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Note on optimal sampling strategy for structural variant detection using optical mapping

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arXiv 2019年

作者： Li, Weiwei Hannig, Jan Jones, Corbin D. Department of Statistics and Operations Research University of North Carolina Chapel Hill United States Department of Biology and Integrative Program for Biological Genome Sciences University of North Carolina Chapel Hill United States

Structural variants compose the majority of human genetic variation, but are difficult to assess using current genomic sequencing technologies. Optical mapping technologies, which measure the size of chromosomal fragments between labeled markers, offer an alternative approach. As these technologies mature towards becoming clinical tools, there is a need to develop an approach for determining the optimal strategy for sampling biological material in order to detect a variant at some threshold. Here we develop an optimization approach using a simple, yet realistic, model of the genomic mapping process using a hyper-geometric distribution and probabilistic concentration inequalities. Our approach is both computationally and analytically tractable and includes a novel approach to getting tail bounds of hyper-geometric distribution. We show that if a genomic mapping technology can sample most of the chromosomal fragments within a sample, comparatively little biological material is needed to detect a variant at high confidence. Copyright © 2019, The Authors. All rights reserved.

关键词： Probability distributions

Effect of Tailored Coaching on Physicians’ Electronic Health Record Proficiency and User Experience: A Randomized Crossover Study

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Mayo Clinic Proceedings: Digital Health 2023年第2期1卷 94-104页

作者： Khairat, Saif Chourasia, Prabal Kwong, Elizabeth Choi, Ji Min Seashore, Carl Carolina Health Informatics Program University of North Carolina at Chapel Hill Chapel Hill NC United States School of Nursing University of North Carolina at Chapel Hill Chapel Hill NC United States Department of Statistics and Operations Research University of North Carolina at Chapel Hill Chapel Hill NC United States Division of General Pediatrics and Adolescent Medicine University of North Carolina at Chapel Hill Chapel Hill NC United States

Objective: To examine the effect of a tailored EHR coaching intervention, informed by audit log data, on physicians’ EHR proficiency, and user experience among pediatricians. Patients and Methods: A 12-month (August 2020 – August 2021) randomized crossover quality improvement study of a tailored EHR coaching was conducted on 34 pediatric physicians at a major medical center. Participants were randomized into Group AB or Group BA. The intervention was a single 1-hour, one-on-one coaching session. An Epic certified pediatrician tailored each coaching session to meet each physician needs using their EHR audit log data. We analyzed EHR audit log data for 3 months pre- and post-intervention. Results: Out of the 34 physicians, 15 (44%) were primary care pediatricians, 19 (56%) were female, 24 (70%) practiced at the medical center. During the initial intervention, the average proficiency score for the Group AB increased by 8.9% (pre-post difference: 0.37, 95% CI: −0.35 to 1.09;P-value=.381). For the crossover intervention, the average proficiency score for Group BA significantly increased by 11.2% (pre-post difference: 0.31, 95% CI: −0.11 to 0.74;P-value=.05). The average perceived EHR workload decreased post coaching sessions compared to pre-session (50.89 vs 46.66, P-value=.06). Post-coaching intervention, the average score for perceived EHR usability improved compared to pre-intervention (4.10 vs 4.34;P-value=.1). Conclusion: Electronic health record audit log data can be used to inform tailored coaching to improve physicians’ EHR proficiency levels and user experience. Tailored EHR coaching can increase awareness about efficiency tools available in the EHR. These findings are relevant to decisionmakers and learning health systems interested in provider well-being by optimizing EHR use. © 2023 The Authors

关键词： CRT classroom training EHR electronic health record NASA-TLX NASA Task Load Index SD standard deviation USE Usability Satisfaction and Ease of Use

Using Cluster Analysis and Dynamic programming for Demand Response Applied to Electricity Load in Residential Homes

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Journal of Engineering for Sustainable Buildings and Cities 2020年第1期1卷 011006页

作者： Chanpiwat, Pattanun Gabriel, Steven A. Moglen, Rachel L. Siemann, Michael J. Department of Mechanical Engineering University of Maryland College Park 20742 MD United States Department of Mechanical Engineering and the Applied Mathematics Statistics and Scientific Computation Program University of Maryland College Park 20742 MD United States Department of Industrial Economics and Technology Management Norwegian University of Science and Technology Trondheim NO-7491 Norway Operations Research and Industrial Engineering The University of Texas at Austin Austin 78712 TX United States Resideo Technologies Austin 78702 TX United States

This paper develops means to analyze and cluster residential households into homogeneous groups based on the electricity load. Classifying customers by electricity load profiles is a top priority for retail electric providers (REPs), so they can plan and conduct demand response (DR) effectively. We present a practical method to identify the most DR-profitable customer groups as opposed to tailoring DR programs for each separate household, which may be computationally prohibitive. Electricity load data of 10,000 residential households from 2017 located in Texas was used. The study proposed the clustered load-profile method (CLPM) to classify residential customers based on their electricity load profiles in combination with a dynamic program for DR scheduling to optimize DR profits. The main conclusions are that the proposed approach has an average 2.3% profitability improvement over a business-as-usual heuristic. In addition, the proposed method on average is approximately 70 times faster than running the DR dynamic programming separately for each household. Thus, our method not only is an important application to provide computational business insights for REPs and other power market participants but also enhances resilience for power grid with an advanced DR scheduling tool. Copyright © 2020 by ASME.

关键词： cluster analysis customer classification demand response dynamic programming energy efficiency integrated systems occupant behavior optimization residential household

Manifold learning with arbitrary norms

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arXiv 2020年

作者： Kileel, Joe Moscovich, Amit Zelesko, Nathan Singer, Amit Department of Mathematics Oden Institute University of Texas at Austin United States Department of Statistics and Operations Research Tel-Aviv University Israel Department of Mathematics Brown University United States Department of Mathematics and Program in Applied and Computational Mathematics Princeton University

Manifold learning methods play a prominent role in nonlinear dimensionality reduction and other tasks involving high-dimensional data sets with low intrinsic dimensionality. Many of these methods are graph-based: they associate a vertex with each data point and a weighted edge with each pair. Existing theory shows that the Laplacian matrix of the graph converges to the Laplace-Beltrami operator of the data manifold, under the assumption that the pairwise affinities are based on the Euclidean norm. In this paper, we determine the limiting differential operator for graph Laplacians constructed using any norm. Our proof involves an interplay between the second fundamental form of the manifold and the convex geometry of the given norm's unit ball. To demonstrate the potential benefits of non-Euclidean norms in manifold learning, we consider the task of mapping the motion of large molecules with continuous variability. In a numerical simulation we show that a modified Laplacian eigenmaps algorithm, based on the Earthmover's distance, outperforms the classic Euclidean Laplacian eigenmaps, both in terms of computational cost and the sample size needed to recover the intrinsic geometry. Copyright © 2020, The Authors. All rights reserved.

关键词： Mathematical operators

Cost-Effectiveness Analysis for Disease Prevention – A Case Study on Colorectal Cancer Screening

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arXiv 2024年

作者： Xiong, Yi Chan, Kwun C.G. Gorfine, Malka Hsu, Li Department of Biostatistics University at Buffalo BuffaloNY United States Department of Biostatistics University of Washington SeattleWA United States Department of Statistics and Operations Research Tel Aviv University Tel Aviv Israel Biostatistics Program Fred Hutchinson Cancer Center SeattleWA United States

Cancer Screening has been widely recognized as an effective strategy for preventing the disease. Despite its effectiveness, determining when to start screening is complicated, because starting too early increases the number of screenings over lifetime and thus costs but starting too late may miss the cancer that could have been prevented. Therefore, to make an informed recommendation on the age to start screening, it is necessary to conduct cost-effectiveness analysis to assess the gain in life years relative to the cost of screenings. As more large-scale observational studies become accessible, there is growing interest in evaluating cost-effectiveness based on empirical evidence. In this paper, we propose a unified measure for evaluating cost-effectiveness and a causal analysis for the continuous intervention of screening initiation age, under the multi-state modeling with semi-competing risks. Extensive simulation results show that the proposed estimators perform well in realistic scenarios. We perform a cost-effectiveness analysis of the colorectal cancer screening, utilizing data from the large-scale Women’s Health Initiative. Our analysis reveals that initiating screening at age 50 years yields the highest quality-adjusted life years with an acceptable incremental cost-effectiveness ratio compared to no screening, providing real-world evidence in support of screening recommendation for colorectal cancer. © 2024, CC BY.

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CEMRACS 2017: numerical probabilistic approach to MFG

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arXiv 2018年

作者： Angiuli, Andrea Graves, Christy V. Li, Houzhi Chassagneux, Jean-François Delarue, François Carmona, René Department of Statistics and Applied Probability University of California Santa Barbara Program in Applied and Computational Mathematics Princeton University Laboratoire de Probabilités Modélisation et Statistiques Université Paris Diderot Laboratoire Jean-Alexandre Dieudonné Université de Nice Sophia-Antipolis Operations Research and Financial Engineering Bendheim Center for Finance Princeton University

This project investigates numerical methods for solving fully coupled forward-backward stochastic differential equations (FBSDEs) of McKean-Vlasov type. Having numerical solvers for such mean field FBSDEs is of interest because of the potential application of these equations to optimization problems over a large population, say for instance mean field games (MFG) and optimal mean field control problems. Theory for this kind of problems has met with great success since the early works on mean field games by Lasry and Lions, see [27], and by Huang, Caines, and Malhamé, see [24]. Generally speaking, the purpose is to understand the continuum limit of optimizers or of equilibria (say in Nash sense) as the number of underlying players tends to infinity. When approached from the probabilistic viewpoint, solutions to these control problems (or games) can be described by coupled mean field FBSDEs, meaning that the coefficients depend upon the own marginal laws of the solution. In this note, we detail two methods for solving such FBSDEs which we implement and apply to five benchmark problems. The first method uses a tree structure to represent the pathwise laws of the solution, whereas the second method uses a grid discretization to represent the time marginal laws of the solutions. Both are based on a Picard scheme;importantly, we combine each of them with a generic continuation method that permits to extend the time horizon (or equivalently the coupling strength between the two equations) for which the Picard iteration converges. Copyright © 2018, The Authors. All rights reserved.

关键词： Numerical methods

Enhancing the sustainability and effectiveness of non-governmental organizations: An integrated neutrosophic decision-making model for determining the most effective corporate governance strategies

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Engineering Applications of Artificial Intelligence 2025年 156卷

作者： Emrah Ayhan Hakan Gökhan Gündoğdu Ahmet Aytekin Ahmet Furkan Karakaya Vladimir Simic Dragan Pamucar Department of Political Science and Public Administration Faculty of Economics and Administrative Sciences Anadolu University Tepebaşı 26470 Eskişehir Türkiye Department of Business Administration Hopa Faculty of Economics and Administrative Sciences Artvin Çoruh University Hopa 08100 Artvin Türkiye Public Administration Master Program Graduate Education Institute Anadolu University Tepebaşı 26470 Eskişehir Türkiye University of Belgrade Faculty of Transport and Traffic Engineering Vojvode Stepe 305 11010 Belgrade Serbia Yuan Ze University College of Engineering Department of Industrial Engineering and Management Taoyuan City 320315 Taiwan Department of Computer Science and Engineering College of Informatics Korea University 145 Anam-ro Seongbuk-gu Seoul 02841 Republic of Korea Department of Operations Research and Statistics Faculty of Organizational Sciences University of Belgrade Belgrade Serbia Department of Mechanics and Mathematics Western Caspian University Baku Azerbaijan İstinye University Faculty of Engineering and Natural Sciences Industrial Engineering Department Sarıyer 34396 İstanbul Türkiye

This research explores the development of effective corporate governance strategies for non-governmental organizations (NGOs) by evaluating both critical decision criteria and innovative organizational models. Based on an extensive literature review, seven governance criteria were identified: credibility and non-profit orientation, regular information flow and transparency, level of institutionalization, frequency of leadership turnover, internal and external stakeholder relations, annual budget, and ideological or religious motivation. In addition, five innovative organizational models were selected as strategic alternatives: continuous learning organization, technology-oriented policy development, income diversification, pluralistic governance, and transformational leadership. The empirical data were gathered through interviews with 16 experts from academia, civil society, and public institutions in Türkiye. To address the complexity and uncertainty of decision-making processes, a hybrid type-2 neutrosophic number (T2NN) multi-criteria decision-making methodology is introduced. The T2NN-ranking comparison and T2NN-criteria importance through intercriteria correlation methods are used to determine the weight of criteria, while T2NN-stable preference ordering towards ideal solution is utilized to rank the alternative models. Results show that the level of institutionalization is the most significant criterion, and income diversification is the most effective organizational model for improving NGO sustainability. The study not only provides practical guidance for NGO leaders but also introduces a robust methodological approach applicable to governance challenges under uncertain conditions.

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Accuracy of commercial geocoding: Assessment and implications

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Epidemiologic Perspectives and Innovations 2006年第1期3卷 1-12页

作者： Whitsel, Eric A. Quibrera, P. Miguel Smith, Richard L. Catellier, Diane J. Liao, Duanping Henley, Amanda C. Heiss, Gerardo Departments of Epidemiology and Medicine University of North Carolina Cardiovascular Disease Program Chapel Hill NC 27514 137 East Franklin Street United States Department of Epidemiology University of North Carolina Cardiovascular Disease Program Chapel Hill NC 27514 137 East Franklin Street United States Department of Statistics and Operations Research University of North Carolina 201 Smith Building 128 Chapel Hill NC 27599 United States Department of Biostatistics University of North Carolina Collaborative Studies Coordinating Center Chapel Hill NC 27514 137 East Franklin Street United States Department of Health Evaluation Sciences Pennsylvania State University College of Medicine Hershey PA 17033 600 Centerview Drive United States University of North Carolina Reference Department Geographic Information Services Chapel Hill NC 27599 United States

Background: Published studies of geocoding accuracy often focus on a single geographic area, address source or vendor, do not adjust accuracy measures for address characteristics, and do not examine effects of inaccuracy on exposure measures. We addressed these issues in a Women's Health Initiative ancillary study, the Environmental Epidemiology of Arrhythmogenesis in WHI. Results: Addresses in 49 U.S. states (n = 3,615) with established coordinates were geocoded by four vendors (A-D). There were important differences among vendors in address match rate (98%;82%;81%;30%), concordance between established and vendor-assigned census tracts (85%;88%;87%;98%) and distance between established and vendor-assigned coordinates (mean ρ [meters]: 1809;748;704;228). Mean ρ was lowest among street-matched, complete, zip-coded, unedited and urban addresses, and addresses with North American Datum of 1983 or World Geodetic System of 1984 coordinates. In mixed models restricted to vendors with minimally acceptable match rates (A-C) and adjusted for address characteristics, within-address correlation, and among-vendor heteroscedasticity of ρ, differences in mean ρ were small for street-type matches (280;268;275), i.e. likely to bias results relying on them about equally for most applications. In contrast, differences between centroid-type matches were substantial in some vendor contrasts, but not others (5497;4303;4210) p _interaction < 10^-4, i.e. more likely to bias results differently in many applications. The adjusted odds of an address match was higher for vendor A versus C (odds ratio = 66, 95% confidence interval: 47, 93), but not B versus C (OR = 1.1, 95% CI: 0.9, 1.3). That of census tract concordance was no higher for vendor A versus C (OR = 1.0, 95% CI: 0.9, 1.2) or B versus C (OR = 1.1, 95% CI: 0.9, 1.3). Misclassification of a related exposure measure - distance to the nearest highway - increased with mean ρ and in the absence of confounding, non-dif

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Evaluation of Marginal and Average Sectorial Ghgs Emissions Abatement Costs Using an Open-Source Energy System Optimization Model: The Italian Case Study

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SSRN

SSRN 2024年

作者： Nicoli, Matteo Colucci, Gianvito Faria, Victor Augusto Duraes Lerede, Daniele de Queiroz, Anderson Rodrigo Savoldi, Laura MAHTEP Group Dipartimento Energia "Galileo Ferraris" Politecnico di Torino Torino Italy Department of Civil Construction & Environmental Engineering NC State University RaleighNC United States Graduate Program on Operations Research NC State University RaleighNC United States Department of Economics and Statistics "Cognetti de Martiis" Università degli Studi di Torino Italy School of Business NC Central University DurhamNC United States

To achieve the goal of transforming Europe into a carbon-neutral continent by 2050, it is essential that emission reduction efforts are supported by well-informed decision-making processes and models. This paper proposes a methodology to evaluate the curves of the marginal GHGs abatement cost through energy system optimization models. The analysis is performed by comparing the marginal cost associated with progressively stricter decarbonization pathways from 2020 to 2050 with the emission reduction benefit. Moreover, average sectorial and sub-sectorial abatement costs are computed to assess the role of different sectors and technologies in the decarbonization process. In the light of its international commitment towards GHGs emission reduction, the selected case study is the Italian energy system, being Italy one of the largest emitting countries in Europe. The maximum marginal cost associated with the -90% emission reduction target in 2050 with respect to the reference scenario is approximately 1600 €/t. From our findings, the power sector turns out to be the cheapest sector to decarbonize (~ 170 €/t), while the industrial sector is the most expensive (~ 620 €/t). The values obtained for the abatement cost suggest that a carbon tax around 160 €/t would be sufficient to strongly reduce the emissions from the Italian energy system. © 2024, The Authors. All rights reserved.

关键词： Carbon