next steps to verify our model on the individual gene level in an assumption-free manner.

q-bio.GN↗

arXiv2021

Accelerating Optimal Experimental Design for Robust Synchronization of Uncertain Kuramoto Oscillator Model Using Machine Learning

Recent advances in objective-based uncertainty quantification (objective-UQ) have shown that such a goal-driven approach for quantifying model uncertainty is extremely useful in real-world problems that aim at achieving specific objectives based on complex uncertain systems. Central to this objective-UQ is the concept of mean objective cost of uncertainty (MOCU), which provides effective means of quantifying the impact of uncertainty on the operational goals at hand. MOCU is especially useful for optimal experimental design (OED) as the potential efficacy of an experimental (or data acquisition) campaign can be quantified by estimating the MOCU that is expected to remain after the campaign. However, MOCU-based OED tends to be computationally expensive, which limits its practical applicability. In this paper, we propose a novel machine learning (ML) scheme that can significantly accelerate MOCU computation and expedite MOCU-based experimental design. The main idea is to use an ML model to efficiently search for the optimal robust operator under model uncertainty, a necessary step for computing MOCU. We apply the proposed ML-based OED acceleration scheme to design experiments aimed at optimally enhancing the control performance of uncertain Kuramoto oscillator models. Our results show that the proposed scheme results in up to 154-fold speed improvement without any degradation of the OED performance.

math.OC↗

arXiv2021

Adaptive Group Testing with Mismatched Models

Accurate detection of infected individuals is one of the critical steps in stopping any pandemic. When the underlying infection rate of the disease is low, testing people in groups, instead of testing each individual in the population, can be more efficient. In this work, we consider noisy adaptive group testing design with specific test sensitivity and specificity that select the optimal group given previous test results based on pre-selected utility function. As in prior studies on group testing, we model this problem as a sequential Bayesian Optimal Experimental Design (BOED) to adaptively design the groups for each test. We analyze the required number of group tests when using the updated posterior on the infection status and the corresponding Mutual Information (MI) as our utility function for selecting new groups. More importantly, we study how the potential bias on the ground-truth noise of group tests may affect the group testing sample complexity.

stat.ME↗

arXiv2021

Robust Importance Sampling for Error Estimation in the Context of Optimal Bayesian Transfer Learning

Classification has been a major task for building intelligent systems as it enables decision-making under uncertainty. Classifier design aims at building models from training data for representing feature-label distributions--either explicitly or implicitly. In many scientific or clinical settings, training data are typically limited, which makes designing accurate classifiers and evaluating their classification error extremely challenging. While transfer learning (TL) can alleviate this issue by incorporating data from relevant source domains to improve learning in a different target domain, it has received little attention for performance assessment, notably in error estimation. In this paper, we fill this gap by investigating knowledge transferability in the context of classification error estimation within a Bayesian paradigm. We introduce a novel class of Bayesian minimum mean-square error (MMSE) estimators for optimal Bayesian transfer learning (OBTL), which enables rigorous evaluation of classification error under uncertainty in a small-sample setting. Using Monte Carlo importance sampling, we employ the proposed estimator to evaluate the classification accuracy of a broad family of classifiers that span diverse learning capabilities. Experimental results based on both synthetic data as well as real-world RNA sequencing (RNA-seq) data show that our proposed OBTL error estimation scheme clearly outperforms standard error estimators, especially in a small-sample setting, by tapping into the data from other relevant domains.

stat.ML↗

arXiv2021

Quantifying the multi-objective cost of uncertainty

Various real-world applications involve modeling complex systems with immense uncertainty and optimizing multiple objectives based on the uncertain model. Quantifying the impact of the model uncertainty on the given operational objectives is critical for designing optimal experiments that can most effectively reduce the uncertainty that affect the objectives pertinent to the application at hand. In this paper, we propose the concept of mean multi-objective cost of uncertainty (multi-objective MOCU) that can be used for objective-based quantification of uncertainty for complex uncertain systems considering multiple operational objectives. We provide several illustrative examples that demonstrate the concept and strengths of the proposed multi-objective MOCU. Furthermore, we present a real-world example based on the mammalian cell cycle network to demonstrate how the multi-objective MOCU can be used for quantifying the operational impact of model uncertainty when there are multiple, possibly competing, objectives.

math.OC↗

arXiv2021

Optimal Experimental Design for Uncertain Systems Based on Coupled Differential Equations

We consider the optimal experimental design problem for an uncertain Kuramoto model, which consists of N interacting oscillators described by coupled ordinary differential equations. The objective is to design experiments that can effectively reduce the uncertainty present in the coupling strengths between the oscillators, thereby minimizing the cost of robust control of the uncertain Kuramoto model. We demonstrate the importance of quantifying the operational impact of the potential experiments in designing optimal experiments.

math.OC↗

arXiv2021

Geometric Affinity Propagation for Clustering with Network Knowledge

Clustering data into meaningful subsets is a major task in scientific data analysis. To date, various strategies ranging from model-based approaches to data-driven schemes, have been devised for efficient and accurate clustering. One important class of clustering methods that is of a particular interest is the class of exemplar-based approaches. This interest primarily stems from the amount of compressed information encoded in these exemplars that effectively reflect the major characteristics of the respective clusters. Affinity propagation (AP) has proven to be a powerful exemplar-based approach that refines the set of optimal exemplars by iterative pairwise message updates. However, a critical limitation is its inability to capitalize on known networked relations between data points often available for various scientific datasets. To mitigate this shortcoming, we propose geometric-AP, a novel clustering algorithm that effectively extends AP to take advantage of the network topology. Geometric-AP obeys network constraints and uses max-sum belief propagation to leverage the available network topology for generating smooth clusters over the network. Extensive performance assessment reveals a significant enhancement in the quality of the clustering results when compared to benchmark clustering schemes. Especially, we demonstrate that geometric-AP performs extremely well even in cases where the original AP fails drastically.

cs.LG↗