Category Archives: Phil

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 7.18.19

7:00 – 5:00 ASRC GEOS

  • Started to fold Wayne’s comments in
  • Working on the Kauffman section
  • Tried making it so K can be higher than N with resampling and I still can’t keep the system from converging, which makes me think that there is something wrong with the code.
  • Send reviews to Antonio – done
  • Back to work on the physics model. Make sure to include a data dictionary mapping system to support Bruce’s concept
  • Sent links to Panda3D to Vadim
  • Code autocompletion using deep learning
  • A lot of flailing today but no good progress:


Phil 7.17.19

7:00 – 7:00 ASRC GEOS

  • Got some nice NK model network plots working:
  • Added a long jump mutation when plateaus are hit:
  • Generally, fixed a lot of bugs in the code, but I think I understand the NK model thing. I do want to try and find how they did the traveling salesman problem
  • AI/ML Meeting
    • NASA? Air Force(?) are putting together a reinforcement learning model for autonomous spacecraft control, that requires a simulator.
  • Meeting with Wayne
    • Lots of work on the dissertation
    • Walked through JuryRoom prototype

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 7,11,19

7:00 – 4:30 ASRC GEOS

  • Ping Antonio – Done
  • Dissertation
    • More Bones in a Hut. Found the online version of the Hi-Lo chapter from BIC. Explaining why Hi-Lo is different from IPD.
  • More reaction wheel modeling
  • Get flight and hotel for July 30 trip – Done
  • So this is how you should install Panda3d and examples:
    • First, make sure that you have Python 3.7 (64 bit! The default is 32 bit). Make sure that your path environment points to this, and not any other 3.x versions that you’re hoarding on your machine.
    • pip install panda3d==1.10.3
    • Then download the installer and DON’T select the python 3.7 support: Panda3d_install
    • Finish the install and verify that the demos run (e.g. python \Panda3D-1.10.3-x64\samples\asteroids\ asteroids
    • That’s it!
  • Discussed DARPA solicitation HR001119S0053 with Aaron. We know the field of study – logistics and supply chain, but BD has totally dropped the ball on deadlines and setting up any kind of relationship with the points of contact. We countered that we could write a paper and present at a venue to gain access and credibility that way.
    • There is a weekly XML from the FBO. Downloading this week’s to see if it’s easy to parse and search

Phil 7.10.19

7:00 – 5:00 ASRC

  • BP&S is up! Need to ping Antonio
  • Need to fix DfS to de-emphasize the mapping part. Including things like, uh, changing the title…
  • Pix at HQ – Done
  • Greenbelt today, which means getting Panda3D up and running on my laptop – Done. Had to point the IDE at the python in the install.
  • Need to add some thoughts to JuryRoom concepts
  • Send dungeon invites for the 23rd, and ping Aaron M. Done. Wayne can’t make it! Drat!
  • Dissertation working on the Bacharach section
  • Got the sim working on the laptop. I realize that the reaction wheel can be modeled as weights on a stick. Long discussion with Bruce T

Phil 7.9.19

7:00 – 5:30 ASRC GEOS

  • BP&S is “on hold” in ArXiv. Hoping that it’s overlap with DfS. I took the mapping text out of the DfS paper and resubmitted. Once that’s done I can send Antonio a link and get advice.
  • Code review with Chris
  • Contact David and see if he’s ok with July 23 – Nope. Trying Aaron M. as a replacement
  • More dissertation. Folded in most of the BP&S paper
  • Look! More mapping of latent spaces! Unsupervised word embeddings capture latent knowledge from materials science literature41586_2019_1335_fig4_esm
    • Here we show that materials science knowledge present in the published literature can be efficiently encoded as information-dense word embeddings11,12,13 (vector representations of words) without human labelling or supervision. Without any explicit insertion of chemical knowledge, these embeddings capture complex materials science concepts such as the underlying structure of the periodic table and structure–property relationships in materials. Furthermore, we demonstrate that an unsupervised method can recommend materials for functional applications several years before their discovery. This suggests that latent knowledge regarding future discoveries is to a large extent embedded in past publications. Our findings highlight the possibility of extracting knowledge and relationships from the massive body of scientific literature in a collective manner, and point towards a generalized approach to the mining of scientific literature.
  • More Panda3D
    • Intervals and sequences
    • Panda3D forum
    • Programming with Panda3D
      • Well, this is looking a lot like the way I would have written it
      • You can convert a NodePath into a “regular” pointer at any time by calling nodePath.node(). However, there is no unambiguous way to convert back. That’s important: sometimes you need a NodePath, sometimes you need a node pointer. Because of this, it is recommended that you store NodePaths, not node pointers. When you pass parameters, you should probably pass NodePaths, not node pointers. The callee can always convert the NodePath to a node pointer if it needs to.
      • Nodepath
    • Huh. It looks like there is no support for procedurally generated primitives. Well, I know what I’m going to be doing…
      • Origin – done
      • Grid
      • Cube (x, y, z size), color (texture?), Boolean for endcaps
      • Cylinder (radius+steps, length), color
      • Sphere  (radius+steps), color
      • Skybox (texture)
      • Then try making a satellite from parts
    • JuryRoom Meeting
      • A lot of discussion on UI issues – how to vote for/against, the right panel layout, and the questions that should be asked for Chris’ studyCapture

Phil 7.8.19

7:00 – 4:30 ASRC GEOS

  • Read and commented on Shimei’s proposal. It’s interesting to see how she’s weaving all these smaller threads together into one larger narrative. I find that my natural approach is to start with an encompassing vision and figure out how to break it down into its component parts. Which sure seems like stylistic vs. primordial. Interestingly, this implies that stylistic is more integrative? Transdisciplinary, primordial work, because it has no natural home, is more disruptive. It makes me think of this episode of Shock of the New about Paul Cezanne.
  • Working on getting BP&S into one file for ArXiv, then back to the dissertation.
    • Flailed around with some package mismatches, and had a upper/lowercase (.PNG vs. .png) problem. Submitted!
  • Need to ping Antonio about BP&S potential venues
  • The Redirect Method uses Adwords targeting tools and curated YouTube videos uploaded by people all around the world to confront online radicalization. It focuses on the slice of ISIS’ audience that is most susceptible to its messaging, and redirects them towards curated YouTube videos debunking ISIS recruiting themes. This open methodology was developed from interviews with ISIS defectors, respects users’ privacy and can be deployed to tackle other types of violent recruiting discourses online.
  • Pushed TimeSeriesML to the git repo, so we’re redundently backed up. Did not send data yet
  • Starting on the PyBullet tutorial
    • Trying to install pybullet.
      • Got this error: error: command ‘C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\x86_amd64\\link.exe’ failed with exit status 1158
      • Updating my Visual Studio (suggested here), in the hope that it fixes that. Soooooo Slooooow
      • Link needs rc.exe/rc.dll
      • Copied the most recent rc.exe and rcdll.dll (from into C:\\Program Files (x86)\\Microsoft Visual Studio 14.0\\VC\\BIN\\x86_amd64\
      • Giving up
  • Trying Panda3d
    • Downloaded and ran the installer. It couldn’t tell that I had Python 3.7.x, but otherwise was fine. Maybe that’s because my Python is on my D: drive?
    • Ran:
      pip install panda3d==1.10.3

      Which worked just fine

    • Had to add the D:\Panda3D-1.10.3-x64\bin and D:\Panda3D-1.10.3-x64\panda3d to the path to get all the imports to work right. This could be because I’m using a global, separately installed Python 3.7.x
    • Hmmm. Getting ModuleNotFoundError: No module named ‘panda3d.core.Point3’; ‘panda3d.core’ is not a package. The IDE can find it though….
    • In a very odd sequence of events, I tried using
      • from pandac.PandaModules import Point3, which worked, but gave me a deprecated warning.
    • Then, while fooling around, I tried the preferred
      • from panda3d.core import Point3, which now works. No idea what fixed it. Here’s the config that I’m using to run: Panda3dConfig
    • Nice performance, too: Pandas3D
    • And it has bullet in it, so maybe it will work here?
    • Starting on the manual

Phil 7.5.19

7:00 – 5:00 ASRC GEOS

  • Got a desk reject from JASSS. Finding a home for this is turning out to be hard
  • Adjust Belief Places and Spaces for a straight ArXiv submission (article, endquote, fix cites). I’m doing this partially out of spite – I don’t want to see JASSS looking back at me in my svn repo. But I also need to get all the parts fixed so that it can be folded into the dissertation. \citep doesn’t play well, and I need to replace all the quotes with \enquote{}.
  • Start folding BP&S into dissertation
  • Look for Collective Intelligence venue?
  • Updated Pandas, which was where I got hung on Tuesday. Now I can use DataFrame.to_numpy() instead of Dataframe.values
  • Continuing on TimeSeriesNormalizer – done! Below is the original file with the data in columns (left) and the normalized file with the data in rows (right): Normalized
  • Learning about PyBullet
  • Thought for the day. Find the snippet for each room/group with the most positive and most negative sentiment, and use that instead of the three words.

Phil 7.3.19

Continuing with the ICML 2019 Tutorial: Recent Advances in Population-Based Search for Deep Neural Networks. Wow. Lots of implications for diversity science. They need to read Martindale though.

This also looks good, using the above concepts of Quality Diversity to create map-like structures in low dimensions

  • Autonomous skill discovery with Quality-Diversity and Unsupervised Descriptors
    • Quality-Diversity optimization is a new family of optimization algorithms that, instead of searching for a single optimal solution to solving a task, searches for a large collection of solutions that all solve the task in a different way. This approach is particularly promising for learning behavioral repertoires in robotics, as such a diversity of behaviors enables robots to be more versatile and resilient. However, these algorithms require the user to manually define behavioral descriptors, which is used to determine whether two solutions are different or similar. The choice of a behavioral descriptor is crucial, as it completely changes the solution types that the algorithm derives. In this paper, we introduce a new method to automatically define this descriptor by combining Quality-Diversity algorithms with unsupervised dimensionality reduction algorithms. This approach enables robots to autonomously discover the range of their capabilities while interacting with their environment. The results from two experimental scenarios demonstrate that robot can autonomously discover a large range of possible behaviors, without any prior knowledge about their morphology and environment. Furthermore, these behaviors are deemed to be similar to handcrafted solutions that uses domain knowledge and significantly more diverse than when using existing unsupervised methods.

Back to the Dissertation

  • Added notes from Monday’s dungeon run
  • Added adversarial herding
  • At 111 pages!

Phil 7.2.19

7:00 – 3:30 ASRC GEOS

  • Wrote up some preliminary notes about the run yesterday
  • Need to set up a schedule for another run in the last half of July
  • Added a “Bones in a Hut” section that follows the main lit review
  • Clustering today
    • Wrote up a workflow.txt file for the whole process.
    • Building TimeSeriesNormalizer class
    • Looks like I lost admin. Stalled

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