To see the other types of publications on this topic, follow the link: Single Player Monte Carlo Tree Search.

Journal articles on the topic 'Single Player Monte Carlo Tree Search'

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 22 journal articles for your research on the topic 'Single Player Monte Carlo Tree Search.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

Schadd, Maarten P. D., Mark H. M. Winands, Mandy J. W. Tak, and Jos W. H. M. Uiterwijk. "Single-player Monte-Carlo tree search for SameGame." Knowledge-Based Systems 34 (October 2012): 3–11. http://dx.doi.org/10.1016/j.knosys.2011.08.008.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Xia, Yu-Wei, Chao Yang, and Bing-Qiu Chen. "A Path Planning Method Based on Improved Single Player-Monte Carlo Tree Search." IEEE Access 8 (2020): 163694–702. http://dx.doi.org/10.1109/access.2020.3021748.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Furuoka, Ryota, and Shimpei Matsumoto. "Worker’s knowledge evaluation with single-player Monte Carlo tree search for a practical reentrant scheduling problem." Artificial Life and Robotics 22, no. 1 (September 23, 2016): 130–38. http://dx.doi.org/10.1007/s10015-016-0325-2.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Wang, Mingyan, Hang Ren, Wei Huang, Taiwei Yan, Jiewei Lei, and Jiayang Wang. "An efficient AI-based method to play the Mahjong game with the knowledge and game-tree searching strategy." ICGA Journal 43, no. 1 (May 26, 2021): 2–25. http://dx.doi.org/10.3233/icg-210179.

Full text
Abstract:
The Mahjong game has widely been acknowledged to be a difficult problem in the field of imperfect information games. Because of its unique characteristics of asymmetric, serialized and multi-player game information, conventional methods of dealing with perfect information games are difficult to be applied directly on the Mahjong game. Therefore, AI (artificial intelligence)-based studies to handle the Mahjong game become challenging. In this study, an efficient AI-based method to play the Mahjong game is proposed based on the knowledge and game-tree searching strategy. Technically, we simplify the Mahjong game framework from multi-player to single-player. Based on the above intuition, an improved search algorithm is proposed to explore the path of winning. Meanwhile, three node extension strategies are proposed based on heuristic information to improve the search efficiency. Then, an evaluation function is designed to calculate the optimal solution by combining the winning rate, score and risk value assessment. In addition, we combine knowledge and Monte Carlo simulation to construct an opponent model to predict hidden information and translate it into available relative probabilities. Finally, dozens of experiments are designed to prove the effectiveness of each algorithm module. It is also worthy to mention that, the first version of the proposed method, which is named as KF-TREE, has won the silver medal in the Mahjong tournament of 2019 Computer Olympiad.
APA, Harvard, Vancouver, ISO, and other styles
5

Guo, Jian, Yaoyao Shi, Zhen Chen, Tao Yu, Bijan Shirinzadeh, and Pan Zhao. "Improved SP-MCTS-Based Scheduling for Multi-Constraint Hybrid Flow Shop." Applied Sciences 10, no. 18 (September 8, 2020): 6220. http://dx.doi.org/10.3390/app10186220.

Full text
Abstract:
As a typical non-deterministic polynomial (NP)-hard combinatorial optimization problem, the hybrid flow shop scheduling problem (HFSSP) is known to be a very common layout in real-life manufacturing scenarios. Even though many metaheuristic approaches have been presented for the HFSSP with makespan criterion, there are limitations of the metaheuristic method in accuracy, efficiency, and adaptability. To address this challenge, an improved SP-MCTS (single-player Monte-Carlo tree search)-based scheduling is proposed for the hybrid flow shop to minimize the makespan considering the multi-constraint. Meanwhile, the Markov decision process (MDP) is applied to transform the HFSSP into the problem of shortest time branch path. The improvement of the algorithm includes the selection policy blending standard deviation, the single-branch expansion strategy and the 4-Rule policy simulation. Based on this improved algorithm, it could accurately locate high-potential branches, economize the resource of the computer and quickly optimize the solution. Then, the parameter combination is introduced to trade off the selection and simulation with the intention of balancing the exploitation and exploration in the search process. Finally, through the analysis of the calculated results, the validity of improved SP-MCTS (ISP-MCTS) for solving the benchmarks is proven, and the ISP-MCTS performs better than the other algorithms in solving large-scale problems.
APA, Harvard, Vancouver, ISO, and other styles
6

Fabbri, André, Frédéric Armetta, Éric Duchêne, and Salima Hassas. "A Self-Acquiring Knowledge Process for MCTS." International Journal on Artificial Intelligence Tools 25, no. 01 (February 2016): 1660007. http://dx.doi.org/10.1142/s0218213016600071.

Full text
Abstract:
MCTS (Monte Carlo Tree Search) is a well-known and efficient process to cover and evaluate a large range of states for combinatorial problems. We choose to study MCTS for the Computer Go problem, which is one of the most challenging problem in the field of Artificial Intelligence. For this game, a single combinatorial approach does not always lead to a reliable evaluation of the game states. In order to enhance MCTS ability to tackle such problems, one can benefit from game specific knowledge in order to increase the accuracy of the game state evaluation. Such a knowledge is not easy to acquire. It is the result of a constructivist learning mechanism based on the experience of the player. That is why we explore the idea to endow the MCTS with a process inspired by constructivist learning, to self-acquire knowledge from playing experience. In this paper, we propose a complementary process for MCTS called BHRF (Background History Reply Forest), which allows to memorize efficient patterns in order to promote their use through the MCTS process. Our experimental results lead to promising results and underline how self-acquired data can be useful for MCTS based algorithms.
APA, Harvard, Vancouver, ISO, and other styles
7

Maes, Francis, David Lupien St-Pierre, and Damien Ernst. "Monte Carlo Search Algorithm Discovery for Single-Player Games." IEEE Transactions on Computational Intelligence and AI in Games 5, no. 3 (September 2013): 201–13. http://dx.doi.org/10.1109/tciaig.2013.2239295.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Spoerer, Kristian. "BI-DIRECTIONAL MONTE CARLO TREE SEARCH." Asia-Pacific Journal of Information Technology and Multimedia 10, no. 01 (June 1, 2021): 17–26. http://dx.doi.org/10.17576/apjitm-2021-1001-02.

Full text
Abstract:
This paper describes a new algorithm called Bi-Directional Monte Carlo Tree Search. The essential idea of Bi-directional Monte Carlo Tree Search is to run an MCTS forwards from the start state, and simultaneously run an MCTS backwards from the goal state, and stop when the two searches meet. Bi-Directional MCTS is tested on 8-Puzzle and Pancakes Problem, two single-agent search problems, which allow control over the optimal solution length d and average branching factor b respectively. Preliminary results indicate that enhancing Monte Carlo Tree Search by making it Bi-Directional speeds up the search. The speedup of Bi-directional MCTS grows with increasing the problem size, in terms of both optimal solution length d and also branching factor b. Furthermore, Bi-Directional Search has been applied to a Reinforcement Learning algorithm. It is hoped that the speed enhancement of Bi-directional Monte Carlo Tree Search will also apply to other planning problems.
APA, Harvard, Vancouver, ISO, and other styles
9

Lisy, Viliam. "ALTERNATIVE SELECTION FUNCTIONS FOR INFORMATION SET MONTE CARLO TREE SEARCH." Acta Polytechnica 54, no. 5 (October 31, 2014): 333–40. http://dx.doi.org/10.14311/ap.2014.54.0333.

Full text
Abstract:
We evaluate the performance of various selection methods for the Monte Carlo Tree Search algorithm in two-player zero-sum extensive-form games with imperfect information. We compare the standard Upper Confident Bounds applied to Trees (UCT) along with the less common Exponential Weights for Exploration and Exploitation (Exp3) and novel Regret matching (RM) selection in two distinct imperfect information games: Imperfect Information Goofspiel and Phantom Tic-Tac-Toe. We show that UCT after initial fast convergence towards a Nash equilibrium computes increasingly worse strategies after some point in time. This is not the case with Exp3 and RM, which also show superior performance in head-to-head matches.
APA, Harvard, Vancouver, ISO, and other styles
10

Roberson, Christian, and Katarina Sperduto. "A Monte Carlo Tree Search Player for Birds of a Feather Solitaire." Proceedings of the AAAI Conference on Artificial Intelligence 33 (July 17, 2019): 9700–9705. http://dx.doi.org/10.1609/aaai.v33i01.33019700.

Full text
Abstract:
Artificial intelligence in games serves as an excellent platform for facilitating collaborative research with undergraduates. This paper explores several aspects of a research challenge proposed for a newly-developed variant of a solitaire game. We present multiple classes of game states that can be identified as solvable or unsolvable. We present a heuristic for quickly finding goal states in a game state search tree. Finally, we introduce a Monte Carlo Tree Search-based player for the solitaire variant that can win almost any solvable starting deal efficiently.
APA, Harvard, Vancouver, ISO, and other styles
11

Mehat, Jean, and Tristan Cazenave. "Combining UCT and Nested Monte Carlo Search for Single-Player General Game Playing." IEEE Transactions on Computational Intelligence and AI in Games 2, no. 4 (December 2010): 271–77. http://dx.doi.org/10.1109/tciaig.2010.2088123.

Full text
APA, Harvard, Vancouver, ISO, and other styles
12

Fu, Michael C. "Simulation-Based Algorithms for Markov Decision Processes: Monte Carlo Tree Search from AlphaGo to AlphaZero." Asia-Pacific Journal of Operational Research 36, no. 06 (December 2019): 1940009. http://dx.doi.org/10.1142/s0217595919400098.

Full text
Abstract:
AlphaGo and its successors AlphaGo Zero and AlphaZero made international headlines with their incredible successes in game playing, which have been touted as further evidence of the immense potential of artificial intelligence, and in particular, machine learning. AlphaGo defeated the reigning human world champion Go player Lee Sedol 4 games to 1, in March 2016 in Seoul, Korea, an achievement that surpassed previous computer game-playing program milestones by IBM’s Deep Blue in chess and by IBM’s Watson in the U.S. TV game show Jeopardy. AlphaGo then followed this up by defeating the world’s number one Go player Ke Jie 3-0 at the Future of Go Summit in Wuzhen, China in May 2017. Then, in December 2017, AlphaZero stunned the chess world by dominating the top computer chess program Stockfish (which has a far higher rating than any human) in a 100-game match by winning 28 games and losing none (72 draws) after training from scratch for just four hours! The deep neural networks of AlphaGo, AlphaZero, and all their incarnations are trained using a technique called Monte Carlo tree search (MCTS), whose roots can be traced back to an adaptive multistage sampling (AMS) simulation-based algorithm for Markov decision processes (MDPs) published in Operations Research back in 2005 [Chang, HS, MC Fu, J Hu and SI Marcus (2005). An adaptive sampling algorithm for solving Markov decision processes. Operations Research, 53, 126–139.] (and introduced even earlier in 2002). After reviewing the history and background of AlphaGo through AlphaZero, the origins of MCTS are traced back to simulation-based algorithms for MDPs, and its role in training the neural networks that essentially carry out the value/policy function approximation used in approximate dynamic programming, reinforcement learning, and neuro-dynamic programming is discussed, including some recently proposed enhancements building on statistical ranking & selection research in the operations research simulation community.
APA, Harvard, Vancouver, ISO, and other styles
13

Gu, Bonwoo, and Yunsick Sung. "Enhanced Reinforcement Learning Method Combining One-Hot Encoding-Based Vectors for CNN-Based Alternative High-Level Decisions." Applied Sciences 11, no. 3 (February 1, 2021): 1291. http://dx.doi.org/10.3390/app11031291.

Full text
Abstract:
Gomoku is a two-player board game that originated in ancient China. There are various cases of developing Gomoku using artificial intelligence, such as a genetic algorithm and a tree search algorithm. Alpha-Gomoku, Gomoku AI built with Alpha-Go’s algorithm, defines all possible situations in the Gomoku board using Monte-Carlo tree search (MCTS), and minimizes the probability of learning other correct answers in the duplicated Gomoku board situation. However, in the tree search algorithm, the accuracy drops, because the classification criteria are manually set. In this paper, we propose an improved reinforcement learning-based high-level decision approach using convolutional neural networks (CNN). The proposed algorithm expresses each state as One-Hot Encoding based vectors and determines the state of the Gomoku board by combining the similar state of One-Hot Encoding based vectors. Thus, in a case where a stone that is determined by CNN has already been placed or cannot be placed, we suggest a method for selecting an alternative. We verify the proposed method of Gomoku AI in GuPyEngine, a Python-based 3D simulation platform.
APA, Harvard, Vancouver, ISO, and other styles
14

Kővári, Bálint, Ferenc Hegedüs, and Tamás Bécsi. "Design of a Reinforcement Learning-Based Lane Keeping Planning Agent for Automated Vehicles." Applied Sciences 10, no. 20 (October 14, 2020): 7171. http://dx.doi.org/10.3390/app10207171.

Full text
Abstract:
Reinforcement learning-based approaches are widely studied in the literature for solving different control tasks for Connected and Autonomous Vehicles, from which this paper deals with the problem of lateral control of a dynamic nonlinear vehicle model, performing the task of lane-keeping. In this area, the appropriate formulation of the goals and environment information is crucial, for which the research outlines the importance of lookahead information, enabling to accomplish maneuvers with complex trajectories. Another critical part is the real-time manner of the problem. On the one hand, optimization or search based methods, such as the presented Monte Carlo Tree Search method, can solve the problem with the trade-off of high numerical complexity. On the other hand, single Reinforcement Learning agents struggle to learn these tasks with high performance, though they have the advantage that after the training process, they can operate in a real-time manner. Two planning agent structures are proposed in the paper to resolve this duality, where the machine learning agents aid the tree search algorithm. As a result, the combined solution provides high performance and low computational needs.
APA, Harvard, Vancouver, ISO, and other styles
15

West, Todd, John Sessions, and Bogdan M. Strimbu. "Heuristic Optimization of Thinning Individual Douglas-Fir." Forests 12, no. 3 (February 28, 2021): 280. http://dx.doi.org/10.3390/f12030280.

Full text
Abstract:
Research Highlights: (1) Optimizing mid-rotation thinning increased modeled land expectation values by as much as 5.1–10.1% over a representative reference prescription on plots planted at 2.7 and 3.7 m square spacings. (2) Eight heuristics, five of which were newly applied to selecting individual trees for thinning, produced thinning prescriptions of near identical quality. (3) Based on heuristic sampling properties, we introduced a variant of the hero heuristic with a 5.3–20% greater computational efficiency. Background and Objectives: Thinning, which is arguably the most subjective human intervention in the life of a stand, is commonly executed with limited decision support in tree selection. This study evaluated heuristics’ ability to support tree selection in a factorial experiment that considered the thinning method, tree density, thinning age, and rotation length. Materials and Methods: The Organon growth model was used for the financial optimization of even age Douglas-fir (Pseudotsuga menziesii (Mirb.) Franco) harvest rotations consisting of a single thinning followed by clearcutting on a high-productivity site. We evaluated two versions of the hero heuristic, four Monte Carlo heuristics (simulated annealing, record-to-record travel, threshold accepting, and great deluge), a genetic algorithm, and tabu search for their efficiency in maximizing land expectation value. Results: With 50–75 years rotations and a 4% discount rate, heuristic tree selection always increased land expectation values over other thinning methods. The two hero heuristics were the most computationally efficient methods. The four Monte Carlo heuristics required 2.8–3.4 times more computation than hero. The genetic algorithm and the tabu search required 4.2–8.4 and 21–52 times, respectively, more computation than hero. Conclusions: The accuracy of the resulting thinning prescriptions was limited by the quality of stand measurement, and the accuracy of the growth and yield models was linked to the heuristics rather than to the choice of heuristic. However, heuristic performance may be sensitive to the chosen models.
APA, Harvard, Vancouver, ISO, and other styles
16

Lee, Gwangho, Gun Hyuk Jang, Ho Young Kang, and Giltae Song. "Predicting aptamer sequences that interact with target proteins using an aptamer-protein interaction classifier and a Monte Carlo tree search approach." PLOS ONE 16, no. 6 (June 25, 2021): e0253760. http://dx.doi.org/10.1371/journal.pone.0253760.

Full text
Abstract:
Oligonucleotide-based aptamers, which have a three-dimensional structure with a single-stranded fragment, feature various characteristics with respect to size, toxicity, and permeability. Accordingly, aptamers are advantageous in terms of diagnosis and treatment and are materials that can be produced through relatively simple experiments. Systematic evolution of ligands by exponential enrichment (SELEX) is one of the most widely used experimental methods for generating aptamers; however, it is highly expensive and time-consuming. To reduce the related costs, recent studies have used in silico approaches, such as aptamer-protein interaction (API) classifiers that use sequence patterns to determine the binding affinity between RNA aptamers and proteins. Some of these methods generate candidate RNA aptamer sequences that bind to a target protein, but they are limited to producing candidates of a specific size. In this study, we present a machine learning approach for selecting candidate sequences of various sizes that have a high binding affinity for a specific sequence of a target protein. We applied the Monte Carlo tree search (MCTS) algorithm for generating the candidate sequences using a score function based on an API classifier. The tree structure that we designed with MCTS enables nucleotide sequence sampling, and the obtained sequences are potential aptamer candidates. We performed a quality assessment using the scores of docking simulations. Our validation datasets revealed that our model showed similar or better docking scores in ZDOCK docking simulations than the known aptamers. We expect that our method, which is size-independent and easy to use, can provide insights into searching for an appropriate aptamer sequence for a target protein during the simulation step of SELEX.
APA, Harvard, Vancouver, ISO, and other styles
17

Baier, Hendrik, and Mark H. M. Winands. "MCTS-Minimax Hybrids with State Evaluations." Journal of Artificial Intelligence Research 62 (June 7, 2018): 193–231. http://dx.doi.org/10.1613/jair.1.11208.

Full text
Abstract:
Monte-Carlo Tree Search (MCTS) has been found to show weaker play than minimax-based search in some tactical game domains. This is partly due to its highly selective search and averaging value backups, which make it susceptible to traps. In order to combine the strategic strength of MCTS and the tactical strength of minimax, MCTS-minimax hybrids have been introduced, embedding shallow minimax searches into the MCTS framework. Their results have been promising even without making use of domain knowledge such as heuristic evaluation functions. This article continues this line of research for the case where evaluation functions are available. Three different approaches are considered, employing minimax with an evaluation function in the rollout phase of MCTS, as a replacement for the rollout phase, and as a node prior to bias move selection. The latter two approaches are newly proposed. Furthermore, all three hybrids are enhanced with the help of move ordering and k-best pruning for minimax. Results show that the use of enhanced minimax for computing node priors results in the strongest MCTS-minimax hybrid investigated in the three test domains of Othello, Breakthrough, and Catch the Lion. This hybrid, called MCTS-IP-M-k, also outperforms enhanced minimax as a standalone player in Breakthrough, demonstrating that at least in this domain, MCTS and minimax can be combined to an algorithm stronger than its parts. Using enhanced minimax for computing node priors is therefore a promising new technique for integrating domain knowledge into an MCTS framework.
APA, Harvard, Vancouver, ISO, and other styles
18

Zheng, Guangcong, Cong Wang, Weijie Shao, Ying Yuan, Zejie Tian, Sancheng Peng, Ali Kashif Bashir, and Shahid Mumtaz. "A single-player Monte Carlo tree search method combined with node importance for virtual network embedding." Annals of Telecommunications, June 19, 2020. http://dx.doi.org/10.1007/s12243-020-00772-5.

Full text
APA, Harvard, Vancouver, ISO, and other styles
19

Christian, Eunike Thirza Hanitya, R. Gunawan Santoso, and Erick Purwanto. "IMPLEMENTASI MONTE CARLO TREE SEARCH PADA PERMAINAN KARTU “DAIFUGO”." Jurnal Informatika 11, no. 1 (November 12, 2015). http://dx.doi.org/10.21460/inf.2015.111.424.

Full text
Abstract:
Daifugo is climbing card game that is originated from Japan. AI player of Daifugo card game can be implemented using Monte Carlo Tree Search to get optimal result from random simulation. Monte Carlo Tree Search has 4 step, selection, expansion, simulation and backpropagation that is executed until maximal loop is reached. Objective of using Monte Carlo Tree Search on AI player in Daifugo card game is to get move with high winning rate and to observe the effect of number of loop on the method to winning rate
APA, Harvard, Vancouver, ISO, and other styles
20

Rossi, Leonardo, Mark H. M. Winands, and Christoph Butenweg. "Monte Carlo Tree Search as an intelligent search tool in structural design problems." Engineering with Computers, February 26, 2021. http://dx.doi.org/10.1007/s00366-021-01338-2.

Full text
Abstract:
AbstractMonte Carlo Tree Search (MCTS) is a search technique that in the last decade emerged as a major breakthrough for Artificial Intelligence applications regarding board- and video-games. In 2016, AlphaGo, an MCTS-based software agent, outperformed the human world champion of the board game Go. This game was for long considered almost infeasible for machines, due to its immense search space and the need for a long-term strategy. Since this historical success, MCTS is considered as an effective new approach for many other scientific and technical problems. Interestingly, civil structural engineering, as a discipline, offers many tasks whose solution may benefit from intelligent search and in particular from adopting MCTS as a search tool. In this work, we show how MCTS can be adapted to search for suitable solutions of a structural engineering design problem. The problem consists of choosing the load-bearing elements in a reference reinforced concrete structure, so to achieve a set of specific dynamic characteristics. In the paper, we report the results obtained by applying both a plain and a hybrid version of single-agent MCTS. The hybrid approach consists of an integration of both MCTS and classic Genetic Algorithm (GA), the latter also serving as a term of comparison for the results. The study’s outcomes may open new perspectives for the adoption of MCTS as a design tool for civil engineers.
APA, Harvard, Vancouver, ISO, and other styles
21

Cazenave, Tristan, Jean-Yves Lucas, Thomas Triboulet, and Hyoseok Kim. "Policy adaptation for vehicle routing." AI Communications, December 22, 2020, 1–15. http://dx.doi.org/10.3233/aic-201577.

Full text
Abstract:
Nested Rollout Policy Adaptation (NRPA) is a Monte Carlo search algorithm that learns a playout policy in order to solve a single player game. In this paper we apply NRPA to the vehicle routing problem. This problem is important for large companies that have to manage a fleet of vehicles on a daily basis. Real problems are often too large to be solved exactly. The algorithm is applied to standard problem of the literature and to the specific problems of EDF (Electricité De France, the main French electric utility company). These specific problems have peculiar constraints. NRPA gives better result than the algorithm previously used by EDF.
APA, Harvard, Vancouver, ISO, and other styles
22

Scotch, Matthew, Arjun Magge, and Matteo Valente. "ZooPhy: A bioinformatics pipeline for virus phylogeography and surveillance." Online Journal of Public Health Informatics 11, no. 1 (May 30, 2019). http://dx.doi.org/10.5210/ojphi.v11i1.9729.

Full text
Abstract:
ObjectiveWe will describe the ZooPhy system for virus phylogeography and public health surveillance [1]. ZooPhy is designed for public health personnel that do not have expertise in bioinformatics or phylogeography. We will show its functionality by performing case studies of different viruses of public health concern including influenza and rabies virus. We will also provide its URL for user feedback by ISDS delegates.IntroductionSequence-informed surveillance is now recognized as an important extension to the monitoring of rapidly evolving pathogens [2]. This includes phylogeography, a field that studies the geographical lineages of species including viruses [3] by using sequence data (and relevant metadata such as sampling location). This work relies on bioinformatics knowledge. For example, the user first needs to find a relevant sequence database, navigate through it, and use proper search parameters to obtain the desired data. They also must ensure that there is sufficient metadata such as collection date and sampling location. They then need to align the sequences and integrate everything into specific software for phylogeography. For example, BEAST [4] is a popular tool for discrete phylogeography. For proper use, the software requires knowledge of phylogenetics and utilization of BEAUti, its XML processing software. The user then needs to use other software, like TreeAnnotator [4], to produce a single (“representative”) maximum clade credibility (MCC) tree. Even then, the evolutionary spread of the virus can be difficult to interpret via a simple tree viewer. There is software (such as SpreaD3 [5]) for visualizing a tree within a geographic context, yet for novice users, it might not be easy to use. Currently, there are only a few systems designed to automate these types of tasks for virus surveillance and phylogeography.MethodsWe have developed ZooPhy, a pipeline for sequence-informed surveillance and phylogeography [1]. It is designed for health agency personnel that do not have expertise in bioinformatics or phylogeography. We created a large database of all virus sequences and metadata from GenBank [6] as well as a smaller database for selected viruses perceived to be of great interest for health agencies including: influenza (A, B, and C), Ebola, rabies, West Nile virus, and Zika virus.In Figure 1A, we show our front-end architecture, created in the style of the influenza research database [7], that enables the user to search by: virus, gene name, host, time-frame, and geography. We also allow users to upload their own list of GenBank accessions or unpublished sequences. Hitting “Search” produces a Results tab which includes the metadata of the sequences. We provide a feature to randomly down-sample by a specified percentage or number. We also allow the user to download the metadata in CSV format or the unaligned sequences in FASTA format.The final tab, "Run", includes a text box for specifying an email in order to send job updates and final results on virus spread. We also enable for the user to study the influence of predictors on virus spread (via a generalized linear model). Currently, we have predictors such as temperature, great circle distance, population, and sample size for selected countries. We also offer experts the ability to specify advanced modeling parameters including the molecular clock type (strict vs. relaxed), coalescent tree prior, and chain length and sampling frequency for the Markov-chain Monte Carlo. When the user selects “Start ZooPhy”, a pre-processor eliminates incomplete or non-disjoint record locations and sends the rest for analysis.ResultsWhen initiated, the ZooPhy pipeline includes sequence alignment via Mafft [8] and creation of an XML template via BEASTGen for input into BEAST for discrete phylogeography. It then uses TreeAnnotator [3] to create an MCC tree from the posterior distribution of sampled trees. ZooPhy uses the MCC as input into SpreaD3 for a recreation of the time-estimated migration via a map. If the user selects the GLM option, the system runs an R script to calculate the Bayes factor of the inclusion probability for each predictor and draws a plot including the regression coefficient and its 95% Bayesian credible interval. We are currently working on new visualization techniques such as those demonstrated by Dudas et al. that combine time-oriented spread via a map and evolution on a phylogenetic tree annotated by discrete locations [9].ConclusionsRecent advances in phylodynamics, bioinformatics, and visualization have demonstrated the potential of pipelines to support surveillance. One example is NextStrain which can perform real-time virus phylodynamics [10]. The system has recently been added as an app to the Global Initiative on Sharing Avian Influenza Data (GISAID) database for influenza tracking using DNA sequences [11]. This presentation will highlight a pipeline for virus phylogeography designed for epidemiologists who are not experts in bioinformatics but wish to leverage virus sequence data as part of routine surveillance. We will describe the development and implementation of our system, ZooPhy, and use real-world case studies to demonstrate its functionality. We invite ISDS delegates to use the system via our web portal, https://zodo.asu.edu/zoophy/ and provide feedback on system utilization.References1. Scotch, M., et al., At the intersection of public-health informatics and bioinformatics: using advanced Web technologies for phylogeography. Epidemiology, 2010. 21(6), 764-768.2. Gardy, J.L. and N.J. Loman, Towards a genomics-informed, real-time, global pathogen surveillance system. Nat Rev Genet, 2018. 19: p. 9-20.3. Avise, J.C., Phylogeography : the history and formation of species. 2000, Cambridge, Mass.: Harvard University Press.4. Suchard, M.A., et al., Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol, 2018. 4.5. Bielejec, F., et al., SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes. Mol Biol Evol, 2016. 33(8): p. 2167-9.6. Benson, D. A.,et al., GenBank. Nucleic Acids Res, 2018. 46, p. D41-D47.7. Zhang, Y., et al., Influenza Research Database: An integrated bioinformatics resource for influenza virus research. Nucleic Acids Res, 2017. 45: p. D466-D474.8. Katoh, K. and D.M. Standley, MAFFT: iterative refinement and additional methods. Methods Mol Biol, 2014. 1079: p. 131-46.9. Dudas, G., et al., Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature, 2017. 544(7650): p. 309-315.10. Hadfield, J., et al., Nextstrain: real-time tracking of pathogen evolution. Bioinformatics, 2018.11. NextFlu. 2018; Available from: https://www.gisaid.org/epiflu-applications/nextflu-app/.
APA, Harvard, Vancouver, ISO, and other styles
We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!

To the bibliography