Category Archives: research

Phil 7.29.19

7:00 – 4:30 ASRC GEOS

  • Dissertation
    • Added paragraph on movement through information
    • Fill in section on my hut/contributions
    • Register for 899, check that I got the reimbursement
  • Get boarding pass at 9:35 – done
  • More data ingestor – done
  • Create TAAS folder and add Anthill and mapping papers, put in overleaf – done
  • Ping Aaron on IEEE paper and map comments – done
    • Aaaaaaaaaaaaand rejected, with no comments. Need to look for another venue. The Atlantic?
  • Ping David on Map comments and Tues/Wed cat sitting – done
  • Generalize cube, size in 3 dimensions and normals from cross products
  • Change cylinder so that normals are from cross products
  • Start on sphere and cone?
  • Rank JR ideas and send sql to Panos, Chris – done
  • Look at Panos paper? – not yet

Phil 7.24.19

7:00 – 4:00 ASRC GEOS

  • Write up my impression of yesterday’s game – done
  • Put together a Google Form to get everyone else’s impression – done
    • Understanding the map
    • Using the map
    • The effect of the map on gameplay and enjoyment
  • Send Don routes for ebike – done
  • Maybe get started on Martindale?
  • Start setting up Heera’s github – done
  • More graphics at Mission drive (bring fixee from home!)
    • Adding class to handle mouse button events – done
    • Refactoring the classes out of the file
    • Working on caps for the cylinder
  • Send Chris and Panos the anonymized sql, and rank the questions for difficulty
  • Various meetings

Phil 7.23.19

7:00 – 7:00 ASRC PhD

Phil 7.19.19

7:00 – 4:30 ASRC GEOS


  • Still looking at what’s wrong with my NK model. I found Random Boolean Networks, when looking for “random binary networks kauffman example“. It also has a bibliography that looks helpful as well
    • Introduction to Random Boolean Networks
      • The goal of this tutorial is to promote interest in the study of random Boolean networks (RBNs). These can be very interesting models, since one does not have to assume any functionality or particular connectivity of the networks to study their generic properties. Like this, RBNs have been used for exploring the configurations where life could emerge. The fact that RBNs are a generalization of cellular automata makes their research a very important topic. The tutorial, intended for a broad audience, presents the state of the art in RBNs, spanning over several lines of research carried out by different groups. We focus on research done within artificial life, as we cannot exhaust the abundant research done over the decades related to RBNs.
      • I can add a display that shows this: Trajectory
      • Got that working
      • Rewrote so that there is an evolve without a fitness test. Trying to set up transition patterns like this: Transitions
      • The thing is, I don’t see how the K part works here…
      • I think I got it working!
    • Complex and Adaptive Dynamical Systems: A Primer
      • An thorough introduction is given at an introductory level to the field of quantitative complex system science, with special emphasis on emergence in dynamical systems based on network topologies. Subjects treated include graph theory and small-world networks, a generic introduction to the concepts of dynamical system theory, random Boolean networks, cellular automata and self-organized criticality, the statistical modeling of Darwinian evolution, synchronization phenomena and an introduction to the theory of cognitive systems. 
        It inludes chapter on Graph Theory and Small-World Networks, Chaos, Bifurcations and Diffusion, Complexity and Information Theory, Random Boolean Networks, Cellular Automata and Self-Organized Criticality, Darwinian evolution, Hypercycles and Game Theory, Synchronization Phenomena and Elements of Cognitive System Theory.

Phil 7.16.19

7:00 – 6:30ASRC GEOS

  • Working more on NK Models. I have the original paper – Towards a general theory of adaptive walks on rugged landscapes, and I’ve pulled out my copy of The Origins of Order
    • Determine if I have the evaluation function right
    • Add mutation
    • Draw the networks
    • Draw an N/K/Fitness landscape?
    • As an aside, I think that an NK model can be modified to use backpropagation rather than mutation. That could be interesting.
    • Ok, here’s everything working the way I think it should work, but I’m not sure it’s right….
  • Need to get back to Antonio about authorship and roles. I think that it makes sense if he can get a sense of what – done
  • Discovered the trumptwitterarchive, which is downloadable. Would like to build a network of the retweets and tagging by sentiment, gender and race.
  • Code review with Chris. Unfortunately, it was more like an interrogation than a tour. My sense is that he was expecting us to ask questions and we were expecting a presentation.
    • It went ok, but the audio connection was terrible

Phil 7.15.19

7:00 – 5:30 ASRC GEOS

  • Talked to David about his experience in the dungeon and with the map on the way down to Skyline Drive yesterday. It didn’t work for him, and I asked hip to write up his thoughts, particularly:
    • How you approach problems (quiet, listen, if the point bets mentioned by someone else, that’s sufficient)
    • A brief description of your experience (learning that you don’t talk to goblins, etc)
    • A paragraph that talks about your reaction to the map during gameplay. Why you think it didn’t work, and the observations of how the other players seemed to use it based on questionable assumptions?
  • Dissertation. Finished up the first pass at Bacharach
    • Started Kaufmann. Tried to get Mathpix to work, but NVIDIA is grabbing the ctrl-alt-m and it seems I can’t stop that
  • Working on adding network visualization to timeseriesML, which we’ll need for visualizing cluster membership changes, and I need it for NK models
    • Writing up some code that will produce visualizable NK Models, which doesn’t seem to be out there?

Phil 7/1/19

7:00 –  6:00 ASRC

  • Updated ADP Job performance
  • Submitted JASSS Paper
  • Discovered the ComSES Network. It’s a repository for models, a job board, and a schedule with deadlines for ABM-related conferences and workshops!
  • First Tymora run with the map today!
    • It went well, I think. My main takeaway is that the place terms are working fine, but the space terms may need more context. It may be that an excerpt from the story that reflects the most common terms may be better than the terms in isolation.
    • The players stayed away from the stairs, and actually turned them to their advantage, using them as a defensive position.
    • The players went through the orb room very fast, and seemed to base their thinking on aspects of the map.
    • The crypticness of the map seems to help the games aspects. The terms are interpretable, and the ambiguity supports the agency of the players

Phil 6.28.19

7:00 – 8:00 ASRC GEOS

  • Early timesheet
  • Sent Aaron a writeup on the clustering results

8:00 – 5:00 PhD

  • Made a poster of the map for the run on Monday
  • Dissertation for the rest of the day
    • Created a chapter and equation directory. Things are getting messy
    • Working on the simulation study chapter – I think the main part of the work is in there. Now I need to add the adversarial herding

Phil 4.4.19

6:00 – 1:30, 3:30 – 7:00 ASRC PhD 1:30 – 2:30 NASA

    • Woke up early, so here we are
    • I have the permutation code running, but I don’t like it. I can tell the overall stability of the terms, which is really good. We go from the terms in one set:
      ---------------- [('Group 1',), ('tymora1',), ('tymora2',), ('tymora3',), ('tymora4',)]
      new_set = {'something', 'dragon', 'grogg'}, master_set = {'something', 'dragon', 'grogg'}, sub_channel_list = ['Group 1']
      new_set = {'light', 'dragon', 'coins'}, master_set = {'light', 'dragon', 'grogg', 'something', 'coins'}, sub_channel_list = ['tymora1']
      new_set = {'eyes', 'coins', 'barrier'}, master_set = {'light', 'dragon', 'eyes', 'grogg', 'something', 'coins', 'barrier'}, sub_channel_list = ['tymora2']
      new_set = {'dragon', 'coins', 'barrier'}, master_set = {'grogg', 'something', 'coins', 'barrier', 'light', 'eyes', 'dragon'}, sub_channel_list = ['tymora3']
      new_set = {'platform', 'dragon', 'coins'}, master_set = {'grogg', 'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora4']
    • To just two groups
      ---------------- [('Group 1', 'tymora1'), ('Group 1', 'tymora2'), ('Group 1', 'tymora3'), ('Group 1', 'tymora4'), ('tymora1', 'Group 1'), ('tymora1', 'tymora2'), ('tymora1', 'tymora3'), ('tymora1', 'tymora4'), ('tymora2', 'Group 1'), ('tymora2', 'tymora1'), ('tymora2', 'tymora3'), ('tymora2', 'tymora4'), ('tymora3', 'Group 1'), ('tymora3', 'tymora1'), ('tymora3', 'tymora2'), ('tymora3', 'tymora4'), ('tymora4', 'Group 1'), ('tymora4', 'tymora1'), ('tymora4', 'tymora2'), ('tymora4', 'tymora3')]
      new_set = {'light', 'something', 'dragon', 'coins'}, master_set = {'light', 'dragon', 'something', 'coins'}, sub_channel_list = ['Group 1', 'tymora1']
      new_set = {'eyes', 'dragon', 'something', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'dragon'}, sub_channel_list = ['Group 1', 'tymora2']
      new_set = {'dragon', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'dragon'}, sub_channel_list = ['Group 1', 'tymora3']
      new_set = {'platform', 'something', 'dragon', 'coins'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['Group 1', 'tymora4']
      new_set = {'light', 'something', 'dragon', 'coins'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora1', 'Group 1']
      new_set = {'light', 'dragon', 'coins'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora1', 'tymora2']
      new_set = {'light', 'dragon', 'coins'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora1', 'tymora3']
      new_set = {'light', 'dragon', 'coins'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora1', 'tymora4']
      new_set = {'eyes', 'dragon', 'something', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora2', 'Group 1']
      new_set = {'eyes', 'dragon', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora2', 'tymora1']
      new_set = {'eyes', 'dragon', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora2', 'tymora3']
      new_set = {'eyes', 'dragon', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora2', 'tymora4']
      new_set = {'dragon', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora3', 'Group 1']
      new_set = {'dragon', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora3', 'tymora1']
      new_set = {'dragon', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora3', 'tymora2']
      new_set = {'platform', 'dragon', 'coins', 'barrier'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora3', 'tymora4']
      new_set = {'platform', 'something', 'dragon', 'coins'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora4', 'Group 1']
      new_set = {'platform', 'dragon', 'coins'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora4', 'tymora1']
      new_set = {'platform', 'dragon', 'coins'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora4', 'tymora2']
      new_set = {'platform', 'dragon', 'coins'}, master_set = {'something', 'coins', 'barrier', 'light', 'eyes', 'platform', 'dragon'}, sub_channel_list = ['tymora4', 'tymora3']
    • As you can see, it settles very fast. I’d just like to figure out a way to get intermediate numbers out of it.
    • Creativity Machine
      • Summary – An artificial neural network that has been trained upon some body of knowledge, and then perturbed in a specially prescribed way, tends to activate into concepts and/or strategies (e.g., new ideas) generalized from that conceptual space. These continuously perturbed networks are called ‘imagination engines‘ or ‘imagitrons‘. If another computational agent, such as a traditional rule-based algorithm or, even better, another trained neural network is allowed to filter for the very best of these emerging ideas, in terms of novelty, utility, or value, we arrive at an extremely valuable neural architecture, the patented Creativity Machine. Optional feedback connections between this latter computational agent and the imagination engine assure swift convergence toward useful ideas or strategies. This new AI paradigm is vastly more powerful than genetic algorithms (GA), efficiently generating new concepts on mere desktop computers rather than on the computational clusters required of GAs. This generative neural network paradigm can and has been extended to whole assemblies of perturbed neural nets generating complex ideas as a multitude of neural modules watch, selectively reinforcing those notions offering novelty, utility, or value of any kind.
    • node2vec: Scalable Feature Learning for Networks


Phil 4.3.19

7:00 – 1:30, ASRC PhD 1:30 – 4:30 NASA, 4:30 – 8:00 PhD

Phil 3.28.19

7:00 – 1:30 ASRC PhD 1:30 – 6:00 NASA AIMES

  • Downloaded an amoeba eating a bacteria. Need to edit
  • Fixed some bugs in the analytic code and downloaded some images and text. There is banding in the space name embeddings, which is pretty interesting
  • Worked on the paper. I think I have an entry point now. It seems to be flowing nicely
  • Dungeons & Dragons Single Volume Edition By Gary Gygax & Dave Arneson
  • GOES-R AI Kickoff meeting
  • More work on slides. Incorporated Wayne’s comments (I think?). Also got the video edited

Phil 3.26.19

7:00 – ASRC PhD

  • BBC Business Daily on “essay mills”. Apparently 7% of students use these?
  • Got 8 results on the survey so far!
  • Add query on place/space/channel(?) terms to find post. It could be an iteration until the one post that returns the most terms is found.
  • Evolving place names. Remarkable how few passes it takes for convergence (of at least the first 3 terms):
    • Group 1: (12 new terms)
      • ‘goblin’, ‘fire’, ‘orc’
      • ‘orb’, ‘statues’, ‘see’
      • ‘grogg’, ‘troll’, ‘box’
      • ‘dragon’, ‘grogg’, ‘something’
    • Group 1, tymora1: (2 new terms)
      • ‘goblin’, ‘orc’, ‘see’ – 1
      • ‘orb’, ‘gate’, ‘statues’ – 1
      • ‘troll’, ‘box’, ‘grogg’ – 0
      • ‘dragon’, ‘coins’, ‘something’ – 0
    • Group 1, tymora1, tymora2 (2 new terms)
      • ‘goblin’, ‘orc’, ‘stairs’ – 1
      • ‘rope’, ‘gate’, ‘orb’ – 2
      • ‘box’, ‘troll’, ‘grogg’ – 0
      • ‘coins’, ‘dragon’, ‘something’ – 0
    • Group 1, tymora1, tymora2, tymora3 (1 new term)
      • ‘goblin’, ‘orc’, ‘stairs’ – 0
      • ‘rope’, ‘gate’, ‘orb’ – 0
      • ‘troll’, ‘box’, ‘grogg’ – 0
      • ‘dragon’, ‘coins’, ‘barrier’ – 1
    • Group 1, tymora1, tymora2, tymora3, tymora4 (0 new terms)
      • ‘goblin’, ‘orc’, ‘stairs’ – 0
      • ‘rope’, ‘gate’, ‘orb’ – 0
      • ‘troll’, ‘grogg’, ‘box’ – 0
      • coins’, ‘dragon’, ‘barrier’  – 0
  • Checking to see if changing the order looks different
    • tymora4 (12 new terms)
      • ‘orc’, ‘goblin’, ‘vines’
      • ‘orb’, ‘trap’, ‘statues’
      • ‘grogg’, ‘troll’, ‘box’
      • ‘dragon’, ‘coins’, ‘platform’
    • tymora3, tymora4 (1 new term)
      • ‘vines’, ‘orc’, ‘goblin’ – 0
      • ‘rope’, ‘statues’, ‘orb’ – 1
      • ‘grogg’, ‘troll’, ‘box’ – 0
      • ‘dragon’, ‘coins’, ‘platform’ – 0
    • tymora2, tymora3, tymora4 (4 new terms)
      • ‘goblin’, ‘stairs’, ‘orc’ – 1
      • ‘rope’, ‘gate’, ‘across’ – 2
      • ‘grogg’, ‘troll’, ‘box’ – 0
      • ‘coins’, ‘dragon’, ‘barrier’ – 1
    • tymora1, tymora2, tymora3, tymora4 (1 new term)
      • ‘goblin’, ‘orc’, ‘stairs’ – 0
      • ‘rope’, ‘gate’, ‘orb’ – 1
      • ‘troll’, ‘box’, ‘grogg’ – 0
      • ‘coins’, ‘dragon’, ‘barrier’ – 0
    • Group 1, tymora1, tymora2, tymora3, tymora4 (0 new terms)
      • ‘goblin’, ‘orc’, ‘stairs’ – 0
      • ‘rope’, ‘gate’, ‘orb’ – 0
      • ‘troll’, ‘grogg’, ‘box’ – 0
      • coins’, ‘dragon’, ‘barrier’ – 0
  • Made a really nice map. This is entirely based on data and patterns found by the software, just arranged using a human-assisted layout:


  • JuryRoom meeting. Chris is getting the schema right, and is looking at IBM’s cloud service for hosting. We spent some time walking through the map. Panos is eager to read the paper

Phil 3.25.19

7:00 – ASRC PhD

  • Realized that the blue sky papers are only referenced by a link in the preface of the proceedings, so I think very few people will have read it. Going to make the slide deck review the paper first, then add in the rest of the content
  • Need to make a survey for past players asking them if a map would have helped, and what kind of map?
  • Added more mapping types. We now have
    • simplesimple
    • place-edgesplace-edges
    • space-edgesspace_edges
    • all-edgesall_edges
  • Create maps with linked spaces for each room for a “zoomed in” room
  • Need to play around with labeling nodes, but that may be after writing the paper. I think I’ll need a different mapping tool