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1. Accelerating Progress Towards the 2030 Neglected Tropical Diseases Targets: How Can Quantitative Modeling Support Programmatic Decisions?

Author

Borlase, Anna, Brady, Oliver, Browning, Raiha, Chitnis, Nakul, Coffeng, Luc, Crowley, Emily, Cucunubá, Zulma, Cummings, Derek, Davis, Christopher, Davis, Emma, Dixon, Matthew, Dobson, Andrew, Dyson, Louise, French, Michael, Fronterre, Claudio, Giorgi, Emanuele, Huang, Ching-I, Jain, Saurabh, James, Ananthu, Kim, Sung, Kura, Klodeta, Lucianez, Ana, Marks, Michael, Mbabazi, Pamela, Medley, Graham, Michael, Edwin, Montresor, Antonio, Mutono, Nyamai, Mwangi, Thumbi, Rock, Kat, Saboyá-Díaz, Martha-Idalí, Sasanami, Misaki, Schwehm, Markus, Spencer, Simon, Srivathsan, Ariktha, Stawski, Robert, Stolk, Wilma, Sutherland, Samuel, Tchuenté, Louis-Albert, de Vlas, Sake, Walker, Martin, Brooker, Simon, Hollingsworth, T, Solomon, Anthony, Fall, Ibrahima, Vasconcelos, Andreia, King, Jonathan, Nunes-Alves, Cláudio, Anderson, Roy, Argaw, Daniel, Basáñez, Maria-Gloria, Bilal, Shakir, Blok, David, and Blumberg, Seth

Subjects
control, elimination, mathematical models, neglected tropical diseases, policy-making, Neglected Diseases, Humans, Tropical Medicine, COVID-19, Models, Theoretical, World Health Organization, SARS-CoV-2, Decision Making, Global Health
Abstract

Over the past decade, considerable progress has been made in the control, elimination, and eradication of neglected tropical diseases (NTDs). Despite these advances, most NTD programs have recently experienced important setbacks; for example, NTD interventions were some of the most frequently and severely impacted by service disruptions due to the coronavirus disease 2019 (COVID-19) pandemic. Mathematical modeling can help inform selection of interventions to meet the targets set out in the NTD road map 2021-2030, and such studies should prioritize questions that are relevant for decision-makers, especially those designing, implementing, and evaluating national and subnational programs. In September 2022, the World Health Organization hosted a stakeholder meeting to identify such priority modeling questions across a range of NTDs and to consider how modeling could inform local decision making. Here, we summarize the outputs of the meeting, highlight common themes in the questions being asked, and discuss how quantitative modeling can support programmatic decisions that may accelerate progress towards the 2030 targets.

Published
2024

4. Manipulating Deformable Objects by Interleaving Prediction, Planning, and Control

Author

McConachie, Dale, Dobson, Andrew, Ruan, Mengyao, and Berenson, Dmitry

Subjects
Computer Science - Robotics
Abstract

We present a framework for deformable object manipulation that interleaves planning and control, enabling complex manipulation tasks without relying on high-fidelity modeling or simulation. The key question we address is when should we use planning and when should we use control to achieve the task? Planners are designed to find paths through complex configuration spaces, but for highly underactuated systems, such as deformable objects, achieving a specific configuration is very difficult even with high-fidelity models. Conversely, controllers can be designed to achieve specific configurations, but they can be trapped in undesirable local minima due to obstacles. Our approach consists of three components: (1) A global motion planner to generate gross motion of the deformable object; (2) A local controller for refinement of the configuration of the deformable object; and (3) A novel deadlock prediction algorithm to determine when to use planning versus control. By separating planning from control we are able to use different representations of the deformable object, reducing overall complexity and enabling efficient computation of motion. We provide a detailed proof of probabilistic completeness for our planner, which is valid despite the fact that our system is underactuated and we do not have a steering function. We then demonstrate that our framework is able to successfully perform several manipulation tasks with rope and cloth in simulation which cannot be performed using either our controller or planner alone. These experiments suggest that our planner can generate paths efficiently, taking under a second on average to find a feasible path in three out of four scenarios. We also show that our framework is effective on a 16 DoF physical robot, where reachability and dual-arm constraints make the planning more difficult., Comment: Accepted to The International Journal of Robotics Research

Published
2020
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6. dRRT*: Scalable and Informed Asymptotically-Optimal Multi-Robot Motion Planning

Author

Shome, Rahul, Solovey, Kiril, Dobson, Andrew, Halperin, Dan, and Bekris, Kostas E.

Subjects
Computer Science - Robotics
Abstract

Many exciting robotic applications require multiple robots with many degrees of freedom, such as manipulators, to coordinate their motion in a shared workspace. Discovering high-quality paths in such scenarios can be achieved, in principle, by exploring the composite space of all robots. Sampling-based planners do so by building a roadmap or a tree data structure in the corresponding configuration space and can achieve asymptotic optimality. The hardness of motion planning, however, renders the explicit construction of such structures in the composite space of multiple robots impractical. This work proposes a scalable solution for such coupled multi-robot problems, which provides desirable path-quality guarantees and is also computationally efficient. In particular, the proposed \drrtstar\ is an informed, asymptotically-optimal extension of a prior sampling-based multi-robot motion planner, \drrt. The prior approach introduced the idea of building roadmaps for each robot and implicitly searching the tensor product of these structures in the composite space. This work identifies the conditions for convergence to optimal paths in multi-robot problems, which the prior method was not achieving. Building on this analysis, \drrt\ is first properly adapted so as to achieve the theoretical guarantees and then further extended so as to make use of effective heuristics when searching the composite space of all robots. The case where the various robots share some degrees of freedom is also studied. Evaluation in simulation indicates that the new algorithm, \drrtstar\, converges to high-quality paths quickly and scales to a higher number of robots where various alternatives fail. This work also demonstrates the planner's capability to solve problems involving multiple real-world robotic arms.

Published
2019
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7. Association of Environmental Factors with Seasonal Intensity of Erysipelothrix rhusiopathiae Seropositivity among Arctic Caribou

Author

Aleuy, O. Alejandro, Anholt, Michele, Orsel, Karin, Mavrot, Fabien, Gagnon, Catherine A., Beckmen, Kimberlee, Cote, Steeve D., Cuyler, Christine, Dobson, Andrew, Elkin, Brett, Leclerc, Lisa-Marie, Taillon, Joelle, and Kutz, Susan

Subjects
Reindeer -- Diseases -- Environmental aspects, Caribou -- Diseases -- Environmental aspects, Mycoplasmatales -- Identification and classification -- Environmental aspects, Emerging communicable diseases -- Risk factors -- Environmental aspects, Health
Abstract

A 2021 report of the Intergovernmental Panel on Climate Change (1) reinforced that anthropogenic influences on climate systems are causing increases in temperature and extremes of weather and climate events [...]

Published
2022
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10. Evidence gaps and diversity among potential win–win solutions for conservation and human infectious disease control

Author

Hopkins, Skylar R, Lafferty, Kevin D, Wood, Chelsea L, Olson, Sarah H, Buck, Julia C, De Leo, Giulio A, Fiorella, Kathryn J, Fornberg, Johanna L, Garchitorena, Andres, Jones, Isabel J, Kuris, Armand M, Kwong, Laura H, LeBoa, Christopher, Leon, Ariel E, Lund, Andrea J, MacDonald, Andrew J, Metz, Daniel C G, Nova, Nicole, Peel, Alison J, Remais, Justin V, Stewart Merrill, Tara E, Wilson, Maya, Bonds, Matthew H, Dobson, Andrew P, Lopez Carr, David, Howard, Meghan E, Mandle, Lisa, and Sokolow, Susanne H

Published
2022
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12. Scalable Asymptotically-Optimal Multi-Robot Motion Planning

Author

Dobson, Andrew, Solovey, Kiril, Shome, Rahul, Halperin, Dan, and Bekris, Kostas E.

Subjects
Computer Science - Multiagent Systems, Computer Science - Robotics
Abstract

Finding asymptotically-optimal paths in multi-robot motion planning problems could be achieved, in principle, using sampling-based planners in the composite configuration space of all of the robots in the space. The dimensionality of this space increases with the number of robots, rendering this approach impractical. This work focuses on a scalable sampling-based planner for coupled multi-robot problems that provides asymptotic optimality. It extends the dRRT approach, which proposed building roadmaps for each robot and searching an implicit roadmap in the composite configuration space. This work presents a new method, dRRT* , and develops theory for scalable convergence to optimal paths in multi-robot problems. Simulated experiments indicate dRRT* converges to high-quality paths while scaling to higher numbers of robots where the naive approach fails. Furthermore, dRRT* is applicable to high-dimensional problems, such as planning for robot manipulators, Comment: 8 pages, 12 figures, submitted to the first International Symposium on Multi-Robot and Multi-Agent Systems (MRS)

Published
2017

13. A solution scan of societal options to reduce transmission and spread of respiratory viruses: SARS-CoV-2 as a case study

Author

Sutherland, William J., Taylor, Nigel G., Aldridge, David C., Martin, Philip, Rhodes, Catherine, Shackelford, Gorm, Beard, Simon, Belfield, Haydn, Bladon, Andrew J., Brick, Cameron, Christie, Alec P., Dobson, Andrew P., Downey, Harriet, Hood, Amelia S.C., Hua, Fangyuan, Hughes, Alice C., Jarvis, Rebecca M., MacFarlane, Douglas, Morgan, William H., Mupepele, Anne-Christine, Marciniak, Stefan J., Nelson, Cassidy, Ó hÉigeartaigh, Seán, Rios Rojas, Clarissa, Sainsbury, Katherine A., Smith, Rebecca K., Sundaram, Lalitha S., Thornton, Ann, Watkins, John, White, Thomas B., Willott, Kate, and Petrovan, Silviu O.

Published
2021
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16. Lyme disease ecology in a changing world: consensus, uncertainty and critical gaps for improving control

Author

Kilpatrick, A Marm, Dobson, Andrew DM, Levi, Taal, Salkeld, Daniel J, Swei, Andrea, Ginsberg, Howard S, Kjemtrup, Anne, Padgett, Kerry A, Jensen, Per M, Fish, Durland, Ogden, Nick H, and Diuk-Wasser, Maria A

Subjects
Vector-Borne Diseases, Infectious Diseases, Prevention, Lyme Disease, Emerging Infectious Diseases, Infection, Good Health and Well Being, Animals, Borrelia burgdorferi, Communicable Disease Control, Humans, Incidence, Ixodes, Risk, epidemiology, emerging infectious disease, dilution effect, Biological Sciences, Medical and Health Sciences, Evolutionary Biology
Abstract

Lyme disease is the most common tick-borne disease in temperate regions of North America, Europe and Asia, and the number of reported cases has increased in many regions as landscapes have been altered. Although there has been extensive work on the ecology and epidemiology of this disease in both Europe and North America, substantial uncertainty exists about fundamental aspects that determine spatial and temporal variation in both disease risk and human incidence, which hamper effective and efficient prevention and control. Here we describe areas of consensus that can be built on, identify areas of uncertainty and outline research needed to fill these gaps to facilitate predictive models of disease risk and the development of novel disease control strategies. Key areas of uncertainty include: (i) the precise influence of deer abundance on tick abundance, (ii) how tick populations are regulated, (iii) assembly of host communities and tick-feeding patterns across different habitats, (iv) reservoir competence of host species, and (v) pathogenicity for humans of different genotypes of Borrelia burgdorferi Filling these knowledge gaps will improve Lyme disease prevention and control and provide general insights into the drivers and dynamics of this emblematic multi-host-vector-borne zoonotic disease.This article is part of the themed issue 'Conservation, biodiversity and infectious disease: scientific evidence and policy implications'.

Published
2017

17. Transformational Principles for NEON Sampling of Mammalian Parasites and Pathogens: A Response to Springer and Colleagues

Author

Cook, Joseph A, Greiman, Stephen E, Agosta, Salvatore J, Anderson, Robert P, Arbogast, Brian S, Baker, Robert J, Boeger, Walter, Bradley, Robert D, Brooks, Daniel R, Cole, Rebecca, Demboski, John R, Dobson, Andrew P, Dunnum, Jonathan L, Eckerlin, Ralph P, Esselstyn, Jacob, Galbreath, Kurt E, Hawdon, John, Hoekstra, Hopi E, Kutz, Susan J, Light, Jessica E, Olson, Link E, Patterson, Bruce D, Patton, James L, Phillips, Anna J, Rickart, Eric, Rogers, Duke S, Siddall, Mark E, Tkach, Vasyl V, and Hoberg, Eric P

Subjects
Environmental Sciences, Biological Sciences, Ecology
Published
2016

18. Similar Part Rearrangement With Pebble Graphs

Author

Krontiris, Athanasios, Shome, Rahul, Dobson, Andrew, Kimmel, Andrew, Yochelson, Issac, and Bekris, Kostas

Subjects
Computer Science - Robotics
Abstract

This work proposes a method for effectively computing manipulation paths to rearrange similar objects in a cluttered space. The solution can be used to place similar products in a factory floor in a desirable arrangement or for retrieving a particular object from a shelf blocked by similarly sized objects. These are challenging problems as they involve combinatorially large, continuous configuration spaces due to the presence of multiple moving bodies and kinematically complex manipulators. This work leverages ideas from algorithmic theory, multi-robot motion planning and manipulation planning to propose appropriate graphical representations for this challenge. These representations allow to quickly reason whether manipulation paths allow the transition between entire sets of objects arrangements without having to explicitly enumerate the path for each pair of arrangements. The proposed method also allows to take advantage of precomputation given a manipulation roadmap for transferring a single object in the same cluttered space. The resulting approach is evaluated in simulation for a realistic model of a Baxter robot and executed in open-loop on the real system, showing that the approach solves complex instances and is promising in terms of scalability and success ratio., Comment: 11 pages

Published
2014

19. Sampling-based Roadmap Planners are Probably Near-Optimal after Finite Computation

Author

Dobson, Andrew, Moustakides, George V., and Bekris, Kostas E.

Subjects
Computer Science - Robotics
Abstract

Sampling-based motion planners have proven to be efficient solutions to a variety of high-dimensional, geometrically complex motion planning problems with applications in several domains. The traditional view of these approaches is that they solve challenges efficiently by giving up formal guarantees and instead attain asymptotic properties in terms of completeness and optimality. Recent work has argued based on Monte Carlo experiments that these approaches also exhibit desirable probabilistic properties in terms of completeness and optimality after finite computation. The current paper formalizes these guarantees. It proves a formal bound on the probability that solutions returned by asymptotically optimal roadmap-based methods (e.g., PRM*) are within a bound of the optimal path length I* with clearance {\epsilon} after a finite iteration n. This bound has the form P(|In - I* | {\leq} {\delta}I*) {\leq} Psuccess, where {\delta} is an error term for the length a path in the PRM* graph, In. This bound is proven for general dimension Euclidean spaces and evaluated in simulation. A discussion on how this bound can be used in practice, as well as bounds for sparse roadmaps are also provided., Comment: 17 pages, 5 figures, 3 tables. Submitted to the Eleventh International Workshop on the Algorithmic Foundations of Robotics (WAFR 2014)

Published
2014

20. Transmission ecology of canine parvovirus in a multi-host, multi-pathogen system

Author

Behdenna, Abdelkader, Lembo, Tiziana, Calatayud, Olga, Cleaveland, Sarah, Halliday, Jo E. B., Packer, Craig, Lankester, Felix, Hampson, Katie, Craft, Meggan E., Czupryna, Anna, Dobson, Andrew P., Dubovi, Edward J., Ernest, Eblate, Fyumagwa, Robert, Hopcraft, J. Grant C., Mentzel, Christine, Mzimbiri, Imam, Sutton, David, Willett, Brian, Haydon, Daniel T., and Viana, Mafalda

Published
2019

22. Eight challenges in modelling disease ecology in multi-host, multi-agent systems

Author

Buhnerkempe, Michael G, Roberts, Mick G, Dobson, Andrew P, Heesterbeek, Hans, Hudson, Peter J, and Lloyd-Smith, James O

Subjects
Aetiology, 2.1 Biological and endogenous factors, Infection, Good Health and Well Being, Communicable Diseases, Ecology, Food Chain, Host-Pathogen Interactions, Humans, Life Cycle Stages, Models, Statistical, Population Dynamics, Multiple hosts, Multiple pathogens, Community ecology, Maintenance, Food webs, Clinical Sciences, Public Health and Health Services
Abstract

Many disease systems exhibit complexities not captured by current theoretical and empirical work. In particular, systems with multiple host species and multiple infectious agents (i.e., multi-host, multi-agent systems) require novel methods to extend the wealth of knowledge acquired studying primarily single-host, single-agent systems. We outline eight challenges in multi-host, multi-agent systems that could substantively increase our knowledge of the drivers and broader ecosystem effects of infectious disease dynamics.

Published
2015

23. Crossing the interspecies barrier: opening the door to zoonotic pathogens.

Author

Gortazar, Christian, Reperant, Leslie A, Kuiken, Thijs, de la Fuente, José, Boadella, Mariana, Martínez-Lopez, Beatriz, Ruiz-Fons, Francisco, Estrada-Peña, Agustin, Drosten, Christian, Medley, Graham, Ostfeld, Richard, Peterson, Townsend, VerCauteren, Kurt C, Menge, Christian, Artois, Marc, Schultsz, Constance, Delahay, Richard, Serra-Cobo, Jordi, Poulin, Robert, Keck, Frederic, Aguirre, A Alonso, Henttonen, Heikki, Dobson, Andrew P, Kutz, Susan, Lubroth, Juan, and Mysterud, Atle

Subjects
Animals, Humans, Zoonoses, Risk Assessment, Disease Reservoirs, Disease Vectors, Health Transition, Models, Biological, Urbanization, Animal Husbandry, Climate Change, Host Specificity, Global Health, Virology, Microbiology, Immunology, Medical Microbiology
Published
2014

27. Ecological Science and Sustainability for the 21st Century

Author

Palmer, Margaret A., Bernhardt, Emily S., Chornesky, Elizabeth A., Collins, Scott L., Dobson, Andrew P., Duke, Clifford S., Gold, Barry D., Jacobson, Robert B., Kingsland, Sharon E., Kranz, Rhonda H., Mappin, Michael J., Martinez, M. Luisa, Micheli, Fiorenza, Morse, Jennifer L., Pace, Michael L., Pascual, Mercedes, Palumbi, Stephen S., Reichman, O. J., Townsend, Alan R., and Turner, Monica G.

Published
2005
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33. Human Health Effects of a Changing Global Nitrogen Cycle

Author

Townsend, Alan R., Howarth, Robert W., Bazzaz, Fakhri A., Booth, Mary S., Cleveland, Cory C., Collinge, Sharon K., Dobson, Andrew P., Epstein, Paul R., Holland, Elisabeth A., Keeney, Dennis R., Mallin, Michael A., Rogers, Christine A., Wayne, Peter, and Wolfe, Amir H.

Published
2003
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34. Seismic modelling for the sub-basalt imaging problem including an analysis and development of the boundary element method

Author

Dobson, Andrew, Ziolkowski, Anton., and Xiang-Yang, Li

Subjects
551.2, Sub-Basalt Imaging, Boundary Element Method
Abstract

The north-east Atlantic margin (NEAM) is important for hydrocarbon exploration because of the growing evidence of hydrocarbon reserves in the region. However, seismic exploration of the sub-surface is hampered by large deposits of flood basalts, which cover possible hydrocarbon-bearing reservoirs underneath. There are several hypotheses as to why imaging beneath basalt is a problem. These include: the high impedance contrast between the basalt and the layers above; the thin-layering of the basalt due to the many flows which make up a basalt succession; and the rough interfaces on the top-basalt interface caused by weathering and emplacement mechanisms. I perform forward modelling to assess the relative importance of these factors for imaging of sub-basalt reflections. The boundary element method (BEM) is used for the rough-interface modelling. The method was selected because only the interfaces between layers need to be discretized, in contrast to grid methods such as finite difference for which the whole model needs to be discretized, and so should lead to fast generation of shot gathers for models which have only a few homogeneous layers. I have had to develop criteria for accurate modelling with the boundary element method and have considered the following: source near an interface, two interfaces close together, removal of model edge effects and precise modelling of a transparent interface. I have improved efficiency of my code by: resampling the model so that fewer discretization elements are required at low frequencies, and suppressing wrap-around so that the time window length can be reduced. I introduce a new scheme which combines domain decomposition and a far-field approximation to improve the efficiency of the boundary element code further. I compare performance with a standard finite difference code. I show that the BEM is well suited to seismic modelling in an exploration environment when there are only a few layers in the model and when a seismic profile containing many shot gathers for one model is required. For many other cases the finite difference code is still the best option. The input models for the forward modelling are based on real seismic data which were acquired in the Faeroe-Shetland Channel in 2001. The modelling shows that roughness on the surface of the basalt has little effect on the imaging in this particular area of the NEAM. The thin layers in the basalt act as a low-pass filter to the seismic wave. For the real-data acquisition, even the topbasalt reflection is a low frequency event. This is most likely to be due to high attenuation in the layers above the basalt. I show that sea-surface multiple energy is considerable and that it could mask possible sub-basalt events on a seismic shot gather, but any shallow sub-basalt events should still be visible even with the presence of multiple energy. This leaves the possibility that there is only one major stratigraphic unit between the base of the basalt and the crystalline basement. The implication of the forward modelling and real data analysis for acquisition is that the acquisition parameters must emphasize the low frequencies, since the high frequencies are attenuated before they even reach the top-basalt interface. The implication for processing is that multiple removal is of prime importance.

Published
2005

50. Dynamics of a morbillivirus at the domestic–wildlife interface : Canine distemper virus in domestic dogs and lions

Author

Viana, Mafalda, Cleaveland, Sarah, Matthiopoulos, Jason, Halliday, Jo, Packer, Craig, Craft, Meggan E., Hampson, Katie, Czupryna, Anna, Dobson, Andrew P., Dubovi, Edward J., Ernest, Eblate, Fyumagwa, Robert, Hoare, Richard, Hopcraft, J. Grant C., Horton, Daniel L., Kaarek, Magai T., Kanellos, Theo, Lankester, Felix, Mentzel, Christine, Mlengeya, Titus, Mzimbiri, Imam, Takahashi, Emi, Willett, Brian, Haydon, Daniel T., and Lembo, Tiziana

Published
2015

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