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# Documentation

## Contributors

Eirene is produced and maintained by

Gregory Henselman-Petrusek \ gh10@princeton.edu \ grh@seas.upenn.edu

Theoretical foundations for this platform lie in matroid optimization; see here for an introduction. The developers make a special acknowledgement to Professor Janche Sang and to Alan Hylton and Robert Short, for their work in performant optimizations. Important contributions have additionally been made by the following individuals.

Ulrich Bauer
Yossi Bokor
Jean-Pierre Both
Paul Breiding
Robert Ghrist
Alan Hylton
Sara Kalisnik
Janche Sang
Robert Short
Ann Sizemore
Primoz Skraba
Christopher Williams

## Installation

Debugging Tip Homebrew and other installers tend to install very old versions, for some reason. The only way to effectively check that you are running the most recent version of Julia is to visit the downloads page (https://julialang.org/downloads/) and compare with your current install.

Installing Julia is simple. Download the most recent version of Julia at https://julialang.org/downloads/. Open a Julia shell and type ] to enter the Package management environment. Then run add Eirene:

(v1.1) pkg> add Eirene


It's fairly common to get error messages when you do this. Generally they will want you to install additional (supporting) packages. Read these messages, and follow the instructions. When in doubt, FIRST check that you are running the latest version of Julia, and use

(v1.1) pkg> update


to ensure that you are using the latest versions of the supporting packages. SECOND, close the Julia shell. Some updates will only take effect after re-opening.

Debugging Tip Pay special attention to red error messages. You can solve nine out of ten installation problems by copy/pasting text from these directly into the REPL.

Debugging Tip Wait times of an hour or more have been reported. The install will finish eventually!

## Example

Let's plot the 1d persistence diagram for a point cloud of 50 points sampled from the uniform distribution on the unit cube, [0,1]3. The second line below generates 3x50 iid matrix and stores it in a variable x. The third asks Eirene to analyze x and store the results in a variable C. The fourth plots the barcode. The fifth plots the persistence diagram. The sixth plots a cycle representative for the first point in this diagram (Eirene numbers the points automatically, so it 'makes sense' to talk about the 'first'). Most of what you can do with Eirene is done with minor modifications to these commands.

julia> using Eirene
julia> x = rand(3,50)
julia> C = eirene(x, model = "pc")
julia> plotbarcode_pjs(C,dim=1)
julia> plotpersistencediagram_pjs(C,dim=1)
julia> plotclassrep_pjs(C,dim=1,class=1)


More examples can be found in EXAMPLES.md!

## Keywords

In the example above, the expression model = "pc" that sits inside C = eirene(x, model = "pc") functions as a declaration to Eirene. It asserts that the columns of x should be treated as points in a Euclidean point cloud. In this context, model is a keyword argument, and "pc" is its value. Every keyword comes with a default value; you only have to declare a value if you want something other than a default.

model = "pc", "vr", "complex"

• States format of the data.
• Possible values: "pc" (point cloud), "vr" (vietoris-rips), "complex". Default value: "vr".
• See 'Complexes' below for special

maxdim = k

• Compute persistent homology in dimensions 0, ..., k.
• Default value: 1.

minrad = t

• Compute homology from time t onward.
• Default value: -Inf.

maxrad = t

• Stop computing homology after time t.
• Devalue value Inf.

numrad = N

• Divide the interval from minrad to maxrad into N equally spaced steps, and compute the homology of each step. If the value of numrad is set to Inf, then homology will computed at every time point.
• Possible values: any positive integer, or Inf. Default value: Inf.
• This keyword argument is currently only available for model = "vr".

record = "cyclerep", "none"

• Determines wether or not to compute generators.
• Possible values: "cyclerep", "none". Default value: "cyclerep".

## Inputs

Eirene computes persistent homology for three types of inputs: distance matrices, point clouds, and complexes. Here are some formats these can come in, and how to analyze them.

#### Distance matrices

julia> C = eirene(x, <keyword arguments>)


Formats for x

• a symmetric matrix in Julia
• a file path to a symmetric matrix, recorded in a comma or space-delimited text file (.csv or .txt)

## Point clouds

julia> C = eirene(x, model = "pc", <keyword arguments>)


Formats for x

• a numeric matrix in Julia (columns will be treated as points in Euclidean space)
• a file path to a numeric matrix, recorded in a comma or space-delimited text file (.csv or .txt)

## Complexes

If you're new to Julia and/or Eirene, formatting for complexes can be a bit overwhelming. We suggest reading the Example and General Formatting sections, ignoring the content on D, rv and cp. Then skip to the section entitled Simple format (from file). This should cover the needs of most users.

### Example

This section gives a practical overview on customized (filtered) topological spaces. For complete details, see the following section. As an example of a (filtered) topological space, we'll use an undirected graph with with two vertices, v1 and v2, and one edge, e1. To begin, let's assign unique ID numbers to the cells of G (see table below).

Debugging tip ID numbers must be assigned in ascending order with respect to the dimension of cells (e.g. cells of dimension 0 receive lower id numbers than cells of dimension 1). **

Debugging tip Numbering must start at 1, not 0.**

i = cell id number (user-assigned)   |   new cell label    |   original cell label
----------------------------------------------------------------------------------
1                                    |   c1                |   v1
2                                    |   c2                |   v2
3                                    |   c3                |   e1
0                                    |   n/a               |   n/a


These ID numbers determine the entries of the boundary matrix D. For example, D[1,3] = 1 because c1 is a face of c3, and D[1,2] = 0 because c1 is not a face of c2.

julia> D = [0 0 1; 0 0 1; 0 0 0]
3×3 Array{Int64,2}:
0  0  1
0  0  1
0  0  0


Suppose that G is the last in a nested sequence of graphs G1, G2, G3 where G1 is just the vertex v1 and G2 is the (unconnected) pair of vertices v1, v2. Suppose that G1, G2, and G3 appear at times t1 =0.01, t2 =0.02, and t3 =0.3, respectively. Then

i = cell id number   |   fv[i]   |   dv[i]   |   ev[i]   |   dp[i]   |   rv[i]   |   cp[i]   |
----------------------------------------------------------------------------------------------
0                      undefined   undefined   undefined   undefined   undefined   undefined
1                        0.01        0           2           1           1           1
2                        0.02        0           1           3           2           1
3                        0.03        1           0           4         undefined     3
4                      undefined   undefined   undefined     4         undefined   undefined
5                      undefined   undefined   undefined   undefined   undefined   undefined


That is,

fv = [0.01,0.02,0.03]
dv = [0,0,1]
ev = [2,1,0]
dp = [1,2,4,4]
rv = [1,2]
cp = [1,1,3]


### General formats

Debugging Tip Julia is 1-indexed. For an example, v[1] is the first entry of a list or vector v. Thus, when assigning unique ID numbers to cells, numbering should start at 1, not 0.

There are several ways to format the data of a cell complex E. Here are the main ingredients.

• number the cells 1, ..., N in ascending order, according to dimension
• let D be the N x N zero/one matrix with D[i,j] = 1 iff i is a face of cell j
• define vectors rv and cp by the following procedure (see Julia documentation for a more direct interpretation) html julia> S = sparse(D) julia> rv = S.rowval julia> cp = S.colptr 

Define vectors dv, ev, and dp such that

• dv[i] is the dimension of cell i
• ev[k] is the total number of cells with dimension k-1
• dp[k] is 1 plus the number of cells of dimension strictly less than k-1

If in addition we have a nested sequence of complexes E_0 ≤ ... ≤ E_n = E, then let fv be the vector such that

• fv[i] is the birthtime of cell i

### Sparse column format

Eirene has a keyword argument for every vector defined in the general formatting section. In the example below, you can substitute either ev = ev or dp=dp in place of dv=dv. Eirene only needs one of the three.

Example computation

julia> C = eirene(rv=rv,cp=cp,dv=dv,fv=fv)


### Simple format (from file)

This format is handy if you need to proof read, or write files by hand.

dv[1], fv[1], <all id #'s for the faces of cell 1, separated by commas>
dv[2], fv[2], <all id #'s for the faces of cell 1, separated by commas>
...
dv[N], fv[N], <all id #'s for the faces of cell 1, separated by commas>


Example file For our example space, this file would take form:

0, 0.01
0, 0.02
1, 0.03, 1, 2


Example computation If this file is saved as Users/Adam/ez.csv, then to compute PH call

julia> C = eirene("Users/Adam/complex.csv",model="complex",entryformat="sp")


### Sparse column format (from file)

You can store E as a comma separated .txt or .csv file with four lines

dp_1, ..., dp_m
fv_1, ..., fv_n
rv_1, ..., rv_p
cp_1, ..., cp_q


where line one is dp, line 2 is fv, line 3 is rv, and line 4 is cp.

• If you know D and want to figure out what rv and cp should be, you can either view the Julia docs on sparse matrices or google "sparse column format".
• Instead of dp, you can put either dv or ev in the first line.

Example files

Recall that

fv = [0.01,0.02,0.03]
dv = [0,0,1]
ev = [2,1,0]
dp = [1,2,4,4]
rv = [1,2]
cp = [1,1,3]


To use the dp format option, you could write a file like so.

1,2,4,4
0.01, 0.02, 0.03
1,2
1,1,3


To use the ev format option, replace the top row with ev:

2,1,0
0.01, 0.02, 0.03
1,2
1,1,3


Example computations

Suppose the first file is saved as desktop/DP.csv. To compute persistent homology, run:

julia> C =eirene("desktop/DP.csv",model="complex",  entryformat=  "dp")


Suppose the second file is saved as desktop/EV.csv. To compute persistent homology, run:

julia> C =eirene("desktop/EV.csv",model="complex",  entryformat=  "ev")


## Barcodes, Betti Curves, and Persistence Diagrams

Eirene stores a list of every persistent homology class (that is, every bar) in the output variable C. To find the birth and death times of each class, run

julia> A = barcode(C, dim=k)


Variable A will be an n x 2 matrix, where n is the number of persistent homology classes of dimension k. The pth persistent homology class in Eirene's list is born at time A[p,1] and dies at time A[p,2]. To obtain the betti curve, run

julia> B = betticurve(C, dim=k)


Variable B is an n x 2 array for which B[j,2] is the kth betti number of the space at time t = B[j,1].

To plot the persistence diagram, betti curve, and barcode in dimension k, run the following. Note that _pjs simply refers to PlotlyJS, with is the Julia package used for graphing.

julia> plotpersistencediagram_pjs(C, dim=k)
julia> plotbetticurve_pjs(C, dim=k)
julia> plotbarcode_pjs(C, dim=k)


• Keyword dim defaults to 1.
• A class that never dies will appear as red dot on the diagonal at the time of its birth.
• Hovering the cursor over a point in the persistence diagram will show a message with its precise Euclidean coordinates (birth and death times) and two additional pieces of information: class and size. Variable class is an integer. If class = p, then the point where the cursor is hovering represents the birth/death time of pth persistent homology class in Eirene's list. It is born at time A[p,1] and dies at time A[p,2]. Variable size is also an integer. It is the number of cells in the cycle representative Eirene computed for this persistent homology class (since Eirene computes homology over the two element field, we always refer to vectors by their support).
• class and size can be displayed permanently, without the need to hover a cursor, via the keyword argument showlabels = true.

### q,p-Wasserstein distances between diagrams

Given two persistence diagramsX and Y, the q,p-Wasserstein Distance W_{q,p}(X,Y) between them is defined as

W_{q,p}(X,Y) := (\inf_{bijections s: X \to Y} \Sigma_{x \in X} ||x - s(x)||_p^q)^(1/q).


To compute the q,p-Wasserstein distance between a pair of persistence diagrams, dgm1 and dgm2, run:

julia> wasserstein_distance(dgm1, dgm2, q=q, p=p)

• Keyword p defaults to 2.
• Keyword q defaults to p.

### Representatives

To compute a cycle representative for the pth persistent homology class in Eirene's list for dimension k, run

julia> S = classrep(C, class=p, dim=k)


By default class = 1 and dim = 1. Recall that, since Eirene computes homology over the two element field, we can always specify a cycle representative by listing the cells that support it. If C was generated from a point cloud or Vietoris-Rips complex, then the cycle representative S will be encoded as an array with k+1 rows. Each column of S represents the set of vertices that make up a k-dimensional simplex. If C was generated from an nxn distance matrix M, then the entries of S correspond to the rows/columns of M. If C is generated from a matrix M whose columns represent points in a point cloud, then the elements of S refer to columns of M. If C was generated with model = "complex", then S will be a vector of integers. These numbers refer to cells in the complex; more precisely, the number q refers to the qth dimension-k cell stored in memory.

Plotting for class representatives is currently supported only for point clouds and Vietoris-Rips complexes. If the input data is a point cloud, coordinates for each vertex will be inferred automatically. If the input data is not a point cloud, or if you would like to overwrite the existing coordinates, set C["inputdata"]["pointlabels"] = N where N is a numeric array whose columns correspond to sample points. Alternatively, you can pass N directly to the plotting function using keyword coords = N (this will not overwrite the existing coordinate data in C).

There are several ways to assign text labels to the points in your figure. If labels were extracted from the input data or file, they are made available automatically for plotting. To create or overwrite existing text labels, set C["inputdata"]["pointlables"] = U, where U is an array of type Any with all string entries. U may also be passed directly to a plotting function using keyword textlabels = U. If no other information is available, Eirene will label data points 1 through n, according to their order in the input array. As in the case of persistence diagrams, both wrappers accept the showlabels keyword argument. Hover-tags in PlotlyJS will still show text labels when showlabels = false. A third option, showlabels = "cycle", will cause plotclassrep_pjs to display the labels of only those vertices incident to the cycle representative being plotted.

### Visualizing non-Euclidean Data

Multidimensional scaling (MDS) is a general approach to generating Euclidean embeddings of non-Euclidean or high-dimensional data which (to the extent possible) faithfully represent distances between points. Most implementations of the MDS algorithm accept a symmetric m x m matrix S and return an ordered set of m points in Rn, with point i corresponding to the ith column of S. These points determine an m x m matrix D, with D[i,j] equal to the Euclidean distance between points i and j. The algorithm aims to to select the points that will make D as similar as possible to S. To use multidmensional scaling with Eirene, pass coords = "mds" to the plotclassrep_pjs function. To specify an embedding of dimension n, use embeddingdim = n.

By default, the input matrix S will be the distance matrix used to generate the filtered complex. However in the special case where only the vertices of a specific class representative are to be shown, that is, when the user specifies showcloud = false, there an additional option. The class to be represented consists of a finite family of simplices, or faces, and the dimension-1 simplices incident to these faces form a graph. The hop distance on this graph yields a new distance matrix, which the user may specify with embeddingobj = "hop". This option often creates cleaner representations.

### Formatting

#### Point clouds and Vietoris Rips complexes

PlotlyJS plots may be exported to the Plotly web API for sharing, storage, and advanced editing. Every function that generates a PlotlyJS visual in the Eirene library returns a PlotlyJS object which may be uploaded via the Plotly. post function. See the documentation for Plotly.jl to learn more.

Arrays can be read from (and written to) text flies using the native readdlm and writedlm (see the Julia wikibooks chapter for text flies). The Julia base includes a number of additional functions for importing data from text flies, and for convenience several of these have been combined in the Eirene wrapper ezread(<pathtofile>).

Import from and export to Matlab flies are available from the packages MATLAB and MAT. Import from and export to Numpy flies is managed by NPZ.

To save an entire dictionary C, the most convenient option by far is the Julia JLD package.

### Performance Tips

The marginal time and memory cost of computing explicit cycle representatives is often small relative to that of computing homological barcodes alone (usually around 10%, for Euclidean point cloud data). Setting the record = "none" may yield significant savings for other spaces, however.

It is common among persistence solvers to round the entries of a user-provided distance matrix to a fixed number of distinct values or significant digits. This is not the default behavior with Eirene, so care must be taken when comparing outputs.

Multidimensional scaling is a blue-chip method in data visualization, but no embedding algorithm is perfect. Particular care must be taken when embeddingobj = "hop" , as performance often decreases appreciably with the number of connected components in the underlying graph. Remember that you can always inspect class representatives directly with the classrep function.

##### Keyword arguments

The following are optional keyword arguments for the main funciton, eirene.

pointlabels = A

• If A is a nonempty array, then assign the pth vertex in the complex a label of A[p], for all p.
• If A is empty, assign the pth vertex a label of p.
• Possible values: A may be any array of numbers or strings. Default value: [].

fastop = true, false

• A value of true allows Eirene to stop computing homology at a given time point t if it can be determined that the homology of the complex does not change after time t. There is no reason to change this setting under normal circumstances.
• Possible values: true, false. Default value: true.
##### Complex formats

Let us say that for any vector v, the symbol v{k} denotes the set of all integers j such that v[k] ≤ j < v[k+1] (you might recall that we used this convention when we explained how to format data for an arbitrary complex). Now let us suppose we have a matrix M with 0 - 1 entries. To save M in computer memory, it suffices to record which rows of each column have nonzero entries. In particular, suppose we are given two vectors, rv (row values) and cp (column pattern). If for all p the set rv[cp{p}] equals the set of rows where column p is nonzero, then we can (essentially) record M in computer memory by saving rv and cp. We call this the column sparse format of M.

When we run the command

C = eirene(rv=rv, cp=cp, fv=fv, dp=dp, <keyword arguments>)


we are passing eirene a pair of vectors (rv and cp) that record the total boundary matrix; this matrix has a row and column for every cell of every dimension. The function of the vector dp is to record the dimension of each cell, and the function of fv is to specify the birth time of each cell.

When Eirene processes these data, they are broken down by dimension. Eirene creates arrays RV, CP, and FV such that (1) RV[p] and CP[p] are column sparse formats for the boundary matrix with columns indexed by the cells of dimension p and rows indexed by cells of dimension p-1, and (2) FV[p][q] is the birth time of the qth p-1-dimensional cell. If you already have access to RV, CP, and FV you can pass them to Eirene directly with the command

C = eirene(rv=RV, cp=CP, fv=FV, dp=[], <keyword arguments>)


### Common Issues

The most common source of technical difficulties in working with Eirene is software update. The best way to check that you are running the most recent version of Julia is to log onto the Julia homepage. To ensure that you have the most recent version of the the various support packages, enter Pkg. update() in a Julia REPL.

The second most common source of technical difficulties rregards operating systems. The fewest issues by far have been reported for Mac OS X. If you have already visited the Julia homepage to make sure your Julia install is up-to-date, it may be worthwhile switching to Mac to see if your issue persists. Windows users have reported encountering an error message that includes the phrase "invalid escape sequence" in reference to file paths. We found that replacing the unary operator \ with \ generally resolves this issue, e.g. C:\Users versus C:\Users`.

Calling the include function twice with the same input will frequently produce a large number of error messages. This is a well documented issue in the current Julia distribution, and does not impact performance.

### Documenting Use

If Eirene has helped your research, teaching, or artistic endeavors, please let us know! You can write us here and copy/paste the following bibtex entry to cite the original tech report. If you have ideas about how Eirene could help with education and outreach, please let us know! We would love to hear from you.

@ARTICLE{henselmanghristl6,
author= {{Henselman}, G. and {Ghrist}, R.},
title= "{Matroid Filtrations and Computational Persistent Homology}",
journal= {ArXiv e-prints},
archivePrefix = "arXiv",
eprint = {1606.00199},
primaryClass = "math.AT",
keywords= {Mathematics -Algebraic Topology, Mathematics -Combinatorics},
year= 2016,
month= jun,
adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

Eirene.jl package for Homological Algebra

Copyright (C) 2016, 2017, 2018 Gregory Henselman

www.gregoryhenselman.org

Eirene is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Eirene is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with Eirene. If not, see http://www.gnu.org/licenses/.

05/30/2017

18 days ago

94 commits