Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
467 lines (405 sloc) 17.5 KB
# File-Name: priority_inbox.R
# Date: 2012-02-10
# Author: Drew Conway (drew.conway@nyu.edu)
# Purpose: Code for Chapter 4. In this case study we will attempt to write a "priority
# inbox" algorithm for ranking email by some measures of importance. We will
# define these measures based on a set of email features, which moves beyond
# the simple work counts used in Chapter 3.
# Data Used: Email messages contained in ../../03-Classification/code/data/
# source: http://spamassassin.apache.org/publiccorpus/
# Packages Used: tm, ggplot2, plyr
# All source code is copyright (c) 2012, under the Simplified BSD License.
# For more information on FreeBSD see: http://www.opensource.org/licenses/bsd-license.php
# All images and materials produced by this code are licensed under the Creative Commons
# Attribution-Share Alike 3.0 United States License: http://creativecommons.org/licenses/by-sa/3.0/us/
# All rights reserved.
# NOTE: If you are running this in the R console you must use the 'setwd' command to set the
# working directory for the console to whereever you have saved this file prior to running.
# Otherwise you will see errors when loading data or saving figures!
# Load libraries
library('tm')
library('ggplot2')
library('plyr')
# Set the global paths
data.path <- file.path("..", "03-Classification", "data")
easyham.path <- file.path(data.path, "easy_ham")
# We define a set of function that will extract the data
# for the feature set we have defined to rank email
# impportance. This includes the following: message
# body, message source, message subject, and date the
# message was sent.
# Simply returns the full text of a given email message
msg.full <- function(path)
{
con <- file(path, open = "rt", encoding = "latin1")
msg <- readLines(con)
close(con)
return(msg)
}
# Retuns the email address of the sender for a given
# email message
get.from <- function(msg.vec)
{
from <- msg.vec[grepl("From: ", msg.vec)]
from <- strsplit(from, '[":<> ]')[[1]]
from <- from[which(from != "" & from != " ")]
return(from[grepl("@", from)][1])
}
# Retuns the subject string for a given email message
get.subject <- function(msg.vec)
{
subj <- msg.vec[grepl("Subject: ", msg.vec)]
if(length(subj) > 0)
{
return(strsplit(subj, "Subject: ")[[1]][2])
}
else
{
return("")
}
}
# Similar to the function from Chapter 3, this returns
# only the message body for a given email.
get.msg <- function(msg.vec)
{
msg <- msg.vec[seq(which(msg.vec == "")[1] + 1, length(msg.vec), 1)]
return(paste(msg, collapse = "\n"))
}
# Retuns the date a given email message was received
get.date <- function(msg.vec)
{
date.grep <- grepl("^Date: ", msg.vec)
date.grep <- which(date.grep == TRUE)
date <- msg.vec[date.grep[1]]
date <- strsplit(date, "\\+|\\-|: ")[[1]][2]
date <- gsub("^\\s+|\\s+$", "", date)
return(strtrim(date, 25))
}
# This function ties all of the above helper functions together.
# It returns a vector of data containing the feature set
# used to categorize data as priority or normal HAM
parse.email <- function(path)
{
full.msg <- msg.full(path)
date <- get.date(full.msg)
from <- get.from(full.msg)
subj <- get.subject(full.msg)
msg <- get.msg(full.msg)
return(c(date, from, subj, msg, path))
}
# In this case we are not interested in classifiying SPAM or HAM, so we will take
# it as given that is is being performed. As such, we will use the EASY HAM email
# to train and test our ranker.
easyham.docs <- dir(easyham.path)
easyham.docs <- easyham.docs[which(easyham.docs != "cmds")]
easyham.parse <- lapply(easyham.docs,
function(p) parse.email(file.path(easyham.path, p)))
# Convert raw data from list to data frame
ehparse.matrix <- do.call(rbind, easyham.parse)
allparse.df <- data.frame(ehparse.matrix, stringsAsFactors = FALSE)
names(allparse.df) <- c("Date", "From.EMail", "Subject", "Message", "Path")
# Convert date strings to POSIX for comparison. Because the emails data
# contain slightly different date format pattners we have to account for
# this by passining them as required partmeters of the function.
date.converter <- function(dates, pattern1, pattern2)
{
pattern1.convert <- strptime(dates, pattern1)
pattern2.convert <- strptime(dates, pattern2)
pattern1.convert[is.na(pattern1.convert)] <- pattern2.convert[is.na(pattern1.convert)]
return(pattern1.convert)
}
pattern1 <- "%a, %d %b %Y %H:%M:%S"
pattern2 <- "%d %b %Y %H:%M:%S"
allparse.df$Date <- date.converter(allparse.df$Date, pattern1, pattern2)
# Convert emails and subjects to lower-case
allparse.df$Subject <- tolower(allparse.df$Subject)
allparse.df$From.EMail <- tolower(allparse.df$From.EMail)
# Order the messages chronologically
priority.df <- allparse.df[with(allparse.df, order(Date)), ]
# We will use the first half of the priority.df to train our priority in-box algorithm.
# Later, we will use the second half to test.
priority.train <- priority.df[1:(round(nrow(priority.df) / 2)), ]
# The first step is to create rank weightings for all of the features.
# We begin with the simpliest: who the email is from.
# Calculate the frequency of correspondence with all emailers in the training set
from.weight <- melt(with(priority.train, table(From.EMail)),
value.name="Freq")
from.weight <- from.weight[with(from.weight, order(Freq)), ]
# We take a subset of the from.weight data frame to show our most frequent
# correspondents.
from.ex <- subset(from.weight, Freq > 6)
from.scales <- ggplot(from.ex) +
geom_rect(aes(xmin = 1:nrow(from.ex) - 0.5,
xmax = 1:nrow(from.ex) + 0.5,
ymin = 0,
ymax = Freq,
fill = "lightgrey",
color = "darkblue")) +
scale_x_continuous(breaks = 1:nrow(from.ex), labels = from.ex$From.EMail) +
coord_flip() +
scale_fill_manual(values = c("lightgrey" = "lightgrey"), guide = "none") +
scale_color_manual(values = c("darkblue" = "darkblue"), guide = "none") +
ylab("Number of Emails Received (truncated at 6)") +
xlab("Sender Address") +
theme_bw() +
theme(axis.text.y = element_text(size = 5, hjust = 1))
ggsave(plot = from.scales,
filename = file.path("images", "0011_from_scales.pdf"),
height = 4.8,
width = 7)
# Log weight scheme, very simple but effective
from.weight <- transform(from.weight,
Weight = log(Freq + 1),
log10Weight = log10(Freq + 1))
from.rescaled <- ggplot(from.weight, aes(x = 1:nrow(from.weight))) +
geom_line(aes(y = Weight, linetype = "ln")) +
geom_line(aes(y = log10Weight, linetype = "log10")) +
geom_line(aes(y = Freq, linetype = "Absolute")) +
scale_linetype_manual(values = c("ln" = 1,
"log10" = 2,
"Absolute" = 3),
name = "Scaling") +
xlab("") +
ylab("Number of emails Receieved") +
theme_bw() +
theme(axis.text.y = element_blank(), axis.text.x = element_blank())
ggsave(plot = from.rescaled,
filename = file.path("images", "0012_from_rescaled.pdf"),
height = 4.8,
width = 7)
# To calculate the rank priority of an email we should calculate some probability that
# the user will respond to it. In our case, we only have one-way communication data.
# In this case, we can calculate a weighting based on words in threads that have a lot
# of activity.
# This function is used to find threads within the data set. The obvious approach
# here is to use the 're:' cue from the subject line to identify message threads.
find.threads <- function(email.df)
{
response.threads <- strsplit(email.df$Subject, "re: ")
is.thread <- sapply(response.threads,
function(subj) ifelse(subj[1] == "", TRUE, FALSE))
threads <- response.threads[is.thread]
senders <- email.df$From.EMail[is.thread]
threads <- sapply(threads,
function(t) paste(t[2:length(t)], collapse = "re: "))
return(cbind(senders,threads))
}
threads.matrix <- find.threads(priority.train)
# Using the matrix of threads generated by the find.threads function this function
# creates a data from of the sender's email, the frequency of emails from that
# sender, and a log-weight for that sender based on the freqeuncy of corresponence.
email.thread <- function(threads.matrix)
{
senders <- threads.matrix[, 1]
senders.freq <- table(senders)
senders.matrix <- cbind(names(senders.freq),
senders.freq,
log(senders.freq + 1))
senders.df <- data.frame(senders.matrix, stringsAsFactors=FALSE)
row.names(senders.df) <- 1:nrow(senders.df)
names(senders.df) <- c("From.EMail", "Freq", "Weight")
senders.df$Freq <- as.numeric(senders.df$Freq)
senders.df$Weight <- as.numeric(senders.df$Weight)
return(senders.df)
}
senders.df <- email.thread(threads.matrix)
# As an additional weight, we can enhance our notion of a thread's importance
# by measuring the time between responses for a given email. This function
# takes a given thread and the email.df data frame to generate a weighting
# based on this activity level. This function returns a vector of thread
# activity, the time span of a thread, and its log-weight.
thread.counts <- function(thread, email.df)
{
# Need to check that we are not looking at the original message in a thread,
# so we check the subjects against the 're:' cue.
thread.times <- email.df$Date[which(email.df$Subject == thread |
email.df$Subject == paste("re:", thread))]
freq <- length(thread.times)
min.time <- min(thread.times)
max.time <- max(thread.times)
time.span <- as.numeric(difftime(max.time, min.time, units = "secs"))
if(freq < 2)
{
return(c(NA, NA, NA))
}
else
{
trans.weight <- freq / time.span
log.trans.weight <- 10 + log(trans.weight, base = 10)
return(c(freq, time.span, log.trans.weight))
}
}
# This function uses the threads.counts function to generate a weights
# for all email threads.
get.threads <- function(threads.matrix, email.df)
{
threads <- unique(threads.matrix[, 2])
thread.counts <- lapply(threads,
function(t) thread.counts(t, email.df))
thread.matrix <- do.call(rbind, thread.counts)
return(cbind(threads, thread.matrix))
}
# Now, we put all of these function to work to generate a training set
# based on our thread features.
thread.weights <- get.threads(threads.matrix, priority.train)
thread.weights <- data.frame(thread.weights, stringsAsFactors = FALSE)
names(thread.weights) <- c("Thread", "Freq", "Response", "Weight")
thread.weights$Freq <- as.numeric(thread.weights$Freq)
thread.weights$Response <- as.numeric(thread.weights$Response)
thread.weights$Weight <- as.numeric(thread.weights$Weight)
thread.weights <- subset(thread.weights, is.na(thread.weights$Freq) == FALSE)
# Similar to what we did in Chapter 3, we create a simple function to return a
# vector of word counts. This time, however, we keep the TDM as a free
# parameter of the function.
term.counts <- function(term.vec, control)
{
vec.corpus <- Corpus(VectorSource(term.vec))
vec.tdm <- TermDocumentMatrix(vec.corpus, control = control)
return(rowSums(as.matrix(vec.tdm)))
}
thread.terms <- term.counts(thread.weights$Thread,
control = list(stopwords = TRUE))
thread.terms <- names(thread.terms)
term.weights <- sapply(thread.terms,
function(t) mean(thread.weights$Weight[grepl(t, thread.weights$Thread, fixed = TRUE)]))
term.weights <- data.frame(list(Term = names(term.weights),
Weight = term.weights),
stringsAsFactors = FALSE,
row.names = 1:length(term.weights))
# Finally, create weighting based on frequency of terms in email.
# Will be similar to SPAM detection, but in this case weighting
# high words that are particularly HAMMMY.
msg.terms <- term.counts(priority.train$Message,
control = list(stopwords = TRUE,
removePunctuation = TRUE,
removeNumbers = TRUE))
msg.weights <- data.frame(list(Term = names(msg.terms),
Weight = log(msg.terms, base = 10)),
stringsAsFactors = FALSE,
row.names = 1:length(msg.terms))
# Remove words that have a zero weight
msg.weights <- subset(msg.weights, Weight > 0)
# This function uses our pre-calculated weight data frames to look up
# the appropriate weightt for a given search.term. We use the 'term'
# parameter to dertermine if we are looking up a word in the weight.df
# for it message body weighting, or for its subject line weighting.
get.weights <- function(search.term, weight.df, term = TRUE)
{
if(length(search.term) > 0)
{
if(term)
{
term.match <- match(names(search.term), weight.df$Term)
}
else
{
term.match <- match(search.term, weight.df$Thread)
}
match.weights <- weight.df$Weight[which(!is.na(term.match))]
if(length(match.weights) < 1)
{
return(1)
}
else
{
return(mean(match.weights))
}
}
else
{
return(1)
}
}
# Our final step is to write a function that will assign a weight to each message based
# on all of our, we create a function that will assign a weight to each message based on
# the mean weighting across our entire feature set.
rank.message <- function(path)
{
msg <- parse.email(path)
# Weighting based on message author
# First is just on the total frequency
from <- ifelse(length(which(from.weight$From.EMail == msg[2])) > 0,
from.weight$Weight[which(from.weight$From.EMail == msg[2])],
1)
# Second is based on senders in threads, and threads themselves
thread.from <- ifelse(length(which(senders.df$From.EMail == msg[2])) > 0,
senders.df$Weight[which(senders.df$From.EMail == msg[2])],
1)
subj <- strsplit(tolower(msg[3]), "re: ")
is.thread <- ifelse(subj[[1]][1] == "", TRUE, FALSE)
if(is.thread)
{
activity <- get.weights(subj[[1]][2], thread.weights, term = FALSE)
}
else
{
activity <- 1
}
# Next, weight based on terms
# Weight based on terms in threads
thread.terms <- term.counts(msg[3], control = list(stopwords = TRUE))
thread.terms.weights <- get.weights(thread.terms, term.weights)
# Weight based terms in all messages
msg.terms <- term.counts(msg[4],
control = list(stopwords = TRUE,
removePunctuation = TRUE,
removeNumbers = TRUE))
msg.weights <- get.weights(msg.terms, msg.weights)
# Calculate rank by interacting all weights
rank <- prod(from,
thread.from,
activity,
thread.terms.weights,
msg.weights)
return(c(msg[1], msg[2], msg[3], rank))
}
# Find splits again
train.paths <- priority.df$Path[1:(round(nrow(priority.df) / 2))]
test.paths <- priority.df$Path[((round(nrow(priority.df) / 2)) + 1):nrow(priority.df)]
# Now, create a full-featured training set.
train.ranks <- suppressWarnings(lapply(train.paths, rank.message))
train.ranks.matrix <- do.call(rbind, train.ranks)
train.ranks.matrix <- cbind(train.paths, train.ranks.matrix, "TRAINING")
train.ranks.df <- data.frame(train.ranks.matrix, stringsAsFactors = FALSE)
names(train.ranks.df) <- c("Message", "Date", "From", "Subj", "Rank", "Type")
train.ranks.df$Rank <- as.numeric(train.ranks.df$Rank)
# Set the priority threshold to the median of all ranks weights
priority.threshold <- median(train.ranks.df$Rank)
# Visualize the results to locate threshold
threshold.plot <- ggplot(train.ranks.df, aes(x = Rank)) +
stat_density(aes(fill="darkred")) +
geom_vline(xintercept = priority.threshold, linetype = 2) +
scale_fill_manual(values = c("darkred" = "darkred"), guide = "none") +
theme_bw()
ggsave(plot = threshold.plot,
filename = file.path("images", "01_threshold_plot.pdf"),
height = 4.7,
width = 7)
# Classify as priority, or not
train.ranks.df$Priority <- ifelse(train.ranks.df$Rank >= priority.threshold, 1, 0)
# Now, test our ranker by performing the exact same procedure on the test data
test.ranks <- suppressWarnings(lapply(test.paths,rank.message))
test.ranks.matrix <- do.call(rbind, test.ranks)
test.ranks.matrix <- cbind(test.paths, test.ranks.matrix, "TESTING")
test.ranks.df <- data.frame(test.ranks.matrix, stringsAsFactors = FALSE)
names(test.ranks.df) <- c("Message","Date","From","Subj","Rank","Type")
test.ranks.df$Rank <- as.numeric(test.ranks.df$Rank)
test.ranks.df$Priority <- ifelse(test.ranks.df$Rank >= priority.threshold, 1, 0)
# Finally, we combine the data sets.
final.df <- rbind(train.ranks.df, test.ranks.df)
final.df$Date <- date.converter(final.df$Date, pattern1, pattern2)
final.df <- final.df[rev(with(final.df, order(Date))), ]
# Save final data set and plot results.
write.csv(final.df, file.path("data", "final_df.csv"), row.names = FALSE)
testing.plot <- ggplot(subset(final.df, Type == "TRAINING"), aes(x = Rank)) +
stat_density(aes(fill = Type, alpha = 0.65)) +
stat_density(data = subset(final.df, Type == "TESTING"),
aes(fill = Type, alpha = 0.65)) +
geom_vline(xintercept = priority.threshold, linetype = 2) +
scale_alpha(guide = "none") +
scale_fill_manual(values = c("TRAINING" = "darkred", "TESTING" = "darkblue")) +
theme_bw()
ggsave(plot = testing.plot,
filename = file.path("images", "02_testing_plot.pdf"),
height = 4.7,
width = 7)
You can’t perform that action at this time.