This project is an implementation of the streaming, one-pass histograms described in Ben-Haim's Streaming Parallel Decision Trees. Inspired by Tyree's Parallel Boosted Regression Trees, the histograms are extended so that they may track multiple values.
The histograms act as an approximation of the underlying dataset. They can be used for learning, visualization, discretization, or analysis. The histograms may be built independently and merged, making them convenient for parallel and distributed algorithms.
While the core of this library is implemented in Java, it includes a
full featured Clojure wrapper. This readme focuses on the Clojure
interface, but Java developers can find documented methods in
com.bigml.histogram.Histogram.
histogram is available as a Maven artifact from
Clojars.
For Leiningen:
For Maven:
<repository>
<id>clojars.org</id>
<url>http://clojars.org/repo</url>
</repository>
<dependency>
<groupId>bigml</groupId>
<artifactId>histogram</artifactId>
<version>4.1.2</version>
</dependency>In the following examples we use Incanter to generate data and for charting.
The simplest way to use a histogram is to create one and then
insert! points. In the example below, ex/normal-data refers to a
sequence of 200K samples from a normal distribution (mean 0, variance
1).
user> (ns examples
(:use [bigml.histogram.core])
(:require (bigml.histogram.test [examples :as ex])))
examples> (def hist (reduce insert! (create) ex/normal-data))You can use the sum fn to find the approximate number of points less
than a given threshold:
examples> (sum hist 0)
99814.63248The density fn gives us an estimate of the point density at the
given location:
examples> (density hist 0)
80936.98291The uniform fn returns a list of points that separate the
distribution into equal population areas. Here's an example that
produces quartiles:
examples> (uniform hist 4)
(-0.66904 0.00229 0.67605)Arbritrary percentiles can be found using percentiles:
examples> (percentiles hist 0.5 0.95 0.99)
{0.5 0.00229, 0.95 1.63853, 0.99 2.31390}We can plot the sums and density estimates as functions. The red line represents the sum, the blue line represents the density. If we normalized the values (dividing by 200K), these lines approximate the cumulative distribution function and the probability distribution function for the normal distribution.
examples> (ex/sum-density-chart hist) ;; also see (ex/cdf-pdf-chart hist)
The histogram approximates distributions using a constant number of
bins. This bin limit is a parameter when creating a histogram
(:bins, defaults to 64). A bin contains a :count of the points
within the bin along with the :mean for the values in the bin. The
edges of the bin aren't captured. Instead the histogram assumes that
points of a bin are distributed with half the points less than the bin
mean and half greater. This explains the fractional sum in the example
below:
examples> (def hist (-> (create :bins 3)
(insert! 1)
(insert! 2)
(insert! 3)))
examples> (bins hist)
({:mean 1.0, :count 1} {:mean 2.0, :count 1} {:mean 3.0, :count 1})
examples> (sum hist 2)
1.5As mentioned earlier, the bin limit constrains the number of unique bins a histogram can use to capture a distribution. The histogram above was created with a limit of just three bins. When we add a fourth unique value it will create a fourth bin and then merge the nearest two.
examples> (bins (insert! hist 0.5))
({:mean 0.75, :count 2} {:mean 2.0, :count 1} {:mean 3.0, :count 1})A larger bin limit means a higher quality picture of the distribution, but it also means a larger memory footprint. In the chart below, the red line represents a histogram with 8 bins and the blue line represents 64 bins.
examples> (ex/multi-pdf-chart
[(reduce insert! (create :bins 8) ex/mixed-normal-data)
(reduce insert! (create :bins 64) ex/mixed-normal-data)])
Another option when creating a histogram is to use gap
weighting. When :gap-weighted? is true, the histogram is encouraged
to spend more of its bins capturing the densest areas of the
distribution. For the normal distribution that means better resolution
near the mean and less resolution near the tails. The chart below
shows a histogram without gap weighting in blue and with gap weighting
in red. Near the center of the distribution, red uses more bins and
better captures the gaussian distribution's true curve.
examples> (ex/multi-pdf-chart
[(reduce insert! (create :bins 8 :gap-weighted? true)
ex/normal-data)
(reduce insert! (create :bins 8 :gap-weighted? false)
ex/normal-data)])
A strength of the histograms is their ability to merge with one another. Histograms can be built on separate data streams and then combined to give a better overall picture.
In this example, the blue line shows a density distribution from a histogram after merging 300 noisy histograms. The red shows one of the original histograms:
examples> (let [samples (partition 1000 ex/mixed-normal-data)
hists (map #(reduce insert! (create) %) samples)
merged (reduce merge! (create) (take 300 hists))]
(ex/multi-pdf-chart [(first hists) merged]))
While a simple histogram is nice for capturing the distribution of a single variable, it's often important to capture the correlation between variables. To that end, the histograms can track a second variable called the target.
The target may be either numeric or categorical. The insert! fn is
overloaded to accept either type of target. Each histogram bin will
contain information summarizing the target. For numeric targets the
sum and sum-of-squares are tracked. For categoricals, a map of
counts is maintained.
examples> (-> (create)
(insert! 1 9)
(insert! 2 8)
(insert! 3 7)
(insert! 3 6)
(bins))
({:target {:sum 9.0, :sum-squares 81.0, :missing-count 0.0},
:mean 1.0,
:count 1}
{:target {:sum 8.0, :sum-squares 64.0, :missing-count 0.0},
:mean 2.0,
:count 1}
{:target {:sum 13.0, :sum-squares 85.0, :missing-count 0.0},
:mean 3.0,
:count 2})
examples> (-> (create)
(insert! 1 :a)
(insert! 2 :b)
(insert! 3 :c)
(insert! 3 :d)
(bins))
({:target {:counts {:a 1.0}, :missing-count 0.0},
:mean 1.0,
:count 1}
{:target {:counts {:b 1.0}, :missing-count 0.0},
:mean 2.0,
:count 1}
{:target {:counts {:d 1.0, :c 1.0}, :missing-count 0.0},
:mean 3.0,
:count 2})Mixing target types isn't allowed:
examples> (-> (create)
(insert! 1 :a)
(insert! 2 999))
Can't mix insert types
[Thrown class com.bigml.histogram.MixedInsertException]insert-numeric! and insert-categorical! allow target types to be
set explicitly:
examples> (-> (create)
(insert-categorical! 1 1)
(insert-categorical! 1 2)
(bins))
({:target {:counts {2 1.0, 1 1.0}, :missing-count 0.0}, :mean 1.0, :count 2})The extended-sum fn works similarly to sum, but returns a result
that includes the target information:
examples> (-> (create)
(insert! 1 :a)
(insert! 2 :b)
(insert! 3 :c)
(extended-sum 2))
{:sum 1.5, :target {:counts {:c 0.0, :b 0.5, :a 1.0}, :missing-count 0.0}}The average-target fn returns the average target value given a
point. To illustrate, the following histogram captures a dataset where
the input field is a sample from the normal distribution while the
target value is the sine of the input. The density is in red and the
average target value is in blue:
examples> (def make-y (fn [x] (Math/sin x)))
examples> (def hist (let [target-data (map (fn [x] [x (make-y x)])
ex/normal-data)]
(reduce (fn [h [x y]] (insert! h x y))
(create)
target-data)))
examples> (ex/pdf-target-chart hist)
Continuing with the same histogram, we can see that average-target
produces values close to original target:
examples> (def view-target (fn [x] {:actual (make-y x)
:approx (:sum (average-target hist x))}))
examples> (view-target 0)
{:actual 0.0, :approx -0.00051}
examples> (view-target (/ Math/PI 2))
{:actual 1.0, :approx 0.9968169965429206}
examples> (view-target Math/PI)
{:actual 0.0, :approx 0.00463}Information about missing values is captured whenever the input field
or the target is nil. The missing-bin fn retrieves information
summarizing the instances with a missing input. For a basic histogram,
that is simply the count:
examples> (-> (create)
(insert! nil)
(insert! 7)
(insert! nil)
(missing-bin))
{:count 2}For a histogram with a target, the missing-bin includes target
information:
examples> (-> (create)
(insert! nil :a)
(insert! 7 :b)
(insert! nil :c)
(missing-bin))
{:target {:counts {:a 1.0, :c 1.0}, :missing-count 0.0}, :count 2}Targets can also be missing, in which case the target missing-count
is incremented:
examples> (-> (create)
(insert! nil :a)
(insert! 7 :b)
(insert! nil nil)
(missing-bin))
{:target {:counts {:a 1.0}, :missing-count 1.0}, :count 2}By default a histogram with categorical targets stores the category
counts as Java HashMaps. Building and merging HashMaps can be
expensive. Alternatively the category counts can be backed by an
array. This can give better performance but requires the set of
possible categories to be declared when the histogram is created. To
do this, set the :categories parameter:
examples> (def categories (map (partial str "c") (range 50)))
examples> (def data (vec (repeatedly 100000
#(vector (rand) (str "c" (rand-int 50))))))
examples> (doseq [hist [(create) (create :categories categories)]]
(time (reduce (fn [h [x y]] (insert! h x y))
hist
data)))
"Elapsed time: 1295.402 msecs"
"Elapsed time: 516.72 msecs"Group targets allow the histogram to track multiple targets at the same time. Each bin contains a sequence of target information. Optionally, the target types in the group can be declared when creating the histogram. Declaring the types on creation allows the targets to be missing in the first insert:
examples> (-> (create :group-types [:categorical :numeric])
(insert! 1 [:a nil])
(insert! 2 [:b 8])
(insert! 3 [:c 7])
(insert! 1 [:d 6])
(bins))
({:target
({:counts {:d 1.0, :a 1.0}, :missing-count 0.0}
{:sum 6.0, :sum-squares 36.0, :missing-count 1.0}),
:mean 1.0,
:count 2}
{:target
({:counts {:b 1.0}, :missing-count 0.0}
{:sum 8.0, :sum-squares 64.0, :missing-count 0.0}),
:mean 2.0,
:count 1}
{:target
({:counts {:c 1.0}, :missing-count 0.0}
{:sum 7.0, :sum-squares 49.0, :missing-count 0.0}),
:mean 3.0,
:count 1})There are multiple ways to render the charts, see examples.clj. An example of rendering a single function, namely cumulative probability:
examples> (def hist (reduce hst/insert! (hst/create) [1 1 2 3 4 4 4 5]))
examples> (let [{:keys [min max]} (hst/bounds hist)]
(core/view (charts/function-plot (hst/cdf hist) min max)))(core and charts are Incanter namespaces.)
To render multiple functions on the same chart, you would use
add-function with the result of function-plot:
examples> (core/view (-> (charts/function-plot (hst/cdf hist) min max :legend true)
(charts/add-function (hst/pdf hist) min max)))While the ability to adapt to non-stationary data streams is a
strength of the histograms, it is also computationally expensive. If
your data stream is stationary, you can increase the histogram's
performance by setting the :freeze parameter. After the number of
inserts into the histogram have exceeded the :freeze parameter, the
histogram bins are locked into place. As the bin means no longer
shift, inserts become computationally cheap. However the quality of
the histogram can suffer if the :freeze parameter is too small.
examples> (time (reduce insert! (create) ex/normal-data))
"Elapsed time: 333.5 msecs"
examples> (time (reduce insert! (create :freeze 1024) ex/normal-data))
"Elapsed time: 166.9 msecs"There are two implementations of bin reservoirs (which support the
insert! and merge! functions). Either of the two implementations,
:tree and :array, can be explicitly selected with the :reservoir
parameter. The :tree option is useful for histograms with many bins
as the insert time scales at O(log n) with respect to the # of
bins. The :array option is good for small number of bins since
inserts are O(n) but there's a smaller overhead. If :reservoir is
left unspecified then :array is used for histograms with <= 256 bins
and :tree is used for anything larger.
examples> (time (reduce insert! (create :bins 16 :reservoir :tree)
ex/normal-data))
"Elapsed time: 554.478 msecs"
examples> (time (reduce insert! (create :bins 16 :reservoir :array)
ex/normal-data))
"Elapsed time: 183.532 msecs"Insert times using reservoir defaults:
![timing chart] (https://docs.google.com/spreadsheet/oimg?key=0Ah2oAcudnjP4dG1CLUluRS1rcHVqU05DQ2Z4UVZnbmc&oid=2&zx=mppmmoe214jm)
Copyright (C) 2013 BigML Inc.
Distributed under the Apache License, Version 2.0.
