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README.md

README.md

shepard

This repository contains data and code from Carr, Smith, Culbertson, and Kirby (submitted). It includes Python code for running a Bayesian iterated learning model of the emergence of semantic categories (plus the raw data that we generated from this model), and code for running online experiments that test the predictions of the model (plus the participant data we collected).

Various other Python and R scripts are also included for replicating the analysis. All Python code in this repo was written for Python 3 and much of it requires NumPy, SciPy, and matplotlib to be installed.

The top-level structure of the repo is:

  • code/: All Python code used for the model and analysis

  • data/: All the raw data files

  • experiments/: Node.js code for the experiments

  • illustrations/: Illustrations created in Affinity Designer

  • manuscript/: LaTeX source and EPS figures for the manuscript

  • stats/: R scripts for reproducing the statistics

  • supplementary/: Various supplementary items

  • visuals/: Various visualizations

Data

All experimental data can be found in the data/experiments/ directory. This includes the following files:

  • exp1_participants.json: Raw JSON data for all participants in Experiment 1 (one participant per line). Personal information has been removed from the original file, such as participant IP addresses and user IDs.

  • exp1_stats.csv: CSV data for Experiment 1 (used by the R script to compute the stats). This file may be regenerated using the generate_csv_for_stats() function in code/exp1_results.py.

  • exp2_chains.json: JSON data for all chains in Experiment 2. This is flattened version of the original file (giving it a similar structure to the model result JSON files) and removes personal participant information.

  • exp2_participants.json: Raw JSON data for all participants in Experiment 2 (one participant per line). Personal information has been removed from the original file, such as participant IP addresses and user IDs.

  • exp2_stats.csv: CSV data for Experiment 2 (used by the R script to compute the stats). This file may be regenerated using the generate_csv_for_stats() function in code/exp2_results.py.

The model and model-fit data has been compressed into zip files. Uncompressed, this data consumes about 1GB of disk space. If you wish to access the raw model or model-fit data, you will need to uncompress the following files:

  • data/model_inf.zip: 97 JSON files, each for a different run of the model under the informativeness prior. Each JSON file contains 100 chains of 50 generations. Files are named following the pattern weight_noise_bottleneck_exposures.json.

  • data/model_sim.zip: 49 JSON files, each for a different run of the model under the simplicity prior. Each JSON file contains 100 chains of 50 generations. Files are named following the pattern weight_noise_bottleneck_exposures.json.

  • data/modelfit.zip: Various raw data files and pickled scikit-optimize result objects. Includes the data_in–data_out pairs for 168 participants (generated by code/mf_extract_data_in_out.py) and log likelihood results under random and candidate parameter settings (generated by code/mf_sample.py).

The data directory also contains:

  • 8x8_solutions.json: Cached rectangular decomposition solutions for Experiment 2 data.

  • rectlang.zip: The raw data (generated by exp2_chunkify.py) used to compute 8x8_solutions.json (this raw data should not be of much interest).

  • sim_comp_cost.zip: Complexity and communicative cost of simulated convex and nonconvex category systems. This is discussed in my thesis.

  • test_modelfit.zip: Raw data used to test the model fit procedure. This is discussed in my thesis.

The structure of the JSON and CSV files should be self-explanatory from inspecting the files. However, to give a few examples, most of the JSON files may be loaded using the function read_json_file() in tools.py, for example:

>>> import tools
>>> model_dataset = tools.read_json_file('../data/model_sim/1.0_0.01_2_2.json')
>>> exp2_dataset = tools.read_json_file('../data/experiments/exp2_chains.json')
>>> # Complexity of chain 16, generation 32 in the model dataset
>>> model_dataset['chains'][16]['generations'][32]['lang_complexity']
49.44161477482669
>>> # Transmission errors for tenth generations across all chains in Experiment 2
>>> [chain['generations'][10]['prod_error'] for chain in exp2_dataset['chains']]
[3.653458818052006, 0.0, 0.11611507530476972, 0.6877694482804536, 3.050944842557372, 1.0529841448544655, 1.1603143477694449, 0.366849896644455, 0.7086360622147698, 0.8754503193229525, 1.8341556081932127, 3.082350200874642]

In the two by-participant data files (exp1_participants.json and exp2_participants.json), which hold more detailed information about individual participants, each line is a JSON record (exported from the MongoDB database). These should be accessed using the function read_json_lines(). For example, to calculate average reaction times by category system, you could do:

>>> exp1_dataset = tools.read_json_lines('../data/experiments/exp1_participants.json')
>>> test_reaction_times = {'angle':[], 'size':[], 'both':[]}
>>> for participant in exp1_dataset:
...     test_reaction_times[participant['condition']].extend(participant['test_reaction_times'])
... 
>>> sum(test_reaction_times['angle']) / len(test_reaction_times['angle'])
3600.316015625
>>> sum(test_reaction_times['size']) / len(test_reaction_times['size'])
3642.93844126506
>>> sum(test_reaction_times['both']) / len(test_reaction_times['both'])
4580.0734375

Model

Various functions are provided in code/model_resuts.py to reproduce figures and visualizations for the model. Generally, these functions can produce SVG, PDF, EPS, or PNG files, but formats other than SVG require Inkscape to be installed on your machine. Producing animated gifs requires the Python package imageio.

The code to run the model is in code/model.py. This Python script is well documented and should allow the reader to run a simple iterated learning chain. The script is designed to be run from the command line. For example, the following command will run a single chain of 50 generations under the simplicity prior and the same basic parameter settings reported in the paper.

$ python model.py my/results/directory/ 1 --generations 50 --height 8 --width 8 --mincats 1 --maxcats 4 --prior simplicity --weight 1.0 --noise 0.01 --bottleneck 2 --exposures 2 --mcmc_iterations 5000

The results will be written out to the file my/results/directory/1 (the number 1 in the above command represents the chain number and can be varied to write each chain to a different file). Depending on the parameter settings you choose, running a single chain can take several hours. In general, the simplicity prior is slower to compute than the informativeness prior. Running a large number of chains is best performed on a cluster (for example, run one chain per CPU core). Each line in the output file gives the results from a single generation. A collection of output files (i.e., one file per chain) can be merged into a single JSON file using model_process.py, which is then suitable for analysis using various functions in model_results.py and il_results.py.

Example: Creating agents that learn from data

If you just want to experiment with the model, it might be more convenient to run the code from an interactive Python shell. Here we run through a few examples to get you started.

>>> import model
>>> my_agent = model.Agent(shape=(4,4), prior='simplicity', weight=1.0, noise=0.01, exposures=2)
>>> my_data = [((0,0), 0), ((1,0), 0), ((0,2), 1), ((1,2), 1), ((2,1), 2), ((3,1), 2), ((2,3), 3), ((3,3), 3)]
>>> my_agent.learn(my_data)
>>> my_agent.language
array([[0, 2, 1, 3],
       [0, 2, 1, 3],
       [0, 2, 1, 3],
       [0, 2, 1, 3]])

In this example, we first created an agent with various parameters (the shape parameter determines the size of the universe – here a 4×4 universe). We then constructed some data (data is a list of meaning–signal pairs, where each meaning is a point in the universe). We then got the agent to learn from this data. Finally, we took a look at what language the agent inferred. Languages are Numpy arrays representing the two-dimensional space; each number represents a category/signal, so in this case, the agent has inferred a language which breaks the space up into four vertical stripes. Contrast with what happens when an agent has a strong informativeness prior and is exposed to the same data:

>>> my_inf_agent = model.Agent(shape=(4,4), prior='informativeness', weight=200.0, noise=0.01, exposures=2)
>>> my_inf_agent.learn(my_data)
>>> my_inf_agent.language
array([[0, 0, 1, 1],
       [0, 0, 1, 1],
       [2, 2, 3, 3],
       [2, 2, 3, 3]])

The agent infers a quadrant partition of the space. We can ask an agent to produce a signal for a particular meaning like this:

>>> my_agent.speak((3,3))
3

Asked to produce a signal for meaning (3,3), the agent produces signal 3. Of course, there is a small probability that the agent might make a production error, which is determined by the noise parameter we set above (in this example, 1%). To ask the agent to produce signals for all meanings, use speak_all():

>>> my_agent.speak_all()
array([[0, 0, 1, 3],
       [0, 2, 1, 3],
       [0, 2, 1, 3],
       [0, 2, 1, 3]])

In this example, the agent has made a production error; meaning (0,1) has been mislabeled as 0 rather than 2.

Example: Running an iterated learning chain

We can now do some iterated learning. First, we'll construct a new dataset derived from the previous agent:

>>> new_data = [(meaning, my_agent.speak(meaning)) for meaning in [(0,0), (1,1), (2,2), (3,3)]]
>>> new_data
[((0, 0), 0), ((1, 1), 2), ((2, 2), 1), ((3, 3), 3)]

Now we'll create a new agent, who will learn from this rather impoverished dataset:

>>> my_agent2 = model.Agent(shape=(4,4), prior='simplicity', weight=1.0, noise=0.01, exposures=2)
>>> my_agent2.learn(new_data)
>>> my_agent2.language
array([[0, 2, 1, 3],
       [0, 2, 1, 3],
       [0, 2, 1, 3],
       [0, 2, 1, 3]])

Even though the new agent only saw signals for four of the meanings (the meanings on the diagonal), it still managed to infer exactly the same language hypothesis as the previous agent. This is because it has a simplicity prior: Given a small amount of data, it looks for the simplest explanation for that data, which is the stripy partition.

We could continue in this fashion, creating a new agent who learns from new data generated by the previous agent. Instead, we will use a Chain object to automatically run an iterated learning chain starting from an initially random language. We set up and run a chain like this:

>>> my_chain = model.Chain(generations=10, shape=(4,4), prior='simplicity', weight=1.0, noise=0.01, bottleneck=2, exposures=2)
>>> my_chain.simulate()

specifying whatever particular parameters we want to test. Under the parameters above, this will take around 20 seconds to run. The results are stored in the list my_chain.generations (you can also pass a filename to the simulate() method in order to have the results written out to a file). Let's have a look at generation 0:

>>> my_chain.generations[0]
{'language': array([[0, 2, 1, 2], [1, 3, 0, 1], [1, 0, 3, 3], [2, 0, 3, 2]]), 'productions': array([[0, 2, 1, 2], [1, 3, 0, 1], [1, 0, 3, 3], [2, 0, 3, 2]]), 'data_out': [((0, 1), 2), ((1, 0), 1), ((0, 3), 2), ((1, 3), 1), ((2, 1), 0), ((3, 1), 0), ((2, 3), 3), ((3, 3), 2)], 'filtered_agent': False, 'lang_expressivity': 4, 'prod_expressivity': 4, 'lang_error': None, 'prod_error': None, 'lang_complexity': 96.9399527356992, 'prod_complexity': 96.9399527356992, 'lang_cost': 2.9863784237091693, 'prod_cost': 2.9863784237091693, 'model_parameters': {'shape': (4, 4), 'mincats': 1, 'maxcats': 4, 'prior': 'simplicity', 'weight': 1.0, 'noise': 0.01, 'bottleneck': 2, 'exposures': 2, 'mcmc_iterations': 5000}}

These results are for a dummy agent that was used to initialize the chain. In particular, we might be interested in looking at the initial random language and its complexity:

>>> my_chain.generations[0]['language']
array([[0, 2, 1, 2],
       [1, 3, 0, 1],
       [1, 0, 3, 3],
       [2, 0, 3, 2]])
>>> my_chain.generations[0]['lang_complexity']
96.9399527356992

Quite a complex language, which is to be expected because it's random. Now, lets take a look at generation 10:

>>> my_chain.generations[10]['language']
array([[2, 2, 2, 2],
       [2, 2, 3, 3],
       [2, 2, 3, 3],
       [2, 2, 3, 3]])
>>> my_chain.generations[10]['lang_complexity']
20.1357092861044

Much simpler! The language has simplified to two contiguous categories and the complexity is now about 20 bits. Finally, lets make a quick and dirty plot showing how complexity varies with generation:

>>> import matplotlib.pyplot as plt
>>> complexity_scores = [generation['lang_complexity'] for generation in my_chain.generations]
>>> plt.plot(complexity_scores)
>>> plt.show()

For nicer plots, visualizations, and animations, code can be found in code/il_visualize.py, code/il_animations.py, code/il_results.py, and code/visualize.py. However, most of this code is specific to the 8×8 case.

Experiments

Various functions are provided in code/exp1_results.py and code/exp2_results.py to reproduce figures and visualizations for the experiments. Generally, these functions can produce SVG, PDF, EPS, or PNG files, but formats other than SVG require Inkscape to be installed on your machine. Producing animated gifs requires the Python package imageio. The model fit figure can be reproduced from code/mf_results.py and requires scikit-optimize to be installed. The model fit analysis was performed by code/mf_collect.py and code/mf_sample.py – reproducing the model fit analysis could be tricky because it's extremely resource intensive (it took about three weeks on an HPC cluster) and the code is somewhat tailored to our specific HPC cluster.

Reproducing the experimental statistics

All statistics were done in R using the lme4 package. They can be reproduced by running the R scripts stats/exp1.R and stats/exp2.R. Our canonical output of these scripts can be found in stats/exp1.R.out and stats/exp2.R.out.

Running the experiments

All the code for the experiments is in the experiments/ directory. The experiments are written in Node.js. server.js is the script that runs on the server-side and does most of the experiment logic (randomization, iteration, participant exclusion, writing to the database, etc.). The script contains several parameters at the top of the code for controlling how the experiment works – these are fairly well documented. client.js is the script that runs on the client side and mostly deals with rendering of the stimuli, responding to button clicks, and so forth. The port numbers at the top of server.js and client.js must match. The code is also able to handle a live communication experiment which we never actually ran (this has not been tested in depth).

To run the experiments you will need a web server with Node.js and MongoDB installed. On a Mac, this can be accomplished by doing something like:

$ brew install node
$ brew install mongodb

Launch MongoDB by doing:

$ mongod

and leave it running in the background or set it up as a system service. Place the contents of the experiments/ directory on your server and install the Node.js dependencies:

$ npm install

Start the Node.js server using:

$ node server.js
Listening on port 9000

Measures

There are three key measures used in the paper: complexity, communicative cost, and variation of information. These are handled by code/rectlang.py, code/commcost.py, and code/varofinf.py.

Complexity

code/rectlang.py implements Fass & Feldman's (2002) “rectangle language”. We use this as a meta-language to describe the languages that arise in our models and experiments; the longer the description, the more complex the language is. Here we provide a few examples of how it may be used. We start by constructing a Space object, which specifies the dimensionality of the universe:

>>> import rectlang
>>> universe = rectlang.Space((4,4))

We may then calculate the complexity of some language we're interested in (languages are represented as Numpy arrays):

>>> import numpy as np
>>> lang = np.array([[1,1,1,2], [0,1,1,2], [0,0,1,2], [0,0,2,2]], dtype=int)
>>> lang
array([[1, 1, 1, 2],
       [0, 1, 1, 2],
       [0, 0, 1, 2],
       [0, 0, 2, 2]])

This is one of the example languages depicted in the paper (a three-contiguous-category language). To compute its complexity, we do:

>>> universe.complexity(lang)
48.593346667096164

To return the set of rectangles that minimize complexity:

>>> universe.compress_language(lang)
(48.593346667096164, [[((1, 0), (1, 1), (2, 0), (2, 1), (1, 1)), ((2, 0), (2, 2), (4, 0), (4, 2), (2, 2))], [((0, 0), (0, 1), (1, 0), (1, 1), (1, 1)), ((0, 1), (0, 3), (2, 1), (2, 3), (2, 2)), ((2, 2), (2, 3), (3, 2), (3, 3), (1, 1))], [((0, 3), (0, 4), (4, 3), (4, 4), (4, 1)), ((3, 2), (3, 3), (4, 2), (4, 3), (1, 1))]])

To look at the codelength and rectangles of individual categories within the language:

>>> universe.compress_concept(lang == 1)
(21.1357092861044, [((0, 0), (0, 1), (1, 0), (1, 1), (1, 1)), ((0, 1), (0, 3), (2, 1), (2, 3), (2, 2)), ((2, 2), (2, 3), (3, 2), (3, 3), (1, 1))])

To obtain binary strings for concepts, you can do:

>>> universe.encode_concept(lang == 1)
'00011001011010100101001'

Such strings are purely for illustrative purposes, but note that a given binary string uniquely picks out a particular category (i.e., this binary string picks out concept 1 from our language):

>>> universe.decode_concept('00011001011010100101001')
array([[ True,  True,  True, False],
       [False,  True,  True, False],
       [False, False,  True, False],
       [False, False, False, False]])

Finally, you can produce a tabulation of codelengths like this:

>>> universe.tabulate()
Class    N locations    Probability            Codelength (bits)
-------  -------------  ---------------------  --------------------
1x1      16             1/10 x 1/16 = 0.00625  -log 1/160 = 7.32193
1x2      24             1/10 x 1/24 = 0.00417  -log 1/240 = 7.90689
1x3      16             1/10 x 1/16 = 0.00625  -log 1/160 = 7.32193
1x4      8              1/10 x 1/8 = 0.0125    -log 1/80 = 6.32193
2x2      9              1/10 x 1/9 = 0.01111   -log 1/90 = 6.49185
2x3      12             1/10 x 1/12 = 0.00833  -log 1/120 = 6.90689
2x4      6              1/10 x 1/6 = 0.01667   -log 1/60 = 5.90689
3x3      4              1/10 x 1/4 = 0.025     -log 1/40 = 5.32193
3x4      4              1/10 x 1/4 = 0.025     -log 1/40 = 5.32193
4x4      1              1/10 x 1/1 = 0.1       -log 1/10 = 3.32193

Various other methods and options are available; study the code for more detail.

Communicative cost

code/commcost.py implements Regier and colleagues' communicative cost measure (e.g., Regier, Kemp, & Kay, 2015). This measures how informative a language is in terms of the extent to which there is a loss of information during communicative interaction. Here we provide a few examples of how it may be used. We start by constructing a Space object, which specifies the dimensionality of the universe:

>>> import commcost
>>> universe = commcost.Space((4,4), gamma=1, mu=2)

Optionally, the parameters gamma (how quickly similarity decays with distance) and mu (the Minkowski exponent; 1 = Manhattan distance, 2 = Euclidean distance) can be passed. We may then calculate the communicative cost of some language we're interested in (languages are represented as Numpy arrays):

>>> import numpy as np
>>> lang = np.array([[1,1,1,2], [0,1,1,2], [0,0,1,2], [0,0,2,2]], dtype=int)
>>> lang
array([[1, 1, 1, 2],
       [0, 1, 1, 2],
       [0, 0, 1, 2],
       [0, 0, 2, 2]])

This is one of the example languages depicted in the paper (a three-contiguous-category language). To compute its communicative cost, we do:

>>> universe.cost(lang)
2.8555467613130343

The commcost module provides various other classes and methods for doing more advanced things, such as changing the need distribution and modeling speaker uncertainty; study the code for more detail.

Variation of information

code/varofinf.py implements Meilă's (2007) variation of information, an information theoretic measure of the distance between two set partitions, which is used as the measure of transmission error between consecutive languages. Simply pass in two languages, represented as Numpy arrays, to the variation_of_information() function:

>>> import varofinf
>>> lang1 = np.array([[1,1,1,2], [0,1,1,2], [0,0,1,2], [0,0,2,2]], dtype=int)
>>> lang2 = np.array([[1,1,1,2], [0,1,1,2], [0,0,1,2], [0,0,2,1]], dtype=int)
>>> varofinf.variation_of_information(lang1, lang2)
0.484459370282069

References

Carr, Smith, Culbertson, & Kirby (submitted). Simplicity and informativeness in semantic category systems.

Fass, D., & Feldman, J. (2002). Categorization under complexity: A unified MDL account of human learning of regular and irregular categories. In S. Becker, S. Thrun, & K. Obermayer (Eds.), Advances in neural information processing systems 15 (pp. 35–42). Cambridge, MA: MIT Press.

Meilă, M. (2007). Comparing clusterings—an information based distance. Journal of Multivariate Analysis, 98, 873–895. doi: 10.1016/j.jmva.2006.11.013

Regier, T., Kemp, C., & Kay, P. (2015). Word meanings across languages support efficient communication. In B. MacWhinney & W. O’Grady (Eds.), The handbook of language emergence (pp. 237–263). Hoboken, NJ: John Wiley & Sons. doi: 10.1002/9781118346136.ch11

License

Except where otherwise noted, this repository is licensed under a Creative Commons Attribution 4.0 license. You are free to share and adapt the material for any purpose, even commercially, as long as you give appropriate credit, provide a link to the license, and indicate if changes were made. See LICENSE.md for full details.

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