Category Archives: Writing

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 7.10.19

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 6.25.19

7:00 – 7:00 ASRC GEOS

  • Scheduled the map run for Monday, July 1, 12:30 – 4:30
  • Asked wayne for a 100-word bio by the end of the month. Working on mine today
  • What use are computational models of cognitive processes?
    • Computational modelers are not always explicit about their motivations for constructing models, nor are they always explicit about the theoretical implications of their models once constructed. Perhaps in part due to this, models have been criticized as “black-box” exercises which can play little or no role in scientific explanation. This paper argues that models are useful, and that the motivations for constructing computational models can be made clear by considering the roles that tautologies can play in the development of explanatory theories. From this, additionally, I propose that although there are diverse benefits of model building, only one class of benefits — those which relate to explanation — can provide justification for the activity.
  • DTW run looks good. It took 8 1/2 hours to run: fulldtw
  • Fixed a lot of things to get the clustering to behave, but it all looks good
  • Spend a while arguing online about ketchup vs. mustard with Aaron JuryRoom
  • Waikato meeting
    • Test with a few thousand posts using lorem ipsum
    • Maybe double the character count
    • Scroll to offscreen posts
    • Context-sensitive text
    • Toggle vote button
    • 500 default chars, variable

Phil 6.24.19

Done with a week of riding my bike around:PANJ

On a related note, in talking to the other members of the group about the dissertation and research, the resonant points seem to involve network density and stiffness, and the mathematical similarities of animal motion and human text usage

7:30 – 3:30 ASRC NASA GEOS

  • Working on the JASSS submission process. Need to get 100-word bios for all authors
    • When submitting your article through the web (see below), you will also be asked to provide:
      • the names, affiliations, addresses, home web pages and emails addresses of all authors;
      • a brief biography (about 100 words) for each of the authors;
      • confirmation that the article has not been published or submitted elsewhere for publication.
  • Re-did the waveforms for DTW with the full data and 100 samples. I’ll fire it up on the way out the door today
  • Starting to build an automated pipeline for producing time-series data for ML
  • Started meta-skills document

Phil 6.12.19

7:00 – 5:30 ASRC GEOS

Phil 6.11.19

ASRC GEOS 7:00 – 5:30

  • Some interesting stuff from ICML 2019
    • The Evolved Transformer
      • Recent works have highlighted the strength of the Transformer architecture on sequence tasks while, at the same time, neural architecture search (NAS) has begun to outperform human-designed models. Our goal is to apply NAS to search for a better alternative to the Transformer. We first construct a large search space inspired by the recent advances in feed-forward sequence models and then run evolutionary architecture search with warm starting by seeding our initial population with the Transformer. To directly search on the computationally expensive WMT 2014 EnglishGerman translation task, we develop the Progressive Dynamic Hurdles method, which allows us to dynamically allocate more resources to more promising candidate models. The architecture found in our experiments – the Evolved Transformer – demonstrates consistent improvement over the Transformer on four well-established language tasks: WMT 2014 English-German, WMT 2014 English-French, WMT 2014 EnglishCzech and LM1B. At a big model size, the Evolved Transformer establishes a new state-ofthe-art BLEU score of 29.8 on WMT’14 EnglishGerman; at smaller sizes, it achieves the same quality as the original “big” Transformer with 37.6% less parameters and outperforms the Transformer by 0.7 BLEU at a mobile-friendly model size of ~7M parameters.
    • DBSCAN++: Towards fast and scalable density clustering
      • DBSCAN is a classical density-based clustering procedure with tremendous practical relevance. However, DBSCAN implicitly needs to compute the empirical density for each sample point, leading to a quadratic worst-case time complexity, which is too slow on large datasets. We propose DBSCAN++, a simple modification of DBSCAN which only requires computing the densities for a chosen subset of points. We show empirically that, compared to traditional DBSCAN, DBSCAN++ can provide not only competitive performance but also added robustness in the bandwidth hyperparameter while taking a fraction of the runtime. We also present statistical consistency guarantees showing the trade-off between computational cost and estimation rates. Surprisingly, up to a certain point, we can enjoy the same estimation rates while lowering computational cost, showing that DBSCAN++ is a sub-quadratic algorithm that attains minimax optimal rates for level-set estimation, a quality that may be of independent interest
    • Garbage In, Reward Out: Bootstrapping Exploration in Multi-Armed Bandits
      • We propose a bandit algorithm that explores by randomizing its history of rewards. Specifically, it pulls the arm with the highest mean reward in a non-parametric bootstrap sample of its history with pseudo rewards. We design the pseudo rewards such that the bootstrap mean is optimistic with a sufficiently high probability. We call our algorithm Giro, which stands for garbage in, reward out. We analyze Giro in a Bernoulli bandit and derive a bound on its n-round regret, where ? is the difference in the expected rewards of the optimal and the best suboptimal arms, and K is the number of arms. The main advantage of our exploration design is that it easily generalizes to structured problems. To show this, we propose contextual Giro with an arbitrary reward generalization model. We evaluate Giro and its contextual variant on multiple synthetic and real-world problems, and observe that it performs well.
    • Guided evolutionary strategies: Augmenting random search with surrogate gradients
      • Many applications in machine learning require optimizing a function whose true gradient is inaccessible, but where surrogate gradient information (directions that may be correlated with, but not necessarily identical to, the true gradient) is available instead. This arises when an approximate gradient is easier to compute than the full gradient (e.g. in meta-learning or unrolled optimization), or when a true gradient is intractable and is replaced with a surrogate (e.g. in certain reinforcement learning applications or training networks with discrete variables). We propose Guided Evolutionary Strategies, a method for optimally using surrogate gradient directions along with random search. We define a search distribution for evolutionary strategies that is elongated along a subspace spanned by the surrogate gradients. This allows us to estimate a descent direction which can then be passed to a first-order optimizer. We analytically and numerically characterize the trade-offs that result from tuning how strongly the search distribution is stretched along the guiding subspace, and use this to derive a setting of the hyperparameters that works well across problems. Finally, we apply our method to example problems, demonstrating an improvement over both standard evolutionary strategies and first-order methods that directly follow the surrogate gradient
    • 2019 Workshop on Human In the Loop Learning (HILL)
      • This workshop is a joint effort between the 4th ICML Workshop on Human Interpretability in Machine Learning (WHI) and the ICML 2019 Workshop on Interactive Data Analysis System (IDAS). We have combined our forces this year to run Human in the Loop Learning (HILL) in conjunction with ICML 2019!
      • The workshop will bring together researchers and practitioners who study interpretable and interactive learning systems with applications in large scale data processing, data annotations, data visualization, human-assisted data integration, systems and tools to interpret machine learning models as well as algorithm designs for active learning, online learning, and interpretable machine learning algorithms. The target audience for the workshop includes people who are interested in using machines to solve problems by having a human be an integral part of the process. This workshop serves as a platform where researchers can discuss approaches that bridge the gap between humans and machines and get the best of both worlds.
    • More JASS paper
    • Start on clustering hyperparameter search
      • Created ClusterEvaluator. Going to use learning_optimizer as the search space evaluator – Done
    • Waikato meeting
      • Extract data from the PHP and Slack DBs for Tony and JASSS

Phil 6.10.19

ASRC GEOS 7:00 – 3:00

  • I’ve been thinking about the implications of this article: Training a single AI model can emit as much carbon as five cars in their lifetimes
    • There is something in this that has to do with the idea of cost. NN architectures have no direct concept of cost. Inevitably the “current best network” takes a building full of specialized processors 200 hours. This has been true for Inception, AmeoebaNet, and AlphaGo. I wonder what would happen if there was a cost for computation that was part of the fitness function?
    • My sense is that evolution, has two interrelated parameters
      • a mutation needs to “work better” (whatever that means in the context) than the current version
      • the organism that embodies the mutation has to reproduce
    • In other words, neural structures in our brains have an unbroken chain of history to the initial sensor neurons in multicellular organisms. All the mutations that didn’t live to make an effect. Those that weren’t able to reproduce didn’t get passed on.
    • Randomness is important too. Systems that are too similar, like Aspen trees that have given up on sexual reproduction and are essentially all clones reproducing by rhizome. These live long enough to have an impact on the environment, particularly where they can crowd out other species, but the species itself is doomed.
    • I’d like to see an approach to developing NNs that involves more of the constraints of “natural” evolution. I think it would lead to better, and potentially less destructive results.
  • SHAP (SHapley Additive exPlanations) is a unified approach to explain the output of any machine learning model. SHAP connects game theory with local explanations, uniting several previous methods [1-7] and representing the only possible consistent and locally accurate additive feature attribution method based on expectations (see our papers for details).
  • Working on clustering. I’ve been going around in circles on how to take a set of relative distance measures and use them as a basis for clustering. To revisit, here’s a screenshot of a spreadsheet containing the DTW distances from every sequence to every other sequence: DTW
  • My approach is to treat each line of relative distances as a high-dimensional coordinate ( in this case, 50 dimensions), and cluster with respect to the point that defines. This takes care of the problem that the data in this case is very symmetric about the diagonal. Using this approach, an orange/green coordinate is in a different location from the mirrored green/orange coordinate. It’s basically the difference between (1, 2) and (2, 1). That should be a reliable clustering mechanism. Here are the results:
    ts_0            0
    ts_1            0
    ts_2            0
    ts_3            0
    ts_4            0
    ts_5            0
    ts_6            0
    ts_7            0
    ts_8            0
    ts_9            0
    ts_10           0
    ts_11           0
    ts_12           0
    ts_13           0
    ts_14           0
    ts_15           0
    ts_16           0
    ts_17           0
    ts_18           0
    ts_19           0
    ts_20           0
    ts_21           0
    ts_22           0
    ts_23           0
    ts_24           0
    ts_25           1
    ts_26           1
    ts_27           1
    ts_28           1
    ts_29           1
    ts_30           1
    ts_31           1
    ts_32           1
    ts_33           1
    ts_34           1
    ts_35           1
    ts_36           1
    ts_37           1
    ts_38           1
    ts_39           1
    ts_40           1
    ts_41           1
    ts_42           1
    ts_43           1
    ts_44           1
    ts_45           1
    ts_46           1
    ts_47           1
    ts_48           1
    ts_49           1
  • First-Order Adversarial Vulnerability of Neural Networks and Input Dimension
    • Carl-Johann Simon-Gabriel, Yann Ollivier, Bernhard Scholkopf, Leon BottouDavid Lopez-Paz
    • Over the past few years, neural networks were proven vulnerable to adversarial images: Targeted but imperceptible image perturbations lead to drastically different predictions. We show that adversarial vulnerability increases with the gradients of the training objective when viewed as a function of the inputs. Surprisingly, vulnerability does not depend on network topology: For many standard network architectures, we prove that at initialization, the l1-norm of these gradients grows as the square root of the input dimension, leaving the networks increasingly vulnerable with growing image size. We empirically show that this dimension-dependence persists after either usual or robust training, but gets attenuated with higher regularization.
  • More JASSS paper. Through the corrections up to the Results section. Kind of surprised to be leaning so hard on Homer, but I need a familiar story from before world maps.
  • Oh yeah, the Age Of discovery correlates with the development of the Mercator projection and usable world maps

Phil 6.6.19

7:00 – 3:00 ASRC PM Summit

  • 75th anniversary of D-day 640px-Naval_Bombardments_on_D-Day
  • Research talk today at the conference. Much networking yesterday.
    • The talk went well. More opportunities for networking. Mayne some ML for 3D printing?
  • Copied the CHIPLAY paper to a new GROUP 2020 folder and change to the acm small article format
  • Simplicial models of social contagion
    • Complex networks have been successfully used to describe the spread of diseases in populations of interacting individuals. Conversely, pairwise interactions are often not enough to characterize social contagion processes such as opinion formation or the adoption of novelties, where complex mechanisms of influence and reinforcement are at work. Here we introduce a higher-order model of social contagion in which a social system is represented by a simplicial complex and contagion can occur through interactions in groups of different sizes. Numerical simulations of the model on both empirical and synthetic simplicial complexes highlight the emergence of novel phenomena such as a discontinuous transition induced by higher-order interactions. We show analytically that the transition is discontinuous and that a bistable region appears where healthy and endemic states co-exist. Our results help explain why critical masses are required to initiate social changes and contribute to the understanding of higher-order interactions in complex systems.
  • This is wild: Randomly wired neural networks and state-of-the-art accuracy? Yes it works.
  • This is sad: Training a single AI model can emit as much carbon as five cars in their lifetimes
  • Came home and slept 2 1/2 hours. Very cooked.

Phil 6.4.19

7:00 – 4:00 ASRC NASA GEOS

  • Continuing to read Colin Martindale’s Cognitive Psychology, a Neural Network Approach, which is absolutely bonkers for something written decades ago. Ordered two more copies.
  • JASSS Paper. Adding footnotes to figures, which is tricky.
  • Dissertation
    • Took the chapter numbers out of the file names, since these things seem to be sliding around quite a bit
  • Registered for Politics and Computational Social Science (PACSS) Conference
  • GROUP paper?
  • Waveform clustering
    • Adding noise to the float_functions class. Here’s the waveform without and with some (0.1) noise:
    • Installed fastdtw for python
    • DTW is working on the lines in the csv. Identical lines have zero distance, noise has some. Need to think about some kind of normalizing measure. Maybe divide by the number of points?
    • Need to iterate as nested loops over all the rows. Skip when i == j – done
    • Need to build a Dataframe of distances from one row to the next – done
    • Here are the two curves to compare: TwoCurves
    • And here’s the DTW result: DTW
  • Good Waikato meeting. We’ll try to run a jury next week. Also, meetings have been moved to 6:30 EST

Phil 5.31.19

7:00 – 3:00 NASA GEOS

  • Got a proposal from Panos and his group. Michael Mayo is interested in running Google’s Universal Sentence Encoder on the data
  • Defending Against Neural Fake News
    • Recent progress in natural language generation has raised dual-use concerns. While applications like summarization and translation are positive, the underlying technology also might enable adversaries to generate neural fake news: targeted propaganda that closely mimics the style of real news. 
      Modern computer security relies on careful threat modeling: identifying potential threats and vulnerabilities from an adversary’s point of view, and exploring potential mitigations to these threats. Likewise, developing robust defenses against neural fake news requires us first to carefully investigate and characterize the risks of these models. We thus present a model for controllable text generation called Grover. Given a headline like `Link Found Between Vaccines and Autism,’ Grover can generate the rest of the article; humans find these generations to be more trustworthy than human-written disinformation. 
    • Developing robust verification techniques against generators like Grover is critical. We find that best current discriminators can classify neural fake news from real, human-written, news with 73% accuracy, assuming access to a moderate level of training data. Counterintuitively, the best defense against Grover turns out to be Grover itself, with 92% accuracy, demonstrating the importance of public release of strong generators. We investigate these results further, showing that exposure bias — and sampling strategies that alleviate its effects — both leave artifacts that similar discriminators can pick up on. We conclude by discussing ethical issues regarding the technology, and plan to release Grover publicly, helping pave the way for better detection of neural fake news.
  • Retooling CHIPLAY for GROUP. Deadline is June 21
  • More JASS tweaking:
    • Switch the urls in the paper to antibubbles to anonymize – done

Phil 5.30.19

7:00 – 2:30 NASA GEOS

  • CHI Play reviews should come back today!
    • Darn – rejected. From the reviews, it looks like we are in the same space, but going a different direction – an alignment problem. Need to read the reviews in detail though.
    • Some discussion with Wayne about GROUP
  • More JASSS paper
    • Added some broader thoughts to the conclusion and punched up the subjective/objective map difference
  • Start writing proposal for Bruce
    • Simple simulation baseline for model building
    • Develop models for
      • Extrapolating multivariate (family) values, including error conditions
      • Classify errors
      • Explainable model, that has sensor inputs drive the controls of the model that produce outputs that are evaluated against the original inputs using RL
      • “Safer” ML using Sanhedrin approach
  • EfficientNet: Improving Accuracy and Efficiency through AutoML and Model Scaling
    • In our ICML 2019 paper, “EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks”, we propose a novel model scaling method that uses a simple yet highly effective compound coefficient to scale up CNNs in a more structured manner. Unlike conventional approaches that arbitrarily scale network dimensions, such as width, depth and resolution, our method uniformly scales each dimension with a fixed set of scaling coefficients. Powered by this novel scaling method and recent progress on AutoML, we have developed a family of models, called EfficientNets, which superpass state-of-the-art accuracy with up to 10x better efficiency (smaller and faster). EfficientNet