Category Archives: Python

Phil 12.20.18

7:00 – 4:00 ASRC NASA/PhD

  • Goal-directed navigation based on path integration and decoding of grid cells in an artificial neural network
    • As neuroscience gradually uncovers how the brain represents and computes with high-level spatial information, the endeavor of constructing biologically-inspired robot controllers using these spatial representations has become viable. Grid cells are particularly interesting in this regard, as they are thought to provide a general coordinate system of space. Artificial neural network models of grid cells show the ability to perform path integration, but important for a robot is also the ability to calculate the direction from the current location, as indicated by the path integrator, to a remembered goal. This paper presents a neural system that integrates networks of path integrating grid cells with a grid cell decoding mechanism. The decoding mechanism detects differences between multi-scale grid cell representations of the present location and the goal, in order to calculate a goal-direction signal for the robot. The model successfully guides a simulated agent to its goal, showing promise for implementing the system on a real robot in the future.
  • Path integration and the neural basis of the ‘cognitive map’
    • Accumulating evidence indicates that the foundation of mammalian spatial orientation and learning is based on an internal network that can keep track of relative position and orientation (from an arbitrary starting point) on the basis of integration of self-motion cues derived from locomotion, vestibular activation and optic flow (path integration).
    • Place cells in the hippocampal formation exhibit elevated activity at discrete spots in a given environment, and this spatial representation is determined primarily on the basis of which cells were active at the starting point and how far and in what direction the animal has moved since then. Environmental features become associatively bound to this intrinsic spatial framework and can serve to correct for cumulative error in the path integration process.
    • Theoretical studies suggested that a path integration system could involve cooperative interactions (attractor dynamics) among a population of place coding neurons, the synaptic coupling of which defines a two-dimensional attractor map. These cells would communicate with an additional group of neurons, the activity of which depends on the conjunction of movement speed, location and orientation (head direction) information, allowing position on the attractor map to be updated by self-motion information.
    • The attractor map hypothesis contains an inherent boundary problem: what happens when the animal’s movements carry it beyond the boundary of the map? One solution to this problem is to make the boundaries of the map periodic by coupling neurons at each edge to those on the opposite edge, resulting in a toroidal synaptic matrix. This solution predicts that, in a sufficiently large space, place cells would exhibit a regularly spaced grid of place fields, something that has never been observed in the hippocampus proper.
    • Recent discoveries in layer II of the medial entorhinal cortex (MEC), the main source of hippocampal afferents, indicate that these cells do have regularly spaced place fields (grid cells). In addition, cells in the deeper layers of this structure exhibit grid fields that are conjunctive for head orientation and movement speed. Pure head direction neurons are also found there. Therefore, all of the components of previous theoretical models for path integration appear in the MEC, suggesting that this network is the core of the path integration system.
    • The scale of MEC spatial firing grids increases systematically from the dorsal to the ventral poles of this structure, in much the same way as is observed for hippocampal place cells, and we show how non-periodic hippocampal place fields could arise from the combination of inputs from entorhinal grid cells, if the inputs cover a range of spatial scales rather than a single scale. This phenomenon, in the spatial domain, is analogous to the low frequency ‘beats’ heard when two pure tones of slightly different frequencies are combined.
    • The problem of how a two-dimensional synaptic matrix with periodic boundary conditions, postulated to underlie grid cell behaviour, could be self-organized in early development is addressed. Based on principles derived from Alan Turing’s theory of spontaneous symmetry breaking in chemical systems, we suggest that topographically organized, grid-like patterns of neural activity might be present in the immature cortex, and that these activity patterns guide the development of the proposed periodic synaptic matrix through a mechanism involving competitive synaptic plasticity.
  • Wormholes in virtual space: From cognitive maps to cognitive graphs
    • Cognitive maps are thought to have a metric Euclidean geometry.
    • Participants learned a non-Euclidean virtual environment with two ‘wormholes’.
    • Shortcuts reveal that spatial knowledge violates metric geometry.
    • Participants were completely unaware of the wormholes and geometric inconsistencies.
    • Results contradict a metric Euclidean map, but support a labelled ‘cognitive graph’.
  • Back to TimeSeriesML
    • Encryption class – done
      • Create a key and save it to file
      • Read a key in from a file into global variable
      • Encrypt a string if there is a key
      • Decrypt a string if there is a key
    • Postgres class – reading part is done
      • Open a global connection and cursor based on a config string
      • Run queries and return success
      • Fetch results of queries as lists of JSON objects

Phil 12.19.18

7:00 – 4:30 ASRC PhD/NASA

  • I think the IEEE paper with Antonio should be something on the math behind diversity/chaos <-> ensembles <-> hierarchies/stampedes
  • Continuing with Normal Accidents
  • Thinking about costly signalling (economics, and more generally) WRT stampede theory. It’s a form of friction. Proof-of-work could be adaptively added to a system to inhibit stampedes?
    • In contract theorysignalling is the idea that one party (termed the agent) credibly conveys some information about itself to another party (the principal). For example, in Michael Spence’s job-market signalling model, (potential) employees send a signal about their ability level to the employer by acquiring education credentials. The informational value of the credential comes from the fact that the employer believes the credential is positively correlated with having greater ability and difficult for low ability employees to obtain. Thus the credential enables the employer to reliably distinguish low ability workers from high ability workers.
  • Tweak optimizer. Change callback method to replace_with_your_method(), and add some documentation on how to use the classes
  • Move clustering paper to LaTex folder – done!
  • Pinged Antonio about the new paper ideas
  • More predictive analytics? Kind of – setting up to read and write out time series to db
  • Upgrading my postgreSQL, to read/write from a table
    • Installed drivers and python packages
    • Reading and writing in the IDE
      • Created and populated a dummy data table
    • Reading in python. Writing is next
  • I was thinking that if we run out of D&D data for other map configurations, that I can use the current data with some repurposing (replace orc with xxx) to create conversations about other environments using human speech. Kind of like PCA for DNA.

Phil 12.17.18

7:00 – 4:30 ASRC NASA/PhD

  • Ted Radio Hour interview with Margaret Heffernan, who spoke about her book, Willful Blindness:
    • “Companies that have been studied for willful blindness can be asked questions like, are there issues at work that people are afraid to raise? And when academics have done studies like this of corporations in the United States, what they find is 85 percent of people say yes. Eighty-five percent of people know there’s a problem, but they won’t say anything. And when I duplicated the research in Europe, asking all the same questions, I found exactly the same number. And what’s really interesting is that when I go to companies in Switzerland, they tell me this is a uniquely Swiss problem. And when I go to Germany, they say, oh yes, this is the German disease. And when I go to companies in England they say, oh yeah, the British are really bad at this. And the truth is, this is a human problem. We’re all, under certain circumstances, willfully blind.”
    • I’ve been thinking about this a lot because when I say, well, why don’t people speak up? What I get is, oh, it’s the culture. And I think, well, what is the culture? The culture is the accumulation of everybody’s actions. And in many of the organizations I work with, change starts in very unexpected places because people just decide, I want to do this or I want to try this. And then they discover they don’t get shot. And then they discover that, actually, now, they’ve got a really exciting project. You know, I think the most dangerous thing in organizations is silence. It’s all those brains whizzing around full of observations and insight and ideas that are not being articulated.
    • I think that that the 15% who do speak out are Nomads. They are mis-aligned with the culture and as such it’s 1) Easier to see problems and solutions. 2) an inability to not behave independently.
  • Bayesian Layers: A Module for Neural Network Uncertainty
    • We describe Bayesian Layers, a module designed for fast experimentation with neural network uncertainty. It extends neural network libraries with layers capturing uncertainty over weights (Bayesian neural nets), pre-activation units (dropout), activations (“stochastic output layers”), and the function itself (Gaussian processes). With reversible layers, one can also propagate uncertainty from input to output such as for flow-based distributions and constant-memory backpropagation. Bayesian Layers are a drop-in replacement for other layers, maintaining core features that one typically desires for experimentation. As demonstration, we fit a 10-billion parameter “Bayesian Transformer” on 512 TPUv2 cores, which replaces attention layers with their Bayesian counterpart.
  • Continuing with Normal Accidents
  • Nice interactive on disinformation on Twitter
  • The universal decay of collective memory and attention
    • Collective memory and attention are sustained by two channels: oral communication (communicative memory) and the physical recording of information (cultural memory). Here, we use data on the citation of academic articles and patents, and on the online attention received by songs, movies and biographies, to describe the temporal decay of the attention received by cultural products. We show that, once we isolate the temporal dimension of the decay, the attention received by cultural products decays following a universal biexponential function. We explain this universality by proposing a mathematical model based on communicative and cultural memory, which fits the data better than previously proposed log-normal and exponential models. Our results reveal that biographies remain in our communicative memory the longest (20–30 years) and music the shortest (about 5.6 years). These findings show that the average attention received by cultural products decays following a universal biexponential function.
  • Zach walkthough
    • Yarn Workspaces
    • NextJS – Tools for developing React Apps – check the github repo to see, for example, how to roll your own web server
    • REACT hooks api
  • Got the basic recursion piece of the optimizer working right. Works for ints, floats, and strings:
    def cascading_step(self):
        self.cur_val = self.range_array[self.index]
        print("{} cur_val = {}".format(, self.cur_val))
        child_complete = True
        if self.child:
            child_complete = self.child.cascading_step()
        if child_complete:
            self.index += 1
            if self.index >= len(self.range_array):
                self.index = 0
                return True
        return False
  • And here’s the first working test:
    v3 cur_val = v3_0
    v2 cur_val = v2_0
    v1 cur_val = v1_0
    step 0 -----------
    v3 cur_val = v3_0
    v2 cur_val = v2_0
    v1 cur_val = v1_1
    step 1 -----------
    v3 cur_val = v3_0
    v2 cur_val = v2_0
    v1 cur_val = v1_2
    step 2 -----------
    v3 cur_val = v3_0
    v2 cur_val = v2_0
    v1 cur_val = v1_3
    step 3 -----------
    v3 cur_val = v3_0
    v2 cur_val = v2_1
    v1 cur_val = v1_0


Phil 12.14.18

7:00 – 4:30 ASRC PhD/NASA

  • Sent Greg a couple of quick notes on using CNNs to match bacteria to phages.
  • Continuing with Normal Accidents
  • A Digital Test of the News: Checking the Web for Public Facts – Workshop report, December 2018
    • The Digital Test of the News workshop brought together digital sociologists, data visualisation and new media researchers at the Centre for Interdisciplinary Methodologies at the University of Warwick on 8 and 9 May 2018. The workshop is part of a broader research collaboration between the Centre for Interdisciplinary Methodologies and the Public Data Lab which investigates the changing nature of public knowledge formation in digital societies and develops inventive methods to capture and visualise knowledge dynamics online. Below we outline the workshop’s aims and outcomes.
  • Added plots to the NN code. Everything seems to look right. Looking at the individual weights in a layer is very informative. Need to add this kind of plotting to our keras code somehow:
  • Changing the coherence code so that the row values are zero or one. Actually, as the amount of data grows, BOW is getting more useful raw. This spreadsheet shows all posts, including the DM. Note that the word frequency is power law (R squared = .9352): All_posts
  • Started the optimizer and excel utils classes
  • NOAA meeting
  • NOAA meeting 2
  • Some thoughts from Aaron on our initial ML approach
    • I think for the first pass we do 1-2 models based on contract type focused on the $500k+ award contracts (120ish total).
    • We construct the inputs like sentences in the word generation LSTM with padded lengths equal to the longest running contract of that type, sorted by length. The model can be tested against current contracts held out in a test set using point by point prediction so we can show accuracy of the model against existing data and use that to set our accuracy threshold.
    • My guess is this will be at least an ORF/PAC model (two different primary contract types) which we can work on tuning with the to get as accurate as possible in the timeframe we have.
    • One of the things we advertise as “next steps” is a detailed analysis of contracts based on similarity measures to identify a series of more accurate models. We can pair this with additional models such as Exponential Smoothing and ARIMA which use fundamentally the exact same pipeline.
    • The GUI will be plumbed up to show these analytic outputs on a per contract basis and we can show by the end of January a simple linear model and the LSTM model to demonstrate how Exponential Smoothing / ARIMA or model averages could be displayed. Once we have these outputs we can take the top 5 highest predicted UDO and display in a summary page so they can use those as a launching off point.
    • If we do it this way it means we only have to focus on the completion of TimeSeriesML LSTM and it’s data pipeline with a maximum of 2 initial models (contract type). I think that is a far more reasonable thing to complete in the timeframe and should still be really exciting to show off.

Phil 12.12.18

7:00 – 4:30 ASRC NASA/PhD

  • Do a dungeon analytic with new posts and DM for Aaron – done!
  • Send email to Shimei for registration and meeting after grading is finished
  • Start review of Normal Accidents – started!
  • Debug NN code – in process. Very tricky figuring out the relationships between the layers in backpropagation
  • Sprint planning
  • NASA meeting
  • Talked to Zach about the tagging project. Looks good, but I wonder how much time we’ll have. Got a name though – TaggerML

Phil 12.11.18

7:00 – 4:30 ASRC PhD/NASA


Somehow, this needs to get into a discussion of the trustworthiness of maps

  • I realized that we can hand-code these initial dungeons, learn a lot and make this a baseline part of the study. This means that we can compare human and machine data extraction for map making. My initial thoughts as to the sequence are:
    • Step 1: Finish running the initial dungeon
    • Step 2: researchers determine a set of common questions that would be appropriate for each room. Something like:
      • Who is the character?
      • Where is the character?
      • What is the character doing?
      • Why is the character doing this?
    • Each answer should also include a section of the text that the reader thinks answers that question. Once this has been worked out on paper, a simple survey website (simpler) can be built that automates this process and supports data collection at moderate scales.
    • Use answers to populate a “Trajectories” sheet in an xml file and build a map!
    • Step 3: Partially automate the extraction to give users a generated survey that lets them select the most likely answer/text for the who/where/what/why questions. Generate more maps!
    • Step 4: Full automation
  • Added these thoughts to the analysis section of the google doc
  • The 11th International Natural Language Generation Conference
    • The INLG conference is the main international forum for the presentation and discussion of all aspects of Natural Language Generation (NLG), including data-to-text, concept-to-text, text-to-text and vision to-text approaches. Special topics of interest for the 2018 edition included:
      • Generating Text with Affect, Style and Personality,
      • Conversational Interfaces, Chatbots and NLG, and
      • Data-driven NLG (including the E2E Generation Challenge)
  • Back to grokking DNNs
    • Still building a SimpleLayer class that will take a set of neurons and create a weight array that will point to the next layer
    • array formatting issues. Tricky
    • I think I’m done enough to start debugging. Tomorrow
  • Sprint review

Phil 12.10.18

7:00 – 5:30 ASRC NASA/PhD

  • For my morning academic work, I am cooking delicious things.
  • There is text in the dungeon! Here’s what happened when I ran the analytics against 3 posts and held back the dungeon master. Rather than put up a bunch of screenshots, here’s the spreadsheet: Day_1_Dungeon_1
  • Russell Richie (twitter) (Scholar) One of my favorite results in the paper is that you can compress the embeddings 10x or more while preserving prediction performance, suggesting that the type of knowledge used to make these kind of judgments may only vary along a relative handful of latent dimensions.
    • dtwstpluuaasaa4
    • dtwqzvwv4aa7kot
  • Ok, back to grokking DNNs
    • Building a SimpleLayer class that will take a set of neurons and create a weight array that will point to the next layer
  • Fika and meeting with Wayne
    • Ade might be interested in doing some coding work!
    • Went over the initial results spreadsheet with Wayn. Overall, progress seems on track. He had an additional thought for venues that I didn’t note.
    • Ping Shimei about 899

Phil 12.7.18

7:00 – 4:30 ASRC NASA/PhD

Phil 12.6.18

7:00 – 4:00 ASRC PhD/NASA

  • Looks like Aaron has added two users
  • Create a “coherence” matrix, where the threshold is based on an average of one or more previous cells. The version shown below uses the tf-idf matrix as a source and checks to see if there are any non-zero values within an arbitrary span. If there are, then the target matrix (initialized with zeroes) is incremented by one on that span. This process iterates from a step of one (the default), to the specified step size. As a result, the more contiguous nonzero values are, the larger and more bell-curved the row sequences will be: spreadsheet3
  • Create a “details” sheet that has information about the database, query, parameters, etc. Done.
  • Set up a redirect so that users have to go through the IRB page if they come from outside the antibubbles site
  • It’s the End of News As We Know It (and Facebook Is Feeling Fine)
    • And as the platforms pumped headlines into your feed, they didn’t care whether the “news” was real. They didn’t want that responsibility or expense. Instead, they honed in on engagement—did you click or share, increasing value to advertisers?
      • Diversity (responsibility, expense), Stampede (engagement, share)
  • Finished Analyzing Discourse and Text Complexity for Learning and Collaborating, and created this entry for the notes.
  • Was looking at John Du Bois paper Towards a dialogic syntax, which looks really interesting, but seems like it might be more appropriate for spoken dialog. Instead, I think I’ll go to Claire Cardie‘s presentation on chat argument analysis at UMD tomorrow and see if that has better alignment.
    • Argument Mining with Structured SVMs and RNNs
      • We propose a novel factor graph model for argument mining, designed for settings in which the argumentative relations in a document do not necessarily form a tree structure. (This is the case in over 20% of the web comments dataset we release.) Our model jointly learns elementary unit type classification and argumentative relation prediction. Moreover, our model supports SVM and RNN parametrizations, can enforce structure constraints (e.g., transitivity), and can express dependencies between adjacent relations and propositions. Our approaches outperform unstructured baselines in both web comments and argumentative essay datasets.

Phil 12.5.18

7:00 – 4:30 ASRC PhD/NASA

Phil 12.3.18

7:00 – 6:00 ASRC PhD

  • Reading Analyzing Discourse and Text Complexity for Learning and Collaborating, basically to find methods that show important word frequency varying over time.
  • Just in searching around, I also found a bunch of potentially useful resources. I’m emphasizing Python at the moment, because that’s the language I’m using at work right now.
    • 5agado has a bunch of nice articles on Medium, linked to code. In particular, there’s Conversation Analyzer – An Introduction, with associated code.
    • High frequency word entrainment in spoken dialogue
      • Cognitive theories of dialogue hold that entrainment, the automatic alignment between dialogue partners at many levels of linguistic representation, is key to facilitating both production and comprehension in dialogue. In this paper we examine novel types of entrainment in two corpora—Switchboard and the Columbia Games corpus. We examine entrainment in use of high-frequency words (the most common words in the corpus), and its association with dialogue naturalness and flow, as well as with task success. Our results show that such entrainment is predictive of the perceived naturalness of dialogues and is significantly correlated with task success; in overall interaction flow, higher degrees of entrainment are associated with more overlaps and fewer interruptions.
    • Looked some more at the Cornel Toolkit, but it seems focussed on other conversation attributes, with more lexical analysis coming later
    • There is a github topic on discourse-analysis, of which John W. DuBoisrezonator project looks particularly interesting. Need to ask Wayne about how to reach out to someone like that.
      • Recently I’ve been interested in what happens when participants in conversation build off each other, reusing words, structures and other linguistic resources just used by a prior speaker. In dialogic syntax, as I call it, parallelism of structure across utterances foregrounds similarities in function, but also brings out differences. Participants notice even the subtlest contrasts in stance–epistemic, affective, illocutionary, and so on–generated by the resonance between juxtaposed utterances. The theories of dialogic syntax and stance are closely related, and I’m currently working on exploring this linkage–one more example of figuring out how language works on multiple levels simultaneously, uniting structure, meaning, cognition, and social interaction.
  • From Computational Propaganda: If You Make It Trend, You Make It True
    • As an example, searching for “Vitamin K shot” (a routine health intervention for newborns) returns almost entirely anti-vaccine propaganda; anti-vaccine conspiracists write prolific quantities of content about that keyword, actively selling the myth that the shot is harmful, causes cancer, causes SIDS. Searches for the phrase are sparse because medical authorities are not producing counter-content or fighting the SEO battle in response.
    • This is literally a use case where a mapping interface would show that something funny was going on in this belief space
  • Yuanyuan’s proposal defense
    • Surgical telementoring, trainee performing the operation is monitored remotely by expert.
    • These are physical models!
    • Manual coding
    • Tracks communication intention, not lexical content
    • Linear Mixed Model
      • Linear mixed models are an extension of simple linear models to allow both fixed and random effects, and are particularly used when there is non independence in the data, such as arises from a hierarchical structure. For example, students could be sampled from within classrooms, or patients from within doctors.
    • DiCoT: a methodology for applying Distributed Cognition to the design of team working systems <– might be worth looking at for dungeon teams
    • Note, a wireless headset mic is nice if there are remote participants and you need to move around the room
    • GLIMMPSE power analysis
  • Add list of publications to the dissertation?
  • Good meeting with Wayne. Brought him up to speed on We discussed chiplay 2019 as a good next venue. We also went over what the iConference presentation might be. More as this develope, since it’s not all that clear. Certainly a larger emphasis on video. Also, it will be in the first batch of presentations.

Phil 11.30.18

7:00 – 3:00 ASRC NASA

  • Started Second Person, and learned about GURPS
  • Added a section on navigating belief places and spaces to the dissertation
  • It looks like I’m doing Computational Discourse Analysis, which has more to do with how the words in a discussion shift over time. Requested this chapter through ILL
  • Looking at Cornell Conversational Analysis Toolkit
  • More Grokking today so I don’t lose too much focus on understanding NNs
        • Important numpy rules:
          import numpy as np
          val = np.array([[0.6]])
          row = np.array([[-0.59, 0.75, -0.94,0.34 ]])
          col = np.array([[-0.59], [ 0.75], [-0.94], [ 0.34]])
          print ("{}, {}) = {}".format(val, row,, row)))
          print ("{}, {}) = {}".format(col, val,, val)))
          note the very different results:
[[0.6]], [[-0.59  0.75 -0.94  0.34]]) = [[-0.354  0.45  -0.564  0.204]]
[[-0.59], [ 0.75], [-0.94], [ 0.34]], [[0.6]]) = [[-0.354], [ 0.45 ], [-0.564], [ 0.204]]
        • So here’s the tricky bit that I don’t get yet
          # Multiply the values of the relu'd layer [[0, 0.517, 0, 0]] by the goal-output_layer [.61]
          weight_mat =, layer_1_to_output_delta) # e.g. [[0], [0.31], [0], [0]]
          weights_layer_1_to_output_col_array += alpha * weight_mat # add the scaled deltas in
          # Multiply the streetlights [[1], [0], [1] times the relu2deriv'd input_to_layer_1_delta [[0, 0.45, 0, 0]]
          weight_mat =, input_to_layer_1_delta) # e.g. [[0, 0.45, 0, 0], [0, 0, 0, 0], [0, 0.45, 0, 0]]
          weights_input_to_layer_1_array += alpha * weight_mat # add the scaled deltas in
        • It looks to me that as we work back from the output layer, we multiply our layer’s weights by the manipulated (relu in this case) for the last layer, and the derivative in the next layer forward?  I know that we are working out how to distribute the adjustment of the weights via something like the chain rule…


Phil 11.29.18

7:00 – 4:30 ASRC PhD/NASA

    • Listening to repeat of America Abroad Sowing Chaos: Russia’s Disinformation Wars. My original notes are here
    • Finished World without End: The Delta Green Open Campaign Setting, by A. Scott Glancey
      • Overall, this describes the creation of the cannon of the Delta Green playspace. The goal as described was to root the work in existing fiction (Lovecraft’s Cthulhu) and historical fact. This provides the core of the space that players can move out from or fill in. Play does not produce more cannon, so it produces a trajectory that may have high influence for the actual players, but may not move beyond that. The article discusses Agent Angela, as an example of a thumbnail sketch that has become a mythical character, independent of the work of the authors with respect to Cannon. My guess is as the Agent Angela space became “stiffer” that it could also be shared more.
      • As a role-playing game, Delta Green’s narrative differs from the traditional narratives of literature, theater, and film because it offers only plot without characters to drive the story forward. It’s up to the role-players to provide the characters. Role-playing game settings are narratives not built around any specific protagonist, yet capable of accommodating multiple protagonists. Thus, role-playing games, particularly the classic paper-and-dice ones, are by their very nature vast narratives. (page 77)
      • During the designing of the Delta Green vast narrative it was decided that we would publish more open-ended source material than scenarios. Source material is usually built around an enemy of Delta Green with a particular agenda or set of goals, much like a traditional role-playing game scenario is set up, only without the framework of scenes and set pieces designed to channel the players through to a resolution of the scenario. The reason for emphasizing open ended source material over scenarios is that we were trying to encourage Keepers to design their own scenarios without pinning them down with too much canon. That is always a danger with creating a role-playing game background. You want to create a rich environment, but you don’t want to fill in so many details that there is nothing new for the players and Keepers to create with their own games. (Page 81)
      • If the players in a role-playing game campaign start to think that their characters are more disposable than the villain, they are going to feel marginalized After all, whose story is this-theirs or a non-player character’s? The fastest way to alienate a group of players is to give them the impression that they are not the center of the story. If they are not the ones driving the action forward, then what’s the point in playing a role-playing game? They might as well be watching a movie if they cannot affect the pacing, action, and outcome of a story. (Page 83)
    • Going to create a bag of words collection for post subjects and posts that are not from the DM, and then plot the use of the words over time (by sequential post). I think that once stop words are removed, that patterns might be visible.
      • Pulling out the words
      • Have the overall counts
      • Building the count mats
      • Stop words worked, needed to drop punctuation and caps
    • Yoast has an array that looks immediately usable:
      [ "a", "about", "above", "after", "again", "against", "all", "am", "an", "and", "any", "are", "as", "at", "be", "because", "been", "before", "being", "below", "between", "both", "but", "by", "could", "did", "do", "does", "doing", "down", "during", "each", "few", "for", "from", "further", "had", "has", "have", "having", "he", "he'd", "he'll", "he's", "her", "here", "here's", "hers", "herself", "him", "himself", "his", "how", "how's", "i", "i'd", "i'll", "i'm", "i've", "if", "in", "into", "is", "it", "it's", "its", "itself", "let's", "me", "more", "most", "my", "myself", "nor", "of", "on", "once", "only", "or", "other", "ought", "our", "ours", "ourselves", "out", "over", "own", "same", "she", "she'd", "she'll", "she's", "should", "so", "some", "such", "than", "that", "that's", "the", "their", "theirs", "them", "themselves", "then", "there", "there's", "these", "they", "they'd", "they'll", "they're", "they've", "this", "those", "through", "to", "too", "under", "until", "up", "very", "was", "we", "we'd", "we'll", "we're", "we've", "were", "what", "what's", "when", "when's", "where", "where's", "which", "while", "who", "who's", "whom", "why", "why's", "with", "would", "you", "you'd", "you'll", "you're", "you've", "your", "yours", "yourself", "yourselves" ]
    • Good, progress. I’m using TF-IDF to determine the importance of the term in the timeline. That’s ok, but not great. Here’s a plot: room_terms
    • You can see the three rooms, but they don’t stand out all that well. Maybe a low-pass filter on top of this? Anyway, done for the day.


Phil 11.21.18

7:00 – 4:00 ASRC PhD/NASA

  • More adversarial herding: Bots increase exposure to negative and inflammatory content in online social systems
    • Social media can deeply influence reality perception, affecting millions of people’s voting behavior. Hence, maneuvering opinion dynamics by disseminating forged content over online ecosystems is an effective pathway for social hacking. We propose a framework for discovering such a potentially dangerous behavior promoted by automatic users, also called “bots,” in online social networks. We provide evidence that social bots target mainly human influencers but generate semantic content depending on the polarized stance of their targets. During the 2017 Catalan referendum, used as a case study, social bots generated and promoted violent content aimed at Independentists, ultimately exacerbating social conflict online. Our results open challenges for detecting and controlling the influence of such content on society.
    • Bot detection appendix
      • It occurs to me that if bots can be detected, then they can be mapped in aggregate on the belief map. This could show what types of beliefs are being artificially enhanced or otherwise influenced
  • Migrating Characterizing Online Public Discussions through Patterns of Participant Interactions to Phlog. Done!
  • Working my way through Grokking. Today’s progress:
    # based on
    import numpy as np
    import matplotlib.pyplot as plt
    import typing
    # methods --------------------------------------------
    # sets all negative numbers to zero
    def relu(x: np.array) -> np.array :
        return (x > 0) * x
    def relu2deriv(output: float) -> float:
        return output > 0 # returns 1 for input > 0
        # return 0 otherwise
    def nparray_to_list(vals: np.array) -> typing.List[float]:
        data = []
        for x in np.nditer(vals):
        return data
    def plot_mat(title: str, var_name: str, fig_num: int, mat: typing.List[float], transpose: bool = False):
        f = plt.figure(fig_num)
        np_mat = np.array(mat)
        if transpose:
            np_mat = np_mat.T
        names = []
        for i in range(len(np_mat)):
            names.append("{}[{}]".format(var_name, i))
    # variables ------------------------------------------
    hidden_size= 4
    alpha = 0.2
    weights_input_to_1_array = 2 * np.random.random((3, hidden_size)) - 1
    weights_1_to_output_array = 2 * np.random.random((hidden_size, 1)) - 1
    # the samples. Columns are the things we're sampling
    streetlights_array = np.array( [[ 1, 0, 1 ],
                                    [ 0, 1, 1 ],
                                    [ 0, 0, 1 ],
                                    [ 1, 1, 1 ] ] )
    # The data set we want to map to. Each entry in the array matches the corresponding streetlights_array roe
    walk_vs_stop_array = np.array([1, 1, 0, 0]).T # and why are we using the transpose here?
    error_plot_mat = [] # for drawing plots
    weights_l1_to_output_plot_mat = [] # for drawing plots
    weights_input_to_l1_plot_mat = [] # for drawing plots
    iter = 0
    max_iter = 1000
    epsilon = 0.001
    layer_2_error = 2 * epsilon
    while layer_2_error > epsilon:
        layer_2_error = 0
        for row_index in range(len(streetlights_array)):
            # input holds one instance of the data set at a time
            input_layer_array = streetlights_array[row_index:row_index + 1]
            # layer one holds the results of the NONLINEAR transformation of the input layer's values (multiply by weights and relu)
            layer_1_array = relu(, weights_input_to_1_array))
            # output layer takes the LINEAR transformation of the values in layer one and sums them (mult)
            output_layer =, weights_1_to_output_array)
            # the error is the difference of the output layer and the goal squared
            goal = walk_vs_stop_array[row_index:row_index + 1]
            layer_2_error += np.sum((output_layer - goal) ** 2)
            # compute the amount to adjust the transformation weights for layer one to output
            layer_1_to_output_delta = (goal - output_layer)
            # compute the amount to adjust the transformation weights for input to layer one
            input_to_layer_1_delta= * relu2deriv(layer_1_array)
            #Still need to figure out why the transpose, but this is where we incrementally adjust the weights
            l1t_array = layer_1_array.T
            ilt_array = input_layer_array.T
            weights_1_to_output_array += alpha *
            weights_input_to_1_array += alpha *
            print("[{}] Error: {:.3f}, L0: {}, L1: {}, L2: {}".format(iter, layer_2_error, input_layer_array, layer_1_array, output_layer))
            #print("[{}] Error: {}, Weights: {}".format(iter, total_error, weight_array))
            iter += 1
            # stop even if we don't converge
            if iter > max_iter:
    for row_index in range(len(streetlights_array)):
        input_layer_array = streetlights_array[row_index:row_index + 1]
        layer_1_array = relu(, weights_input_to_1_array))
        output_layer =, weights_1_to_output_array)
        print("{} = {:.3f} vs. {}".format(input_layer_array, float(output_layer), walk_vs_stop_array[row_index]))
    # plots ----------------------------------------------
    f1 = plt.figure(1)
    plot_mat("input to layer 1 weights", "weight", 2, weights_input_to_l1_plot_mat)
    plot_mat("layer 1 to output weights", "weight", 3, weights_l1_to_output_plot_mat)