4,101 results on '"Reeb AN"'
Search Results
2. Service-Learning: An Empirically Driven and Transformational Pedagogy to Develop Psychologically Literate Citizens for Contemporary Challenges
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Ana I. Ruiz, Roger N. Reeb, Tia N. Turner, Robert G. Bringle, and Patti H. Clayton
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Service-learning can produce timely paradigmatic shifts in the psychology curriculum and in teaching practices. This innovative pedagogy enhances students' academic learning, personal growth, civic development, and professional development. Service-learning pedagogy also has the potential of enhancing students' understanding of, and commitment to, "glocal" (global-local) issues as expressed in the United Nations' Sustainable Development Goals. Service-learning is defined and proffered to transform the undergraduate psychology curriculum by engaging the department faculty to align course outcomes and scaffold community-engaged activities from the introductory to capstone courses. This transformation is illustrated with a major contemporary challenge: climate change.
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- 2024
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3. Startups’ demand for accounting expertise: evidence from a randomized field experiment
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Gefen, Ofir, Reeb, David, and Sulaeman, Johan
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- 2024
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4. Tighter Confidence Bounds for Sequential Kernel Regression
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Flynn, Hamish and Reeb, David
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Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
Confidence bounds are an essential tool for rigorously quantifying the uncertainty of predictions. They are a core component in many sequential learning and decision-making algorithms, with tighter confidence bounds giving rise to algorithms with better empirical performance and better performance guarantees. In this work, we use martingale tail inequalities to establish new confidence bounds for sequential kernel regression. Our confidence bounds can be computed by solving a conic program, although this bare version quickly becomes impractical, because the number of variables grows with the sample size. However, we show that the dual of this conic program allows us to efficiently compute tight confidence bounds. We prove that our new confidence bounds are always tighter than existing ones in this setting. We apply our confidence bounds to kernel bandit problems, and we find that when our confidence bounds replace existing ones, the KernelUCB (GP-UCB) algorithm has better empirical performance, a matching worst-case performance guarantee and comparable computational cost., Comment: 34 pages, 7 figures
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- 2024
5. TALENT PIPELINES FOR THE FOURTH INDUSTRIAL REVOLUTION: How California PaCE Units Can Bridge Critical KSA Gaps
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Reeb, Tyler, Swarat, Chris, and Taylor, Barbara
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- 2024
6. Integrate-and-fire circuit for converting analog signals to spikes using phase encoding
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Lopez-Randulfe, Javier, Reeb, Nico, and Knoll, Alois
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Computer Science - Emerging Technologies ,Computer Science - Neural and Evolutionary Computing ,Electrical Engineering and Systems Science - Signal Processing - Abstract
Processing sensor data with spiking neural networks on digital neuromorphic chips requires converting continuous analog signals into spike pulses. Two strategies are promising for achieving low energy consumption and fast processing speeds in end-to-end neuromorphic applications. First, to directly encode analog signals to spikes to bypass the need for an analog-to-digital converter (ADC). Second, to use temporal encoding techniques to maximize the spike sparsity, which is a crucial parameter for fast and efficient neuromorphic processing. In this work, we propose an adaptive control of the refractory period of the leaky integrate-and-fire (LIF) neuron model for encoding continuous analog signals into a train of time-coded spikes. The LIF-based encoder generates phase-encoded spikes that are compatible with digital hardware. We implemented the neuron model on a physical circuit and tested it with different electric signals. A digital neuromorphic chip processed the generated spike trains and computed the signal's frequency spectrum using a spiking version of the Fourier transform. We tested the prototype circuit on electric signals up to 1 KHz. Thus, we provide an end-to-end neuromorphic application that generates the frequency spectrum of an electric signal without the need for an ADC or a digital signal processing algorithm., Comment: 13 pages
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- 2023
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7. Emerging Logistic Challenges, Health Disparities, and Bioethical Concerns in Kidney Xenotransplantation: A Literature Review
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Klapholz, J., Eickel, G., Reeb, M., Jaffe, I., Klitenic, S., Alejo, J., Lonze, B., and Levan, M.
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- 2024
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8. Improved Algorithms for Stochastic Linear Bandits Using Tail Bounds for Martingale Mixtures
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Flynn, Hamish, Reeb, David, Kandemir, Melih, and Peters, Jan
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Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
We present improved algorithms with worst-case regret guarantees for the stochastic linear bandit problem. The widely used "optimism in the face of uncertainty" principle reduces a stochastic bandit problem to the construction of a confidence sequence for the unknown reward function. The performance of the resulting bandit algorithm depends on the size of the confidence sequence, with smaller confidence sets yielding better empirical performance and stronger regret guarantees. In this work, we use a novel tail bound for adaptive martingale mixtures to construct confidence sequences which are suitable for stochastic bandits. These confidence sequences allow for efficient action selection via convex programming. We prove that a linear bandit algorithm based on our confidence sequences is guaranteed to achieve competitive worst-case regret. We show that our confidence sequences are tighter than competitors, both empirically and theoretically. Finally, we demonstrate that our tighter confidence sequences give improved performance in several hyperparameter tuning tasks., Comment: Accepted at NeurIPS 2023. 35 pages, 6 figures
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- 2023
9. Diversity and distribution of ferns and clubmosses in the eastern canyons of Isalo National Park, Madagascar
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Randrianarimanana, Rivoharifara, Rakotondrainibe, France, Boucheron-Dubuisson, Elodie, Marline, Lovanomenjanahary, Rakotoarinivo, Mijoro, and Reeb, Catherine
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- 2024
10. PAC-Bayes Bounds for Bandit Problems: A Survey and Experimental Comparison
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Flynn, Hamish, Reeb, David, Kandemir, Melih, and Peters, Jan
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
PAC-Bayes has recently re-emerged as an effective theory with which one can derive principled learning algorithms with tight performance guarantees. However, applications of PAC-Bayes to bandit problems are relatively rare, which is a great misfortune. Many decision-making problems in healthcare, finance and natural sciences can be modelled as bandit problems. In many of these applications, principled algorithms with strong performance guarantees would be very much appreciated. This survey provides an overview of PAC-Bayes bounds for bandit problems and an experimental comparison of these bounds. On the one hand, we found that PAC-Bayes bounds are a useful tool for designing offline bandit algorithms with performance guarantees. In our experiments, a PAC-Bayesian offline contextual bandit algorithm was able to learn randomised neural network polices with competitive expected reward and non-vacuous performance guarantees. On the other hand, the PAC-Bayesian online bandit algorithms that we tested had loose cumulative regret bounds. We conclude by discussing some topics for future work on PAC-Bayesian bandit algorithms., Comment: 32 pages, 8 figures
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- 2022
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11. Validation of Composite Systems by Discrepancy Propagation
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Reeb, David, Patel, Kanil, Barsim, Karim, Schiegg, Martin, and Gerwinn, Sebastian
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
Assessing the validity of a real-world system with respect to given quality criteria is a common yet costly task in industrial applications due to the vast number of required real-world tests. Validating such systems by means of simulation offers a promising and less expensive alternative, but requires an assessment of the simulation accuracy and therefore end-to-end measurements. Additionally, covariate shifts between simulations and actual usage can cause difficulties for estimating the reliability of such systems. In this work, we present a validation method that propagates bounds on distributional discrepancy measures through a composite system, thereby allowing us to derive an upper bound on the failure probability of the real system from potentially inaccurate simulations. Each propagation step entails an optimization problem, where -- for measures such as maximum mean discrepancy (MMD) -- we develop tight convex relaxations based on semidefinite programs. We demonstrate that our propagation method yields valid and useful bounds for composite systems exhibiting a variety of realistic effects. In particular, we show that the proposed method can successfully account for data shifts within the experimental design as well as model inaccuracies within the simulation., Comment: 21 pages incl. 11 pages appendix; camera-ready version at UAI 2023
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- 2022
12. Glutamate transporters in health and disease
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L. Reeb, Katelyn, primary, K. Gill, Simran, additional, Temmermand, Rhea, additional, and C.K. Fontana, Andréia, additional
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- 2024
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13. One dimensional non-Hausdorff manifolds and foliations of the plane
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Haefliger, André and Reeb, Georges
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Mathematics - Geometric Topology - Abstract
The original article titled "Vari\'et\'es (non s\'epar\'ees) \`a une dimension et structures feuillet\'ees du plan" was published in 1957 in French in L'Enseignement Math\'ematique. It establishes a beautiful connection between foliations of the plane and non-Hausdorff $1$-dimensional manifolds arising naturally as leaf spaces of the foliations. Since its appearance, this theory has paved the way for several results concerning dynamical systems and foliations of the plane and $2$-manifolds. Haefliger and Reeb's article inspires many results in the theory of foliation of $3$-manifolds as well: we refer the interested reader to Danny Calegari's book on the topic. Haefliger and Reeb's article also has been applied to areas outside topological dynamics. This article has been referenced in $43$ papers to-date and has helped build many nice results. In the literature, the main theorem of this article has been commonly referred to as Haefliger-Reeb theory or "a classical result by Haefliger and Reeb". However, to the best of our knowledge, no English version of this article is currently available. We have kept the article entirely unchanged except to add figures and correct a few typographical errors. We hope that this translation will be useful for the broader audience., Comment: Original work is in French. Translated to English by Gangotryi Sorcar
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- 2022
14. The Impact of Service-Oriented Undergraduate Research on an Ongoing Participatory Community Action Research Project at Homeless Shelters
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Zicka, Jennifer L. and Reeb, Roger N.
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This article is a genuine contribution between an undergraduate student (Jennifer Zicka) and her mentor (Dr. Roger Reeb). Jennifer made unique contributions to an ongoing project that empowers and supports guests at homeless shelters as they strive to overcome personal challenges and obstacles related to homelessness. After a brief description of the Project, we celebrate Jennifer's unique contributions, which sets the stage for the centerpiece of the article -- Jennifer's heartfelt reflection on how this experiential learning contributed to her civic-related development, personal growth, and the pursuit of her dream career.
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- 2021
15. Legume cover crop as a primary nitrogen source in an organic crop rotation in Ontario, Canada: impacts on corn, soybean and winter wheat yields
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Yang, Xueming, Drury, Craig F., Dan Reynolds, W., and Reeb, Mary-Anne D.
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- 2024
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16. Utilizing Expert Features for Contrastive Learning of Time-Series Representations
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Nonnenmacher, Manuel, Oldenburg, Lukas, Steinwart, Ingo, and Reeb, David
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Computer Science - Machine Learning ,Computer Science - Artificial Intelligence ,Statistics - Machine Learning - Abstract
We present an approach that incorporates expert knowledge for time-series representation learning. Our method employs expert features to replace the commonly used data transformations in previous contrastive learning approaches. We do this since time-series data frequently stems from the industrial or medical field where expert features are often available from domain experts, while transformations are generally elusive for time-series data. We start by proposing two properties that useful time-series representations should fulfill and show that current representation learning approaches do not ensure these properties. We therefore devise ExpCLR, a novel contrastive learning approach built on an objective that utilizes expert features to encourage both properties for the learned representation. Finally, we demonstrate on three real-world time-series datasets that ExpCLR surpasses several state-of-the-art methods for both unsupervised and semi-supervised representation learning.
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- 2022
17. PAC-Bayesian Lifelong Learning For Multi-Armed Bandits
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Flynn, Hamish, Reeb, David, Kandemir, Melih, and Peters, Jan
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Computer Science - Machine Learning ,Statistics - Machine Learning - Abstract
We present a PAC-Bayesian analysis of lifelong learning. In the lifelong learning problem, a sequence of learning tasks is observed one-at-a-time, and the goal is to transfer information acquired from previous tasks to new learning tasks. We consider the case when each learning task is a multi-armed bandit problem. We derive lower bounds on the expected average reward that would be obtained if a given multi-armed bandit algorithm was run in a new task with a particular prior and for a set number of steps. We propose lifelong learning algorithms that use our new bounds as learning objectives. Our proposed algorithms are evaluated in several lifelong multi-armed bandit problems and are found to perform better than a baseline method that does not use generalisation bounds., Comment: 29 pages, 5 figures
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- 2022
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18. Time-coded Spiking Fourier Transform in Neuromorphic Hardware
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López-Randulfe, Javier, Reeb, Nico, Karimi, Negin, Liu, Chen, Gonzalez, Hector A., Dietrich, Robin, Vogginger, Bernhard, Mayr, Christian, and Knoll, Alois
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Computer Science - Neural and Evolutionary Computing ,Electrical Engineering and Systems Science - Signal Processing - Abstract
After several decades of continuously optimizing computing systems, the Moore's law is reaching itsend. However, there is an increasing demand for fast and efficient processing systems that can handlelarge streams of data while decreasing system footprints. Neuromorphic computing answers thisneed by creating decentralized architectures that communicate with binary events over time. Despiteits rapid growth in the last few years, novel algorithms are needed that can leverage the potential ofthis emerging computing paradigm and can stimulate the design of advanced neuromorphic chips.In this work, we propose a time-based spiking neural network that is mathematically equivalent tothe Fourier transform. We implemented the network in the neuromorphic chip Loihi and conductedexperiments on five different real scenarios with an automotive frequency modulated continuouswave radar. Experimental results validate the algorithm, and we hope they prompt the design of adhoc neuromorphic chips that can improve the efficiency of state-of-the-art digital signal processorsand encourage research on neuromorphic computing for signal processing., Comment: Accepted version on IEEE Transactions on Computers (early access). Added copyright notice
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- 2022
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19. Positive allosteric modulation of glutamate transporter reduces cocaine-induced locomotion and expression of cocaine conditioned place preference in rats
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Reeb, Katelyn L., Wiah, Sonita, Patel, Bhumiben P., Lewandowski, Stacia I., Mortensen, Ole V., Salvino, Joseph M., Rawls, Scott M., and Fontana, Andréia C.K.
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- 2024
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20. Wildfire, Smoke Exposure, Human Health, and Environmental Justice Need to be Integrated into Forest Restoration and Management
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D’Evelyn, Savannah M, Jung, Jihoon, Alvarado, Ernesto, Baumgartner, Jill, Caligiuri, Pete, Hagmann, R Keala, Henderson, Sarah B, Hessburg, Paul F, Hopkins, Sean, Kasner, Edward J, Krawchuk, Meg A, Krenz, Jennifer E, Lydersen, Jamie M, Marlier, Miriam E, Masuda, Yuta J, Metlen, Kerry, Mittelstaedt, Gillian, Prichard, Susan J, Schollaert, Claire L, Smith, Edward B, Stevens, Jens T, Tessum, Christopher W, Reeb-Whitaker, Carolyn, Wilkins, Joseph L, Wolff, Nicholas H, Wood, Leah M, Haugo, Ryan D, and Spector, June T
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Epidemiology ,Public Health ,Health Sciences ,Lung ,Climate-Related Exposures and Conditions ,Respiratory ,Air Pollution ,Child ,Environmental Exposure ,Environmental Justice ,Forests ,Humans ,Smoke ,United States ,Wildfires ,Wildland fire ,Public health ,Air quality ,Exposure ,Ecological restoration ,Prescribed burning ,Environmental justice ,Interdisciplinary ,Collaborative partnerships - Abstract
Purpose of reviewIncreasing wildfire size and severity across the western United States has created an environmental and social crisis that must be approached from a transdisciplinary perspective. Climate change and more than a century of fire exclusion and wildfire suppression have led to contemporary wildfires with more severe environmental impacts and human smoke exposure. Wildfires increase smoke exposure for broad swaths of the US population, though outdoor workers and socially disadvantaged groups with limited adaptive capacity can be disproportionally exposed. Exposure to wildfire smoke is associated with a range of health impacts in children and adults, including exacerbation of existing respiratory diseases such as asthma and chronic obstructive pulmonary disease, worse birth outcomes, and cardiovascular events. Seasonally dry forests in Washington, Oregon, and California can benefit from ecological restoration as a way to adapt forests to climate change and reduce smoke impacts on affected communities.Recent findingsEach wildfire season, large smoke events, and their adverse impacts on human health receive considerable attention from both the public and policymakers. The severity of recent wildfire seasons has state and federal governments outlining budgets and prioritizing policies to combat the worsening crisis. This surging attention provides an opportunity to outline the actions needed now to advance research and practice on conservation, economic, environmental justice, and public health interests, as well as the trade-offs that must be considered. Scientists, planners, foresters and fire managers, fire safety, air quality, and public health practitioners must collaboratively work together. This article is the result of a series of transdisciplinary conversations to find common ground and subsequently provide a holistic view of how forest and fire management intersect with human health through the impacts of smoke and articulate the need for an integrated approach to both planning and practice.
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- 2022
21. Advancing Seaport Environmental Sustainability: Case Studies from the San Pedro Bay Ports Clean Air Action Plan
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Matsumoto, Deanna, Mace, Caitlin, Reeb, Tyler, and O’Brien, Thomas
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Air quality management ,Case studies ,Environmental policy ,Freight transportation ,Intermodal transportation ,Ports - Abstract
The Port of Los Angeles and Port of Long Beach, together referred to as the San Pedro Bay Port Complex, are an important source of regional economic activity in southern California. However, the port complex is also the single largest fixed source of air pollution in the region. In response to pressure from regulatory agencies and local communities, the two ports developed a Clean Air Action Plan in 2006.The research team assembled three case studies of programs implemented under the Clean Air Action Plan: the Technology Advancement Program, voluntary Vessel Speed Reduction programs, and the Clean Trucks Program. An additional case study featured a proposed private-sector infrastructure project: the Southern California International Gateway project. Each case study describes the program, stakeholders involved, barriers to implementation, and outcomes. These cases highlight the institutional challenges the ports face while working with a multitude of stakeholders and regulatory bodies to address both environmental sustainability and economic competitiveness. View the NCST Project Webpage
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- 2022
22. SOSP: Efficiently Capturing Global Correlations by Second-Order Structured Pruning
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Nonnenmacher, Manuel, Pfeil, Thomas, Steinwart, Ingo, and Reeb, David
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Computer Science - Machine Learning ,Computer Science - Computer Vision and Pattern Recognition ,Statistics - Machine Learning - Abstract
Pruning neural networks reduces inference time and memory costs. On standard hardware, these benefits will be especially prominent if coarse-grained structures, like feature maps, are pruned. We devise two novel saliency-based methods for second-order structured pruning (SOSP) which include correlations among all structures and layers. Our main method SOSP-H employs an innovative second-order approximation, which enables saliency evaluations by fast Hessian-vector products. SOSP-H thereby scales like a first-order method despite taking into account the full Hessian. We validate SOSP-H by comparing it to our second method SOSP-I that uses a well-established Hessian approximation, and to numerous state-of-the-art methods. While SOSP-H performs on par or better in terms of accuracy, it has clear advantages in terms of scalability and efficiency. This allowed us to scale SOSP-H to large-scale vision tasks, even though it captures correlations across all layers of the network. To underscore the global nature of our pruning methods, we evaluate their performance not only by removing structures from a pretrained network, but also by detecting architectural bottlenecks. We show that our algorithms allow to systematically reveal architectural bottlenecks, which we then remove to further increase the accuracy of the networks.
- Published
- 2021
23. Life Transition Events and Depressive Symptom Trajectories during Young Adulthood: The Influence of Adverse Family and Individual Contexts in Adolescence
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Lee, Tae Kyoung, Wickrama, Kandauda A. S., O'Neal, Catherine Walker, Neppl, Tricia K., and Reeb, Ben T.
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Because sequential patterns of multiple transition events (i.e., college graduation, full-time employment, marriage, and parenthood) are associated with turning points in depressive symptom trajectories during young adulthood, the present study used a sample of 446 White adolescents (52.3% females; 15.58 years old, on average) over 18 years (1992 to 2010) to (a) identify distinct "longitudinal joint processes" between these sequential patterns of life transition events and turning points of depressive symptom trajectories by using a person-centered modeling approach and (b) investigate the influence of adverse family and individual contexts (negative family economic events, hostile relationships with parents, and impulsive sensation seeking) in adolescence on these longitudinal joint processes. We identified six longitudinal joint processes: (a) traditional transition pattern with no turning points in depressive symptom trajectories, (b) traditional transition pattern with turning points in depressive symptom trajectories in the mid-to-late 20s, (c) early parenthood transition pattern with no turning points in depressive symptom trajectories, (d) early parenthood transition pattern with turning points in depressive symptom trajectories in the mid-to-late 20s, (e) precocious transition pattern with no turning points in depressive symptom trajectories, and (f) precocious transition pattern with depressive symptom turning points (or fluctuations) throughout young adulthood. Negative family economic events, hostile relationships with parents, and impulsive sensation seeking in adolescence influenced these longitudinal joint processes. Hostile relationships with parents also uniquely influenced turning points in depressive symptoms during young adulthood while impulsive sensation seeking uniquely influence sequential patterns of life transition events. Clinical implications are discussed.
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- 2023
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24. Diversity and distribution of ferns and clubmosses in the eastern canyons of Isalo National Park, Madagascar
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Rivoharifara Randrianarimanana, France Rakotondrainibe, Elodie Boucheron-Dubuisson, Lovanomenjanahary Marline, Mijoro Rakotoarinivo, and Catherine Reeb
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Plant ecology ,QK900-989 - Abstract
Background and aims – In contrast to the flowering plants, the pteridophyte flora of Madagascar is still understudied. While several studies have been published on the eastern and central parts of the island, there are currently few works dedicated to the pteridophytes of southwestern Madagascar. The aim of this work is to increase the knowledge of the pteridophyte flora of the Isalo massif in southwestern Madagascar. It presents a checklist of Isalo’s pteridophytes and an analysis of the diversity and distribution patterns of pteridophyte communities across ecological gradients in the eastern canyons of Isalo. Material and methods – Eighty plots were placed in six canyons. In each plot, pteridophyte species abundance was inventoried, as well as several ecological and geomorphological variables. A census in the field and observations on specimens in herbaria were carried to make a checklist of all the pteridophyte species known for Isalo. Statistical analysis was carried out to understand the pteridophyte diversity and distribution patterns in the Isalo’s canyons: (1) exploratory analysis (FAMD and HCPC) highlights the general patterns of ecological gradients, (2) a rarefaction curve was used to compare species diversity, and (3) co-inertia analysis investigated the relationship between ecological gradient and pteridophyte communities. Key results – In total, 60 species of ferns and lycophytes have been recorded in the massif, including ten endemic species to Madagascar and 11 species reported for the first time in the Isalo massif. Species diversity is especially high in the northern canyons (Anjofo, Andramanero, Antsifotra) in contrast to the middle (Maki and Rats) and southern (Namaza) canyons. Fern distribution patterns were correlated to a combination of environmental factors, highlighting species-specific ecological preferences.
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- 2024
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25. Workforce Implications of Transitioning to Zero-Emission Buses in Public Transit
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Jakovich, Scott and Reeb, Tyler
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Complete streets ,Economic impacts ,Environmental impacts ,Life cycle analysis ,Social factors - Abstract
This white paper provides educational and policy-driven approaches to sustainable transportation workforce development in the transit sector with a focus on knowledge transfer and training strategies for zero-emission bus technologies. The authors draw from a comprehensive survey of national research, interviews with transit leaders, and case studies to identify the most critical technology transfer gaps in the adoption of zero-emission bus technologies. The paper concludes with strategic transit workforce priorities and related recommendations for transit leaders, educational partners, and policy makers.View the NCST Project Webpage
- Published
- 2022
26. Studying Bioluminescence Flashes with the ANTARES Deep Sea Neutrino Telescope
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Reeb, N., Hutschenreuter, S., Zehetner, P., Ensslin, T., Alves, S., André, M., Anghinolfi, M., Anton, G., Ardid, M., Aubert, J. -J., Aublin, J., Baret, B., Basa, S., Belhorma, B., Bendahman, M., Bertin, V., Biagi, S., Bissinger, M., Boumaaza, J., Bouta, M., Bouwhuis, M. C., Brânzaş, H., Bruijn, R., Brunner, J., Busto, J., Caiffi, B., Capone, A., Caramete, L., Carr, J., Carretero, V., Celli, S., Chabab, M., Chau, T. N., Moursli, R. Cherkaoui El, Chiarusi, T., Circella, M., Coleiro, A., Colomer-Molla, M., Coniglione, R., Coyle, P., Creusot, A., Díaz, A. F., de Wasseige, G., Deschamps, A., Distefano, C., Di Palma, I., Domi, A., Donzaud, C., Dornic, D., Drouhin, D., Eberl, T., van Eeden, T., Khayati, N. El, Enzenhöfer, A., Fermani, P., Ferrara, G., Filippini, F., Fusco, L., Gatelet, Y., Gay, P., Glotin, H., Gozzini, R., Ruiz, R. Gracia, Graf, K., Guidi, C., Hallmann, S., van Haren, H., Heijboer, A. J., Hello, Y., Hernández-Rey, J. J., Hößl, J., Hofestädt, J., Huang, F., Illuminati, G., James, C. W., Jisse-Jung, B., Jong, M. d., Jong, P. d., Jongen, M., Kadler, M., Kalekin, O., Katz, U., Khan-Chowdhury, N. R., Kouchner, A., Kreykenbohm, I., Kulikovskiy, V., Lahmann, R., Breton, R. Le, Lefèvre, D., Leonora, E., Levi, G., Lincetto, M., Lopez-Coto, D., Loucatos, S., Maderer, L., Manczak, J., Marcelin, M., Margiotta, A., Marinelli, A., Martínez-Mora, J. A., Melis, K., Migliozzi, P., Moussa, A., Muller, R., Nauta, L., Navas, S., Nezri, E., Fearraigh, B. Ó, Organokov, M., Păvălaş, G. E., Pellegrino, C., Perrin-Terrin, M., Piattelli, P., Pieterse, C., Poirè, C., Popa, V., Pradier, T., Randazzo, N., Reck, S., Riccobene, G., Romanov, A., Sánchez-Losa, A., Greus, F. Salesa, Samtleben, D. F. E., Sanguineti, M., Sapienza, P., Schnabel, J., Schumann, J., Schüssler, F., Spurio, M., Stolarczyk, Th., Taiuti, M., Tayalati, Y., Tingay, S. J., Vallage, B., Van Elewyck, V., Versari, F., Viola, S., Vivolo, D., Wilms, J., Zavatarelli, S., Zegarelli, A., Zornoza, J. D., and Zúñiga, J.
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Physics - Atmospheric and Oceanic Physics ,Astrophysics - Instrumentation and Methods for Astrophysics ,Quantitative Biology - Populations and Evolution - Abstract
We develop a novel technique to exploit the extensive data sets provided by underwater neutrino telescopes to gain information on bioluminescence in the deep sea. The passive nature of the telescopes gives us the unique opportunity to infer information on bioluminescent organisms without actively interfering with them. We propose a statistical method that allows us to reconstruct the light emission of individual organisms, as well as their location and movement. A mathematical model is built to describe the measurement process of underwater neutrino telescopes and the signal generation of the biological organisms. The Metric Gaussian Variational Inference algorithm is used to reconstruct the model parameters using photon counts recorded by the neutrino detectors. We apply this method to synthetic data sets and data collected by the ANTARES neutrino telescope. The telescope is located 40 km off the French coast and fixed to the sea floor at a depth of 2475 m. The runs with synthetic data reveal that we can reliably model the emitted bioluminescent flashes of the organisms. Furthermore, we find that the spatial resolution of the localization of light sources highly depends on the configuration of the telescope. Precise measurements of the efficiencies of the detectors and the attenuation length of the water are crucial to reconstruct the light emission. Finally, the application to ANTARES data reveals the first precise localizations of bioluminescent organisms using neutrino telescope data.
- Published
- 2021
27. Environmental Plans and Freight Movement at the San Pedro Bay Ports: A Quick Strike Analysis
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Matsumoto, Deanna, Mace, Caitlin, Reeb, Tyler, and O'Brien, Thomas
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Air quality management ,Case studies ,Environmental policy ,Freight transportation ,Intermodal transportation ,Ports - Abstract
Critical to freight movement in Southern California are environmental plans at the Port of Los Angeles (POLA) and Port of Long Beach (POLB). The combined port complex is the single largest fixed source of air pollution in the South Coast Air Basin. This white paper presents three case studies from the San Pedro Bay Ports Clean Air Action Plan (CAAP), including brief analyses of their effects on freight movement in the region. This research also includes a case study of a private-sector, yet-to-be-built infrastructure project designed to support the faster movement of freight out of the San Pedro Bay Ports called the Southern California International Gateway (SCIG). The case studies are provided to elucidate how self-regulating agreements and operator-led programs contribute to regional environmental goals for freight operations. The findings indicate in part that stakeholder power relationships influence the ability to both develop environmental strategies and determine their outcomes. They also indicate that port-focused plans are more effective when their impact on the entire supply chain is considered. The research also helps to illustrate examples of unintended consequences of freight-related environmental measures which will prove useful to policymakers and operators alike.View the NCST Project Webpage
- Published
- 2022
28. Which Minimizer Does My Neural Network Converge To?
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Nonnenmacher, Manuel, Reeb, David, and Steinwart, Ingo
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Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
The loss surface of an overparameterized neural network (NN) possesses many global minima of zero training error. We explain how common variants of the standard NN training procedure change the minimizer obtained. First, we make explicit how the size of the initialization of a strongly overparameterized NN affects the minimizer and can deteriorate its final test performance. We propose a strategy to limit this effect. Then, we demonstrate that for adaptive optimization such as AdaGrad, the obtained minimizer generally differs from the gradient descent (GD) minimizer. This adaptive minimizer is changed further by stochastic mini-batch training, even though in the non-adaptive case, GD and stochastic GD result in essentially the same minimizer. Lastly, we explain that these effects remain relevant for less overparameterized NNs. While overparameterization has its benefits, our work highlights that it induces sources of error absent from underparameterized models.
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- 2020
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29. Deep Learning-based Pipeline for Module Power Prediction from EL Measurements
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Hoffmann, Mathis, Buerhop-Lutz, Claudia, Reeb, Luca, Pickel, Tobias, Winkler, Thilo, Doll, Bernd, Würfl, Tobias, Peters, Ian Marius, Brabec, Christoph, Maier, Andreas, and Christlein, Vincent
- Subjects
Computer Science - Computer Vision and Pattern Recognition ,Computer Science - Machine Learning ,Electrical Engineering and Systems Science - Image and Video Processing - Abstract
Automated inspection plays an important role in monitoring large-scale photovoltaic power plants. Commonly, electroluminescense measurements are used to identify various types of defects on solar modules but have not been used to determine the power of a module. However, knowledge of the power at maximum power point is important as well, since drops in the power of a single module can affect the performance of an entire string. By now, this is commonly determined by measurements that require to discontact or even dismount the module, rendering a regular inspection of individual modules infeasible. In this work, we bridge the gap between electroluminescense measurements and the power determination of a module. We compile a large dataset of 719 electroluminescense measurementsof modules at various stages of degradation, especially cell cracks and fractures, and the corresponding power at maximum power point. Here,we focus on inactive regions and cracks as the predominant type of defect. We set up a baseline regression model to predict the power from electroluminescense measurements with a mean absolute error of 9.0+/-3.7$W_P$ (4.0+/-8.4%). Then, we show that deep-learning can be used to train a model that performs significantly better (7.3+/-2.7$W_P$ or 3.2+/-6.5%) and propose a variant of class activation maps to obtain the per cell power loss, as predicted by the model. With this work, we aim to open a new research topic. Therefore, we publicly release the dataset, the code and trained models to empower other researchers to compare against our results. Finally, we present a thorough evaluation of certain boundary conditions like the dataset size and an automated preprocessing pipeline for on-site measurements showing multiple modules at once.
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- 2020
30. Beyond the Mean-Field: Structured Deep Gaussian Processes Improve the Predictive Uncertainties
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Lindinger, Jakob, Reeb, David, Lippert, Christoph, and Rakitsch, Barbara
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Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
Deep Gaussian Processes learn probabilistic data representations for supervised learning by cascading multiple Gaussian Processes. While this model family promises flexible predictive distributions, exact inference is not tractable. Approximate inference techniques trade off the ability to closely resemble the posterior distribution against speed of convergence and computational efficiency. We propose a novel Gaussian variational family that allows for retaining covariances between latent processes while achieving fast convergence by marginalising out all global latent variables. After providing a proof of how this marginalisation can be done for general covariances, we restrict them to the ones we empirically found to be most important in order to also achieve computational efficiency. We provide an efficient implementation of our new approach and apply it to several benchmark datasets. It yields excellent results and strikes a better balance between accuracy and calibrated uncertainty estimates than its state-of-the-art alternatives., Comment: 12 pages main text, 20 pages appendix. v2: changes due to NeurIPS review process. Camera-ready version to be published at NeurIPS 2020
- Published
- 2020
31. Validation of composite systems by discrepancy propagation.
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David Reeb, Kanil Patel, Karim Said Barsim, Martin Schiegg, and Sebastian Gerwinn
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- 2023
32. Service Learning : An Innovative Pedagogy for the Psychology Curriculum
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Bringle, Robert G., Reeb, Roger N., Naudé, Luzelle, Ruiz, Ana I., Ong, Faith, Zumbach, Joerg, Section editor, Narciss, Susanne, Section editor, Bernstein, Douglas A., Section editor, Marsico, Giuseppina, Section editor, Zumbach, Joerg, editor, Bernstein, Douglas A., editor, Narciss, Susanne, editor, and Marsico, Giuseppina, editor
- Published
- 2023
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33. Tighter Confidence Bounds for Sequential Kernel Regression.
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Hamish Flynn and David Reeb
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- 2024
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34. Cellular states are coupled to genomic and viral heterogeneity in HPV-related oropharyngeal carcinoma
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Puram, Sidharth V., Mints, Michael, Pal, Ananya, Qi, Zongtai, Reeb, Ashley, Gelev, Kyla, Barrett, Thomas F., Gerndt, Sophie, Liu, Ping, Parikh, Anuraag S., Ramadan, Salma, Law, Travis, Mroz, Edmund A., Rocco, James W., Adkins, Doug, Thorstad, Wade L., Gay, Hiram A., Ding, Li, Paniello, Randal C., Pipkorn, Patrik, Jackson, Ryan S., Wang, Xiaowei, Mazul, Angela, Chernock, Rebecca, Zevallos, Jose P., Silva-Fisher, Jessica, and Tirosh, Itay
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- 2023
- Full Text
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35. Primary Care Support Tools for Digestive Health Care: A Mixed Method Study
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Mubashir Arain, Leanne Reeb, Rebecca C. Miyagishima, Julia Carter, and Kerri L. Novak
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Diseases of the digestive system. Gastroenterology ,RC799-869 - Abstract
Background. To address the increasing demands for gastroenterology specialty care and increasing wait times, centralized access and triage (CAT) systems, telephone support, and clinical care pathways were implemented to streamline referrals and support management of low-risk gastrointestinal (GI) conditions in the primary care medical home. This study aimed to understand primary care providers (PCPs) and GI specialists’ perceptions of these supports, factors that affect support implementation and identify barriers and facilitators for implementing supports from both PCP and GI specialists’ perspectives. Methods. We conducted a mixed method study including surveys and interviews with PCPs and GI specialists. Online surveys and semistructured qualitative interviews were conducted from July 2022 to September 2022. All interviews were transcribed and coded to perform a thematic analysis. Survey data were analyzed in SPSS version 25. Descriptive statistics were employed to summarize and describe the data collected. Inferential statistics were used to identify associations and relationships within the dataset. T-test and chi-square tests were applied at 95% confidence level, with a p value
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- 2024
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36. Controlling the properties of metakaolin-based geopolymer/liquid organic waste emulsions: A rheological approach
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Hasnaoui, Abdelaziz, Reeb, Charles, De Campos, Matthieu, Davy, Catherine A., and Lambertin, David
- Published
- 2023
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37. A refinement of Reznick's Positivstellensatz with applications to quantum information theory
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Müller-Hermes, Alexander, Nechita, Ion, and Reeb, David
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Quantum Physics ,Mathematical Physics - Abstract
In his solution of Hilbert's 17th problem Artin showed that any positive definite polynomial in several variables can be written as the quotient of two sums of squares. Later Reznick showed that the denominator in Artin's result can always be chosen as an $N$-th power of the squared norm of the variables and gave explicit bounds on $N$. By using concepts from quantum information theory (such as partial traces, optimal cloning maps, and an identity due to Chiribella) we give simpler proofs and minor improvements of both real and complex versions of this result. Moreover, we discuss constructions of Hilbert identities using Gaussian integrals and we review an elementary method to construct complex spherical designs. Finally, we apply our results to give improved bounds for exponential quantum de Finetti theorems in the real and in the complex setting.
- Published
- 2019
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38. A Maturity Model for Intraorganizational Online Collaboration.
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Samuel Reeb
- Published
- 2023
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39. Machine learning reveals genetic modifiers of the immune microenvironment of cancer
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Riley-Gillis, Bridget, Tsaih, Shirng-Wern, King, Emily, Wollenhaupt, Sabrina, Reeb, Jonas, Peck, Amy R., Wackman, Kelsey, Lemke, Angela, Rui, Hallgeir, Dezso, Zoltan, and Flister, Michael J.
- Published
- 2023
- Full Text
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40. Micro embossing of graphite-based anodes for lithium-ion batteries to improve cell performance
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Sandherr, Jens, Kleefoot, Max-Jonathan, Nester, Sara, Weisenberger, Christian, DeSilva, Anjali K.M., Michel, Dominik, Reeb, Sarah, Fingerle, Mathias, Riegel, Harald, and Knoblauch, Volker
- Published
- 2023
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41. Incorporation of environmental covariates to nonlinear mixed models describing fruit growth
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D. Del Brio, V. Tassile, S.J. Bramardi, and P.D. Reeb
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peras ,curvas de crecimiento ,pronóstico de producción ,efectos aleatorios ,Agriculture ,Agriculture (General) ,S1-972 - Abstract
El pronóstico de cosecha es un gran desafío en la producción de peras. Estimar el tamaño de los frutos a partir de curvas de crecimiento permite predecir tanto la cantidad como la calidad de la fruta para cosecha. Este trabajo tuvo como objetivo ajustar modelos mixtos no lineales multiniveles (MMNL) basados en la curva logística para describir el crecimiento de peras “William´s” en el Alto Valle de Río Negro y Neuquén, Argentina. Los modelos ajustados incorporaron diferentes índices termoacumulativos que contemplan los efectos de la temperatura en la fisiología del crecimiento de los frutos. De esta manera, se logra no solo describir el crecimiento de los frutos, sino también se pueden observar las variaciones ambientales a lo largo de las temporadas de crecimiento. El estudio se realizó en perales “William´s” durante 16 temporadas. Se seleccionaron e identificaron al azar numerosos árboles y frutos. A cada fruto se le midió su diámetro ecuatorial semanalmente con un calibre digital electrónico. Los datos climáticos se obtuvieron de la estación meteorológica del INTA Alto Valle y los índices termoacumulativos se calcularon a partir de los datos de temperaturas. Los mejores modelos fueron seleccionados según los criterios de información. El MMNL multinivel permitió discernir y cuantificar las fuentes de variabilidad estocástica en diferentes niveles, lo que permitió obtener mejores criterios de información en comparación con los modelos que solo consideraron un único nivel de variabilidad entre los efectos aleatorios. La incorporación de índices termoacumulativos mejoró notablemente la performance de los modelos obtenidos.
- Published
- 2023
- Full Text
- View/download PDF
42. Trapping performance of alkali-activated materials incorporating a hydrogen/tritium getter for the conditioning of tritiated organic liquids
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Reeb, Charles, Davy, Catherine, Pierlot, Christel, and Lambertin, David
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- 2023
- Full Text
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43. ESSA, Low-Wage Migrants, and the Persistent Neoliberal Education Structure: A Critical Review
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Reeb-Reascos, Kathleen K. and Serniuk, Jennifer
- Abstract
Through discriminatory policies and neoliberal practices, public institutions have historically marginalized low-wage migrants on the basis of race, ethnicity, class, and English-language ability. Under the Trump administration and Republican-led Congress, anti-immigrant practices and rhetoric have intensified. This paper explores the impact of current educational policies as they exist in a structure dominated by anti-immigrant ideology. In a critical review of scholarly literature, this paper examines the Every Student Succeeds Act (ESSA) in the context of past legislation and the position of these groups within the structure of U.S. education. Our investigation acknowledges that the ESSA attempts to improve educational opportunities for low-wage migrants, but the policy's shift toward state and local control creates uncertainty for these students. Specifically, we conclude that policy implementation for migrant populations will remain ineffective without fundamental changes to the climate and organization of state and local systems.
- Published
- 2018
44. Apple (Malus domestica) and pear (Pyrus communis) yield prediction after tree image analysis
- Author
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Dolores del Brio, Valentin Tassile, Sergio Jorge Bramardi, Darío Eduardo Fernández, and Pablo Daniel Reeb
- Subjects
fruit detection ,artificial vision ,yield forecast ,Malus domestica ,Pyrus communis ,Agriculture ,Food processing and manufacture ,TP368-456 - Abstract
Yield forecasting depends on accurate tree fruit counts and mean size estimation. This information is generally obtained manually, requiring many hours of work. Artificial vision emerges as an interesting alternative to obtaining more information in less time. This study aimed to test and train YOLO pre-trained models based on neural networks for the detection and count of pears and apples on trees after image analysis; while also estimating fruit size. Images of trees were taken during the day and at night in apple and pear trees while fruits were manually counted. Trained models were evaluated according to recall, precision and F1score. The correlation between detected and counted fruits was calculated while fruit size estimation was made after drawing straight lines on each fruit and using reference elements. The precision, recall and F1score achieved by the models were up to 0.86, 0.83 and 0.84, respectively. Correlation coefficients between fruit sizes measured manually and by images were 0.73 for apples and 0.80 for pears. The proposed methodologies showed promising results, allowing forecasters to make less time consuming and accurate estimates compared to manual measurements. Highlights: • The number of fruits in apple and pear trees, could be estimated from images with promising results. • The possibility of estimating the fruit numbers from images could reduce the time spent on this task, and above all, the costs. This allow growers to increase the number of trees sampled to make yield forecasts.
- Published
- 2023
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- View/download PDF
45. Parallel evolution of linezolid-resistant Staphylococcus aureus in patients with cystic fibrosis
- Author
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Nicholas J. Pitcher, Andries Feder, Nicholas Bolden, Christian F. Zirbes, Anthony J. Pamatmat, Linda Boyken, Jared J. Hill, Alyssa R. Bartels, Andrew L. Thurman, Valerie C. Reeb, Harry S. Porterfield, Ahmed M. Moustafa, Paul J. Planet, and Anthony J. Fischer
- Subjects
Staphylococcus aureus ,linezolid ,MRSA ,ribosomal RNA ,hypermutation ,Microbiology ,QR1-502 - Abstract
ABSTRACT Linezolid is an antibiotic used to treat serious Staphylococcus aureus infections. Resistance to linezolid is considered rare but could emerge with repeated dosing. We recently reported widespread prescription of linezolid for a cohort of patients with cystic fibrosis (CF). The goals of this study were to determine the incidence of linezolid-resistant methicillin-resistant Staphylococcus aureus (MRSA) in CF and identify molecular mechanisms for linezolid resistance. We identified patients who cultured S. aureus resistant to linezolid with minimum inhibitory concentration (MIC) >4 at the University of Iowa CF Center between 2008 and 2018. We obtained isolates from these patients and retested susceptibility to linezolid using broth microdilution. We used whole genome sequencing to perform phylogenetic analysis of linezolid-resistant isolates and examine sequences for mutations or accessory genes that confer linezolid resistance. Between 2008 and 2018, 111 patients received linezolid, and 4 of these patients cultured linezolid-resistant S. aureus. We sequenced 11 resistant and 21 susceptible isolates from these 4 subjects. Phylogenetic analysis indicated that linezolid resistance developed in ST5 or ST105 backgrounds. Three individuals had linezolid-resistant S. aureus with a G2576T mutation in 23S rRNA. One of these subjects additionally had a mutS− mutL− hypermutating S. aureus that produced five resistant isolates with multiple ribosomal subunit mutations. In one subject, the genetic basis for linezolid resistance was unclear. We conclude that linezolid resistant S. aureus can occur through multiple genetic mechanisms in patients with repeated exposure to this antibiotic. IMPORTANCE Patients with cystic fibrosis have persistent lung infections with Staphylococcus aureus that require extensive antibiotic treatments. Linezolid, an antibiotic given by oral or intravenous route, is prescribed repeatedly for patients whose lung disease has progressed. After treatment with linezolid, S. aureus strains can evolve antibiotic resistance through multiple genetic mechanisms. In addition to a common mutation in the 23S ribosomal RNA known to confer linezolid resistance, S. aureus strains can evolve novel resistance based on a combination of mutations affecting the bacterial ribosome. This combination of mutations was observed in a strain that exhibited hypermutation owing to the loss of the DNA repair genes mutS and mutL. In this cohort of patients with cystic fibrosis, linezolid resistance was transient, possibly due to the growth disadvantage of resistant strains. However, ongoing chronic exposure to linezolid may create optimal conditions for the future emergence of resistance to this critical antibiotic.
- Published
- 2023
- Full Text
- View/download PDF
46. Utilizing Expert Features for Contrastive Learning of Time-Series Representations.
- Author
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Manuel T. Nonnenmacher, Lukas Oldenburg, Ingo Steinwart, and David Reeb
- Published
- 2022
47. Learning Gaussian Processes by Minimizing PAC-Bayesian Generalization Bounds
- Author
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Reeb, David, Doerr, Andreas, Gerwinn, Sebastian, and Rakitsch, Barbara
- Subjects
Statistics - Machine Learning ,Computer Science - Machine Learning - Abstract
Gaussian Processes (GPs) are a generic modelling tool for supervised learning. While they have been successfully applied on large datasets, their use in safety-critical applications is hindered by the lack of good performance guarantees. To this end, we propose a method to learn GPs and their sparse approximations by directly optimizing a PAC-Bayesian bound on their generalization performance, instead of maximizing the marginal likelihood. Besides its theoretical appeal, we find in our evaluation that our learning method is robust and yields significantly better generalization guarantees than other common GP approaches on several regression benchmark datasets., Comment: 11 pages main text, 12 pages appendix. v2: minor changes, new NeurIPS style file. Final camera-ready version submitted to NeurIPS 2018
- Published
- 2018
48. Improved Algorithms for Stochastic Linear Bandits Using Tail Bounds for Martingale Mixtures.
- Author
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Hamish Flynn, David Reeb, Melih Kandemir, and Jan R. Peters
- Published
- 2023
49. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
- Author
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Zhou, Naihui, Jiang, Yuxiang, Bergquist, Timothy R, Lee, Alexandra J, Kacsoh, Balint Z, Crocker, Alex W, Lewis, Kimberley A, Georghiou, George, Nguyen, Huy N, Hamid, Md Nafiz, Davis, Larry, Dogan, Tunca, Atalay, Volkan, Rifaioglu, Ahmet S, Dalkıran, Alperen, Cetin Atalay, Rengul, Zhang, Chengxin, Hurto, Rebecca L, Freddolino, Peter L, Zhang, Yang, Bhat, Prajwal, Supek, Fran, Fernández, José M, Gemovic, Branislava, Perovic, Vladimir R, Davidović, Radoslav S, Sumonja, Neven, Veljkovic, Nevena, Asgari, Ehsaneddin, Mofrad, Mohammad RK, Profiti, Giuseppe, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita, Boecker, Florian, Schoof, Heiko, Kahanda, Indika, Thurlby, Natalie, McHardy, Alice C, Renaux, Alexandre, Saidi, Rabie, Gough, Julian, Freitas, Alex A, Antczak, Magdalena, Fabris, Fabio, Wass, Mark N, Hou, Jie, Cheng, Jianlin, Wang, Zheng, Romero, Alfonso E, Paccanaro, Alberto, Yang, Haixuan, Goldberg, Tatyana, Zhao, Chenguang, Holm, Liisa, Törönen, Petri, Medlar, Alan J, Zosa, Elaine, Borukhov, Itamar, Novikov, Ilya, Wilkins, Angela, Lichtarge, Olivier, Chi, Po-Han, Tseng, Wei-Cheng, Linial, Michal, Rose, Peter W, Dessimoz, Christophe, Vidulin, Vedrana, Dzeroski, Saso, Sillitoe, Ian, Das, Sayoni, Lees, Jonathan Gill, Jones, David T, Wan, Cen, Cozzetto, Domenico, Fa, Rui, Torres, Mateo, Warwick Vesztrocy, Alex, Rodriguez, Jose Manuel, Tress, Michael L, Frasca, Marco, Notaro, Marco, Grossi, Giuliano, Petrini, Alessandro, Re, Matteo, Valentini, Giorgio, Mesiti, Marco, Roche, Daniel B, Reeb, Jonas, Ritchie, David W, Aridhi, Sabeur, Alborzi, Seyed Ziaeddin, Devignes, Marie-Dominique, Koo, Da Chen Emily, Bonneau, Richard, Gligorijević, Vladimir, Barot, Meet, Fang, Hai, Toppo, Stefano, and Lavezzo, Enrico
- Subjects
Human Genome ,Networking and Information Technology R&D (NITRD) ,Genetics ,Generic health relevance ,Animals ,Biofilms ,Candida albicans ,Drosophila melanogaster ,Genome ,Bacterial ,Genome ,Fungal ,Humans ,Locomotion ,Memory ,Long-Term ,Molecular Sequence Annotation ,Pseudomonas aeruginosa ,Protein function prediction ,Long-term memory ,Biofilm ,Critical assessment ,Community challenge ,Environmental Sciences ,Biological Sciences ,Information and Computing Sciences ,Bioinformatics - Abstract
BackgroundThe Critical Assessment of Functional Annotation (CAFA) is an ongoing, global, community-driven effort to evaluate and improve the computational annotation of protein function.ResultsHere, we report on the results of the third CAFA challenge, CAFA3, that featured an expanded analysis over the previous CAFA rounds, both in terms of volume of data analyzed and the types of analysis performed. In a novel and major new development, computational predictions and assessment goals drove some of the experimental assays, resulting in new functional annotations for more than 1000 genes. Specifically, we performed experimental whole-genome mutation screening in Candida albicans and Pseudomonas aureginosa genomes, which provided us with genome-wide experimental data for genes associated with biofilm formation and motility. We further performed targeted assays on selected genes in Drosophila melanogaster, which we suspected of being involved in long-term memory.ConclusionWe conclude that while predictions of the molecular function and biological process annotations have slightly improved over time, those of the cellular component have not. Term-centric prediction of experimental annotations remains equally challenging; although the performance of the top methods is significantly better than the expectations set by baseline methods in C. albicans and D. melanogaster, it leaves considerable room and need for improvement. Finally, we report that the CAFA community now involves a broad range of participants with expertise in bioinformatics, biological experimentation, biocuration, and bio-ontologies, working together to improve functional annotation, computational function prediction, and our ability to manage big data in the era of large experimental screens.
- Published
- 2019
50. Does Intention Matter? Relations between Parent Pointing, Infant Pointing, and Developing Language Ability
- Author
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Salo, Virginia C, Reeb-Sutherland, Bethany, Frenkel, Tahl I, Bowman, Lindsay C, and Rowe, Meredith L
- Subjects
Clinical Research ,Pediatric ,Psychology ,Cognitive Sciences ,Developmental & Child Psychology - Abstract
Infants' pointing is associated with concurrent and later language development. The communicative intention behind the point-i.e., imperative versus declarative-can affect both the nature and strength of these associations, and is therefore a critical factor to consider. Parents' pointing is associated with both infant pointing and infant language; however, less work has examined the intent behind parents' points. We explore relations between parents' and infants' pointing at the level of communicative intention, and examine how pointing relates to concurrent and longitudinal infant language skills. In a sample of 52 mother-infant dyads, we measured mother and infant pointing at infant age 12-months, and infant expressive and receptive language at 12-, 18-, and 24-months. We found that mothers produced points with a variety of intentions, however we did not find relations between mother and infant pointing within the different communicative intentions. Replicating previous research, infant declarative pointing was related both concurrently and longitudinally to their language ability. Mothers' declarative pointing was related to their infants' concurrent language, while their imperative pointing was not. Further, there was an interaction between parent and infant declarative pointing, such that the positive relation between parents' declarative pointing and their infants' concurrent receptive language was present only for those infants who were also producing declarative points themselves. Findings suggest that parents' declarative pointing may support both their infants' early word learning and, perhaps, provides a model for their infant to begin using points as well. This study constitutes an important initial exploration of these relations.
- Published
- 2019
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