Tag Archives: Science

The Journalist’s Guide to Statistics

There are three kinds of lies: lies, damned lies, and statistics.

Mark Twain, “My Autobiography”

Journalists need a good understanding of numbers. Tapping into the power of data would let them create more meaningful and effective stories. But making sense of numbers can be difficult. Reporting on data is often not as straightforward or manageable as other types of journalism. Writers need to separate signal from noise.

What’s more, researchers and writers need to know the context of data to draw appropriate conclusions. You can know everything about how candidates in an election fare against one another through polls and surveys, but, until you know the causes behind why people would vote that way, you can’t say much about those statistics. I’ve written more here on the nature of causation in the context of scientific research. This guide provides a logical, reader-friendly approach to writers wanting to harness the power of statistics.

Table of contents:

  1. Know the numbers
  2. Study the source
  3. Remember the reader
  4. Present the product

1. Know the numbers

Too often, writers throw around numbers not knowing what they mean. Here is a run-down of statistics terms you should know as a journalist:

  • Bayesian statistics
    • If it rains, how does that affect which football team will win? This branch of statistics lets you figure out how likely something may occur based on how it depends on other factors. This lets you account for factors like false positives (when an experiment detects something that doesn’t exist) such as medical screening flagging false cues as cancer. With Bayesian models, you can account for different sources of information in putting together these conditional probabilities.
    • Using Bayesian statistics to predict how likely future events are is “Bayesian inference.”
  • Beta distribution
    • Using a pre-defined distribution, you can determine how well a baseball player will do at the beginning of a season even when you haven’t collected much data so far. Using her batting average of .270, you can create beta distribution (shown above with α = .81 and β = .219. The average is .270 and the standard deviation is σ2 = .115.
    • If you don’t know the exact probability something occurs, you can figure out how which probability is most likely by selecting it from a beta distribution of probabilities. You can use α and β to calculate the mean μ and standard deviation σ with:
    • You’ll also find binomial distributions which use the same probability for all trials instead of letting it change.
  • Chi-square test (χ2 test)
      Suppose you wanted to find the relationship between being HIV positive and sexual preference. You survey 30 males and find the following data (in a contingency table):
      Sexual preference
      MaleFemaleBothTotal
      HIV+4239
      Not HIV+316221
      7185
      Then, you can multiply the raw numbers and divide by the total to calculate how likely it is HIV+ determines sexual preference. This gives you expected values, different from the observed ones as shown below:
      Sexual preference
      MalesFemalesBothTotal
      HIV+
      Observed (O)4239
      Expected (E)(9*7)/30  = 2.1(9*18)/30 = 5.4(9*5)/30=1.5
      (O-E)1.9-3.4-1.5
      (O-E)^23.6111.562.25
      Not HIV+
      Observed (O)316221
      Expected (E)(21*7)/30 = 4.9(21*18)/30 = 12.6(21*5)/30 = 3.5
      (O-E)-1.93.4-1.5
      (O-E)^23.6111.562.25
      30
    • If you have an expectation or prediction of what your results should look like, the chi-square test compares them to what you actually observe to tell you how well your predictions match what happens. This example is borrowed from David Stockburger at Missouri State.
    • Researchers calculate this by finding the difference between observed and expected values using the formula χ2 = (observed − expected)2/expected.
    • Sometimes you’ll see the difference between observed and expected values referred to as the “residual.”
  • Confounding variable
    • If you want to test if texting leads to an increase in crashes, you would want to make sure that text messages, not weather or traffic, cause the crashes. These extra variables the study doesn’t account for are confounding variables.
  • Controlled experiment
    • If you give a drug to students to observe how it affects sleep, you should compare this group (the treatment group) to a controlled group, a set of students under the same conditions, but without the drug. This makes sure you can determine that it was the drug causing differences in sleep and not some other variable.
  • Correlation
    • This tells you how well two variables are related to one another. Two stocks that change in similar ways to one another over time may be correlated.
  • Fisher’s exact test
      CuredNot CuredTotal
      Drug A4258100
      Drug B1486100
      Total56144
    • Similar to the chi-square test, this test compares whether an outcome occurs using a contingency table (shown above). There’s no formal calculation, but it can give you an idea of the probability an effect occurs.
  • Histogram
    • This tells you how data is distributed with the normal distribution shown above. The height of each bar shows you how many data points in the bin along the x-axis or how likely it is to fall in that bin. For probabilities, the area of the bins should equal 100 percent.
  • Margin of error
    • When you make a measurement, the margin of error (sometimes called “uncertainty”) tells you how much that measurement can change due to other factors. You’ll typically find this in a range of a confidence interval, such as “40 percent +/- 1 percent.”
    • If you’re polling a sample of people, the margin of error can tell you how close the sample is as representative of the entire population.
    • Writer Robert Niles defines this as “1 divided by the square root of the number of people in the sample.”
    • You can further break down error into bias and systematic error:
      • The same way standing on a weighing scale while wearing clothes makes you heavier, a bias creates an error based on how you measure something.
      • If, instead, the weighing scale itself isn’t calibrated properly, there’s a systematic error. This affects all results due to the nature of your measuring equipment itself.
  • Mean
    • This is the average of a set of data points, generally written using μ. When dealing with statistics, keep your language precise to communicate the most effective message possible. If the average life expectancy in the U.S. is 79 years, know the standard deviation and sample size. You may not need to report those factors, but they’ll help you put your averages in context.
    • When journalists write about the “average citizen” or the “average voter,” in most cases, they’re not referring to the strict mathematical definition of an average (the sum of each data point divided by the number of data points). Rather, journalists tend to refer to the “average” as a common, representative individual in a population. Keep in mind the statistical average only represents this “average individual” based on how the standard deviation and sample size.
  • Median
    • If you listed your data points from highest to lowest, the value in the middle is the median. Because this doesn’t depend on how far spread out or varied the data points are, the median is, more or less, the “middle.” It doesn’t matter that the richest person in America makes four times as much as the middle-class. What matters is whether it’s greater or lesser than those in the middle.
    • In some cases, the median can give you a more accurate idea of the “average” person in a population when reporting. Make sure you understand where the median falls in the space between the highest and lowest data point. That can tell you more about how the numbers are distributed.
    • Paleontologist Stephen Jay Gould quoted Twain’s “damned lies” quote to argue that using the eight-month median survival time for peritoneal mesothelioma was misleading. Many people, like Gould who lived for two more decades, would live for years and take an optimistic, positive view of statistics in general.
  • Mode
    • The mode is the number occurring most often. This simple and clean measurement can tell you who’s the most popular candidate in an election. You won’t see this much, but it’s helpful for comparing raw numbers against one another like sales figures.
  • Multiplication rule
    • If there’s a 1/2 chance you’ll draw a red card from a deck and a 1/13 chance the card is a King, then there chance to draw aa red King is 1/2*1/13= 1/26. This holds for independent events.
    • Keep track of how one event may affect the other. If you draw red card from a deck (with a 1/2 probability), the chance the next card is red is now 25/51 because you have one less red card in the deck.
  • Normal (or standard or Gaussian) distribution
    • Imagine taking a set of heights in a population and graphing the heights on the x-axis with how many times they occur on the y-axis. If the data is “normally” distributed, then most people should fall around an average height with fewer and fewer heights farther away from this average as shown in the graph above. In the normal distribution, you can define this distribution using the mean and standard deviation with  σ as the standard deviation and μ as the mean.
    • The normal distribution centers on the average and, with a greater standard deviation, it becomes more spread out in both directions. You most likely won’t report the normal distribution explicitly in a news story.
    • The standard deviation lets you compare the mean to the distribution. About 70 percent of people are one standard deviation from the mean (in either direction), 95 percent are two standard deviations away and almost everyone, three standard deviations away. The Z-score also tells you how far away a data point is from the mean.
    • If you wanted to test if a new psychiatric drug changed the frequency of mood swings, you might measure the number of mood swings in a population with the drug and a population without. If you found that the means of the two distributions are separated by a certain number of standard deviations, you can convert that to a p-value. The smaller the p-value, the more likely it is that the drug itself, not some random variable. This gives you a probability that the drug works.
  • Null hypothesis (H0)
    • To figure out if smoking truly causes cancer, scientists look for ways to show that “smoking doesn’t cause cancer” is false. This is a null hypothesis (H0), usually used to show that there is no effect or no relationship between what you want to show. In the words of scientists, they look for ways to “reject the null hypothesis.”
    • When creating a standard distribution, the p-value tells you how likely it is to reject the null hypothesis.
  • Quartile
    • Split the data into four equally sized groups. The lowest quarter is the lower quartile, the highest quarter is the upper quartile and everything in between is the middle quartile. The range of the middle quartile is the interquartile range.
  • Range
    • This is the highest value minus the smallest. Note that the range is a single number, not a range of numbers.
  • Regression
    • Regression tests what causes something to happen. If smoking really does cause an increase in cancer, then you should see it if you make a graph of cancer prevalence vs. smoking like the graph above, usually with a line of best fit (shown in red). Given enough linear regressions, you can separate a scientific observation explain the relationship between into the variables that cause it.
    • Keep in mind correlation does not imply causation. If you find that video game sales rise around similar times when violent crimes occur, you still need to show that one caused the other before drawing conclusions between the two. Otherwise things may be a coincidence or just a matter of randomness.
    • You’ll see an R value (how well one variable explains the other) or an R2 value (how well the model fits the data). The ANOVA (Analysis of Variance) creates an R2 and whether the result is “statistically significant.”
  • Standard deviation
    • The standard deviation is how widely values are spread apart or how much the data varies. This, along with mean, defines a normal distribution.
    • You can calculate the standard deviation of the population the formula above with x̄ as the average of data points x over n number of data points with Σ the sum of each value (xi – x̄)2. If you want the standard deviation of a specific sample, use n-1 instead of n in the denominator because you only know the mean of that sample, not the population.
    • The standard deviation squared gives you the variance. Sometimes researchers use “deviation” and “variance” interchangeably so keep in mind the difference.
  • Stochastic models
    • These are ways to predict future data like financial portfolios or weather forecasts that depend on randomness. Using distributions like the normal or beta distributions, you can simulate what future data will look like and form predictions.
  • Variable
    • Variables are anything that differs from person to person or sample to sample.
    • Categorical variables are ways of labeling people into groups (like biological sex or state of residence), continuous ones lie on a scale (like age or temperature), qualitative ones use adjectives (like colors) and random variables are what scientists measure as outcomes of experiments (like flipping a coin).

    • 2. Study the source

    The Society for Professional Journalists dictates you should remain accountable and transparent, seek the truth and report it and act independently. In the context of numbers, this means remaining open and honest in data analysis, scrutinizing findings and mathematical methods and doing so free from anything that my interfere with an investigation. After you know the definitions of statistics, you need to know where those numbers came from. This means not only knowing how data was collected, but appealing to statistics in a way that reflects the current principles of journalism.

    Writer William Davies argued the authority of statistics and the researchers who study them is declining. In a post-statistical society, journalists need to remain objective and skeptical to statistics while still appreciating them for what they are. It won’t be a battle between elite facts and populist feelings, but, rather, public rhetoric and the forces against it.

    Remember to keep numbers in context of their original source or how they were measured. If someone asks where you got your information from or how a number was calculated, you should have an appropriate answer. If you’re reporting a p-value for biomedical study, which variables were measured? How does the standard deviation affect the certainty of the results? Make sure that, for whatever claim or argument a scientist has put forward in a study, you can be responsible for however you report on it.

    As you become more statistically literate, you’ll naturally reevaluate how you reason. Becoming aware of common fallacies and pitfalls journalists fall into can make you more prepared to present accurate scientific findings. Be careful when you read a study suggesting that, because people are losing jobs, the economy must be doing poorly or that, if a study found no evidence on the link between fossil fuels and climate change that you conclude there’s evidence of absence. You can begin to see through the arguments that the majority of people saying something is true makes it true and, instead, take a more empirical approach to forming an opinion.

    Much more sinister are those who prey on individuals without a strong statistical or mathematical literacy. Showing that the cost of attending college is a smaller percent of the national debt now than it was in the 1960s doesn’t show that today’s college students pay less for their education. As you study the context and nuances of scientific findings, you’ll become better prepared to separate signal from noise in these situations.

    If there’s a 20 percent chance of rain, does that mean it will rain 20 percent of the time? If a medical procedure has a false positive rate of 1 out of 10 trials, how does that change its effectiveness? It’s easy to appeal to the authority of statistics and science without investigating for yourself. Check what experiments were performed or the historical use of tests like the Fisher’s exact test.

    This way, you’re acting as both a writer and a researcher. The key here is to avoid resorting to phrases like “studies show” or “survey says,” and, instead, ask yourself if you really know what the scientific studies purport. Many times scientists will refer to terms like “standard deviation” or “variance” interchangeably so make sure you know what’s being reported.

    3. Remember the reader

    Now that you have a deep understanding of what you’re reporting and what it means, you need to put it in a context that a general audience can understand.

    If you ask a drunkard what number is larger, 2/3 or 3/5, he won’t be able to tell you. But if you rephrase the question: what is better, 2 bottles of vodka for 3 people or 3 bottles of vodka for 5 people, he will tell you right away: 2 bottles for 3 people, of course.

    Edward Frenkel, “Love and Math: The Heart of Hidden Reality”

    In the quote above, how does drunkard arrive at the correct answer? The statistics are presented differently. In the rephrased question, he has a more “tangible,” usable way of understanding how the proportions of vodka would be arise from the distribution among people.

    How well do you understand what you write? Try answering this question to find out.

    Imagine you conduct a breast cancer screening using mammography in a certain region. You know the following information about the women in this region: The probability that a woman has breast cancer is 1 percent (known as “prevalence”). If a woman has breast cancer, the probability that she tests positive is 90 percent (“sensitivity”). If a woman does not have breast cancer, the probability that she nevertheless tests positive is 9 percent (false-positive rate). A woman tests positive. She wants to know from you whether that means that she has breast cancer for sure, or what the chances are. What is the best answer?

      A. The probability that she has breast cancer is about 81 percent.
      B. Out of 10 women with a positive mammogram, about 9 have breast cancer.
      C. Out of 10 women with a positive mammogram, about 1 has breast cancer.
      D. The probability that she has breast cancer is about 1 percent.

    When German psychologist Gerd Gigerezner posed the question to about 1000 gynecologists, about 21 percent chose the correct answer, C. While that is a little worse than random guessing, I must admit that, on my first attempt, I failed to answer this question correctly, as well. Through his research, Gigerezner has crafted a theory of understanding statistics that would help us in situations like this.

    Similar to Frenkel’s example of the fractions of vodka, psychologists like Daniel Kahneman and Gerd Gigerezner have shown that asking statistics questions in different ways can influence the ways we understand them. For example, when the information preceding the question is framed differently (as shown below), 87 percent of gynecologists answered correctly.

    Assume you conduct breast cancer screening using mammography in a certain region. You know the following information about the women in this region:

    • Ten out of every 1,000 women have breast cancer
    • Of these 10 women with breast cancer, 9 test positive
    • Of the 990 women without cancer, about 89 nevertheless test positive

    In both examples (of breast cancer screening and of bottles of vodka), when we change from “conditional probabilities” to “natural frequencies,” we suddenly understand statistics much better. Like Gigerezner, I believe we can teach the appropriate way to interpret statistics, and, with the effect it has on our health and society, we have a moral imperative to do so.

    You can use a confusion matrix like the one above to keep track of the accuracy metrics of an experiment when presenting information to colleagues.

    This isn’t a simple case of deliberately communicating false information or lying about the statistics we use. While there may be agendas and conflicts-of-interests between professionals (including scientists), we simply don’t understand how to interpret statistics. And, in the field of medicine, this can have disastrous results. We make poor decisions about how long a patient may live, how prevalence of cancer among smokers, and understanding the harms and benefits of screening for breast cancer.

    4. Present the product

    Many ways of visualizing, illustrating or explaining statistics exist no matter the medium. Looking across FiveThirtyEight, The Guardian‘s Data section or other data journalism publications, you can find effective ways of communicating complicated concepts either to the audience of your publication or to colleagues. Use figures and graphs to explain take-home messages and conclusions from your reporting. Make sure they’re easy to read and follow.

    Python and R offer ways of visualizing statistical findings with R providing much more extensive libraries for statistics than Python. My work in creating interactive network graphs, word clouds and even periodic tables show some examples. To produce a confusion matrix like the one shown below, you can use this code.

    Compare this confusion matrix to the Null hypothesis table above. Though it might be too complicated for someone reading a newspaper, you can use it to present findings to other researchers.

    It’s a good idea to value openness and transparency with your code and work in creating visualizations. This gives other researchers and writers ways to check and re-examine what you’ve done. The chart below shows how much the University of California Santa Cruz Science Communication class of 2020 used Slack during their fall quarter (with its code here). Interactive graphs give the reader a better sense of data and let you communicate more information as effective as possible.

    Make sure to perform statistical tests to confirm results from research when you report. In the movie “Rosencrantz and Guildenstern Are Dead,” the two protagonists flip a coin heads 92 times in a row. The chances this may happen is about 1 in 5 octillion. In a more realistic setting, the Dallas Cowboys have won 6 out of 8 coin tosses in the history of Super Bowls. In R, you can use a binomial distribution to return the value 0.109375. 

    probability <- .5 # Set the odds of getting heads to .5. 
wins <- 6 # number of winning coin flips
totalFlips <- 8 # total coin flips
dbinom(wins, totalFlips, probability)
> 0.109375

    In the code, the comments are written with a # in front of them explaining what each line does. These comments are notes programmers write to explain things without affecting the code.

    With enough coin tosses you can make a graph of how these probabilities are based on the number of heads and flips. When you only have two outcomes (heads or tails), it’s a Bernoulli distribution.

    How likely is it the coin is fair? (Code found here.)

    Not all visuals are created equal. Statisticians William Cleveland and Robert McGill found that people can tell differences between length and angles much more easily than shapes and colors. This means, where appropriate, you should use charts and plots that rely on lines slopes when possible and avoid pie charts.

    No matter the code or plot you make, taking an independent investigative approach to statistics can let you harness the power of data in your stories. Becoming more savvy with numbers and calculations can let you present more accurate, verified findings. Though you can’t just drop statistics without context or understanding of how they came about, newsrooms and other workplaces for publications can use a more empirical approach in their findings in presenting scientific research for what it is. Whether its journalists themselves or a hired analyst creating statistical models of disease prevalence, they should adhere to the established standards of journalism.

    Life expectancy: visualized. (Code found here.)

    Journalism emphasizes quick, easy-to-understand conclusions and messages. While some projects can require more complicated work flows such as Bayesian models, bootstrapping or exploratory data analysis, sometimes all that matters is whether an experiment worked or didn’t. In many cases, you simply don’t have the time or capacity to explain what a p-value or regression test is. Still, becoming statistically literate and understanding the mathematics behind calculations involved in research can make you all the more prepared in presenting stories. Being able to tell the difference between causation and correlation can save you from drawing false conclusions and make your arguments more justified on the basis of statistics. It can give you the power to check the work of others and move journalism into a domains of peer-reviewed, egalitarian work. In writing this guide, I hope to do so as well.

    The Emergent Beauty of Mathematics

    The first 30 seconds of a Brownian tree (code can be found here).

    Like a flower in full bloom, nature reveals its patterns shaped by mathematics. Or as particles collide with one another, they create snowflake-like fractals through emergence. How do fish swarm in schools or consciousness come about from the brain? Simulations can provide answers.

    Through code, you can simulate how living cells or physical particles would interact with one another. Using equations that govern the behavior of how cells act when they meet one another or how they would grow and evolve into larger structures. In the gif above, you can use diffusion-limited aggregation to create Brownian trees. These are the structures that emerge when particles move randomly with respect to one another. Particles in fluid (like dropping color dye into water) take these patterns when you look at them under a microscope. As the particles collide and form trees, they create shapes and patterns like water crystals on glass. These visuals can give you a way of appreciating how beautiful mathematics is. The way mathematical theory can borrow from nature and how biological communities of living organisms themselves depend on physical laws shows how such an interdisciplinary approach provides a way to bridge different disciplines.

    After about 20 minutes, the branches of the Brownian tree take form.

    In the code, the particles are set to move with random velocities in two dimensions and, if they collide with the tree (a central particle at the beginning), they form parts of the tree. As the tree grows bigger over time, it takes the shapes of branches the same way neurons in the brain form trees that send signals between one another. These fractals, in their uniqueness, give them a kind of mathematical beauty.

    Conway’s game of life represents another way something emerges from randomness.

    Flashing lights coming and going away like stars shining in the sky are more than just randomness. These models of cellular interactions are known as cellular automaton. The gif above shows an example of Conway’s game of life, a simulation of how living cells interact with one another.

    These cells “live” and “die” according to four simple rules: (1) live cells with fewer than two live neighbors die, as if by underpopulation, (2) live cells with two or three live neighbors live on to the next generation, (3) live cells with more than three live neighbors die, as if by overpopulation and (4) dead cells with exactly three live neighbors become live cells, as if by reproduction.

    Conus textile shows a similar cellular automaton pattern on its shell.

    Through these rules, specific shapes emerge such as “gliders” or “knightships” you can further describe with rules and equations. You’ll find natural versions of cells obeying rules like the colorful patterns on a seashell. Complex structures emerging from more basic, fundamental sets of rules unite these observations. While the beauty of these structures becomes more and more apparent from the patterns between different disciplines, searching for these patterns in other contexts can be more difficult such as human behavior.

    Recent writing like Genesis: The Deep Origin of Societies by biologist E.O. Wilson take on the debate over how altruism in humans evolved. While the shape of snowflakes can emerge from the interactions between water molecules, humans getting along with one another seems far more complicated and higher-level. Though you can find similar cooperation in ants and termites creating societies, how did science let this happen?

    Biologists have answered that organisms choose to mate with individuals and increase the survival chances of themselves and their offspring while passing on their genes. Though they’ve argued this for decades, Wilson offers a contrary point of view. In groups, selfish organisms defeat altruistic ones, but altruistic groups beat selfish groups overall. This group selection drives the emergence of altruism. Through these arguments, both sides have appealed to the mathematics of nature, showing its growing importance in recognizing the patterns of life.

    Wilson clarifies that data analysis and mathematical modeling should come second to the biology itself. Becoming experts on organisms themselves should be a priority. Regardless of what form it takes, the beauty is still there, even if it’s below the surface.

    How to Create Interactive Network Graphs (from Twitter or elsewhere) with Python

    In this post, a gentle introduction to different Python packages will let you create network graphs users can interact with. Taking a few steps into graph theory, you can apply these methods to anything from links between the severity of terrorist attacks or the prices of taxi cabs. In this tutorial, you can use information from Twitter to make graphs anyone can appreciate.

    The code for steps 1 and 2 can be found on GitHub here, and the code for the rest, here.

    Table of contents:

    1. Get Started
    2. Extract Tweets and Followers
    3. Process the Data
    4. Create the Graph
    5. Evaluate the Graph
    6. Plot the Map

    1. Get Started

    Make sure you’re familiar with using a command line interface such as Terminal and you can download the necessary Python packages (chart-studio, matplotlib, networkx, pandas, plotly and python-twitter). You can use Anaconda to download them. This tutorial will introduce parts of the script you can run from the command line to extract tweets and visualize them.

    If you don’t have a Twitter developer account, you’ll need to login here and get one. Then create an app and find your keys and secret codes for the consumer and access tokens. This lets you extract information from Twitter.

    2. Extract Tweets and Followers

    To extract Tweets, run the script below. In this example, the tweets of the UCSC Science Communication class of 2020 are analyzed (in screennames) so their Twitter handles are used. Replace the variables currently defined as None below with them. Keep these keys and codes safe and don’t share them with others. Set datadir to the output directory to store the data.

    The code begins with import statements to use the required packages including json and os, which should come installed with Python. 

    import json
import os
import pickle
import twitter 

screennames = ["science_ari", "shussainather", "laragstreiff",                  "scatter_cushion", "jessekathan", "jackjlee",                 "erinmalsbury", "joetting13", "jonathanwosen",                 "heysmartash"] 

CONSUMER_KEY = None
CONSUMER_SECRET = None
ACCESS_TOKEN_KEY = None
ACCESS_TOKEN_SECRET = None

datadir = "data/twitter"

    Extract the information we need. This code goes through each screen name and accesses their tweet and follower information. It then saves the data of both of them to output JSON and pickle files. 

    t = twitter.Api(consumer_key = CONSUMER_KEY,
                     consumer_secret = CONSUMER_SECRET,
                     access_token_key = ACCESS_TOKEN_KEY,
                     access_token_secret = ACCESS_TOKEN_SECRET)
     for sn in screennames:
         """
         For each user, get the followers and tweets and save them
         to output pickle and JSON files.
         """
         fo = datadir + "/" + sn + ".followers.pickle"
         # Get the follower information.
         fof = t.GetFollowers(screen_name = sn)
         with open(fo, "w") as fofpickle:
             pickle.dump(fof, fofpickle, protocol = 2)
         with open(fo, "r") as fofpickle:
             with open(fo.replace(".pickle", ".json"), "w") as fofjson:
                 fofdata = pickle.load(fofpickle)
                 json.dump(fofdata, fofjson)  # Get the user's timeline with the 500 most recent tweets.
        timeline = t.GetUserTimeline(screen_name=sn, count=500)
        tweets = [i.AsDict() for i in timeline]
        with open(datadir + "/" + sn + ".tweets.json", "w") as tweetsjson:
             json.dump(tweets, tweetsjson) # Store the informtion in a JSON.

    This should extract the follower and tweets and save them to pickle and JSON files in the datadir.

    3. Process the Data

    Now that you have an input JSON file of tweets, you can set it to the tweetsjson variable in the code below to read it as a pandas DataFrame.

    For the rest of the tutorial, start a new script for convenience. 

    import json 
    import matplotlib.pyplot as plt 
    import networkx as nx 
    import numpy as np 
    import pandas as pd 
    import re 
    from plotly.offline import iplot, plot
    from operator import itemgetter

    Use pandas to import the JSON file as a pandas DataFrame.

    df = pd.read_json(tweetsjson)

    Set tfinal as the final DataFrame to make. 

    tfinal = pd.DataFrame(columns = ["created_at", "id", "in_reply_to_screen_name",                                       "in_reply_to_status_id", "in_reply_to_user_id",                                        "retweeted_id", "retweeted_screen_name", "user_mentions_screen_name",                                       "user_mentions_id", "text", "user_id", "screen_name", "followers_count"])

    Then, extract the columns you’re interested in and add them to tfinal.

    eqcol = ["created_at", "id", "text"]
    tfinal[eqcol] = df[eqcol]
    tfinal = filldf(tfinal)
    tfinal = tfinal.where((pd.notnull(tfinal)), None)

    Use the following functions to extract information from them. Each function extracts information form the input df DataFrame and adds it to the tfinal one.

    First, get the basic information: screen name, user ID and how many followers.

    def getbasics(tfinal):
         """
         Get the basic information about the user.
         """
         tfinal["screen_name"] = df["user"].apply(lambda x: x["screen_name"])
         tfinal["user_id"] = df["user"].apply(lambda x: x["id"])
         tfinal["followers_count"] = df["user"].apply(lambda x: x["followers_count"])
         return tfinal

    Then, get information on which tweets have been retweeted. 

    def getretweets(tfinal):
         """
         Get retweets.
         """
         # Inside the tag "retweeted_status" will find "user" and will get "screen name" and "id". 
         tfinal["retweeted_screen_name"] = df["retweeted_status"].apply(lambda x: x["user"]["screen_name"] if x is not np.nan else np.nan)
         tfinal["retweeted_id"] = df["retweeted_status"].apply(lambda x: x["user"]["id_str"] if x is not np.nan else np.nan)
         return tfinal

    Figure out which tweets are replies and to who they are replying.

    def getinreply(tfinal):
         """
         Get reply info.
         """
         # Just copy the "in_reply" columns to the new DataFrame.
         tfinal["in_reply_to_screen_name"] = df["in_reply_to_screen_name"]
         tfinal["in_reply_to_status_id"] = df["in_reply_to_status_id"]
         tfinal["in_reply_to_user_id"]= df["in_reply_to_user_id"]
         return tfinal

    The following function runs each of these functions to get the information into tfinal.

    def filldf(tfinal):
         """
         Put it all together.
         """
         getbasics(tfinal)
         getretweets(tfinal)
         getinreply(tfinal)
         return tfinal

    You’ll use this getinteractions() function in the next step when creating the graph. This takes the actual information from the tfinal DataFrame and puts it into the format that a graph can use.

    def getinteractions(row):
     """
     Get the interactions between different users.
     """
     # From every row of the original DataFrame.
     # First we obtain the "user_id" and "screen_name".
     user = row["user_id"], row["screen_name"]
     # Be careful if there is no user id.
     if user[0] is None:
         return (None, None), []

    For the remainder of the for loop, get the information if it’s there. 

        # The interactions are going to be a set of tuples.
    interactions = set()

    # Add all interactions. 
    # First, we add the interactions corresponding to replies adding 
    # the id and screen_name.
    interactions.add((row["in_reply_to_user_id"], 
    row["in_reply_to_screen_name"]))
    # After that, we add the interactions with retweets.
    interactions.add((row["retweeted_id"], 
    row["retweeted_screen_name"]))
    # And later, the interactions with user mentions.
    interactions.add((row["user_mentions_id"], 
    row["user_mentions_screen_name"]))

    # Discard if user id is in interactions.
    interactions.discard((row["user_id"], row["screen_name"]))
    # Discard all not existing values.
    interactions.discard((None, None))
    # Return user and interactions.
    return user, interactions

    4. Create the Graph

    Initialize the graph with networkx.

    graph = nx.Graph()

    Loop through the tfinal DataFrame and get the interaction information. Use the getinteractions function to get each user and interaction involved with each tweet. 

    for index, tweet in tfinal.iterrows():
         user, interactions = getinteractions(tweet)
         user_id, user_name = user
         tweet_id = tweet["id"]
         for interaction in interactions:
             int_id, int_name = interaction
             graph.add_edge(user_id, int_id, tweet_id=tweet_id)
             graph.node[user_id]["name"] = user_name
             graph.node[int_id]["name"] = int_name

    5. Evaluate the Graph

    In the field of social network analysis (SNA), researchers use measurements of nodes and edges to tell what graphs re like. This lets you separate the signal from noise when looking at network graphs.

    First, look at the degrees and edges of the graph. The print statements should print out the information about these measurements.

    degrees = [val for (node, val) in graph.degree()]
    print("The maximum degree of the graph is " + str(np.max(degrees))) 
    print("The minimum degree of the graph is " + str(np.min(degrees)))
    print("There are " + str(graph.number_of_nodes()) + " nodes and " + str(graph.number_of_edges()) + " edges present in the graph")
    print("The average degree of the nodes in the graph is " + str(np.mean(degrees)))

    Are all the nodes connected?

    if nx.is_connected(graph):
         print("The graph is connected")
     else:
         print("The graph is not connected")
     print("There are " + str(nx.number_connected_components(graph)) + " connected in the graph.")

    Information about the largest subgraph can tell you what sort of tweets represent the majority. 

    largestsubgraph = max(nx.connected_component_subgraphs(graph), key=len)
     print("There are " + str(largestsubgraph.number_of_nodes()) + " nodes and " + str(largestsubgraph.number_of_edges()) + " edges present in the largest component of the graph.")

    The clustering coefficient tells you how close together the nodes congregate using the density of the connections surrounding a node. If many nodes are connected in a small area, there will be a high clustering coefficient. 

    print("The average clustering coefficient is " + str(nx.average_clustering(largestsubgraph)) + " in the largest subgraph")
    print("The transitivity of the largest subgraph is " + str(nx.transitivity(largestsubgraph)))
    print("The diameter of our graph is " + str(nx.diameter(largestsubgraph)))
    print("The average distance between any two nodes is " + str(nx.average_shortest_path_length(largestsubgraph)))

    Centrality tells you how many direct, “one step,” connections each node has to other nodes in the network, and there are two ways to measure it. “Betweenness centrality” represents which nodes act as “bridges” between nodes in a network by finding the shortest paths and counting how many times each node falls on one. “Closeness centrality,” instead, scores each node based on the sum of the shortest paths.

    graphcentrality = nx.degree_centrality(largestsubgraph)
    maxde = max(graphcentrality.items(), key=itemgetter(1))
    graphcloseness = nx.closeness_centrality(largestsubgraph)
    graphbetweenness = nx.betweenness_centrality(largestsubgraph, normalized=True, endpoints=False)
    maxclo = max(graphcloseness.items(), key=itemgetter(1))
    maxbet = max(graphbetweenness.items(), key=itemgetter(1))

    print("The node with ID " + str(maxde[0]) + " has a degree centrality of " + str(maxde[1]) + " which is the max of the graph.")
    print("The node with ID " + str(maxclo[0]) + " has a closeness centrality of " + str(maxclo[1]) + " which is the max of the graph.")
    print("The node with ID " + str(maxbet[0]) + " has a betweenness centrality of " + str(maxbet[1]) + " which is the max of the graph.")

    6. Plot the Map

    Get the edges and store them in lists Xe and Ye in the x- and y-directions. 

    Xe=[]
    Ye=[]
    for e in G.edges():
        Xe.extend([pos[e[0]][0], pos[e[1]][0], None])
        Ye.extend([pos[e[0]][1], pos[e[1]][1], None])

    Define the Plotly “trace” for nodes and edges. Plotly uses these traces as a way of storing the graph data right before it’s plotted.

    trace_nodes = dict(type="scatter",
                 x=Xn, 
                 y=Yn,
                 mode="markers",
                 marker=dict(size=28, color="rgb(0,240,0)"),
                 text=labels,
                 hoverinfo="text")

trace_edges = dict(type="scatter",                  
                 mode="lines",                  
                 x=Xe,                  
                 y=Ye,                 
                 line=dict(width=1, color="rgb(25,25,25)"),                                         hoverinfo="none")

    Plot the graph with the Fruchterman-Reingold layout algorithm. This image shows an example of a graph plotted with this algorithm, designed to provide clear, explicit ways the nodes are connected.

    The force-directed Fruchterman-Reingold algorithm to draw nodes in an understandable way.

    pos = nx.fruchterman_reingold_layout(G)

    Use the axis and layout variables to customize what appears on the graph. Using the showline=False, option, you will hide the axis line, grid, tick labels and title of the graph. Then the fig variable creates the actual figure.

    axis = dict(showline=False, 
              zeroline=False,
              showgrid=False,
              showticklabels=False,
              title=""
              )

    layout = dict(title= "My Graph",  
                 font= dict(family="Balto"),
                 width=600,
                 height=600,
                 autosize=False,
                 showlegend=False,
                 xaxis=axis,
                 yaxis=axis,
                 margin=dict(
                 l=40,
                 r=40,
                 b=85,
                 t=100,
                 pad=0,   
         ),
         hovermode="closest",
         plot_bgcolor="#EFECEA", # Set background color.           
         )

     fig = dict(data=[trace_edges, trace_nodes], layout=layout)

    Annotate with the information you want others to on each node. Use the labels variable to list (with the same length as pos) what should appear as an annotation.

    labels = range(len(pos))

    def make_annotations(pos, anno_text, font_size=14, font_color="rgb(10,10,10)"):
         L=len(pos)
         if len(anno_text)!=L:
             raise ValueError("The lists pos and text must have the same len")
         annotations = []
         for k in range(L):
             annotations.append(dict(text=anno_text[k], 
                                     x=pos[k][0], 
                                     y=pos[k][1]+0.075,#this additional value is chosen by trial and error
                                     xref="x1", yref="y1",
                                     font=dict(color= font_color, size=font_size),
                                     showarrow=False)
                               )
         return annotations  
    fig["layout"].update(annotations=make_annotations(pos, labels))

    Finally, plot.

    iplot(fig)

    An example graph

    Make a word cloud in a single line of Python

    Moby-Dick, visualized

    This is a concise way to make a word cloud using Python. It can teach you basics of coding while creating a nice graphic.

    It’s actually four lines of code, but making the word cloud only takes one line, the final one. 

    import nltk
from wordcloud import WordCloud
nltk.download("stopwords")
WordCloud(background_color="white", max_words=5000, contour_width=3, contour_color="steelblue").generate_from_text(" ".join([r for r in open("mobydick.txt", "r").read().split() if r not in set(nltk.corpus.stopwords.words("english"))])).to_file("wordcloud.png")

    Just tell me what to do now!

    The first two lines lines specify the required packages you must download with these links: nltk and wordcloud. You may also try these links: nltk and wordcloud to download them. The third line downloads the stop words (common words like “the”, “a” and “in”) that you don’t want in your word cloud.

    The fourth line is complicated. Calling the WordCloud() method, you can specify the background color, contour color and other options (found here). generate_from_text() takes a string of words to put in the word cloud.

    The " ".join() creates this string of words separated by spaces from a list of words. The for loop in the square brackets[] creates this list of each word from the input file (in this case, mobydick.txt) with the r variable letting you use each word one at a time in the list.

    The input file is open(), read() and split() into its words under the condition (using if) they aren’t in nltk.corpus.stopwords.words("english"). Finally, to_file() saves the image as wordcloud.png.

    How to use this code

    In the code, change "mobydick.txt" to the name of your text file (keep the quotation marks). Save the code in a file makewordcloud.py in the text file’s directory, and use a command line interface (such as Terminal) to navigate to the directory.

    Run your script using python makewordcloud.py, and check out your wordcloud.png!

    Global Mapping of Critical Minerals

    The periodic table below illustrates the global abundance of critical minerals in the Earth’s crust in parts per million (ppm). Hover over each element to view! Lanthanides and actinides are omitted due to lack of available data.

    Data is obtained from the USGS handbook “Critical Mineral Resources of the United States— Economic and Environmental Geology and Prospects for Future Supply.” The code used is found here.

    Bokeh Plot

    Because these minerals tend to concentrate in specific countries like niobium in Brazil or antimony in China and remain central to many areas of society such as national defense or engineering, governments like the US have come forward with listing these minerals as “critical.”

    The abundance across different continents is shown in the map above.

    You can find gallium, the most abundant of the critical minerals, in place of aluminum and zinc, elements smaller than gallium. Processing bauxite ore or sphalerite ore (from the sediment-hosted, Mississippi Valley-type and volcanogenic massive sulfide) of zinc yield gallium. The US meets its gallium needs through primary, recycled and refined forms of the element.

    German and indium have uses in electronics, flat-panel display screens, light-emitting diodes (LEDs) and solar power arrays. China, Belgium, Canada, Japan and South Korea are the main producers of indium while germanium production can be more complicated. In many cases, countries import primary germanium from other ones, such as Canada importing from the US or Finland from the Democratic Republic of the Congo, to recover them.

    Rechargable battery cathodes and jet aircraft turbine engines make use of cobalt. While the element is the central atom in vitamin B12, excess and overexposure can cause lung and heart dysfunction and dermatitis.

    As one of only three countries that processes beryllium into products, the US doesn’t put much time or money into exploring for new deposits within its own borders because a single producer dominates the domestic berllyium market. Beryllium finds uses in magnetic resonance imaging (MRI) and medical lasers.

    A Deep Learning Overview with Python

    This course proposes a quick introduction to deep learning and two of its major networks, convolutional neural networks (CNNs) and recurrent neural networks (RNNs). The purpose is to give an intuitive sense of how to implement deep learning approaches for various tasks. To use this iPython notebook, run the python code in separate files for each cell. The content below each cell of this notebook is the output for running those cells.

    Simple perceptron

    In [1]:
    import numpy as np

# sigmoid function
def sigmoid(x,deriv=False):
    if(deriv==True):
        return x*(1-x)
    return 1/(1+np.exp(-x))
    
# input dataset
X = np.array([[0,0,1],
              [0,1,1],
              [1,0,1],
              [1,1,1]])
    
# output dataset            
y = np.array([[0,0,1,1]]).T

# seed random numbers to make calculation
# deterministic (just a good practice)
np.random.seed(1)

# initialize weights randomly with mean 0
syn0 = 2*np.random.random((3,1)) - 1

for j in range(100000):

    # forward propagation
    l0 = X
    l1 = sigmoid(np.dot(l0,syn0))

    # how much did we miss?
    l1_error = y - l1
    if (j% 10000) == 0:
        print("Error:" + str(np.mean(np.abs(l1_error))))

    # multiply how much we missed by the 
    # slope of the sigmoid at the values in l1
    l1_delta = l1_error * sigmoid(l1,True)

    # update weights
    syn0 += np.dot(l0.T,l1_delta)

print()
print("Prediction after Training:")
print(l1)

    Error:0.517208275438
Error:0.00795484506673
Error:0.0055978239634
Error:0.00456086918013
Error:0.00394482243339
Error:0.00352530883742
Error:0.00321610234673
Error:0.00297605968522
Error:0.00278274003022
Error:0.0026227273927

Prediction after Training:
[[ 0.00301758]
 [ 0.00246109]
 [ 0.99799161]
 [ 0.99753723]]

    What is the loss function here? How is it calculated?

    Any idea how it would perform on non-linearly separable data? How could we test it?

    Multilayer perceptron

    Let’s use the fact that the sigmoid is differenciable (while the step function we saw in the slides is not). This allows us to add more layers (hence more modelling power).

    In [2]:
    import numpy as np

def sigmoid(x,deriv=False):
	if(deriv==True):
	    return x*(1-x)

	return 1/(1+np.exp(-x))
    
X = np.array([[0,0,1],
              [0,1,1],
              [1,0,1],
              [1,1,1]])
                
y = np.array([[0],
			  [1],
			  [1],
			  [0]])

np.random.seed(1)

# randomly initialize our weights with mean 0
syn0 = 2*np.random.random((3,4)) - 1
syn1 = 2*np.random.random((4,1)) - 1

for j in range(100000):

	# Feed forward through layers 0, 1, and 2
    l0 = X
    l1 = sigmoid(np.dot(l0,syn0))
    l2 = sigmoid(np.dot(l1,syn1))

    # how much did we miss the target value?
    l2_error = y - l2
    
    if (j% 10000) == 0:
        print("Error:" + str(np.mean(np.abs(l2_error))))
        
    # in what direction is the target value?
    # were we really sure? if so, don't change too much.
    l2_delta = l2_error*sigmoid(l2,deriv=True)

    # how much did each l1 value contribute to the l2 error (according to the weights)?
    l1_error = l2_delta.dot(syn1.T)
    
    # in what direction is the target l1?
    # were we really sure? if so, don't change too much.
    l1_delta = l1_error * sigmoid(l1,deriv=True)

    syn1 += l1.T.dot(l2_delta)
    syn0 += l0.T.dot(l1_delta)
    
print()
print(l2)

    Error:0.496410031903
Error:0.00858452565325
Error:0.00578945986251
Error:0.00462917677677
Error:0.00395876528027
Error:0.00351012256786
Error:0.00318350238587
Error:0.00293230634228
Error:0.00273150641821
Error:0.00256631724004

[[ 0.00199094]
 [ 0.99751458]
 [ 0.99771098]
 [ 0.00294418]]

    Setting up the environment

    We have done toy examples for feedforward networks. Things quickly become complicated, so let’s go deeper by relying on high-level frameworks: TensorFlow and Keras. Most technicalities are thus avoided so that you can directly play with networks.

    In [ ]:
    !conda install tensorflow keras
    In [3]:
    import tensorflow as tf
import keras

    /Users/syedather/.local/lib/python3.6/site-packages/matplotlib/__init__.py:1067: UserWarning: Duplicate key in file "/Users/syedather/.matplotlib/matplotlibrc", line #2
  (fname, cnt))
Using TensorFlow backend.
    In [4]:
    hello = tf.constant('Hello, TensorFlow!')
sess = tf.Session()
print(sess.run(hello))

    b'Hello, TensorFlow!'

    CNNs

    We are going to use the MNIST dataset for our first task. The code below loads the dataset and shows one training example and its label.

    In [5]:
    from __future__ import print_function
import keras
from keras.datasets import mnist
from keras.models import Sequential
from keras.layers import Dense, Dropout, Flatten
from keras.layers import Conv2D, MaxPooling2D
from keras import backend as K
from pylab import *

# the data, split between train and test sets
(x_train, y_train), (x_test, y_test) = mnist.load_data()

print("The first training instance is labeled as: "+str(y_train[0]))

    The first training instance is labeled as: 5
    In [6]:
    figure(1)
imshow(x_train[0], interpolation='nearest')
    Out[6]:
    <matplotlib.image.AxesImage at 0x1259b2320>

    Now study the following code. What is the network we use? How many layers? What hyper parameters?

    In [7]:
    # Setup some hyper parameters
batch_size = 128
num_classes = 10
epochs = 15

# input image dimensions
img_rows, img_cols = 28, 28

# This is some technicality regarding Keras' dataset
if K.image_data_format() == 'channels_first':
    x_train = x_train.reshape(x_train.shape[0], 1, img_rows, img_cols)
    x_test = x_test.reshape(x_test.shape[0], 1, img_rows, img_cols)
    input_shape = (1, img_rows, img_cols)
else:
    x_train = x_train.reshape(x_train.shape[0], img_rows, img_cols, 1)
    x_test = x_test.reshape(x_test.shape[0], img_rows, img_cols, 1)
    input_shape = (img_rows, img_cols, 1)

# We convert the matrices to floats as we will use real numbers
x_train = x_train.astype('float32')[:1000]
x_test = x_test.astype('float32')[:200]
x_train /= 255
x_test /= 255
print('x_train shape:', x_train.shape)
print(x_train.shape[0], 'train samples')
print(x_test.shape[0], 'test samples')

# convert class vectors to binary class matrices
y_train = keras.utils.to_categorical(y_train, num_classes)[:1000]
y_test = keras.utils.to_categorical(y_test, num_classes)[:200]


# Build network
model = Sequential()
model.add(Conv2D(32, kernel_size=(3, 3),
                 activation='relu',
                 input_shape=input_shape))
model.add(Conv2D(64, (3, 3), activation='relu'))
model.add(MaxPooling2D(pool_size=(2, 2)))
# model.add(Dropout(0.25))
model.add(Flatten())
model.add(Dense(128, activation='relu'))
# model.add(Dropout(0.5))
model.add(Dense(num_classes, activation='softmax'))

model.compile(loss=keras.losses.categorical_crossentropy,
              optimizer=keras.optimizers.Adam(),
              metrics=['accuracy'])

# Train
model.fit(x_train, y_train,
          batch_size=batch_size,
          epochs=epochs,
          verbose=1,
          validation_data=(x_test, y_test))

# Evaluate on test data
score = model.evaluate(x_test, y_test, verbose=0)
print()
print('Test loss:', score[0])
print('Test accuracy:', score[1])

# Evaluate on training data
score = model.evaluate(x_train, y_train, verbose=0)
print()
print('Train loss:', score[0])
print('Train accuracy:', score[1])

    x_train shape: (1000, 28, 28, 1)
1000 train samples
200 test samples
Train on 1000 samples, validate on 200 samples
Epoch 1/15
1000/1000 [==============================] - 4s 4ms/step - loss: 1.7244 - acc: 0.5660 - val_loss: 0.9116 - val_acc: 0.7900
Epoch 2/15
1000/1000 [==============================] - 4s 4ms/step - loss: 0.5967 - acc: 0.8320 - val_loss: 0.5148 - val_acc: 0.8100
Epoch 3/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.4394 - acc: 0.8670 - val_loss: 0.3056 - val_acc: 0.8600
Epoch 4/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.3296 - acc: 0.9050 - val_loss: 0.3263 - val_acc: 0.9000
Epoch 5/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.2205 - acc: 0.9360 - val_loss: 0.2092 - val_acc: 0.9200
Epoch 6/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.1684 - acc: 0.9560 - val_loss: 0.1870 - val_acc: 0.9450
Epoch 7/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.1325 - acc: 0.9690 - val_loss: 0.1597 - val_acc: 0.9350
Epoch 8/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.0990 - acc: 0.9740 - val_loss: 0.1617 - val_acc: 0.9400
Epoch 9/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.0636 - acc: 0.9840 - val_loss: 0.1434 - val_acc: 0.9450
Epoch 10/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.0393 - acc: 0.9960 - val_loss: 0.1545 - val_acc: 0.9400
Epoch 11/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.0267 - acc: 0.9950 - val_loss: 0.1444 - val_acc: 0.9400
Epoch 12/15
1000/1000 [==============================] - 4s 4ms/step - loss: 0.0158 - acc: 1.0000 - val_loss: 0.1642 - val_acc: 0.9350
Epoch 13/15
1000/1000 [==============================] - 3s 3ms/step - loss: 0.0090 - acc: 1.0000 - val_loss: 0.1475 - val_acc: 0.9450
Epoch 14/15
1000/1000 [==============================] - 4s 4ms/step - loss: 0.0057 - acc: 1.0000 - val_loss: 0.1556 - val_acc: 0.9350
Epoch 15/15
1000/1000 [==============================] - 4s 4ms/step - loss: 0.0041 - acc: 1.0000 - val_loss: 0.1651 - val_acc: 0.9350

Test loss: 0.165074422359
Test accuracy: 0.935

Train loss: 0.00311407446489
Train accuracy: 1.0

    Is there anything wrong here?

    How do you think a linear classifier performs?

    In [8]:
    # Setup some hyper parameters
batch_size = 128
num_classes = 10
epochs = 15

# input image dimensions
img_rows, img_cols = 28, 28

# This is some technicality regarding Keras' dataset
if K.image_data_format() == 'channels_first':
    x_train = x_train.reshape(x_train.shape[0], 1, img_rows, img_cols)
    x_test = x_test.reshape(x_test.shape[0], 1, img_rows, img_cols)
    input_shape = (1, img_rows, img_cols)
else:
    x_train = x_train.reshape(x_train.shape[0], img_rows, img_cols, 1)
    x_test = x_test.reshape(x_test.shape[0], img_rows, img_cols, 1)
    input_shape = (img_rows, img_cols, 1)

# We convert the matrices to floats as we will use real numbers
x_train = x_train.astype('float32')[:1000]
x_test = x_test.astype('float32')[:200]
x_train /= 255
x_test /= 255
print('x_train shape:', x_train.shape)
print(x_train.shape[0], 'train samples')
print(x_test.shape[0], 'test samples')

# convert class vectors to binary class matrices
y_train = keras.utils.to_categorical(y_train, num_classes)[:1000]
y_test = keras.utils.to_categorical(y_test, num_classes)[:200]


# Build network
model = Sequential()
model.add(Conv2D(32, kernel_size=(3, 3),
                 activation='relu',
                 input_shape=input_shape))
model.add(Conv2D(64, (3, 3), activation='relu'))
model.add(MaxPooling2D(pool_size=(2, 2)))
model.add(Dropout(0.25))
model.add(Flatten())
model.add(Dense(128, activation='relu'))
model.add(Dropout(0.5))
model.add(Dense(num_classes, activation='softmax'))

model.compile(loss=keras.losses.categorical_crossentropy,
              optimizer=keras.optimizers.Adam(),
              metrics=['accuracy'])

# Train
model.fit(x_train, y_train,
          batch_size=batch_size,
          epochs=epochs,
          verbose=1,
          validation_data=(x_test, y_test))

# Evaluate on test data
score = model.evaluate(x_test, y_test, verbose=0)
print()
print('Test loss:', score[0])
print('Test accuracy:', score[1])

# Evaluate on training data
score = model.evaluate(x_train, y_train, verbose=0)
print()
print('Train loss:', score[0])
print('Train accuracy:', score[1])

    x_train shape: (1000, 28, 28, 1)
1000 train samples
200 test samples

    ---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-8-a1470fe28059> in <module>()
     53           epochs=epochs,
     54           verbose=1,
---> 55           validation_data=(x_test, y_test))
     56 
     57 # Evaluate on test data

~/anaconda3/lib/python3.6/site-packages/keras/models.py in fit(self, x, y, batch_size, epochs, verbose, callbacks, validation_split, validation_data, shuffle, class_weight, sample_weight, initial_epoch, steps_per_epoch, validation_steps, **kwargs)
    961                               initial_epoch=initial_epoch,
    962                               steps_per_epoch=steps_per_epoch,
--> 963                               validation_steps=validation_steps)
    964 
    965     def evaluate(self, x=None, y=None,

~/anaconda3/lib/python3.6/site-packages/keras/engine/training.py in fit(self, x, y, batch_size, epochs, verbose, callbacks, validation_split, validation_data, shuffle, class_weight, sample_weight, initial_epoch, steps_per_epoch, validation_steps, **kwargs)
   1628             sample_weight=sample_weight,
   1629             class_weight=class_weight,
-> 1630             batch_size=batch_size)
   1631         # Prepare validation data.
   1632         do_validation = False

~/anaconda3/lib/python3.6/site-packages/keras/engine/training.py in _standardize_user_data(self, x, y, sample_weight, class_weight, check_array_lengths, batch_size)
   1478                                     output_shapes,
   1479                                     check_batch_axis=False,
-> 1480                                     exception_prefix='target')
   1481         sample_weights = _standardize_sample_weights(sample_weight,
   1482                                                      self._feed_output_names)

~/anaconda3/lib/python3.6/site-packages/keras/engine/training.py in _standardize_input_data(data, names, shapes, check_batch_axis, exception_prefix)
    111                         ': expected ' + names[i] + ' to have ' +
    112                         str(len(shape)) + ' dimensions, but got array '
--> 113                         'with shape ' + str(data_shape))
    114                 if not check_batch_axis:
    115                     data_shape = data_shape[1:]

ValueError: Error when checking target: expected dense_4 to have 2 dimensions, but got array with shape (1000, 10, 10)

    Let’s use this model to predict a value for the first training instance we vizualized.

    In [ ]:
    print(model.predict(np.expand_dims(x_train[0], axis=0)))

    Is the model correct here? What is the output of the network?

    RNNs

    We will now switch to RNNs. These require more resources, so we can’t do the fanciest applications during the workshop. We will do some sentiment classification of movie reviews.

    In [9]:
    from __future__ import print_function
import numpy as np
import keras
from keras.preprocessing import sequence
from keras.models import Sequential
from keras.layers import Dense, Dropout, Embedding, LSTM, Bidirectional
from keras.datasets import imdb

# Number of considered words, based on frequencies
max_features = 20000
# cut texts after this number of words
maxlen = 100
batch_size = 32

print('Loading data...')
(x_train, y_train), (x_test, y_test) = keras.datasets.imdb.load_data(num_words=max_features, index_from=3)

# This is just for pretty printing the sentences...
word_to_id = keras.datasets.imdb.get_word_index()
word_to_id = {k:(v+3) for k,v in word_to_id.items()}
word_to_id["<PAD>"] = 0
word_to_id["<START>"] = 1
word_to_id["<UNK>"] = 2
id_to_word = {value:key for key,value in word_to_id.items()}

print("Here's the input for the first training instance:")
print(' '.join(id_to_word[id] for id in x_train[0] ))

    Loading data...
Downloading data from https://s3.amazonaws.com/text-datasets/imdb.npz
17465344/17464789 [==============================] - 2s 0us/step
Downloading data from https://s3.amazonaws.com/text-datasets/imdb_word_index.json
1646592/1641221 [==============================] - 0s 0us/step
Here's the input for the first training instance:
<START> this film was just brilliant casting location scenery story direction everyone's really suited the part they played and you could just imagine being there robert <UNK> is an amazing actor and now the same being director <UNK> father came from the same scottish island as myself so i loved the fact there was a real connection with this film the witty remarks throughout the film were great it was just brilliant so much that i bought the film as soon as it was released for retail and would recommend it to everyone to watch and the fly fishing was amazing really cried at the end it was so sad and you know what they say if you cry at a film it must have been good and this definitely was also congratulations to the two little boy's that played the <UNK> of norman and paul they were just brilliant children are often left out of the praising list i think because the stars that play them all grown up are such a big profile for the whole film but these children are amazing and should be praised for what they have done don't you think the whole story was so lovely because it was true and was someone's life after all that was shared with us all

    What do you think about this text? Is it a positive or negative review?

    In [10]:
    print("Here are the dataset shapes")
print(len(x_train), 'train sequences')
print(len(x_test), 'test sequences')

print("And the input for the first instance is represented as:")
print(x_train[0])

    Here are the dataset shapes
25000 train sequences
25000 test sequences
And the input for the first instance is represented as:
[1, 14, 22, 16, 43, 530, 973, 1622, 1385, 65, 458, 4468, 66, 3941, 4, 173, 36, 256, 5, 25, 100, 43, 838, 112, 50, 670, 2, 9, 35, 480, 284, 5, 150, 4, 172, 112, 167, 2, 336, 385, 39, 4, 172, 4536, 1111, 17, 546, 38, 13, 447, 4, 192, 50, 16, 6, 147, 2025, 19, 14, 22, 4, 1920, 4613, 469, 4, 22, 71, 87, 12, 16, 43, 530, 38, 76, 15, 13, 1247, 4, 22, 17, 515, 17, 12, 16, 626, 18, 19193, 5, 62, 386, 12, 8, 316, 8, 106, 5, 4, 2223, 5244, 16, 480, 66, 3785, 33, 4, 130, 12, 16, 38, 619, 5, 25, 124, 51, 36, 135, 48, 25, 1415, 33, 6, 22, 12, 215, 28, 77, 52, 5, 14, 407, 16, 82, 10311, 8, 4, 107, 117, 5952, 15, 256, 4, 2, 7, 3766, 5, 723, 36, 71, 43, 530, 476, 26, 400, 317, 46, 7, 4, 12118, 1029, 13, 104, 88, 4, 381, 15, 297, 98, 32, 2071, 56, 26, 141, 6, 194, 7486, 18, 4, 226, 22, 21, 134, 476, 26, 480, 5, 144, 30, 5535, 18, 51, 36, 28, 224, 92, 25, 104, 4, 226, 65, 16, 38, 1334, 88, 12, 16, 283, 5, 16, 4472, 113, 103, 32, 15, 16, 5345, 19, 178, 32]

    What do these numbers represent? Is there any limitation you can imagine coming from this?

    In [11]:
    print('Pad sequences (samples x time)')
x_train = sequence.pad_sequences(x_train, maxlen=maxlen)[:5000]
x_test = sequence.pad_sequences(x_test, maxlen=maxlen)[:5000]
print('x_train shape:', x_train.shape)
print('x_test shape:', x_test.shape)
y_train = np.array(y_train)[:5000]
y_test = np.array(y_test)[:5000]

model = Sequential()
model.add(Embedding(max_features, 128, input_length=maxlen))
model.add(Bidirectional(LSTM(64)))
model.add(Dropout(0.5))
model.add(Dense(1, activation='sigmoid'))

model.compile('adam', 'binary_crossentropy', metrics=['accuracy'])

print('Train...')
model.fit(x_train, y_train,
          batch_size=batch_size,
          epochs=4,
          validation_data=[x_test, y_test])

    Pad sequences (samples x time)
x_train shape: (5000, 100)
x_test shape: (5000, 100)
Train...
Train on 5000 samples, validate on 5000 samples
Epoch 1/4
5000/5000 [==============================] - 54s 11ms/step - loss: 0.6032 - acc: 0.6570 - val_loss: 0.4283 - val_acc: 0.8056
Epoch 2/4
5000/5000 [==============================] - 54s 11ms/step - loss: 0.2761 - acc: 0.8918 - val_loss: 0.4403 - val_acc: 0.7948
Epoch 3/4
5000/5000 [==============================] - 61s 12ms/step - loss: 0.1101 - acc: 0.9670 - val_loss: 0.6366 - val_acc: 0.8026
Epoch 4/4
5000/5000 [==============================] - 56s 11ms/step - loss: 0.0478 - acc: 0.9868 - val_loss: 0.6637 - val_acc: 0.7954
    Out[11]:
    <keras.callbacks.History at 0x1392d76d8>
    In [12]:
    print("The neural net predicts that the first instance sentiment is:")
print(model.predict(np.expand_dims(x_train[0], axis=0)))

    The neural net predicts that the first instance sentiment is:
[[ 0.99445081]]

    Remarks? Comments?

    How do the training scores compare to the test scores? How can we improve this? What are the current limitations?

    This RNN use case takes more time to train but it is definitely more impressive. We will model the language, by training on a novel. For each (set of) word(s) in the novel, the objective is to predict the following word. This can be done on any text, and we don’t need annotated data – the text itself is enough.

    Have a look at the following piece of code and try to understand what it does. Then, run it and see the network generating text! At first, the output is not meaningful, but it becomes so over time. This is the magic I was referring to.

    Beware: this will take longer to run on a CPU. A GPU is recommended, but you can still try to run it for a while to see the predictions evolve. On my laptop, an epoch takes 6mins so the full training takes 6hrs. About 20 epochs are required for the generated text to be somewhat meaningful.

    Note, however, that although this seems long, training actual deep learning models for concrete tasks takes days, even on multiple GPUs. This is mostly because of the data size and the much deeper networks.

    In [ ]:
    from __future__ import print_function
from keras.callbacks import LambdaCallback
from keras.models import Sequential
from keras.layers import Dense, Activation
from keras.layers import LSTM
from keras.optimizers import RMSprop
from keras.utils.data_utils import get_file
import numpy as np
import random
import sys
import io

# We load a text from Nietzsche
path = get_file('nietzsche.txt', origin='https://s3.amazonaws.com/text-datasets/nietzsche.txt')
with io.open(path, encoding='utf-8') as f:
    text = f.read().lower()
print('corpus length:', len(text))

# We create dictionaries of character > index and the other way around
chars = sorted(list(set(text)))
print('total chars:', len(chars))
char_indices = dict((c, i) for i, c in enumerate(chars))
indices_char = dict((i, c) for i, c in enumerate(chars))

# cut the text in semi-redundant sequences of maxlen characters
maxlen = 40
step = 3
sentences = []
next_chars = []
for i in range(0, len(text) - maxlen, step):
    sentences.append(text[i: i + maxlen])
    next_chars.append(text[i + maxlen])
print('nb sequences:', len(sentences))

print('Vectorization...')
x = np.zeros((len(sentences), maxlen, len(chars)), dtype=np.bool)
y = np.zeros((len(sentences), len(chars)), dtype=np.bool)
for i, sentence in enumerate(sentences):
    for t, char in enumerate(sentence):
        x[i, t, char_indices[char]] = 1
    y[i, char_indices[next_chars[i]]] = 1


# build the model: a single LSTM
print('Build model...')
model = Sequential()
model.add(LSTM(128, input_shape=(maxlen, len(chars))))
model.add(Dense(len(chars)))
model.add(Activation('softmax'))

optimizer = RMSprop(lr=0.01)
model.compile(loss='categorical_crossentropy', optimizer=optimizer)


def sample(preds, temperature=1.0):
    # helper function to sample an index from a probability array
    preds = np.asarray(preds).astype('float64')
    preds = np.log(preds) / temperature
    exp_preds = np.exp(preds)
    preds = exp_preds / np.sum(exp_preds)
    probas = np.random.multinomial(1, preds, 1)
    return np.argmax(probas)


def on_epoch_end(epoch, logs):
    # Function invoked at end of each epoch. Prints generated text.
    print()
    print('----- Generating text after Epoch: %d' % epoch)

    start_index = random.randint(0, len(text) - maxlen - 1)
    for diversity in [0.2, 0.5, 1.0, 1.2]:
        print('----- diversity:', diversity)

        generated = ''
        sentence = text[start_index: start_index + maxlen]
        generated += sentence
        print('----- Generating with seed: "' + sentence + '"')
        sys.stdout.write(generated)

        for i in range(400):
            x_pred = np.zeros((1, maxlen, len(chars)))
            for t, char in enumerate(sentence):
                x_pred[0, t, char_indices[char]] = 1.

            preds = model.predict(x_pred, verbose=0)[0]
            next_index = sample(preds, diversity)
            next_char = indices_char[next_index]

            generated += next_char
            sentence = sentence[1:] + next_char

            sys.stdout.write(next_char)
            sys.stdout.flush()
        print()

print_callback = LambdaCallback(on_epoch_end=on_epoch_end)

model.fit(x, y,
          batch_size=128,
          epochs=60,
          callbacks=[print_callback])

    Downloading data from https://s3.amazonaws.com/text-datasets/nietzsche.txt
606208/600901 [==============================] - 0s 0us/step
corpus length: 600893
total chars: 57
nb sequences: 200285
Vectorization...
Build model...
Epoch 1/60
200285/200285 [==============================] - 281s 1ms/step - loss: 1.9553

----- Generating text after Epoch: 0
----- diversity: 0.2
----- Generating with seed: "to
agree with many people. "good" is no "
to
agree with many people. "good" is no and it is the the of the same the of the sention of the strenge of the most the self-our of the inderent that the sensive indeed the one of the constitute of the most of the semple of the desire of the sensive of the most of the semple of the sempathy of the one of the into the every to a soul of the some of the persent the free of the semple of the most of the sention of the of the spiritual the 
----- diversity: 0.5
----- Generating with seed: "to
agree with many people. "good" is no "
to
agree with many people. "good" is no may a suptimes and also orage mankind the one of indeed of one streng the possible the sensition and the inderenation of a sul the in a sould be the orting a solitiarity of religions in a man of such and a scient, in every of and the self-to and of a revilued it is the most in the indeed, and it is assual that the ord of the of the distiture in its all the manter of the soul permans the decours of
----- diversity: 1.0
----- Generating with seed: "to
agree with many people. "good" is no "
to
agree with many people. "good" is no causest and hew the fown of every groktulr
destined a the art it noteriness of one it all and
and cothinded of that rendercaterfroe to doe," in the pational the is the onl yutre
allor upitsoon,--one
viburan mused a "master in the that niver if
a pridicle quesiles of
the shoold enss nowxing to
feef ma.t--wute disequerly that then her rewadd finale the eeblive alse rusurefver" a selovery catte he re
----- diversity: 1.2
----- Generating with seed: "to
agree with many people. "good" is no "
to
agree with many people. "good" is no likeurenes, it is novamentstisuser'stone, indos paces. fund, wethel feel the
que let doee new eveny that is that the catel. thotgy is
within ceoks of theregeritades) and itwas brutmes ageteron
clyrelogilabl freephi; its. by an? andaver happ
one of his absuman artificss? itself old a
ooker himsood and bus hray
fined in smuch is sudtirers of rerarder from and
afutty
mest utfered with to "bewnook one
Epoch 2/60
 81664/200285 [===========>..................] - ETA: 2:37 - loss: 1.6395

    Web Scraping with Python Made Easy

    Imagine you run a business selling shoes online and wanted to monitor how your competitors price their products. You could spend hours a day clicking through page after page or write a script for a web bot, an automated piece of software that keeps track a site’s updates. That’s where web scraping comes in.

    Scraping websites lets you extract information from hundreds or thousands of webpages at once. You can search websites like Indeed for job opportunities or Twitter for tweets. In this gentle introduction to web scraping, we’ll go over the basic code to scrape websites such that anyone, regardless of background, can extract and analyze these kinds of results.

    Getting Started

    Using my GitHub repository on web scraping, you can install the software and run the scripts as instructed. Click on the src directory on the repository page to see the README.md file that explains each script and how to run them.

    Examining the Site

    You can use a sitemap file to located where websites upload content without crawling every single web page. Here’s a sample one. You can also find out how large a site is and how much information you can actually extract from it. You can search a site using Google’s Advanced Search to figure out how many pages you may need to scrape. This will come in handy when creating a web scraper that may need to pause for updates or act in a different manner after reaching a certain number of pages.

    You can also run the identify.py script in the src directory to figure out more information bout how each site was built. This should give info about the frameworks, programming languages, and servers used in building each website as well as the registered owner for the domain. This also uses robotparser to check for restrictions.

    Many websites have a robots.txt file with crawling restrictions. Make sure you check out this file for a website for more information about how to crawl a website or any rules that you should follow. The sample protocol can be found here.

    Crawling a Site

    There are three general approaches to crawling a site: Crawling a sitemap, Iterating through an ID for each webpage, and following webpage links. download.py shows how to download a webpage with methods of sitemap crawling, results.py shows you how to scrape those results while iterating through webpage IDs, and indeedScrape.py uses the webpage links for crawling. download.py also contains information on inserting delays, returning a list of links from HTML, and supporting proxies that can let you access websites through blocked requests.

    Scraping the Data

    In the file compare.py, you can compare the efficiency of the three web scraping methods.

    You can use regular expressions (known as regex or regexp) to perform neat tricks with text for getting information from websites. The script regex.py shows how this is done.

    You can also use the browser extension Firebug Lite to get information from a webpage. In Chrome, you can click View >> Developer >> View Source to get the source behind a webpage.

    Beautiful Soup, one of the requried packages to run indeedScrape.py, parses a webpage and provides a convenient interface to navigate the content, as shown in bs4test.py. Lxml also does this in lxmltest.py. A comparison of these three scraping methods are in the following table.

    Scraping methodPerformanceEase of useEase of install
    RegexFastHardEasy
    Beautiful SoupSlowEasyEasy
    lxmlFastEasyHard

    The callback.py script lets you scrape data and save it to an output .csv file.

    Caching Downloads

    Caching crawled webpages lets you store them in a manageablae format while only having to download them once. In download.py, there’s a python class Downloader that shows how to cache URLs after downloading their webpages. cache.py has a python class that maps a URL to a filename when caching.

    Depending on which operating system you’re using, there’s a limit to how much you can cache.

    Operating systemFile systemInvalid filename charactersMax filename length
    LinuxExt3/Ext4/, \0255 bytes
    OS X HFS Plus:, \0255 UT-16 code units
    WindowsNTFS \, /, ?, :, *, >, <, |255 characters

    Though cache.py is easy to use, you can take the hash of the URL itself to use as the filename to ensure your files directly map to the URLs of the saved cache. Using MongoDB, you can build ontop of the current file system database system and avoid the file system limitations. This method is found in mongocache.py using pymongo, a Python wrapper for MongoDB.

    Test out the other scripts such as alexacb.py for downloading information on the top sites by Alexa ranking. mongoqueue.py has functionality for queueing the MongoDB inquiries that can be imported to other scripts.

    You can work with dynamic webpages using the code from browserrender.py. The majority of leading websites using JavScript for functionality, meaning you can’t view all their content in barebones HTML.

    A Comparison of Copper in the U.S.

    As humanity’s oldest metal, copper comes in many forms. People have used copper for thousands of years. When the ancient Romans mined the element “cyprium” from Cyprus, the metal soon became known in English as “copper.” 

    Copper is produced and consumed in many forms, from the lining of electrical motors to the coating of pennies. Thanks to its high thermal and electrical conductivity, the material is frequently used in telecommunication technologies and as a building material.

    The process of copper production includes mining, refining, smelting, and electrowinning. Through smelting and electrolytic refining, engineers and scientists transform mined ores to copper cathodes. Cathodes are thin sheets of pure copper used as raw material for processing the metal into high-quality products. 

    Using data available to the public from the U.S. Geological Survey, the copper market has changed to society’s needs over the past years. 

    The four major types of copper are mined copper, secondary copper, refined copper and refined electrowon copper. Secondary copper comes from recycled and scrap materials such as tubes, sheets, cables, radiators and castings, as well as from residues like dust or slag. 

    Engineers and scientists transform mined pure copper metal and copper from concentrated low-grade ores through smelting and electrolytic refining in creating copper cathodes. Acid leaching of oxidized ores produces more copper.

    Thanks to the chemical and physical properties of copper, the material is suitable for electrical and thermal conductivity. Copper’s high ductility and malleability give it key roles in industrial applications of coil wining, power transmission and generation and telecommunication technologies.

    The different methods of processing copper have remained constant for the most part between 1990 and 2010. The data is from “U.S. Mineral Dependence—Statistical Compilation of U.S. and World Mineral Production, Consumption, and Trade, 1990–2010” by James J. Barry, Grecia R. Matos and W. David Menzie. The rise in refined copper reflects market trends for the rising demand for refined copper, according to a report in Mining.com. Oxide and sulfur ores generally have between 0.5 and 2.0% copper. The process involves concentrating the ore to remove gangue and other materials.


    Differences between reported and apparent processed copper consumption in the U.S. have decreased from 2005 to 2009. Copper consumption itself has dropped.

    The various types of copper produced by the U.S. have remained constant over the time period. 

    Mined copper has remained the dominant copper produced around the world, though refined copper has come close or equal to it from 1996 to 2001. Refined electrowon copper has steadily surpassed secondary copper over the time period, too. 

    The epistemology and metaphysics of causality

    The epistemology of causality

    There are two epistemic approaches to causal theory. Under a hypothetico-deductive account, we hypothesize causal relationships and deduce predictions based on them. We test these hypotheses and predictions by comparing empirical phenomena and other knowledge and information on what actually happens to these theories. We may also take an inductive approach in which we make a large number of appropriate, justified observations (such as a set of data) from which we can induce causal relationships directly from them.

    Hypothetico-Deductive discovery

    The testing phase of this account of discovery and causality uses the views on the nature of causality to determine whether we support or refute the hypothesis. We search for physical processes underlying the causal relationships of the hypothesis. We can use statistics and probability to determine which consequences of hypotheses are verified, like comparing our data to a distribution such as a Gaussian or Dirichlet one. We can further probe these consequences on a probabilistic level and show that changing hypothesized causes can predict, determine, or guarantee effects.

    Philosopher Karl Popper advocated this approach for causal explanations of events that consist of natural laws, which are universal statements about the world. He designated initial conditions, single-case statements, from which we may deduce outcomes and form predictions of various events. These case initial conditions call for effects that we can determine, such as whether a physical system will approach thermodynamic equilibrium or how a population might evolve under the influence of predators or external forces. Popper delineated the method of hypothesizing laws, deducing their consequences, and rejecting laws that aren’t supported as a cyclical process. This is the covering-law account of causal explanation.

    Inductive learning

    Philosopher Francis Bacon promoted the inductive account of scientific learning and reasoning. From a very high number of observations of some phenomenon or event with experimental, empirical evidence where it’s appropriate, we can compile a table of positive instances (in which a phenomenon occurs), negative instances (it doesn’t occur), and partial instances (it occurs to a certain degree). This gives a multidimensionality to phenomena that characterize causal relationships from both a priori and a posterior perspectives.

    Inductivist artificial intelligence (AI) approaches have in common the feature that causal relationships can be determined from statistical relationships. We assume the Causal Markov condition holds of physical causality and physical probability. This Causal Markov Condition plays a significant deterministic role in the various features of the model and the events or phenomena it predicts. A causal net must have the Causal Markov Condition as an assumption or premise. For structural equation models (SEM), Causal Markov Conditions result from representations of each variable as a function of its direct causes and an associated error variable with it. We assume probabilistic independence of each error variable. We then find the class of causal models or a single best causal model with probabilistic independences that are justified by the Causal Markov Condition. They should be consistent with independences we can infer from the data, and we might also make further assumptions about the minimality (no submodel of the causal model also satisfied the Causal Markov Condition), faithfulness (all independences in the data are implied via the Causal Markov Condition), linearity (all variables are linear functions of their direct causes and uncorrelated error variables). We may also define causal sufficiency, whether all common causes of measured variables are measured, and context generality, every individual or node in the model has causal relations of the population. These two features let us describe models and methods of scientific reasoning as causal in nature and, from there, we may apply appropriate causal models such as Bayesian, frequentist, or similar methods of prediction. We may even illustrate a causal diagram or model elements under various conditions such as those given by independence or constraints on variables.

    This way, in the intercorrelatedness of the graph or model, we can’t change the value of a variable without affecting the way it relates to other variables, but there may conditions in which we construct models that have autonomous nodes or variables. The way these features and claims of inductivist AI interact with another is subject to debate by the underlying assumptions, justification, and methods of reasoning behind these models.

    Metaphysics of causality

    We can pose questions about the mathematization of causality even with the research and methods that have dominated the work on probability and its consequences. We can speculate what causality is and the opinions on the nature of causality as they relate to the axioms and definitions that have remained stable in the theories of probability and statistics.

    We can elaborate three types of causality approaches. The first is that causality is only a heuristic and has no role in scientific reasoning and discourse, as philosopher Bertrand Russel argued. Science depends upon functional relationships, not causal laws. The second position is that causality is a fundamental feature of the world, a universal principle. We should, therefore, treat it as a scientific primitive. This position evolved out of conflict with purported philosophical analyses that appealed to asymmetry of time (that it moves in one direction) to explain the asymmetry of causation (that they move in one direction and one direction only). This raises concerns of how to interpret time in terms of causality. The third is we can reduce causal relations to other concepts that don’t involve causal notions. Many philosophers support this position, and, as such, there are four divisions within this position.

    The first schism we discuss is that causality is a relation between variables that are single-case or repeatable according to the interpretation of causality in question. We interpret causality as a mental in nature given that causality is a feature of an agent’s epistemic state and physical if it’s a feature of the external world. We interpret it as subjective if two agents with the same relevant knowledge can disagree on a conclusion of the relationships with both positions correct, as though they were a matter of arbitrary choice. Otherwise we interpret it as objective. The subjective-objective schism raises issues between how different positions would be regarded as correct and what determines the subjective element or role subjectivity plays in these two different positions.

    The second partition is the mechanistic account of causality – that physical processes link cause and effect. We interpret causal statements as giving information about these processes. Philosophers Wesley Salmon and Phil Dowe advocate this position as they argue causal processes transmit or have a conserved physical quantity to them. We may describe the relation between energy and mass (E = mc²) as causal relations from start (cause) to a finish (effect). One may argue against this position on the grounds that these relations in science have no specific direction one way or another and are symmetrical and not subject to causality. It does, however, relate single cases linked by physical processes even if we can induce causal regularities or laws from these connections in an objective manner. If two people disagree on the causal connections, one or both are wrong.

    This approach is difficult to apply. The physics of these quantities aren’t determined by the causal relations themselves. The conservation of these physical quantities may suggest causal links to physicists, they aren’t relevant in the fields that emerge from physics such as chemistry or engineering. This would lead one to believe the epistemology of the causal concepts are irrelevant to their metaphysics. If this were the case, the knowledge of a causal relationship would have little to do with the causal connection itself.

    The third subdivision is probabilistic causality in which we treat causal connections with probabilistic relationships of variables. We can debate which probabilistic relationships among variables of probabilistic causality determine or create causal relationships. One might say the Principle of Common Cause (if two variables are probabilistically dependent, then one causes the other or they’re effects of common causes that make them independent from one another). Philosopher Hans Reichenbach applied this to causality to provide a probabilistic analysis of time in its single direction. More recent philosophers use the Causal Markov Condition as a necessary condition for causality with other less central conditions. We normally apply probabilistic causality to repeatable variables such that probability handles them, but critics may argue the Principle of the Common Cause and the Causal Markov Conditions have counterexamples showing they don’t hold in under all conditions.

    Finally, the fourth subclass is the counterfactual account, as advocated by philosopher David Lewis. In this way, we reduce causal relations to subjunctive conditions such that an effect depends causally on a cause if and only iff (1) if the cause were to occur, then the effect would occur (or its chance to occur would raise significantly) and (2) if the cause didn’t occur then the effect wouldn’t occur. The transitive closure of the Causal Depedendence (that a cause will either increase the probability of a direct effect or, if it’s a preventative, make the effect less likely, as long as the effect’s other direct causes are held fixed) holds. The causal relationships are what goes on in possible worlds that are similar to our own. Lewis introduced counterfactual theory to account of the causal relationships between single-case events and causal relationships that are mind-independent and objective. We may still press this account by arguing that we have no physical contact with these possible worlds or that there isn’t an objective way to determine which worlds are closest to our own or which worlds we should follow and analyze in determining causality. The counterfactualist may respond that the worlds we choose are the ones in which the cause-and-effect relationship occurs as closer to our own world and, from there, determine which appropriate world is closest to our own.