3,153 research outputs found
Recommended from our members
Inference of single-cell phylogenies from lineage tracing data using Cassiopeia.
The pairing of CRISPR/Cas9-based gene editing with massively parallel single-cell readouts now enables large-scale lineage tracing. However, the rapid growth in complexity of data from these assays has outpaced our ability to accurately infer phylogenetic relationships. First, we introduce Cassiopeia-a suite of scalable maximum parsimony approaches for tree reconstruction. Second, we provide a simulation framework for evaluating algorithms and exploring lineage tracer design principles. Finally, we generate the most complex experimental lineage tracing dataset to date, 34,557 human cells continuously traced over 15 generations, and use it for benchmarking phylogenetic inference approaches. We show that Cassiopeia outperforms traditional methods by several metrics and under a wide variety of parameter regimes, and provide insight into the principles for the design of improved Cas9-enabled recorders. Together, these should broadly enable large-scale mammalian lineage tracing efforts. Cassiopeia and its benchmarking resources are publicly available at www.github.com/YosefLab/Cassiopeia
An efficient memetic, permutation-based evolutionary algorithm for real-world train timetabling
Train timetabling is a difficult and very tightly constrained combinatorial
problem that deals with the construction of train schedules. We focus on the
particular problem of local reconstruction of the schedule following a small
perturbation, seeking minimisation of the total accumulated delay by adapting
times of departure and arrival for each train and allocation of resources
(tracks, routing nodes, etc.). We describe a permutation-based evolutionary
algorithm that relies on a semi-greedy heuristic to gradually reconstruct the
schedule by inserting trains one after the other following the permutation.
This algorithm can be hybridised with ILOG commercial MIP programming tool
CPLEX in a coarse-grained manner: the evolutionary part is used to quickly
obtain a good but suboptimal solution and this intermediate solution is refined
using CPLEX. Experimental results are presented on a large real-world case
involving more than one million variables and 2 million constraints. Results
are surprisingly good as the evolutionary algorithm, alone or hybridised,
produces excellent solutions much faster than CPLEX alone
Human-Machine Collaborative Optimization via Apprenticeship Scheduling
Coordinating agents to complete a set of tasks with intercoupled temporal and
resource constraints is computationally challenging, yet human domain experts
can solve these difficult scheduling problems using paradigms learned through
years of apprenticeship. A process for manually codifying this domain knowledge
within a computational framework is necessary to scale beyond the
``single-expert, single-trainee" apprenticeship model. However, human domain
experts often have difficulty describing their decision-making processes,
causing the codification of this knowledge to become laborious. We propose a
new approach for capturing domain-expert heuristics through a pairwise ranking
formulation. Our approach is model-free and does not require enumerating or
iterating through a large state space. We empirically demonstrate that this
approach accurately learns multifaceted heuristics on a synthetic data set
incorporating job-shop scheduling and vehicle routing problems, as well as on
two real-world data sets consisting of demonstrations of experts solving a
weapon-to-target assignment problem and a hospital resource allocation problem.
We also demonstrate that policies learned from human scheduling demonstration
via apprenticeship learning can substantially improve the efficiency of a
branch-and-bound search for an optimal schedule. We employ this human-machine
collaborative optimization technique on a variant of the weapon-to-target
assignment problem. We demonstrate that this technique generates solutions
substantially superior to those produced by human domain experts at a rate up
to 9.5 times faster than an optimization approach and can be applied to
optimally solve problems twice as complex as those solved by a human
demonstrator.Comment: Portions of this paper were published in the Proceedings of the
International Joint Conference on Artificial Intelligence (IJCAI) in 2016 and
in the Proceedings of Robotics: Science and Systems (RSS) in 2016. The paper
consists of 50 pages with 11 figures and 4 table
Battle of Postdisaster Response and Restoration
[EN] The paper presents the results of the Battle of Postdisaster Response and Restoration (BPDRR) presented in a special session at the first International water distribution systems analysis & computing and control in the water industry (WDSA/CCWI) Joint Conference, held in Kingston, Ontario, Canada, in July 2018. The BPDRR problem focused on how to respond and restore water service after the occurrence of five earthquake scenarios that cause structural damage in a water distribution system. Participants were required to propose a prioritization schedule to fix the damages of each scenario while following restrictions on visibility/nonvisibility of damages. Each team/approach was evaluated against six performance criteria: (1) time without supply for hospital/firefighting, (2) rapidity of recovery, (3) resilience loss, (4) average time of no user service, (5) number of users without service for eight consecutive hours, and (6) water loss. Three main types of approaches were identified from the submissions: (1) general-purpose metaheuristic algorithms, (2) greedy algorithms, and (3) ranking-based prioritizations. All three approaches showed potential to solve the challenge efficiently. The results of the participants showed that for this network, the impact of a large-diameter pipe failure on the network is more significant than several smaller pipes failures. The location of isolation valves and the size of hydraulic segments influenced the resilience of the system during emergencies. On average, the interruptions to water supply (hospitals and firefighting) varied considerably among solutions and emergency scenarios, highlighting the importance of private water storage for emergencies. The effects of damages and repair work were more noticeable during the peak demand periods (morning and noontime) than during the low-flow periods; and tank storage helped to preserve functionality of the network in the first few hours after a simulated event. (C) 2020 American Society of Civil Engineers.Paez, D.; Filion, Y.; Castro-Gama, M.; Quintiliani, C.; Santopietro, S.; Sweetapple, C.; Meng, F.... (2020). Battle of Postdisaster Response and Restoration. Journal of Water Resources Planning and Management. 146(8):1-13. https://doi.org/10.1061/(ASCE)WR.1943-5452.0001239S1131468Balut A. R. Brodziak J. Bylka and P. Zakrzewski. 2018. “Battle of post-disaster response and restauration (BPDRR).” In Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. 14. Kingston Canada: Open Journal Systems.Bibok A. 2018. “Near-optimal restoration scheduling of damaged drinking water distribution systems using machine learning.” In Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. 14. Kingston Canada: Open Journal Systems.Castro-Gama M. C. Quintiliani and S. Santopietro. 2018. “After earthquake post-disaster response using a many-objective approach a greedy and engineering interventions.” In Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. 14. Kingston Canada: Open Journal Systems.Cimellaro, G. P., Tinebra, A., Renschler, C., & Fragiadakis, M. (2016). New Resilience Index for Urban Water Distribution Networks. Journal of Structural Engineering, 142(8). doi:10.1061/(asce)st.1943-541x.0001433Cover, T., & Hart, P. (1967). Nearest neighbor pattern classification. IEEE Transactions on Information Theory, 13(1), 21-27. doi:10.1109/tit.1967.1053964Creaco, E., Franchini, M., & Alvisi, S. (2010). Optimal Placement of Isolation Valves in Water Distribution Systems Based on Valve Cost and Weighted Average Demand Shortfall. Water Resources Management, 24(15), 4317-4338. doi:10.1007/s11269-010-9661-5Deb, K., Mohan, M., & Mishra, S. (2005). Evaluating the ε-Domination Based Multi-Objective Evolutionary Algorithm for a Quick Computation of Pareto-Optimal Solutions. Evolutionary Computation, 13(4), 501-525. doi:10.1162/106365605774666895Deuerlein J. D. Gilbert E. Abraham and O. Piller. 2018. “A greedy scheduling of post-disaster response and restoration using pressure-driven models and graph segment analysis.” In Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. 14. Kingston Canada: Open Journal Systems.Deuerlein, J. W. (2008). Decomposition Model of a General Water Supply Network Graph. Journal of Hydraulic Engineering, 134(6), 822-832. doi:10.1061/(asce)0733-9429(2008)134:6(822)Di Nardo, A., Di Natale, M., Giudicianni, C., Santonastaso, G. F., & Savic, D. (2018). Simplified Approach to Water Distribution System Management via Identification of a Primary Network. Journal of Water Resources Planning and Management, 144(2), 04017089. doi:10.1061/(asce)wr.1943-5452.0000885Eliades D. G. M. Kyriakou S. Vrachimis and M. M. Polycarpou. 2016. “EPANET-MATLAB toolkit: An open-source software for interfacing EPANET with MATLAB.” In Proc. 14th Int. Conf. on Computing and Control for the Water Industry (CCWI) 8. The Hague The Netherlands: International Water Conferences. https://doi.org/10.5281/zenodo.831493.Fragiadakis, M., Christodoulou, S. E., & Vamvatsikos, D. (2013). Reliability Assessment of Urban Water Distribution Networks Under Seismic Loads. Water Resources Management, 27(10), 3739-3764. doi:10.1007/s11269-013-0378-0Gilbert, D., Abraham, E., Montalvo, I., & Piller, O. (2017). Iterative Multistage Method for a Large Water Network Sectorization into DMAs under Multiple Design Objectives. Journal of Water Resources Planning and Management, 143(11), 04017067. doi:10.1061/(asce)wr.1943-5452.0000835Hill, D., Kerkez, B., Rasekh, A., Ostfeld, A., Minsker, B., & Banks, M. K. (2014). Sensing and Cyberinfrastructure for Smarter Water Management: The Promise and Challenge of Ubiquity. Journal of Water Resources Planning and Management, 140(7), 01814002. doi:10.1061/(asce)wr.1943-5452.0000449Hwang, H. H. M., Lin, H., & Shinozuka, M. (1998). Seismic Performance Assessment of Water Delivery Systems. Journal of Infrastructure Systems, 4(3), 118-125. doi:10.1061/(asce)1076-0342(1998)4:3(118)Li Y. J. Gao C. Jian C. Ou and S. Hu. 2018. “A two-stage post-disaster response and restoration method for the water distribution system.” In Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. 14. Kingston Canada: Open Journal Systems.Liu, W., Zhao, Y., & Li, J. (2014). Seismic functional reliability analysis of water distribution networks. Structure and Infrastructure Engineering, 11(3), 363-375. doi:10.1080/15732479.2014.887121Luong, H. T., & Nagarur, N. N. (2005). Optimal Maintenance Policy and Fund Allocation in Water Distribution Networks. Journal of Water Resources Planning and Management, 131(4), 299-306. doi:10.1061/(asce)0733-9496(2005)131:4(299)MacQueen J. B. 1967. “Some methods for classification and analysis of multivariate observations.” In Vol. 1 of Proc. 5th Berkeley Symp. on Mathematical Statistics and Probability 281–297. Berkeley: University of California Press.Mahmoud, H. A., Kapelan, Z., & Savić, D. (2018). Real-Time Operational Response Methodology for Reducing Failure Impacts in Water Distribution Systems. Journal of Water Resources Planning and Management, 144(7), 04018029. doi:10.1061/(asce)wr.1943-5452.0000956Meng, F., Fu, G., Farmani, R., Sweetapple, C., & Butler, D. (2018). Topological attributes of network resilience: A study in water distribution systems. Water Research, 143, 376-386. doi:10.1016/j.watres.2018.06.048Ostfeld, A., Uber, J. G., Salomons, E., Berry, J. W., Hart, W. E., Phillips, C. A., … Walski, T. (2008). The Battle of the Water Sensor Networks (BWSN): A Design Challenge for Engineers and Algorithms. Journal of Water Resources Planning and Management, 134(6), 556-568. doi:10.1061/(asce)0733-9496(2008)134:6(556)Paez D. Y. Filion and M. Hulley. 2018a. “Battle of post-disaster response and restoration (BPDRR)—Problem description and rules.” Accessed June 14 2019. https://www.queensu.ca/wdsa-ccwi2018/problem-description-and-files.Paez, D., Suribabu, C. R., & Filion, Y. (2018). Method for Extended Period Simulation of Water Distribution Networks with Pressure Driven Demands. Water Resources Management, 32(8), 2837-2846. doi:10.1007/s11269-018-1961-1Salcedo C. A. Aguilar P. Cuero S. Gonzalez S. Muñoz J. Pérez A. Posada J. Robles and K. Vargas. 2018. “Determination of the hydraulic restoration capacity of b-city involving a multi-criteria decision support model.” In Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. 14. Kingston Canada: Open Journal Systems.Santonastaso G. F. E. Creaco A. Di Nardo and M. Di Natale. 2018. “Post-disaster response and restauration of B-town network based on primary network.” In Vol. 1 of Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. Kingston Canada: Open Journal Systems.Sophocleous S. E. Nikoloudi H. A. Mahmoud K. Woodward and M. Romano. 2018. “Simulation-based framework for the restoration of earthquake-damaged water distribution networks using a genetic algorithm.” In Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. 14. Kingston Canada: Open Journal Systems.Sweetapple C. F. Meng R. Farmani G. Fu and D. Butler. 2018. “A heuristic approach to water network post-disaster response and restoration.” In Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. 14. Kingston Canada: Open Journal Systems.Tabucchi, T., Davidson, R., & Brink, S. (2010). Simulation of post-earthquake water supply system restoration. Civil Engineering and Environmental Systems, 27(4), 263-279. doi:10.1080/10286600902862615Taormina, R., Galelli, S., Tippenhauer, N. O., Salomons, E., Ostfeld, A., Eliades, D. G., … Ohar, Z. (2018). Battle of the Attack Detection Algorithms: Disclosing Cyber Attacks on Water Distribution Networks. Journal of Water Resources Planning and Management, 144(8), 04018048. doi:10.1061/(asce)wr.1943-5452.0000969Walski, T. M. (1993). Water distribution valve topology for reliability analysis. Reliability Engineering & System Safety, 42(1), 21-27. doi:10.1016/0951-8320(93)90051-yWang, Y., Au, S.-K., & Fu, Q. (2010). Seismic Risk Assessment and Mitigation of Water Supply Systems. Earthquake Spectra, 26(1), 257-274. doi:10.1193/1.3276900Yoo, D. G., Kang, D., & Kim, J. H. (2016). Optimal design of water supply networks for enhancing seismic reliability. Reliability Engineering & System Safety, 146, 79-88. doi:10.1016/j.ress.2015.10.001Zhang Q. F. Zheng K. Diao B. Ulanicki and Y. Huang. 2018. “Solving the battle of post-disaster response and restauration (BPDRR) problem with the aid of multi-phase optimization framework.” In Proc. 1st Int. WDSA/CCWI 2018 Joint Conf. 14. Kingston Canada: Open Journal Systems
Iterative Beam Search for Simple Assembly Line Balancing with a Fixed Number of Work Stations
The simple assembly line balancing problem (SALBP) concerns the assignment of
tasks with pre-defined processing times to work stations that are arranged in a
line. Hereby, precedence constraints between the tasks must be respected. The
optimization goal of the SALBP-2 version of the problem concerns the
minimization of the so-called cycle time, that is, the time in which the tasks
of each work station must be completed.
In this work we propose to tackle this problem with an iterative search
method based on beam search. The proposed algorithm is able to obtain optimal,
respectively best-known, solutions in 283 out of 302 test cases. Moreover, for
9 further test cases the algorithm is able to produce new best-known solutions.
These numbers indicate that the proposed iterative beam search algorithm is
currently a state-of-the-art method for the SALBP-2
- …