# Crate kodama[−][src]

This crate provides a fast implementation of agglomerative hierarchical clustering.

The ideas and implementation in this crate are heavily based on the work of
Daniel Müllner, and in particular, his 2011 paper,
Modern hierarchical, agglomerative clustering algorithms.
Parts of the implementation have also been inspired by his C++
library, `fastcluster`

.
Müllner's work, in turn, is based on the hierarchical clustering facilities
provided by MATLAB and
SciPy.

The runtime performance of this library is on par with Müllner's `fastcluster`

implementation.

# Overview

The most important parts of this crate are as follows:

`linkage`

performs hierarchical clustering on a pairwise dissimilarity matrix.`Method`

determines the linkage criteria.`Dendrogram`

is a representation of a "stepwise" dendrogram, which serves as the output of hierarchical clustering.

# Usage

Add this to your `Cargo.toml`

:

```
[dependencies]
kodama = "0.1"
```

and this to your crate root:

extern crate kodama;

# Example

Showing an example is tricky, because it's hard to motivate the use of hierarchical clustering on small data sets, and especially hard without domain specific details that suggest a hierarchical clustering may actually be useful.

Instead of solving the hard problem of motivating a real use case, let's take a look at a toy use case: a hierarchical clustering of a small number of geographic points. We'll measure the distance (by way of the crow) between these points using latitude/longitude coordinates with the Haversine formula.

We'll use a small collection of municipalities from central Massachusetts in our example. Here's the data:

```
Index Municipality Latitude Longitude
0 Fitchburg 42.5833333 -71.8027778
1 Framingham 42.2791667 -71.4166667
2 Marlborough 42.3458333 -71.5527778
3 Northbridge 42.1513889 -71.6500000
4 Southborough 42.3055556 -71.5250000
5 Westborough 42.2694444 -71.6166667
```

Each municipality in our data represents a single observation, and we'd like to
create a hierarchical clustering of them using `linkage`

.
The input to `linkage`

is a *condensed pairwise dissimilarity matrix*. This
matrix stores the dissimilarity between all pairs of observations. The
"condensed" aspect of it means that it only stores the upper triangle (not
including the diagonal) of the matrix. We can do this because hierarchical
clustering requires that our dissimilarities between observations are
reflexive. That is, the dissimilarity between `A`

and `B`

is the same as the
dissimilarity between `B`

and `A`

. This is certainly true in our case with the
Haversine formula.

So let's compute all of the pairwise dissimilarities and create our condensed pairwise matrix:

// See: https://en.wikipedia.org/wiki/Haversine_formula fn haversine((lat1, lon1): (f64, f64), (lat2, lon2): (f64, f64)) -> f64 { const EARTH_RADIUS: f64 = 3958.756; // miles let (lat1, lon1) = (lat1.to_radians(), lon1.to_radians()); let (lat2, lon2) = (lat2.to_radians(), lon2.to_radians()); let delta_lat = lat2 - lat1; let delta_lon = lon2 - lon1; let x = (delta_lat / 2.0).sin().powi(2) + lat1.cos() * lat2.cos() * (delta_lon / 2.0).sin().powi(2); 2.0 * EARTH_RADIUS * x.sqrt().atan() } // From our data set. Each coordinate pair corresponds to a single observation. let coordinates = vec![ (42.5833333, -71.8027778), (42.2791667, -71.4166667), (42.3458333, -71.5527778), (42.1513889, -71.6500000), (42.3055556, -71.5250000), (42.2694444, -71.6166667), ]; // Build our condensed matrix by computing the dissimilarity between all // possible coordinate pairs. let mut condensed = vec![]; for row in 0..coordinates.len() - 1 { for col in row + 1..coordinates.len() { condensed.push(haversine(coordinates[row], coordinates[col])); } } // The length of a condensed dissimilarity matrix is always equal to // `N-choose-2`, where `N` is the number of observations. assert_eq!(condensed.len(), (coordinates.len() * (coordinates.len() - 1)) / 2);

Now that we have our condensed dissimilarity matrix, all we need to do is
choose our *linkage criterion*. The linkage criterion refers to the formula
that is used during hierarchical clustering to compute the dissimilarity
between newly formed clusters and all other clusters. This crate provides
several choices, and the choice one makes depends both on the problem you're
trying to solve and your performance requirements. For example, "single"
linkage corresponds to using the minimum dissimilarity between all pairs of
observations between two clusters as the dissimilarity between those two
clusters. It turns out that doing single linkage hierarchical clustering has
a rough isomorphism to computing the minimum spanning tree, which means the
implementation can be quite fast (`O(n^2)`

, to be precise). However, other
linkage criteria require more general purpose algorithms with higher constant
factors or even worse time complexity. For example, using median linkage has
worst case `O(n^3)`

complexity, although it is often `n^2`

in practice.

In this case, we'll choose average linkage (which is `O(n^2)`

). With that
decision made, we can finally run linkage:

use kodama::{Method, linkage}; let dend = linkage(&mut condensed, coordinates.len(), Method::Average); // The dendrogram always has `N - 1` steps, where each step corresponds to a // newly formed cluster by merging two previous clusters. The last step creates // a cluster that contains all observations. assert_eq!(dend.len(), coordinates.len() - 1);

The output of `linkage`

is a stepwise
`Dendrogram`

.
Each step corresponds to a merge between two previous clusters. Each step is
represented by a 4-tuple: a pair of cluster labels, the dissimilarity between
the two clusters that have been merged and the total number of observations
in the newly formed cluster. Here's what our dendrogram looks like:

```
cluster1 cluster2 dissimilarity size
2 4 3.1237967760688776 2
5 6 5.757158112027513 3
1 7 8.1392602685723 4
3 8 12.483148228609206 5
0 9 25.589444117482433 6
```

Another way to look at a dendrogram is to visualize it (the following image was created with matplotlib):

If you're familiar with the central Massachusetts region, then this dendrogram is probably incredibly boring. But if you're not, then this visualization immediately tells you which municipalities are closest to each other. For example, you can tell right away that Fitchburg is quite far from any other municipality!

# Testing

The testing in this crate is made up of unit tests on internal data structures
and quickcheck properties that check the consistency between the various
clustering algorithms. That is, quickcheck is used to test that, given the
same inputs, the `mst`

, `nnchain`

, `generic`

and `primitive`

implementations
all return the same output.

There are some caveats to this testing strategy:

- Only the
`generic`

and`primitive`

implementations support all linkage criteria, which means some linkage criteria have worse test coverage. - Principally, this testing strategy assumes that at least one of the implementations is correct.
- The various implementations do not specify how ties are handled, which occurs whenever the same dissimilarity value appears two or more times for distinct pairs of observations. That means there are multiple correct dendrograms depending on the input. This case is not tested, and instead, all input matrices are forced to contain distinct dissimilarity values.
- The output of both Müllner's and SciPy's implementations of hierarchical clustering has been hand-checked with the output of this crate. It would be better to test this automatically, but the scaffolding has not been built.

Obviously, this is not ideal and there is a lot of room for improvement!

## Structs

Dendrogram |
A step-wise dendrogram that represents a hierarchical clustering as a binary tree. |

LinkageState |
Mutable scratch space used by the linkage algorithms. |

Step |
A single merge step in a dendrogram. |

## Enums

Error |
An error. |

Method |
A method for computing the dissimilarities between clusters. |

MethodChain |
A method for computing dissimilarities between clusters in the |

## Functions

generic |
Perform hierarchical clustering using Müllner's "generic" algorithm. |

generic_with |
Like |

linkage |
Return a hierarchical clustering of observations given their pairwise dissimilarities. |

linkage_with |
Like |

mst |
Perform hierarchical clustering using the minimum spanning tree algorithm as described in Müllner's paper. |

mst_with |
Like |

nnchain |
Perform hierarchical clustering using the "nearest neighbor chain" algorithm as described in Müllner's paper. |

nnchain_with |
Like |

primitive |
Perform hierarchical clustering using the "primitive" algorithm as described in Müllner's paper. |

primitive_with |
Like |

## Type Definitions

Result |
A type alias for |