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Exploring Replication and Reproducibility in Avida: Understanding Stochastic Systems

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This presentation delves into the critical topics of replication and reproducibility within the context of computational science, specifically using Avida as a case study. It covers the fundamental differences between replication and reproducibility, exploring how identical and similar results can emerge under varying parameters. The presentation also addresses the challenges of replicating results, especially in stochastic systems where random number generators influence outcomes. Key factors affecting reproducibility, such as software versions and hardware, are discussed, emphasizing the importance of consistent experimental conditions for scientific integrity.

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Exploring Replication and Reproducibility in Avida: Understanding Stochastic Systems

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Presentation Transcript

  1. Replication & misc BEACON CLASS Sep 24th

  2. Today’s topics Replication and reproducibility How much memory does Avida use? Saving highly evolved critters.

  3. Replication vs Reproducibility • Replication: identical results. • Same parameters => same results • Reproducibility: similar results. • Similar parameters => similar results • (What’s “similar”?) • Corroboration: • Similar results seen in a different system

  4. First: why did everyone get different results?

  5. Avida is stochastic • You really don’t want to run exactly the same simulation every time you fix parameters…! • But computers aren’t (shouldn’t be) random! So how?? • “Pseudo-random number generator” • Basically, take a number. Generate another number from it using a deterministic process, but make the process return a very different number from the first one, using complex math functions.

  6. Avida is stochastic But this just pushes the problem back – how do you choose that first number differently for each run!? …take the time of day and use that as your random “seed”, from which all your other numbers will be generated. This “seed” can then be used to replicate the run exactly.

  7. Avida is stochastic So, if two of you had run Avida at the same microsecond, you should have gotten the same results!

  8. Suppose… You cannot replicate the results in the 2003 paper. What are your options? (Posit no evildoing)

  9. Suppose… You find a copy of the source from 2003, and run the same program with the same parameters. And you get different results! Why might this happen?

  10. Suppose… You get a copy of the source from 2003, and you run it hardware from 2003, and still get different results!?

  11. What should our standards be? For scientists, reproducibility is extremely important. Replication … less so. It’s very challenging to exactly replicate a given experimental situation. But, there is a pragmatic reason to think about replication, too.

  12. Replication in computational science • We have spent mucho time making sure that computers do the same thing every time, at the micro level. • If you observe unplanned variation in a computational system, then: • You either are using one of the approximate subsystems, like floating point; • Oryou have a bug.

  13. Replication in computational science • So, proximate to an experiment, you should be able to exactly replicate a particular result from a computational experiment. • Then, changing • Data sets • Hardware • Underlying software • …may result in observed differences.

  14. Engineering vs Science mindset Engineering mind set is aimed at construction. They care if it does as they intended it to do, and if they can reproduce the construction process. Scientists are trying to constrain the situation and figure out which characteristics are general and which ones aren’t.

  15. Computer architecture

  16. Example: mowing the lawn

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