Pattern-Oriented Modeling of Agent-Based
Complex Systems: Lessons from Ecology
Volker Grimm,1* Eloy Revilla,2 Uta Berger,3 Florian Jeltsch,4 Wolf M. Mooij,5 Steven F. Railsback,6
Hans-Hermann Thulke,1 Jacob Weiner,7 Thorsten Wiegand,1 Donald L. DeAngelis8
Agent-based complex systems are dynamic networks of many interacting agents; examples
include ecosystems, financial markets, and cities. The search for general principles
underlying the internal organization of such systems often uses bottom-up simulation
models such as cellular automata and agent-based models. No general framework for
designing, testing, and analyzing bottom-up models has yet been established, but recent
advances in ecological modeling have come together in a general strategy we call patternoriented modeling. This strategy provides a unifying framework for decoding the internal
organization of agent-based complex systems and may lead toward unifying algorithmic
theories of the relation between adaptive behavior and system complexity.
W
hat makes James Bond an agent?
He has a clear goal, he is autonomous in his decisions about
achieving the goal, and he adapts these decisions to his rapidly changing situation. We
are surrounded by such autonomous, adaptive
agents: cells of the immune system, plants, citizens, stock market investors, businesses, etc.
The agent-based complex systems (1) (ACSs)
around us are made up of myriad interacting
agents. One of the most important challenges
confronting modern science is to understand
and predict such systems. Bottom-up simulation modeling is one tool for doing so: We
compile relevant information about entities at
a lower level of the system (in Bagent-based
models,[ these are individual agents), formulate theories about their behavior, implement
these theories in a computer simulation, and
observe the emergence of system-level properties related to particular questions (2, 3).
1
UFZ Umweltforschungszentrum Leipzig-Halle, Department Ökologische Systemanalyse, PF 500 136,
04301 Leipzig, Germany. 2Department of Applied Biology, Estación Biológica de Doñana, Spanish Council for
Scientific Research CSIC, Ave. Maria Luisa s/n, E-41013
Seville, Spain. 3Zentrum für Marine Tropenökologie,
Fahrenheitstrasse 6, 28359 Bremen, Germany. 4Institut für Biochemie und Biologie, Universität Potsdam,
Maulbeerallee 2, 14469 Potsdam, Germany. 5Netherlands Institute of Ecology, Centre for Limnology,
Rijksstraatweg 6, 3631 AC Nieuwersluis, Netherlands.
6
Lang, Railsback and Associates and Department of
Mathematics, Humboldt State University, 250 California Avenue, Arcata, CA 95521, USA. 7Botany Section,
Department of Ecology, Royal Veterinary and Agricultural University Rolighedsvej 21, DK-1958 Frederiksberg,
Denmark. 8U.S. Geological Survey/Florida Integrated
Science Centers and Department of Biology, University of Miami, Post Office Box 249118, Coral Gables,
FL 33124, USA.
*To whom correspondence should be addressed.
E-mail: volker.grimm@ufz.de
Bottom-up models have been developed
for many types of ACSs (4), but the identification of general principles underlying the
organization of ACSs has been hampered by
the lack of an explicit strategy for coping
with the two main challenges of bottom-up
modeling: complexity and uncertainty (5, 6).
Consequently, model structure often is chosen
ad hoc, and the focus is often on how to
represent agents without sufficient emphasis
on analyzing and validating the applicability of
models to real problems (5, 7).
A strategy called pattern-oriented modeling
(POM) attempts to make bottom-up modeling
more rigorous and comprehensive (6, 8–10). In
POM, we explicitly follow the basic research
program of science: the explanation of observed patterns (11). Patterns are defining characteristics of a system and often, therefore,
indicators of essential underlying processes
and structures. Patterns contain information on
the internal organization of a system, but in a
Bcoded[ form. The purpose of POM is to
Bdecode[ this information (10).
The motivation for POM is that, for complex systems, a single pattern observed at a
specific scale and hierarchical level is not
sufficient to reduce uncertainty in model structure and parameters. This has long been known
in science. For example, Chargaff_s rule of
DNA base pairing was not sufficient to decode the structure of DNA—until combined
with patterns from x-ray diffraction of DNA
and from the tautomeric properties of the purine and pyrimidine bases (12). Thus, in POM,
multiple patterns observed in real systems at
different hierarchical levels and scales are used
systematically to optimize model complexity
and to reduce uncertainty.
POM was formulated in ecology, a science
with a long tradition of bottom-up modeling.
Ecology, in the past 30 years, has produced as
many individual-based models as all other disciplines together have produced agent-based
models (13), and has focused more on bottomup models that address real systems and problems (14).
We describe here how observed patterns
can be used to optimize model structure, test
and contrast theories for agent behavior, and
reduce parameter uncertainty. Finally, we
discuss POM as a unifying framework for the
science of agent-based complex systems in
general.
Patterns for Model Structure:
The Medawar Zone
Finding the optimal level of resolution in a
bottom-up model’s structure is a fundamental
problem. If a model is too simple, it neglects
essential mechanisms of the real system,
limiting its potential to provide understanding
and testable predictions regarding the problem
it addresses. If a model is too complex, its
analysis will be cumbersome and likely to get
bogged down in detail. We need a way to find
an optimal zone of model complexity, the
‘‘Medawar zone’’ (Fig. 1).
Modeling has to start with specific questions (15). From these questions, we first
formulate a conceptual model that helps us
decide which elements and processes of the
real system to include or ignore. With complex
systems, however, the question addressed by
the model is not sufficient to locate the
Medawar zone because ACSs include too
many degrees of freedom. Moreover, the conceptual model may too much reflect our perspective as external observers, with our specific
interests, beliefs, and scales of perception.
A key idea of POM is to use multiple
patterns observed in real systems to guide
design of model structure. Using observed
patterns for model design directly ties the
model’s structure to the internal organization
of the real system. We do so by asking: What
observed patterns seem to characterize the
system and its dynamics, and what variables
and processes must be in the model so that
these patterns could, in principle, emerge? For
example, if there are patterns in age structure,
sex ratio, and spatial distribution, then age,
sex, and space should be represented in the
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increase model credibility, gain understanding
(18), and address more questions.
In an example from ecological epidemiology, multiple patterns guided the stepwise
design and calibration of a model describing
the spread of rabies among red foxes in central
Europe (22). Observed patterns included the
large-scale wave of rabies prevalence, disease
pockets ahead of the wave, and temporal oscillations of prevalence at local and regional
scales. The resulting model reproduced these
patterns, but not by simply applying a preconceived model structure and then fitting it to
the patterns; instead, one pattern after another
was used to gradually refine model structure
(23). Structural realism of this model is
indicated by the striking match between model
predictions and a long-term data set of hunted
foxes, which combines aspects of rabies epidemiology (before the onset of rabies control),
fox ecology (after control), and their interaction (during control).
In other ACS disciplines, we found only a
few models explicitly addressing multiple patterns, although many models were implicitly based on multiple patterns. A model of
consumer markets (24) addresses three patterns: (i) The statistical distribution of weekly sales of fast-moving consumer goods has
fatter tails and thinner peaks than normal distributions; (ii) there are clusters of high sales
volatility; and (iii) market shares of different
stores follow power-law distributions. Exactly
how these patterns influenced the design of
the model is not clear, but pattern (iii) appears to be why the model is spatially explicit:
Consumer agents only visit stores that are
nearby.
Patterns for Contrasting
Alternative Theories
Agents continuously make decisions to reach
their goals—e.g., survival and reproductive
success, profiting in a stock market, finding
the best place to settle—in an ever-changing
environment. How do we model these decisions? What information do agents have, what
alternatives do they consider, and how do they
predict the consequences of their decisions?
Many studies of ACSs try only one model of
decision-making and attempt to show that it
leads to results compatible with a limited data
set. This practice, however, may lead to the
impression that bottom-up models include so
many parameters that they can be fitted to data
whether or not their structure and processes are
valid.
A more rigorous strategy for modeling
agent decisions, or other bottom-up processes,
is to use ‘‘strong inference’’ (25) by contrasting alternative decision models, or ‘‘theories’’
(3, 6). First, alternative theories of the agent’s
decisions are formulated. Next, characteristic
patterns at both the individual and higher
levels are identified. The alternative theories
Medawar zone
Payoff
model; if we know that agents behave differently at high densities (e.g., are more aggressive), behavior variability should be in the
model. This use of patterns might force us to
include state variables and processes that are
only indirectly linked to the ultimate purpose
of the model and are not part of our initial
conceptual model. Ideally, the patterns used to
design a model occur at different spatial and
temporal scales and different hierarchical levels, because the key to understanding complex
systems often lies in understanding how processes on different scales and hierarchical levels
are bound to each other.
Multiple patterns were key to modeling
spatiotemporal dynamics of the beech forests
of central Europe (Fig. 2). Natural beech forests
are characterized by a spatial mosaic pattern of
successional stages. A cellular automaton model that focused on this pattern only (16) was too
poor in structure to reveal the forest’s internal organization. But the forests have more
characteristic patterns. Different successional
stages have different patterns of vertical structure: e.g., the climax stage has closed canopy
and little understory, and the decaying stage
has canopy gaps and an understory of young
beech. Therefore, a newer model (17, 18) includes four height classes (from seedlings to
upper canopy) (Fig. 2). The model also explicitly represents individual big trees because
canopy gaps are caused by windthrow, an
individual-level process. The model’s structure was thus determined by the multiple
characteristic patterns: The mosaic pattern
determined horizontal spatial scale and resolution, the vertical patterns determined the
need for height classes, and canopy gaps determined that large beeches must be described
individually.
When designed to reproduce multiple patterns, models are more likely to be ‘‘structurally
realistic’’ (10). In particular, model components (e.g., individuals) correspond directly to
observed objects and variables, and processes
correspond to the internal organization of the
real system, so that the model ‘‘not only reproduces the observed real system behavior,
but truly reflects the way in which the real
system operates to produce this behavior’’
[(19), p. 5].
Structurally realistic models can make independent and testable secondary predictions.
The beech forest model, for example, delivered
independent predictions of forest characteristics that were not considered during model
development and testing (20). Predictions of
age structure in the canopy and the spatial
distribution of very old ‘‘giant’’ trees were in
good agreement with observations, considerably increasing the model’s credibility and
justifying a completely new application: tracking woody debris (21). Complexity in patternoriented bottom-up models is not simply a
burden but can provide rich opportunities to
Model complexity
Problem
Multiple
Patterns
Data
Fig. 1. Payoff of bottom-up models versus their
complexity. A model’s payoff is determined not
only by how useful it is for the problem it was
developed for, but also by its structural realism;
i.e., its ability to produce independent predictions
that match observations. If model design is guided
only by the problem to be addressed (which often
is the explanation of a single pattern), the model
will be too simple. If model design is driven by all
the data available, the model will be too complex.
But there is a zone of intermediate complexity
where the payoff is high. We call this the
‘‘Medawar zone’’ because Medawar described a
similar relation between the difficulty of a
scientific problem and its payoff (41). If the very
process of model development is guided by
multiple patterns observed at different scales
and hierarchical levels, the model is likely to end
up in the Medawar zone.
are then implemented in a bottom-up model
and tested by how well they reproduce the
patterns. Decision models that fail to reproduce
the characteristic patterns are rejected, and
additional patterns with more falsifying power
can be used to contrast successful alternatives.
Rigorous techniques can be used to design
experiments and analyze data (6, 26).
As an example, consider the well-known
‘‘boids’’ model (27) that produces schoolinglike behavior from a simple theory: Individual
boids try to avoid collisions, match the velocity
of neighboring individuals, and stay close to
neighbors. The emergence of aggregations
resembling fish schools from this theory (Fig.
3), however, does not prove that boids explains
schooling in real fish.
To define theory for schooling of real fish,
Huth (28) used observed patterns and contrasted alternative theories for fish behavior.
Two patterns characterizing fish schools were
defined and quantified: polarization and nearest neighbor distance (Fig. 3). Eleven alternative theories for how fish adapt swimming
speed and direction were formulated. In the
first nine theories, the influence of neighbors is
averaged; but in two theories, fish adjust their
swimming to only one neighbor—e.g., the one
Fig. 2. Pattern-oriented model design. Observed patterns that characterize old-growth beech forests [(A); images: front, M.
Flade; right, C. Rademacher; top, S. Winter] include a horizontal mosaic of developmental stages [(B); x scale: 400 m; modified
from (42)], the vertical patterns of tree size that define the developmental stages [(C), showing the late decaying stage;
x scale: È60 m; modified from (43)], and distributions of fallen large trees [(D), a map of fallen wood; ellipses indicate crown
projections of standing trees; x scale: È60 m; modified from (43)]. To allow these patterns to emerge from it, the model
includes a grid-based horizontal structure [(E), showing grid cells in three developmental stages; x scale: 570 m], a grid-based
vertical structure [(F), showing each grid cell’s percentage cover for four height classes; total area shown: 1 ha)], and
individual representation of large trees [(G), showing one cell’s trees in the largest two height classes; cell area: 204 m2); (E)
to (G) modified from (18)].
closest in front. These two ‘‘priority’’ theories
failed to reproduce realistic polarization values
(Fig. 3), eliminating them as valid theory.
This example shows that looking at one
pattern may not be sufficient to falsify weak
theory: Looking at nearest neighbor distance
alone suggested that both types of schooling
model produce similar results, but in fact the
priority theories produce schools only as compact, but not as polarized, as real schools.
Moreover, the nine theories based on averaging
differ widely in assumptions, but the fish school’s
properties turned out to be robust to these
assumptions. Demonstrating robustness is also
key to a bottom-up model’s credibility, because it
indicates that we captured the most important
mechanisms. Huth and Wissel’s model also
reproduced several additional patterns not
considered during model development, providing further support for its structural realism.
This pattern-oriented theory development
approach is increasingly used in models of
ACS. Railsback and Harvey (9) used a stream
trout model to contrast three theories for how
individual fish select habitat. Only a new
theory that assumes that fish select habitat to
maximize expected survival over a future
period reproduced observed patterns of feeding
hierarchy, response to competing species and
predatory fish, seasonal habitat shifts, and
response to reduced food availability. Although
these patterns are each qualitative, or ‘‘weak,’’
together they were able to falsify all but one
theory of habitat selection.
In a model exploring what determines the
access of nomadic herdsmen to pasture lands
owned by village farmers in north Cameroon,
herdsmen negotiate with farmers for access to
pastures (29). Two theories of the herdsmen’s
reasoning were contrasted: (i) ‘‘cost priority,’’
in which herdsmen only consider one dimension of their relationship to farmers—costs;
and (ii) ‘‘friend priority,’’ in which herdsmen
remember the number of agreements and
refusals they received in previous negotiations.
Real herdsmen sustain a social network across
many villages through repeated interactions,
a pattern reproduced only by the ‘‘friend
priority’’ theory.
In economics, agent-based model experiments have been used to identify characteristics of artificial stock market investors that
reproduce patterns well known from real stock
markets (30). These patterns include continual
and unpredictable stock price volatility, high
skew and kurtosis in the distribution of profits
among investors, and an inverse relation between current investment profits and future
price instability. Two assumptions were
contrasted about how much historic data
investors use to predict the outcome of their
investment decisions: (i) Investors all use 25year memories of market data, versus (ii)
memory varies from 0.5 to 25 years. Although
ally refine models by
patterns.
none of the simulations reproduced all
the observed market
patterns, the assumption that all investors
use 25-year memories
failed to reproduce
the most basic pattern: price volatility.
This pattern-oriented
analysis indicates
that individual variation in investment
decision-making is
crucial to stock market dynamics.
Testing and contrasting alternative
theories or decision
models has several
bene fits. W e a re
forced to be explicit
about how decision
models are formulated and tested; we
can demonstrate how
important the specific formulation of
a decision—or any
other low-level—
model is; we can explore null models;
and we can continuapplying additional
Patterns for Parameters:
Coping with Uncertainty
Pattern-oriented modeling can reduce uncertainty in model parameters in two ways. First,
it helps make models structurally realistic,
which usually makes them less sensitive to
parameter uncertainty (31). For example, an
individual-based coyote population model
reproduced an array of observed patterns with
no fine-tuning of parameter values taken from
the literature (32). The trout model (9) had
four parameters that were particularly uncertain yet important; each had relatively
independent effects on four different outputs
(size versus abundance, for juveniles versus
adults), so they could be calibrated manually
and independently.
Second, the realism of structure and mechanism of pattern-oriented models helps parameters interact in ways similar to interactions
of real mechanisms. It is therefore possible
to fit all calibration parameters by finding
values that reproduce multiple patterns simultaneously. This technique is known as ‘‘inverse modeling’’ (33). For a spatially explicit
individual-based model of brown bear dispersal from Slovenia into the Alps (34), a
global sensitivity analysis of the uncalibrated
parameter set revealed high uncertainty in
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Polarization
Nearest neighbor
distance
model output. To reA
B 1.5
duce this uncertainty,
two data sets were
1.0
used to identify five
patterns. Quantitative criteria for the
0.5
agreement between
observed and simulated patterns were
0.0
0 1 2 3 4 5 6 7 8 9 10 11
developed. The in60
direct modeling analysis started with 557
50
random parameter
40
sets covering the plausible ranges of all pa30
rameters. The five
20
observed patterns
were used as filters:
10
Only 10 of the 557
0 1 2 3 4 5 6 7 8 9 10 11
parameter sets reModel version
produced all of them.
Fig.
3.
Strong
inference
by
contrasting
alternative
theories
of
the
agents’
behavior.
Boids
(27)
is
a
conceptual model that
This parameter fildemonstrates how schools or flocks can emerge from simple rules for behavior [(A); a version of boids by H. Hildenbrandt (44)]. (B)
tering reduced the
In a similar model of fish schools (28, 45), 11 alternative theories of fish behavior were contrasted by looking at two school-level
model’s global sen- patterns: polarization ( p) and nearest neighbor distance (NND); p is 0- if all fish swim in the same direction and p approaches 90sitivity by a factor if all fish swim in random directions. Values of p observed in real fish schools are 10- to 20-; observed NND is often G1 fish body
of 4 (fig. S1).
length. In model versions 1 to 9, the influence of neighbor fish is averaged; in model version 10 and 11 (shaded), fish select a single
Indirect parame- neighbor fish and orient their swimming to this neighbor only.
terization is routine
in physical process models (i.e., in chemistry,
hydrology, and climate modeling), but rare
so far in models of ACSs. An encouraging
exception is the agent-based model of an
ancient society, the Kayenta Anasazi, who
occupied the Long House Valley in northeastern Arizona (United States) until 1300
A.D. Paleoenvironmental and archaeological
records permitted the development of a detailed, spatially explicit agent-based model of
this society and its history (35). These data
include estimates of annual potential maize
production for each hectare in the study area
for the period 400 to 1400 A.D. and records of
human settlement in the valley. Theories for
agent decisions, for example, splitting households and moving, were based on detailed regional ethnographies.
The model includes variability in mortality,
fertility, splitting of households, and maize
harvest rates; with eight unknown parameters.
To evaluate these parameters indirectly, the
time series of the number of simulated households was compared to the historical record.
The best parameter set reproduced all imFig. 4. Parameterization and independent predictions of an agent-based model of the Anasazi in
portant trends and population sizes in the ar- the Long House Valley [modified from (35)]. The simulation environment consists of an 80 by 120
chaeological record. This parameter set also grid of 1-ha squares. Dark gray represents a higher water table; light gray and blue represent a
reproduced important features of the spatial lower water table. White is nonfarmable land. The red dots represent settlements. (Left) The
distribution of the settlements (Fig. 4) and the historical settlement in 1125 A.D.; (right) prediction of the simulation model for the same year.
gradual northward movement of the popula- The match between data and simulation is imperfect, but the clustering of settlements along the
tion. These spatial patterns can be considered valley boundaries is captured by the model. The model was calibrated not to the settlement
patterns but to the population size time series for 400 to 1450 A.D.
independent predictions, strong indicators of
the model’s structural realism.
entities are physical objects such as atoms agents’’ (36); see also table S1]. However,
Implications and Future Directions
and stars, or are relatively easy to represent, POM is the first attempt to explicitly formulate
Patterns are widely used by many modelers,
such as flocking birds, pedestrians in a a rigorous and comprehensive strategy for
particularly in disciplines where the low-level
panicking crowd, or car drivers [‘‘Brownian
modeling ACSs. The POM strategy is a
way to focus on the most essential information about a complex system’s internal organization. Multiple patterns keep us from
building models that are too simple in structure and mechanism, or too complex and
uncertain. Using patterns to test and contrast
alternative theories for agent behavior or
other low-level processes is a way for the
science of ACS to get beyond clever demonstration models and on to rigorous explanations of how real systems are organized and
how they respond to internal and external
forces. POM is just taking root, and we expect to see its rapid development in the near
future.
Bottom-up models are virtual laboratories
where controlled experiments distinguish
noise from signal in the system’s organization. In particular, experiments contrasting
hypotheses for the behavior of interacting
agents will lead to an accumulation of theory
for how the dynamics of systems from molecules to ecosystems and economies emerge
from bottom-level processes. This approach
may change our whole notion of scientific
theory, which until now has been based on
the theories of physics. Theories of complex
systems may never be reducible to simple
analytical equations, but are more likely to
be sets of conceptually simple mechanisms
(e.g., Darwinian natural selection) that produce different dynamics and outcomes in
different contexts. POM thus may lead us to
an algorithmic (37), rather than analytical,
approach to theory.
References and Notes
1. ‘‘Agent-based complex systems’’ (ACSs) are often
referred to as ‘‘complex adaptive systems,’’ but we
prefer ACS because it is not clear whether systems
are really adaptive, which would require that they
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nonrandom structure and therefore containing information on the mechanisms from which they
emerge. Complex systems contain patterns at different hierarchical levels and scales. Ecosystems, for
example, contain patterns in primary production,
species diversity, spatial structure, dynamics of component species populations, behavior of individual
organisms, resource dynamics, and response of all
these to disturbance events and stress. Useful patterns need not be striking; qualitative or ‘‘weak’’ patterns can be powerful in combination. For example,
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Fischer Verlag, Stuttgart, Jena, New York, 1995).
44. See www.rug.nl/biologie/onderzoek/onderzoekgroepen/
theoreticalbiology/peoplePages/hannoPage.
45. A. Huth, C. Wissel, Ecol. Model. 75–76, 135 (1994).
46. We thank L. Tesfatsion, P. Johnson, B. LeBaron, and
T. Kohler for hints to relevant literature; S. Winter,
M. Flade, and C. Rademacher for providing photos;
H. Hildenbrandt for Fig. 3A; and three anonymous
referees for valuable comments.
Supporting Online Material
www.sciencemag.org/cgi/content/full/310/5750/987/
DC1
SOM Text
Fig. S1
Table S1
References and Notes
10.1126/science.1116681
Supporting Online Material for
Pattern-Oriented Modeling of Agent-Based Complex Systems:
Lessons from Ecology
Volker Grimm,* Eloy Revilla, Uta Berger, Florian Jeltsch, Wolf M. Mooij,
Steven F. Railsback, Hans-Hermann Thulke, Jacob Weiner, Thorsten Wiegand,
Donald L. DeAngelis
*To whom correspondence should be addressed. E-mail: volker.grimm@ufz.de
This PDF file includes:
SOM Text
Fig. S1
Table S1
References and Notes
1
Supporting Online Material
Pattern-oriented Modeling of Agent-based Complex Systems: Lesson from Ecology
Volker Grimm, Eloy Revilla, Uta Berger, Florian Jeltsch, Wolf M. Mooij, Steven
F. Railsback, Hans-Hermann Thulke, Jacob Weiner, Thorsten Wiegand, Donald L. DeAngelis
1. References directly addressing pattern-oriented modeling
2. Recent reviews on bottom-up modeling
3. Example of indirect, pattern-oriented parameterization
4. Use of patterns in bottom-up models of different disciplines
1 References directly addressing pattern-oriented modeling
DeAngelis, D. L., and W. M. Mooij. 2003. In praise of mechanistically-rich models. Pages
63-82 in C. D. Canham, J. J. Cole, and W. K. Lauenroth, editors. Models in Ecosystem
Science. Princeton University Press, Princeton, New Jersey.
Eisinger, D., H.-H. Thulke, T. Selhorst, and T. Müller. 2005. Emergency vaccination of rabies
under limited resources - combating or containing? BMC Infectious Diseases 5 : 10.
Grimm V (1994) Mathematical models and understanding in ecology. Ecological Modelling
75/76:641-51.
Grimm, V., K. Frank, F. Jeltsch, R. Brandl, J. Uchmanski, and C. Wissel. 1996. Patternoriented modelling in population ecology. Science of the Total Environment 183:151166.
Grimm, V., and U. Berger. 2003. Seeing the forest for the trees, and vice versa: patternoriented ecological modelling. Pages 411-428 in L. Seuront, and P. G. Strutton,
editors. Handbook of Scaling Methods in Aquatic Ecology: Measurement, Analysis,
Simulation. CRC Press, Boca Raton.
Grimm V., and S. F. Railsback. 2005. Individual-based Modeling and Ecology. Princeton
University Press, Princeton, N.J.
Grimm V, Railsback SF. In press. Agent-based models in ecology: from patterns to theory. In:
F. Billari, T. Fent, A. Fuernkranz-Prskawetz, J. Scheffran, editors. Agent-based
Modelling in Demography, Economics and Environmental Sciences. Physica Verlag,
Heidelberg.
Kramer-Schadt, S., E. Revilla, T. Wiegand, and U. Breitenmoser. 2004. Fragmented
landscapes, road mortality and patch connectivity: modelling influences on the
dispersal of Eurasian lynx. Journal of Applied Ecology 41:711-723.
Railsback, S. F. 2001. Getting “results”: the pattern-oriented approach to analyzing natural
systems with individual-based models. Natural Resource Modeling 14:465-474.
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Railsback, S. F., and B. C. Harvey. 2002. Analysis of habitat selection rules using an
individual-based model. Ecology 83:1817-1830.
Railsback, S. F., B. C. Harvey, R. H. Lamberson, D. E. Lee, N. J. Claasen, and S. Yoshihara.
2002. Population-level analysis and validation of an individual-based cuthroat trout
model. Natural Resource Modeling 14:465-474.
Railsback, S. F., B. C. Harvey, J. W. Hayse, and K. E. LaGory. 2005. Tests of theory for diel
variation in salmonid feeding activity and habitat use. Ecology 86:947-959.
Revilla, E., T. Wiegand, F. Palomares, P. Ferreras, and M. Delibes. 2004. Effects of matrix
heterogeneity on animal dispersal: from individual behavior to metapopulation-level
parameters. American Naturalist 164:E130-E153.
Schadt, S., F. Knauer, P. Kaczensky, E. Revilla, T. Wiegand, and L. Trepl. 2002. Rule-based
assessment of suitable habitat and patch connectivity for the Eurasian lynx. Ecological
Applications 12:1469-1483.
Wiegand, T., J. Naves, T. Stephan, and A. Fernandez. 1998. Assessing the risk of extinction
for the brown bear (Ursus arctos) in the Cordillera Cantabrica; Spain. Ecological
Monographs 68:539-570.
Wiegand, T., F. Jeltsch, I. Hanski, and V. Grimm. 2003. Using pattern-oriented modeling for
revealing hidden information: a key for reconciling ecological theory and conservation
practice. Oikos 100:209-222.
Wiegand, T., E. Revilla, and F. Knauer. 2004. Dealing with uncertainty in spatially explicit
population models. Biodiversity and Conservation 13:53-78.
2 Recent reviews on bottom-up modeling
Axelrod, R. 2003. Advancing the Art of Simulation in the Social Sciences. Japanese Journal
for Management Information System 12: 16-22.
Bonabeau, E. 2002. Agent-based modeling: methods and techniques for simulating human
systems. P. Natl. Acad. Sci. USA 99, suppl. 3:7280-7287.
Bousquet, F., and C. Le Page. 2004. Multi-agent simulations and ecosystem management: a
review. Ecological Modelling 176:313-332.
DeAngelis, D. L., W. M. Mooij, and A. Basset. 2003. The importance of spatial scale in the
modeling of aquatic ecosystems. Pages 383-400 in L. Seuront, and P. G. Strutton
editors. Handbook of Scaling Methods in Aquatic Ecology: Measurement, Analysis,
Simulation. CRC Press, Boca Raton.
Giske, J., G. Huse, and O. Fiksen. 1998. Modelling spatial dynamics of fish. Reviews in Fish
Biology and Fisheries 8:57-91.
Grimm, V. 1999. Ten years of individual-based modelling in ecology: What have we learned,
and what could we learn in the future? Ecological Modelling 115:129-148.
Huse, G., J. Giske, and A. G. V. Salvanes. 2002. Individual-based modelling. Pages 228-248
in P. J. B. Hart, and J. Reynolds editors. Handbook of Fish and Fisheries. Blackwell,
Oxford.
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Jeltsch, F., and K. A. Moloney. 2003. Spatially-explicit vegetation models: what have we
learned? Progress in Botany 63:326-343.
Kreft, J.-U., C. Picioreanu, J. W. T. Wimpenny, and M. C. M. van Loosdrecht. 2001.
Individual-based modeling of biofilms. Microbiology 147:2897-2912.
LeBaron, B. 2000. Agent-based computational finance: suggested readings and early research.
Journal of Economic Dynamics & Control 24:679-702.
LeBaron, B. 2001. A builder’s guide to agent-based financial markets. Quantitative Finance
1: 254-261.
Macy, M., Willer, R. 2001. From Factors to Actors. Annual Review of Sociology 28: 143-166.
Parker, D. C., S. M. Manson, M. A. Janssen, M. J. Hoffmann, and P. Deadman. 2003. Multiagent systems for the simulation of land-use and land-cover change: a review. Annals
of the Association of American Geographers 93:314-337.
Rosser, J.B. Jr. 1999. On the Complexities of Complex Economic Dynamics. The Journal of
Ecoconomic Perspectives 13: 169-192.
Tesfatsion, L. 2002. Agent-based computational economics: growing economies from the
bottom up. Artificial Life 8:55-82.
Uchmanski, J. 2003. Ecology of individuals. Pages 275-302 in R. S. Ambasht, and N. K.
Ambasht, editors. Modern Trends in Applied Terrestrial Ecology. Plenum Pr., New
York.
Werner, F. E., J. A. Quinlan, R. G. Lough, and D. R. Lynch. 2001. Spatially explicit
individual-based modeling of marine populations: a review of advances in the 1990s.
Sarsia 86:411-421.
Wissel, C. 2000. Grid-based models as tools for ecological research. Pages 94-115 in U.
Dieckmann, R. Law, and J. A. J. Metz, editors. The Geometry of Ecological
Interactions: Simplifying Spatial Complexity. Cambridge University Press,
Cambridge.
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3 Example of pattern-oriented, indirect parameterization
Figure S1. Pattern-oriented parameterization of an individual-based model describing the
spread of brown bears from Slovenia into the Austrian Alps. (A) Filters (=patterns) for
parameterization: (1) area with low female density; observed bear density classes (darker
shading indicates higher density) in (2) Central Austria, (3) the Carnic Alps, (4) and the
Karawanken; (5) time series of females with cubs of the year (COY) in Central Austria; (B)
Number of parameterizations that pass the filters, i.e., reproduce the observed patterns; (C)
Mean (red bars) and coefficient of variation (black bars) of the growth rate of the overall bear
population produced by parameterizations that passed the filters or combinations of filters.
(B-D: Modified after (S1)).
4
5
4 Use of patterns in bottom-up models of different disciplines
Table S1. Example bottom-up models of real complex systems in which multiple observed patterns are used for system identification, hypothesis
testing, or parameterization.
Discipline
Problem
Model type
Observed patterns
Reference
Climate change
Recent southern hemisphere climate
change
Three-dimensional
grid-based
Vertical and horizontal structure and amplitude of
geopotential height and temperature trends, direction
and strength of near-surface winds
(S2)
Ecology
Species composition and spatial
patterns in mussel beds
Grid-based
Gap size distribution; community composition
(S3)
Ecology
Abrupt changes in overwintering
location of Atlantic herring
Individual-based
Abrupt changes in overwintering locations of herring
schools coincide with years of extremely high
recruitment.
(S4)
Ecology
Effects of landscape heterogeneity on Individual- and grid- Twenty-two patterns at three levels of temporal
individual dispersal behaviour in lynx based
resolution; e.g. maximum and final dispersal
distances, habitat selection
Epidemiology
Detection of epidemics, and
vaccination programs in large cities
Agent-based (based
on traffic model
TRANSIM)
Traffic flow density; jam wave propagation; activity
(S6)
patterns; contact patterns among demographic groups,
etc.
Epidemiology
Spread of raccoon rabies in
heterogeneous landscapes
Grid-based
Spatiotemporal pattern of rabies spread into
uninfected areas; times of first infection
Material science
Formation of nanoporosity in
corroding alloys
Individual-based
Nanopore morphology; dissolution current versus
(Kinetic Monte Carlo overpotential
simulation of
individual atoms)
(S8)
Morphogenesis
research
Mutation-induced disruption of
polarity of hair cells of Drosophila
Grid-based with
reaction-diffusion
(S9)
Qualitative features of spatial hair patterns
(S5)
(S7)
5
6
equations
Paleobiology
Human cause of late-Pleistocene
megafaunal mass extinction in
America
Grid-based with
difference equations
Overall extinction rates; human population density;
rates of animal consumption by humans; temporal
overlap of humans and extinct species
(S10)
Statistical
physics
Understanding and managing escape
panics
Agent-based
Nine patterns identified from reports, video materials, (S11)
etc., e.g. “people move or try to move faster than
normal”
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7
Supporting References
S1. Wiegand, T., E. Revilla, and F. Knauer. Dealing with uncertainty in spatially explicit
population models. Biodiversity and Conservation 13:53-78, 2004.)
S2. Gillett, N. P., and D. W. J. Thompson. 2003. Simulation of recent southern hemisphere
limate change. Science 302:273-275.
S3. Wootton, J. T. 2001. Local interactions predict large-scale pattern in empirically derived
cellular automata. Nature 413:841-844.
S4. Huse, G., S. Railsback, and A. Fernö. 2002. Modelling changes in migration pattern of
herring: collective behaviour and numerical domination. Journal of Fish Biology 60:571582.
http://www.humboldt.edu/~ecomodel/clupeoids.htm
S5. Revilla, E., T. Wiegand, F. Palomares, P. Ferreras, and M. Delibes. 2004. Effects of
matrix heterogeneity on animal dispersal: from individual behavior to metapopulationlevel parameters. American Naturalist 164:E130-E153.
http://www.journals.uchicago.edu/AN/journal/issues/v164n5/40364/40364.html
S6. Eubank, S., H. Guclu, V. S. A. Kumar, M. V. Marathe, A. Srinivasan, Z. Toroczkai, and
N. Wang. 2004. Modelling disease outbreaks in realistic urban social networks. Nature
429:180-184.
http://www.nature.com/nature/journal/v429/n6988/extref/nature02541-s1.htm
S7. Russell, C. A., D. L. Smith, L. A. Waller, J. E. Childs, and L. A. Real. 2004. A priori
prediction of disease invasion dynamics in a novel environment. Proceedings of the
Royal Society London B 271:21-25.
S8. Erlebacher, J., M. J. Aziz, A. Karma, N. Dimitrov, and K. Sieradzki. 2001. Evolution of
nanoporosity in dealloying. Nature 410:450-453.
S9. Amonlirdviman, K., N. A. Khare, D. R. P. Tree, W.-S. Chen, J. D. Axelrod, and C. J.
Tomlin. 2005. Mathematical modeling of planar cell polarity to understand domineering
nonautonomy. Science 307:423-426.
http://www.sciencemag.org/cgi/content/full/307/5708/423/DC1
S10.Alroy, J. 2001. A multispecies overkill simulation of the end-pleistocene megafaunal
mass extinction. Science 292:1893-1896.
http://www.sciencemag.org/cgi/content/full/292/5523/1893/DC1
S11.Helbing, D., I. Farkas, and T. Vicsek. 2000. Simulating dynamics features of escape
panic. Nature 407:487-491.
http://www.helbing.org/ http://angel.elte.hu/~panic/
http://www.journals.royalsoc.ac.uk/app/home/contribution.asp?wasp=5n5d6mlqmm3krgl
xgndm&referrer=parent&backto=issue,4,15;journal,28,184;linkingpublicationresults,1:10
2024,1
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