Subsequent application of self-organizing map and hidden Markov models infer community states of stream benthic macroinvertebrates |
Kim, Dong-Hwan
(Department of Integrated Biological Science, Pusan National University)
Nguyen, Tuyen Van (Department of Physics, Pusan National University) Heo, Muyoung (Department of Physics, Pusan National University) Chon, Tae-Soo (Department of Integrated Biological Science, Pusan National University) |
1 | Tucker BC, Anand M. 2004. On the use of stationary versus hidden Markov models to detect simple versus complex ecological dynamics. Ecol Model 185: 177-193. |
2 | Usher MB. 1981. Modelling ecological succession, with particular reference to Markovian models. In: Vegetation Dynamics in Grasslans, Healthlands and Mediterranean Ligneous Formations (Poissonet P, Romane F, Austin MA, van der Maarel E, Schmidt W, eds). Springer Netherlands, Amsterdam, pp11-18. |
3 | Vesanto J, Himberg J, Alhoniemi E, Parhankangas J. 2000. SOM Toolbox for Matlab 5. Helsinki University of Technology, Espoo. |
4 | Visser I, Raijmakers MEJ, Molenaar PCM. 2002. Fitting hidden Markov models to psycological data. Sci Prog 10: 185-199. |
5 | Viovy N, Saint G. 1994. Hidden Markov models applied to vegetation dynamics analysis using satellite remote sensing. IEEE Trans Geosci Remote Sens, 32: 906-917. DOI |
6 | Voegtlin T, Dominey PF. 2001. Learning high-degree sequences in a linear network. In: Neural Networks, 2001. Proceedings. IJCNN '01. International Joint Conference on Jul 15-19. IEEE, Washington, DC, pp 940-944. |
7 | Ward JH. 1963. Hierarchical grouping to optimize an objective function. J Am Stat Assoc 58: 236-244. DOI |
8 | Winston WL. 1994. Operations Research: Applications and Algorithms, 3rd ed. Duxbury Press, Belmont, CA. |
9 | Wiggins GB. 1996. Larvae of the North American Caddisfly Genera (Trichoptera). University of Toronto Press, Toronto. |
10 | Wootton JT. 2001b. Local interactions predict large-scale pattern in empirically derived cellular automata. Nature 413: 841-844. DOI |
11 | Yemshanov D, Perera AH. 2002. A spatially explicit stochastic model to simulate boreal forest cover transitions: general structure and properties. Ecol Model 150: 189-209. DOI |
12 | Yoon IB. 1995. Aquatic Insects of Korea. Jeonghaengsa, Seoul. (in Korean) |
13 | Adriaenssens V, Verdonschot PFM, Goethals PLM, De Pauw N. 2007. Application of clustering techniques for the characterization of macroinvertebrate communities to support river restoration management. Aquat Ecol 41: 387-398. DOI |
14 | Baum LE. 1972. An equality and associated maximization technique in statistical estimation for probabilistic functions of Markov processes. Inequalities 3: 1-8. |
15 | Baum LE, Petrie T. 1966. Statistical inference for probabilistic functions of finite state Markov chains. Ann Math Stat 37: 1554-1563. DOI |
16 | Beche LA, Resh VH. 2007. Short-term climatic trends affect the temporal variability of macroinvertebrates in California 'Mediterranean' streams. Freshw Biol 52: 2317-2339. DOI |
17 | Brigham AR, Brigham WU, Gnilka A. 1982. Aquatic Insects and Oligochaetes of North and South Carolina. Midwest Aquatic Enterprises, Mahomet, IL |
18 | Brinkhurst RO. 1986. Guide to the Freshwater Aquatic Microdrile Oligochaetes of North America. Department of Fisheries and Oceans, Ottawa. |
19 | Cereghino R, Park YS. 2009. Review of self-organizing Map (SOM) approach in water resources: commentary. Environ Model Softw 24: 945-947. DOI |
20 | Collier KJ. 2008. Temporal patterns in the stability, persistence and condition of stream macroinvertebrate communities: relationships with catchment land-use and regional climate. Freshw Biol 53: 603-616. DOI |
21 | Chon TS, Park YS, Park JH. 2000. Determining temporal pattern of community dynamics by using unsupervised learning algorithms. Ecol Model 132: 151-166. DOI |
22 | Durbin R, Eddy S, Krogh A, Mitchison G. 1998. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids . Cambridge University Press, Cambridge. |
23 | Chon TS. 2011. Self-Organizing Maps applied to ecological sciences. Ecol Inform 6: 50-61. DOI |
24 | Chon TS, Kwak IS, Park YS, Kim TH, Kim Y. 2001. Patterning and short-term predictions of benthic macroinvertebrate community dynamics by using a recurrent artificial neural network. Ecol Model 146: 181-193. DOI |
25 | Dale MB, Dale PER, Li C, Biswas G. 2002. Assessing impacts of small perturbations using a model-based approach. Ecol Model 156: 185-199. DOI |
26 | Gauch HG Jr. 1982. Multivariate Analysis in Community Ecology. Cambridge University Press, Cambridge. |
27 | Ghahramani Z, Jordan MI. 1997. Factorial hidden Markov models. Mach Learn 29: 245-275. DOI |
28 | Hawkes HA. 1998. Origin and development of the biological monitoring working party score system. Water Res 32: 964-968. DOI |
29 | Hill MF, Witman JD, Caswell H. 2004. Markov chain analysis of succession in a rocky subtidal community. Am Nat 164: E46-E61. DOI |
30 | Ver Hoef JM, Cressie N. 1997. Using hidden Markov chains and empirical Bayes change-point estimation for transect data. Environ Ecol Stat 4: 247-264. DOI |
31 | Horn HS. 1975. Markovian processes of forest succession. In: Ecology and Evolution of Communities (Cody ML, Diamond JM, eds). Harvard University Press, Cambridge, MA, pp 196-211. |
32 | Hyun K, Song MY, Kim S, Chon TS. 2005. Using an artificial neural network to patternize long-term fisheries data from South Korea. Aquat Sci 67: 382-389. DOI |
33 | Kohonen T. 2001. Self-Organizing Maps. 3rd ed. Springer- Verlag, Heidelberg. |
34 | Jongman RHG, ter Braak CJF, van Tongerenm OFR. 1995. Data Analysis in Community and Landscape Ecology. Cambridge University Press, Cambridge. |
35 | Juang BH, Rabiner LR. 1991. Hidden Markov models for speech recognition. Technometrics 33: 251-272. DOI ScienceOn |
36 | Karplus K, Sjolander K, Barrett C, Cline M, Haussler D, Hughey R, Holm L, Sander C. 1997. Predicting protein structure using hidden Markov models. Proteins Suppl 1: 134-139. |
37 | Krogh A, Brown M, Mian I, Sjolander K, Haussler D. 1994. Hidden Markov models in computational biology: applications to protein modeling. J Mol Biol 235: 1501-1531. DOI |
38 | Legendre P, Legendre L. 1998. Numerical Ecology. 2nd ed. Elsevier, Amsterdam. |
39 | Liu Y, Lee SH, Chon TS. 2011. Analysis of behavioral changes of zebrafish (Danio rerio) in response to formaldehyde using Self-organizing map and a hidden Markov model. Ecol Model 222: 2191-2201. DOI |
40 | MacDonald IL, Raubenheimer D. 1995. Hidden Markov models and animal behaviour. Biomet J 37: 701-712. DOI |
41 | Merritt RW, Cummins KW. 1996. An Introduction to the Aquatic Insects of North America. Kendall Hunt, Dubuque, IA. |
42 | Park YS, Cereghino R, Compin A, Lek S. 2003. Applications of artificial neural networks for patterning and predicting aquatic insect species richness in running waters. Ecol Model 160: 265-280. DOI |
43 | Park YS, Song MY, Park YC, Oh KH, Choe E, Chon TS. 2007. Community patterns of benthic macroinvertebrates collected on the national scale in Korea. Ecol Model 203: 26-33. DOI |
44 | Resh VH, Rosenberg DM. 1984. The Ecology of Aquatic Insects. Praeger Publishers, New York, NY. |
45 | Pennak RW. 1978. Freshwater Invertebrates of the United States. 2nd ed. Wieley, New York, NY. |
46 | Quach QK, Chon TS, Kim HS, Nguyen TV. 2013. One and two-individual movements of fish after chemical exposure. J Korean Phys Soc 63: 18-27. DOI |
47 | Rabiner L. 1989. A tutorial on hidden Markov models and selected applications in speech recognition. P IEEE 77: 257-286. DOI |
48 | Scarsbrook MR. 2002. Persistence and stability of lotic invertebrate communities in New Zealand. Freshw Biol 47: 417-431. DOI |
49 | Shannon CE, Weaver W. 1949. The Mathematical Theory of Information. University of Illinois Press, Urbana, IL. |
50 | Simon G, Lee JA, Cottrell M, Verleysen M. 2007. Forecasting the CATS benchmark with the double vector quantization method. Neurocomputing 70: 2400-2409. DOI |
51 | Taheri A, Tarihi MR, Abad HBB, Bababeyk H. 2005. Fuzzy hidden Markov models for speech recognition on based FEM Algorithm. In: The Second World Enformatika Conference (Cemal, A, ed.). WEC'05, Feb 25-27, 2005. Enformatika, Canakkale, Turkey, pp 59-61. |
52 | Tang H, Song MY, Cho WS, Park YS, Chon TS. 2010. Species abundance distribution of benthic chironomids and other macroinvertebrates across different levels of pollution in streams. Ann Limnol - Int J Lim 46: 53-66. DOI |
53 | Tucker BC, Anand M. 2003. The use of matrix models to detect natural and pollution-induced forest gradients. Comm Ecol 4: 89-110. DOI |