Tag Archives: agent-based modeling

Software tools for ABMs

A key consideration when embarking on an agent-based modelling focused project is ‘what are we going to write the model in?’. The investment of time and effort that goes into learning a new software tool or a language is so considerable that in the vast majority of cases it is the model that has to be adjusted to the modellers skills and knowledge rather than the the other way round.

Browsing through the OpenABM library it is clear that Netlogo is archaeology’s, social sciences and ecology first choice (51 results), with other platforms and languages trailing well behind (Java – 13 results, Repast – 5 results, Python – 5 results)*. But it comes without saying that there are more tools out there. A new paper published in Computer Science Review compares and contrasts 85 ABM platforms and tools.

It classifies each software package according to the easy of development (simple-moderate-hard) as well as its capabilities (light-weight to extreme-scale). It also sorts them according to their scope and possible subjects (purpose-specific, e.g., teaching, social science simulations, cloud computing, etc., or subject-specific, e.g., pedestrian simulation, political phenomena, artificial life) so that you have a handy list of software tools designed for different applications. This is, to the best of my knowledge, the first survey of this kind since this, equally useful but by now badly outdated, report from 2010.

Abar, Sameera, Georgios K. Theodoropoulos, Pierre Lemarinier, and Gregory M.P. O’Hare. 2017. “Agent Based Modelling and Simulation Tools: A Review of the State-of-Art Software.” Computer Science Review 24: 13–33. doi:10.1016/j.cosrev.2017.03.001.

 

* Note that the search terms might have influenced the numbers, e.g., if the simulation is concerned with pythons (the snakes) it would add to the count regardless of the language it was written in.

Image source: wikipedia.org

Simulados: a short video explaining what ABM is and how we use it to understand the past

This video, brought to you by our friends over at the Barcelona Supercomputing Center, does a great job of explaining in easy-to-understand terms what agent-based modeling is, and how it can be useful for both understanding the past and making the past relevant to the present. No small feat to accomplish in about 3 minutes. Have a look!

Wanna learn about ABM? There’s an app for that

You can now procrastinate for hours learn about agent-based modelling by playing a computer game!

Yep, life research doesn’t get any better than this.

Our colleagues from the Supercomputer Centre in Barcelona and Simulpast have released a game! Evolving Planet has an archaeologically inspired plot, easy to grasp interface and cool graphics making it an absolutely outstanding procrastination tool (what do you mean ‘stop wasting time playing computer games’? I’m doing research here!).

You steer a group of bots trying to achieve tasks such as obtaining resource, arriving at a specific location or influencing another group within precise time brackets. You can give them certain qualities (ability to move faster, a boost to fertility, etc) but the internal workings of the bots are set in stone (well, code), which is a nice way of showing the methodology behind simulation. By manipulating the bots characteristics, what you are in fact doing is testing different behavioural scenarios: would a bigger but slower group be more successful in dispersal? Can you achieve the goal faster with a highly militaristic group or with a friendly ‘influencing’ group?

I breezed through the ‘dispersal’ part but struggled in several of the later missions indicating that the game is very well grounded in the most current research. However, archaeologists who do ABM (of dispersal…) on a daily basis are probably not the target audience since the whole point of the game seems to be helping non-modellers understand what the technique can and what it cannot do and what kind of questions can you approach with it (+ having some fun). So get your non-coding friends on board and hopefully, they won’t get an idea that all we do whole day long is gaming. And even if they do, they’ll join rather than cut our funding.

Evolving Planet can be downloaded from the apple and android app stores for free. For more information: http://evolvingplanetgame.com

 

Image source: Evolving Planet presskit . http://evolvingplanetgame.com

CAA in Atlanta: 2017 dates

The Simulating Complexity team is all coming home from a successful conference in Oslo. Highlights include a 2-day workshop on agent-based modeling led by the SimComp team, a roundtable on complexity and simulation approaches in archaeology, and a full-day session on simulation approaches in archaeology.

We are all looking forward to CAA 2017 in Atlanta. Dates were announced at Oslo, so start planning.

CAA2017 will be held at Georgia State University March 13th-18th. This leaves 2 weeks before the SAAs, so we hope to have a good turnout on simulation and complexity approaches at both meetings!

French Wine: Solving Complex Problems with Simple Models

What approach do you use if you have only partial information but you want to learn  more about a subject? In a recent article, I confronted this very problem. Despite knowing quite a bit about Gaulish settlements and distributions of artifacts, we still know relatively little about the beginnings of the wine industry. We know it was a drink for the elite. We know that Etruscans showed up with wine, and later Greeks showed up with wine. But we don’t know why Etruscan wine all but disappears rapidly within a few years. Is this simple economics (Greek wine being cheaper)? Is this simply that Etruscan wine tasted worse? It’s a question and a conundrum; it simply doesn’t make sense that everyone in the region would swap from one wine type to another. Also, the ceramic vessels that were used to carry the wine—amphorae—those are what we find. They should last for a while, but they disappear. Greek wine takes over, Greek amphorae take over, and Etruscan wine and amphorae disappear.

This is a perfect question for agent based modeling. My approach uses a very simple model of preference, coupled with some simple economics, to look at how Gauls could be drivers of the economy. Through parameter testing I show that a complete transition between two types of wine could occur even when less than 100% of the consumers ‘prefer’ one type.

Most importantly in this model, the pattern oriented approach shows how agent-based modeling can be useful for examining a mystery, even when the amount of information available might be small.

Check the article out on the open source MDPI website.

Everything you ever wanted to know about building a simulation, but without the jargon

I think everyone who had anything to do with modelling came across an innocent colleague/supervisor/another academic enthusiastically exclaiming:

“Well, isn’t this a great topic for a simulation? Why don’t we put it together – you do the coding and I’ll take care of the rest. It will be done and dusted in two weeks!”

“Sure! I routinely build well-informed and properly tested simulations in less than two weeks.” – answered no one, ever.

Building a simulation can be a long and frustrating process with unwelcome surprises popping out at every corner. Recently I summarised the 9 phases of developing a model and the most common pitfalls in an paper published in Human Biology: ‘So You Think You Can Model? A Guide to Building and Evaluating Archaeological Simulation Models of Dispersals‘. It is an entirely jargon free overview of the simulation pipeline, predominantly aimed at anyone who want to start building their own archaeological simulation but does not know what does the process entail. It will be equally useful to non-modellers, who want to learn more about the technique before they start trusting the results we throw at them. And, I hope, it may inspire more realistic time management for simulation projects 🙂

You can access the preprint of it here. It is not as nicely typeset as the published version but, hey!, it is open access.

 

Tim Kohler–The Nine Questions

photo by Roger Cozien

I sat down with Tim Kohler, the creator of the Village Ecodynamics Project agent-based model, professor of anthropology at Washington State University, researcher at Crow Canyon Archaeological Center, and external faculty at the Santa Fe Institute, to discuss his philosophy on complexity science and archaeology, and get some tips for going forward studying complex systems.

How did you get introduced to complexity science:

I took a sabbatical in the mid-1990s and was fortunate to be able to do it at the Santa Fe Institute. Being there right when Chris Langton was developing Swarm, and just looking over his shoulder while he was developing it, was highly influential; Swarm was the original language that we programmed the Village Ecodynamics Project in. Having the opportunity to interact with scientists of many different types at the Santa Fe Institute (founded in 1984) was a wonderful opportunity. This was not an opportunity available to many archaeologists, so one of the burdens I bear, which is honestly a joyful burden, is that having had that opportunity I need to promulgate that to others who weren’t so lucky. This really was my motive for writing Complex Systems and Archaeology in “Archaeological Theory Today” (second edition).

What complexity tools do you use and how?

I primarily use agent-based modeling, although in Complex Systems and Archaeology  I recognize the values of the many other tools available. But I’d point out that I do an awful lot of work that is traditional archaeology too. I recently submitted an article that attempts to look at household-level inequality from the Dolores Archaeological Project data, and this is traditional archaeological inquiry. I do these studies because I think that they contribute in an important way to understanding whether or not an exercise in a structure like the development of leadership model, gives us a sensible answer. This feeds in to traditional archaeology.

In 2014 I published an article calculating levels of violence in the American Southwest. This is traditional archaeology, although it does use elements of complexity. I can’t think of other instances where archaeologists have tried to analyze trajectories of things through time in a phase-space like I did there. The other thing that I do that is kind of unusual in archaeology (not just complexity archaeology) is that I have spent a lot of time and effort trying to estimate how much production you can get off of landscapes. Those things have not really been an end in themselves, although they could be seen as such. However, I approached trying to estimate the potential production of landscapes so that it could feed into the agent-based models. Thus these exercises contribute to complex systems approaches.

What do you think is the unique contribution that complexity science has for archaeology?

I got interested in complexity approaches in early to mid 1990s; during that time when you look around the theoretical landscape there were two competing approaches on offer in archaeology: 1) Processualism (the new archaeology), and the reaction to processualism, 2) Post-processualism, which came from the post-modern critique.

First, with processualism. There has been a great deal of interesting and useful work done through that framework, but if you look at some of that work it really left things lacking. An article that really influenced my feelings on that approach was Feinman’s, famous article “Too Many Types: An Overview of Sedentary Prestate Societies in the Americas” from Advances in Archaeological Method and Theory (1984). He does a nice analysis in the currency of variables having to do with maximal community size, comparison of administrative levels, leadership functions, etc. I would argue that these variables are always a sort of abstraction on the point of view of the analyst. And people, as they are living their daily lives, are not aware of channeling their actions along specific dimensions that can be extracted along variables; people act, they don’t make variables, they act! It’s only through secondary inference that some outcome of their actions (and in fact those of many others) can be distilled as a ‘variable.’ My main objection to processualism is that everything is a variable, and more often these variables are distilled at a very high level abstraction for analysis. Leadership functions, the number of administrative levels… but there’s never a sense in processual archaeology (in my view) for how it is through people’s actions that these variables emerge and these high levels came to be. I thought this was a major flaw in processualism

If you look at post-processulism, at its worst people like Tilley and Shanks in the early 1990s, you have this view of agency… People are acting almost without structures. There’s no predictability to their actions. No sense of optimality or adaptation that structure their actions. Although I would admit that these positions did have the effect of exposing some of the weaknesses in processual archaeology, they didn’t offer a positive program to make a path going forward to understand prehistory.

I thought what was needed was a way to think about the archaeological record as being composed of the actions of agents, while giving the proper role to these sorts of structures that these agents had to operate within (people within societies). I also thought that a proper role needed to be given to concepts like evolution and adaptation that were out the window for the early post-processualists. That is what complexity in archaeology tries to achieve. A complex-adaptive system approach honors actions of individuals but also honors that agents have clear goals that provide predictability to their actions, and that these take place within structures, such as landscapes or ecosystems or cities, that structure these in relatively predictable ways.

How does complexity help you understand your system of interest?

Complexity approaches give us the possibility to examine how high-level outcomes emerge from the outcomes of agent-landscape interaction and agent-agent interaction. These approaches to a great measure satisfy the weaknesses of those the two main approaches from 90s (processualism and post-processualism). So we have both high level outcomes (processualism) and agent level actions (post-processualism) but complexity provides a bridge between these two.

What are the barriers we need to break to make complexity science a main-stream part of archaeology?

Obviously barriers need to be broken. Early on, although this is not the case as much any more, many students swallowed the post-processual bait hook, line and sinker, which made it so they wouldn’t be very friendly to complexity approaches. They were, in a sense, blinded by theoretical prejudices. This is much less true now, and becomes less true each year. The biggest barrier now to entry is the fact that very few faculty are proficient in the tools of complex adaptive systems in archaeology, such as agent based modeling, scaling studies, and faculty even are not proficient with posthoc analyses in tools like R that make sense of what’s going on in these complex systems. Until we get a cadre of faculty who are fluent in these approaches this will be a main barrier.

Right now the students are leading the way in complex adaptive systems studies in archaeology. In a way, this is similar to how processual archaeology started—it was the students who led the way then too. Students are leading the way right now, and as they become faculty it will be enormously useful for the spread of those tools. So all of these students need to get jobs to be able to advance archaeology, and that is a barrier.

Do you think that archaeology has something that can uniquely contribute to complexity science (and what is it)?

I would make a strong division between complex adaptive systems (anything that includes biological and cultural agents) and complex nonadaptive systems (spin glasses, etc.) where there is no sense that there is some kind of learning or adaptation. Physical systems are structured by optimality but there is no learning or adaptation.

The one thing that archaeologists have to offer that is unique is the really great time depth that we always are attempting to cope with in archaeology.

The big tradeoff with archaeology is that, along with deep time depth, we have very poor resolution for the societies that we are attempting to study. But this gives us a chance to develop tools and methods that work with complex adaptive systems specifically within social systems; this, of course, is not unique to archaeology, as it is true for economists, biologists, and economists

What do you think are the major limitations of complexity theory?

I don’t think complexity approaches, so far at least, have had much to say about the central construct for anthropology—culture. Agent-based models, for example, and social network analysis are much more attuned to behavior than to culture. They have not, so far, tried to use these tools to try to understand culture change as opposed to behavioral change. It’s an outstanding problem. And this has got to be addressed if the concept of culture remains central to anthropology (which, by definition, it will). Unless complexity can usefully address what culture is and how it changes, complexity will always be peripheral. Strides have been made in that direction, but the citadel hasn’t been taken.

Does applying complexity theory to a real world system (like archaeology) help alleviate the limitations of complexity and make it more easily understandable?

Many people who aren’t very interested in science are really interested in archaeology. So I think archaeology offers a unique possibility for science generally, and complexity specifically, by being applied to understanding something that people are intrinsically interested in, even if they aren’t interested in other applications of same tools to other problems. It’s non-threatening. You can be liberal or conservative and you can be equally interested in what happened to the Ancestral Puebloans; you might have predilection to one answer or another, but you are still generally interested. But these things are non-threatening in an interesting way. They provide a showcase for these powerful tools that might be more threatening if they were used in an immediate fashion.

What do you recommend your graduate students start on when they start studying complexity?

Dynamics in Human and Primate Societies by Kohler and Gummerman is a useful starting point

I am a big enthusiast for many works that John Holland wrote

Complexity: A Guided Tour by Melanie Mitchell’s is a great volume

I learned an enormous amount by a close reading of Stu Kauffman’s “Origins of Order.” I read this during my first sabbatical at SFI, and if you were to look at the copy you’d see all sorts of marginal annotations in that. We don’t see him cited much nowadays, but he did make important contributions to understanding complex systems.

In terms of technology or classes, the most important things would be for them to get analytical and modeling tools as soon as they could and as early as they can. In the case of Washington State University, taking agent-based modeling course and taking the R and Big Data course would be essential. But to be a good archaeologist you need a good grounding in method and theory, so taking courses that fulfill that as early on as possible is essential.

And a final question…

What are two current papers/books/talks that influence your recent work?

I’m always very influenced by the work of my students. One of my favorites is the 2014 Bocinsky and Kohler article in Nature Communications. Another is upcoming foodwebs work from one of my other students. These papers are illustrative of the powers of complexity approaches. Bocinsky’s article is not in and of itself a contribution to complex adaptive systems in archaeology, except that it is in the spirit of starting off from a disaggregated entity (cells on a landscape) and ending up with a production sequence emerging from that for the system as a whole. It shows how we can get high-level trends that can be summarized by amounts within the maize niche. So it deals, in a funny way, with the processes of emergence. It’s a prerequisite for doing the agent-based modeling work.

Some recent works by Tim Kohler

2014 (first author, with Scott G. Ortman, Katie E. Grundtisch, Carly M. Fitzpatrick, and Sarah M. Cole) The Better Angels of Their Nature: Declining Violence Through Time among Prehispanic Farmers of the Pueblo Southwest. American Antiquity 79(3): 444–464.

2014 (first author, with Kelsey M. Reese) A Long and Spatially Variable Neolithic Demographic Transition in the North American Southwest. PNAS (early edition).

2013 How the Pueblos got their Sprachbund. Journal of Archaeological Method and Theory 20:212-234.

2012 (first author, with Denton Cockburn, Paul L. Hooper, R. Kyle Bocinsky, and Ziad Kobti) The Coevolution of Group Size and Leadership: An Agent-Based Public Goods Model for Prehispanic Pueblo Societies. Advances in Complex Systems15(1&2):1150007.

2012 (first editor, with Mark D. Varien) Emergence and Collapse of Early Villages: Models of Central Mesa Verde Archaeology. University of California Press, Berkeley