Archive for the ‘Data Analytics’ Category
The story before the story – a data science fable
It is well-known that data-driven stories are a great way to convey results of data science initiatives. What is perhaps not as well-known is that data science projects often have to begin with stories too. Without this “story before the story” there will be no project, no results and no data-driven stories to tell….
For those who prefer to read, here’s a transcript of the video in full:
In the beginning there is no data, let alone results…but there are ideas. So, long before we tell stories about data or results, we have to tell stories about our ideas. The aim of these stories is to get people to care about our ideas as much as we do and, more important, invest in them. Without their interest or investment there will be no results and no further stories to tell.
So one of the first things one has to do is craft a story about the idea…or the story before the story.
Once upon a time there was a CRM system. The system captured every customer interaction that occurred, whether it was by phone, email or face to face conversation. Many quantitative details of interactions were recorded, time, duration, type. And if the interaction led to a sale, the details of the sale were recorded too.
Almost as an aside, the system also gave sales people the opportunity to record their qualitative impressions as free text notes. As you might imagine, this information, though potentially valuable, was never analysed. Sure managers looked at notes in isolation from time to time when referring.to specific customer interactions, but there was no systematic analysis of the corpus as a whole. Nobody had thought it worthwhile to do this, possibly because it is difficult if not quite impossible to analyse unstructured information in the world of relational databases and SQL.
One day, an analyst was browsing data randomly in the system, as good analysts sometimes do. He came across a note that to him seemed like the epitome of a good note…it described what the interaction was about, the customer’s reactions and potential next steps all in a logical fashion.
This gave him an idea. Wouldn’t it be cool, he thought, if we could measure the quality of notes? Not only would this tell us something about the customer and the interaction, it may tell us something about the sales person as well.
The analyst was mega excited…but he realised he’d need help. He was an IT guy and as we all know, business folks in big corporations stopped listening to their IT guys long ago. So our IT guy had his work cut out for him.
After much cogitation, he decided to enlist the help of his friend, a strategic business analyst in the marketing department. This lady, who worked in marketing had the trust of the head of marketing. If she liked the idea, she might be able to help sell it to the head of marketing.
As it turned out, the business analyst loved the idea…more important, since she knew what the sales people do on a day to day basis, she could give the IT guy more ideas on how he could build quantitative measures of the quality of notes. For example, she suggested looking for emotion-laden words or mentions of competitor’s products and so on. The IT guy now had some concrete things to work on. The initial results gave them even more ideas, and soon they had more than enough to make a convincing pitch to the head of marketing.
It would take us too far afield to discuss details of the pitch, but what we will say is this: they avoided technical details, instead focusing on the strategic and innovative aspects of the work.
The marketing head liked the idea…what was there not to like? He agreed to support the effort, and the idea became a project….
…and yes, within months the project resulted in new insights into customer behaviour. But that is another story.
A gentle introduction to decision trees using R
Introduction
Most techniques of predictive analytics have their origins in probability or statistical theory (see my post on Naïve Bayes, for example). In this post I’ll look at one that has more a commonplace origin: the way in which humans make decisions. When making decisions, we typically identify the options available and then evaluate them based on criteria that are important to us. The intuitive appeal of such a procedure is in no small measure due to the fact that it can be easily explained through a visual. Consider the following graphic, for example:
Figure 1: Example of a simple decision tree (Courtesy: Duncan Hull)
(Original image: https://www.flickr.com/photos/dullhunk/7214525854, Credit: Duncan Hull)
The tree structure depicted here provides a neat, easy-to-follow description of the issue under consideration and its resolution. The decision procedure is based on asking a series of questions, each of which serve to further reduce the domain of possibilities. The predictive technique I discuss in this post,classification and regression trees (CART), works in much the same fashion. It was invented by Leo Breiman and his colleagues in the 1970s.
In what follows, I will use the open source software, R. If you are new to R, you may want to follow this link for more on the basics of setting up and installing it. Note that the R implementation of the CART algorithm is called RPART (Recursive Partitioning And Regression Trees). This is essentially because Breiman and Co. trademarked the term CART. As some others have pointed out, it is somewhat ironical that the algorithm is now commonly referred to as RPART rather than by the term coined by its inventors.
A bit about the algorithm
The rpart algorithm works by splitting the dataset recursively, which means that the subsets that arise from a split are further split until a predetermined termination criterion is reached. At each step, the split is made based on the independent variable that results in the largest possible reduction in heterogeneity of the dependent (predicted) variable.
Splitting rules can be constructed in many different ways, all of which are based on the notion of impurity- a measure of the degree of heterogeneity of the leaf nodes. Put another way, a leaf node that contains a single class is homogeneous and has impurity=0. There are three popular impurity quantification methods: Entropy (aka information gain), Gini Index and Classification Error. Check out this article for a simple explanation of the three methods.
The rpart algorithm offers the entropy and Gini index methods as choices. There is a fair amount of fact and opinion on the Web about which method is better. Here are some of the better articles I’ve come across:
https://www.garysieling.com/blog/sklearn-gini-vs-entropy-criteria
http://www.salford-systems.com/resources/whitepapers/114-do-splitting-rules-really-matter
The answer as to which method is the best is: it depends. Given this, it may be prudent to try out a couple of methods and pick the one that works best for your problem.
Regardless of the method chosen, the splitting rules partition the decision space (a fancy word for the entire dataset) into rectangular regions each of which correspond to a split. Consider the following simple example with two predictors x1 and x2. The first split is at x1=1 (which splits the decision space into two regions x11), the second at x2=2, which splits the (x1>1) region into 2 sub-regions, and finally x1=1.5 which splits the (x1>1,x2>2) sub-region further.
Figure 2: Example of partitioning
It is important to note that the algorithm works by making the best possible choice at each particular stage, without any consideration of whether those choices remain optimal in future stages. That is, the algorithm makes a locally optimal decision at each stage. It is thus quite possible that such a choice at one stage turns out to be sub-optimal in the overall scheme of things. In other words, the algorithm does not find a globally optimal tree.
Another important point relates to well-known bias-variance tradeoff in machine learning, which in simple terms is a tradeoff between the degree to which a model fits the training data and its predictive accuracy. This refers to the general rule that beyond a point, it is counterproductive to improve the fit of a model to the training data as this increases the likelihood of overfitting. It is easy to see that deep trees are more likely to overfit the data than shallow ones. One obvious way to control such overfitting is to construct shallower trees by stopping the algorithm at an appropriate point based on whether a split significantly improves the fit. Another is to grow a tree unrestricted and then prune it back using an appropriate criterion. The rpart algorithm takes the latter approach.
Here is how it works in brief:
Essentially one minimises the cost, 
First, we note that when 
An implication of their tendency to overfit data is that decision trees tend to be sensitive to relatively minor changes in the training datasets. Indeed, small differences can lead to radically different looking trees. Pruning addresses this to an extent, but does not resolve it completely. A better resolution is offered by the so-called ensemble methods that average over many differently constructed trees. I’ll discuss one such method at length in a future post.
Finally, I should also mention that decision trees can be used for both classification and regression problems (i.e. those in which the predicted variable is discrete and continuous respectively). I’ll demonstrate both types of problems in the next two sections.
Classification trees using rpart
To demonstrate classification trees, we’ll use the Ionosphere dataset available in the mlbench package in R. I have chosen this dataset because it nicely illustrates the points I wish to make in this post. In general, you will almost always find that algorithms that work fine on classroom datasets do not work so well in the real world…but of course, you know that already!
We begin by setting the working directory, loading the required packages (rpart and mlbench) and then loading the Ionosphere dataset.
Next we separate the data into training and test sets. We’ll use the former to build the model and the latter to test it. To do this, I use a simple scheme wherein I randomly select 80% of the data for the training set and assign the remainder to the test data set. This is easily done in a single R statement that invokes the uniform distribution (runif) and the vectorised function, ifelse. Before invoking runif, I set a seed integer to my favourite integer in order to ensure reproducibility of results.
In the above, I have also removed the training flag from the training and test datasets.
Next we invoke rpart. I strongly recommend you take some time to go through the documentation and understand the parameters and their defaults values. Note that we need to remove the predicted variable from the dataset before passing the latter on to the algorithm, which is why we need to find the column index of the predicted variable (first line below). Also note that we set the method parameter to “class“, which simply tells the algorithm that the predicted variable is discrete. Finally, rpart uses Gini rule for splitting by default, and we’ll stick with this option.
The resulting plot is shown in Figure 3 below. It is quite self-explanatory so I won’t dwell on it here.
Figure 3: A classification tree for Ionosphere dataset
Next we see how good the model is by seeing how it fares against the test data.
| pred true | bad | good |
| bad | 17 | 2 |
| good | 9 | 43 |
Note that we need to verify the above results by doing multiple runs, each using different training and test sets. I will do this later, after discussing pruning.
Next, we prune the tree using the cost complexity criterion. Basically, the intent is to see if a shallower subtree can give us comparable results. If so, we’d be better of choosing the shallower tree because it reduces the likelihood of overfitting.
As described earlier, we choose the appropriate pruning parameter (aka cost-complexity parameter)
| CP | nsplit | rel error | xerror | xstd | |
| 1 | 0.57 | 0 | 1.00 | 1.00 | 0.080178 |
| 2 | 0.20 | 1 | 0.43 | 0.46 | 0.062002 |
| 3 | 0.02 | 2 | 0.23 | 0.26 | 0.048565 |
| 4 | 0.01 | 4 | 0.19 | 0.35 |
It is clear from the above, that the lowest cross-validation error (xerror in the table) occurs for 
Next, we prune the tree based on this value of CP:
Note that rpart will use a default CP value of 0.01 if you don’t specify one in prune.
The pruned tree is shown in Figure 4 below.
Figure 4: A pruned classification tree for Ionosphere dataset
Let’s see how this tree stacks up against the fully grown one shown in Fig 3.
This seems like an improvement over the unpruned tree, but one swallow does not a summer make. We need to check that this holds up for different training and test sets. This is easily done by creating multiple random partitions of the dataset and checking the efficacy of pruning for each. To do this efficiently, I’ll create a function that takes the training fraction, number of runs (partitions) and the name of the dataset as inputs and outputs the proportion of correct predictions for each run. It also optionally prunes the tree. Here’s the code:
Note that in the above, I have set the default value of the prune_tree to FALSE, so the function will execute the first branch of the if statement unless the default is overridden.
OK, so let’s do 50 runs with and without pruning, and check the mean and variance of the results for both sets of runs.
So we see that there is an improvement of about 3% with pruning. Also, if you were to plot the trees as we did earlier, you would see that this improvement is achieved with shallower trees. Again, I point out that this is not always the case. In fact, it often happens that pruning results in worse predictions, albeit with better reliability – a classic illustration of the bias-variance tradeoff.
Regression trees using rpart
In the previous section we saw how one can build decision trees for situations in which the predicted variable is discrete. Let’s now look at the case in which the predicted variable is continuous. We’ll use the Boston Housing dataset from the mlbench package. Much of the discussion of the earlier section applies here, so I’ll just display the code, explaining only the differences.
Next we invoke rpart, noting that the predicted variable is medv (median value of owner-occupied homes in $1000 units) and that we need to set the method parameter to “anova“. The latter tells rpart that the predicted variable is continuous (i.e that this is a regression problem).
The plot of the tree is shown in Figure 5 below.
Figure 5: A regression tree for Boston Housing dataset
Next, we need to see how good the predictions are. Since the dependent variable is continuous, we cannot compare the predictions directly against the test set. Instead, we calculate the root mean square (RMS) error. To do this, we request rpart to output the predictions as a vector – one prediction per record in the test dataset. The RMS error can then easily be calculated by comparing this vector with the medv column in the test dataset.
Here is the relevant code:
Again, we need to do multiple runs to check on the reliability of the predictions. However, you already know how to do that so I will leave it to you.
Moving on, we prune the tree using the cost complexity criterion as before. The code is exactly the same as in the classification problem.
The tree is unchanged so I won’t show it here. This means, as far as the cost complexity pruning is concerned, the optimal subtree is the same as the original tree. To confirm this, we’d need to do multiple runs as before – something that I’ve already left as as an exercise for you :). Basically, you’ll need to write a function analogous to the one above, that computes the root mean square error instead of the proportion of correct predictions.
Wrapping up
This brings us to the end of my introduction to classification and regression trees using R. Unlike some articles on the topic I have attempted to describe each of the steps in detail and provide at least some kind of a rationale for them. I hope you’ve found the description and code snippets useful.
I’ll end by reiterating a couple points I made early in this piece. The nice thing about decision trees is that they are easy to explain to the users of our predictions. This is primarily because they reflect the way we think about how decisions are made in real life – via a set of binary choices based on appropriate criteria. That said, in many practical situations decision trees turn out to be unstable: small changes in the dataset can lead to wildly different trees. It turns out that this limitation can be addressed by building a variety of trees using different starting points and then averaging over them. This is the domain of the so-called random forest algorithm.We’ll make the journey from decision trees to random forests in a future post.
Postscript, 20th September 2016: I finally got around to finishing my article on random forests.
A gentle introduction to network graphs using R and Gephi
Introduction
Graph theory is the an area of mathematics that analyses relationships between pairs of objects. Typically graphs consist of nodes (points representing objects) and edges (lines depicting relationships between objects). As one might imagine, graphs are extremely useful in visualizing relationships between objects. In this post, I provide a detailed introduction to network graphs using R, the premier open source tool statistics package for calculations and the excellent Gephi software for visualization.
The article is organised as follows: I begin by defining the problem and then spend some time developing the concepts used in constructing the graph Following this, I do the data preparation in R and then finally build the network graph using Gephi.
The problem
In an introductory article on cluster analysis, I provided an in-depth introduction to a couple of algorithms that can be used to categorise documents automatically. Although these techniques are useful, they do not provide a feel for the relationships between different documents in the collection of interest. In the present piece I show network graphs can be used to to visualise similarity-based relationships within a corpus.
Document similarity
There are many ways to quantify similarity between documents. A popular method is to use the notion of distance between documents. The basic idea is simple: documents that have many words in common are “closer” to each other than those that share fewer words. The problem with distance, however, is that it can be skewed by word count: documents that have an unusually high word count will show up as outliers even though they may be similar (in terms of words used) to other documents in the corpus. For this reason, we will use another related measure of similarity that does not suffer from this problem – more about this in a minute.
Representing documents mathematically
As I explained in my article on cluster analysis, a document can be represented as a point in a conceptual space that has dimensionality equal to the number of distinct words in the collection of documents. I revisit and build on that explanation below.
Say one has a simple document consisting of the words “five plus six”, one can represent it mathematically in a 3 dimensional space in which the individual words are represented by the three axis (See Figure 1). Here each word is a coordinate axis (or dimension). Now, if one connects the point representing the document (point A in the figure) to the origin of the word-space, one has a vector, which in this case is a directed line connecting the point in question to the origin. Specifically, the point A can be represented by the coordinates 
Figure 1
As another example consider document, B, which consists of only two words: “five plus” (see Fig 2). Clearly this document shares some similarity with document but it is not identical. Indeed, this becomes evident when we note that document (or point) B is simply the point $latex(1, 1, 0)$ in this space, which tells us that it has two coordinates (words/frequencies) in common with document (or point) A.
Figure 2
To be sure, in a realistic collection of documents we would have a large number of distinct words, so we’d have to work in a very high dimensional space. Nevertheless, the same principle holds: every document in the corpus can be represented as a vector consisting of a directed line from the origin to the point to which the document corresponds.
Cosine similarity
Now it is easy to see that two documents are identical if they correspond to the same point. In other words, if their vectors coincide. On the other hand, if they are completely dissimilar (no words in common), their vectors will be at right angles to each other. What we need, therefore, is a quantity that varies from 0 to 1 depending on whether two documents (vectors) are dissimilar(at right angles to each other) or similar (coincide, or are parallel to each other).
Now here’s the ultra-cool thing, from your high school maths class, you know there is a trigonometric ratio which has exactly this property – the cosine!
What’s even cooler is that the cosine of the angle between two vectors is simply the dot product of the two vectors, which is sum of the products of the individual elements of the vector, divided by the product of the lengths of the two vectors. In three dimensions this can be expressed mathematically as:
where the two vectors are 
The upshot of the above is that the cosine of the angle between the vector representation of two documents is a reasonable measure of similarity between them. This quantity, sometimes referred to as cosine similarity, is what we’ll take as our similarity measure in the rest of this article.
The adjacency matrix
If we have a collection of 
Since every document is identical to itself, the diagonal elements of the matrix will all be 1. These similarities are trivial (we know that every document is identical to itself!) so we’ll set the diagonal elements to zero.
Another important practical point is that visualizing every relationship is going to make a very messy graph. There would be 
Building the adjacency matrix using R
We now have enough background to get down to the main point of this article – visualizing relationships between documents.
The first step is to build the adjacency matrix. In order to do this, we have to build the document term matrix (DTM) for the collection of documents, a process which I have dealt with at length in my introductory pieces on text mining and topic modeling. In fact, the steps are actually identical to those detailed in the second piece. I will therefore avoid lengthy explanations here. However, I’ve listed all the code below with brief comments (for those who are interested in trying this out, the document corpus can be downloaded here and a pdf listing of the R code can be obtained here.)
OK, so here’s the code listing:
docs <- tm_map(docs, toSpace, “-“)
docs <- tm_map(docs, toSpace, “’”)
docs <- tm_map(docs, toSpace, “‘”)
docs <- tm_map(docs, toSpace, “•”)
docs <- tm_map(docs, toSpace, “””)
docs <- tm_map(docs, toSpace, ““”)
pattern = “organiz”, replacement = “organ”)
docs <- tm_map(docs, content_transformer(gsub),
pattern = “organis”, replacement = “organ”)
docs <- tm_map(docs, content_transformer(gsub),
pattern = “andgovern”, replacement = “govern”)
docs <- tm_map(docs, content_transformer(gsub),
pattern = “inenterpris”, replacement = “enterpris”)
docs <- tm_map(docs, content_transformer(gsub),
pattern = “team-“, replacement = “team”)
“also”,”howev”,”tell”,”will”,
“much”,”need”,”take”,”tend”,”even”,
“like”,”particular”,”rather”,”said”,
“get”,”well”,”make”,”ask”,”come”,”end”,
“first”,”two”,”help”,”often”,”may”,
“might”,”see”,”someth”,”thing”,”point”,
“post”,”look”,”right”,”now”,”think”,”‘ve “,
“‘re “,”anoth”,”put”,”set”,”new”,”good”,
“want”,”sure”,”kind”,”larg”,”yes,”,”day”,”etc”,
“quit”,”sinc”,”attempt”,”lack”,”seen”,”awar”,
“littl”,”ever”,”moreov”,”though”,”found”,”abl”,
“enough”,”far”,”earli”,”away”,”achiev”,”draw”,
“last”,”never”,”brief”,”bit”,”entir”,”brief”,
“great”,”lot”)
The rows of a DTM are document vectors akin to the vector representations of documents A and B discussed earlier. The DTM therefore contains all the information we need to calculate the cosine similarity between every pair of documents in the corpus (via equation 1). The R code below implements this, after taking care of a few preliminaries.
A few lines need a brief explanation:
First up, although the DTM is a matrix, it is internally stored in a special form suitable for sparse matrices. We therefore have to explicitly convert it into a proper matrix before using it to calculate similarity.
Second, the names I have given the documents are way too long to use as labels in the network diagram. I have therefore mapped the document names to the row numbers which we’ll use in our network graph later. The mapping back to the original document names is stored in filekey.csv. For future reference, the mapping is shown in Table 1 below.
| File number | Name |
| 1 | BeyondEntitiesAndRelationships.txt |
| 2 | bigdata.txt |
| 3 | ConditionsOverCauses.txt |
| 4 | EmergentDesignInEnterpriseIT.txt |
| 5 | FromInformationToKnowledge.txt |
| 6 | FromTheCoalface.txt |
| 7 | HeraclitusAndParmenides.txt |
| 8 | IroniesOfEnterpriseIT.txt |
| 9 | MakingSenseOfOrganizationalChange.txt |
| 10 | MakingSenseOfSensemaking.txt |
| 11 | ObjectivityAndTheEthicalDimensionOfDecisionMaking.txt |
| 12 | OnTheInherentAmbiguitiesOfManagingProjects.txt |
| 13 | OrganisationalSurprise.txt |
| 14 | ProfessionalsOrPoliticians.txt |
| 15 | RitualsInInformationSystemDesign.txt |
| 16 | RoutinesAndReality.txt |
| 17 | ScapegoatsAndSystems.txt |
| 18 | SherlockHolmesFailedProjects.txt |
| 19 | sherlockHolmesMgmtFetis.txt |
| 20 | SixHeresiesForBI.txt |
| 21 | SixHeresiesForEnterpriseArchitecture.txt |
| 22 | TheArchitectAndTheApparition.txt |
| 23 | TheCloudAndTheGrass.txt |
| 24 | TheConsultantsDilemma.txt |
| 25 | TheDangerWithin.txt |
| 26 | TheDilemmasOfEnterpriseIT.txt |
| 27 | TheEssenceOfEntrepreneurship.txt |
| 28 | ThreeTypesOfUncertainty.txt |
| 29 | TOGAFOrNotTOGAF.txt |
| 30 | UnderstandingFlexibility.txt |
Table 1: File mappings
Finally, the distance function (as.dist) in the cosine similarity function sets the diagonal elements to zero because the distance between a document and itself is zero…which is just a complicated way of saying that a document is identical to itself 🙂
The last three lines of code above simply implement the cutoff that I mentioned in the previous section. The comments explain the details so I need say no more about it.
…which finally brings us to Gephi.
Visualizing document similarity using Gephi
Gephi is an open source, Java based network analysis and visualisation tool. Before going any further, you may want to download and install it. While you’re at it you may also want to download this excellent quick start tutorial.
Go on, I’ll wait for you…
To begin with, there’s a little formatting quirk that we need to deal with. Gephi expects separators in csv files to be semicolons (;) . So, your first step is to open up the adjacency matrix that you created in the previous section (AdjacencyMatrix.csv) in a text editor and replace commas with semicolons.
Once you’ve done that, fire up Gephi, go to File > Open, navigate to where your Adjacency matrix is stored and load the file. If it loads successfully, you should see a feedback panel as shown in Figure 3. By default Gephi creates a directed graph (i.e one in which the edges have arrows pointing from one node to another). Change this to undirected and click OK.
Figure 3: Gephi import feedback
Once that is done, click on overview (top left of the screen). You should end up with something like Figure 4.
Figure 4: Initial overview after loading adjacency matrix
Gephi has sketched out an initial network diagram which depicts the relationships between documents…but it needs a bit of work to make it look nicer and more informative. The quickstart tutorial mentioned earlier describes various features that can be used to manipulate and prettify the graph. In the remainder of this section, I list some that I found useful. Gephi offers many more. Do explore, there’s much more than I can cover in an introductory post.
First some basics. You can:
- Zoom and pan using mouse wheel and right button.
- Adjust edge thicknesses using the slider next to text formatting options on bottom left of main panel.
- Re-center graph via the magnifying glass icon on left of display panel (just above size adjuster).
- Toggle node labels on/off by clicking on grey T symbol on bottom left panel.
Figure 5 shows the state of the diagram after labels have been added and edge thickness adjusted (note that your graph may vary in appearance).
Figure 5: graph with node labels and adjusted edge thicknesses
The default layout of the graph is ugly and hard to interpret. Let’s work on fixing it up. To do this, go over to the layout panel on the left. Experiment with different layouts to see what they do. After some messing around, I found the Fruchtermann-Reingold and Force Atlas options to be good for this graph. In the end I used Force Atlas with a Repulsion Strength of 2000 (up from the default of 200) and an Attraction Strength of 1 (down from the default of 10). I also adjusted the figure size and node label font size from the graph panel in the center. The result is shown in Figure 6.
Figure 6: Graph after using Force Atlas layout
This is much better. For example, it is now evident that document 9 is the most connected one (which table 9 tells us is a transcript of a conversation with Neil Preston on organisational change).
It would be nice if we could colour code edges/nodes and size nodes by their degree of connectivity. This can be done via the ranking panel above the layout area where you’ve just been working.
In the Nodes tab select Degree as the rank parameter (this is the degree of connectivity of the node) and hit apply. Select your preferred colours via the small icon just above the colour slider. Use the colour slider to adjust the degree of connectivity at which colour transitions occur.
Do the same for edges, selecting weight as the rank parameter(this is the degree of similarity between the two douments connected by the edge). With a bit of playing around, I got the graph shown in the screenshot below (Figure 7).
Figure 5: Connectivity-based colouring of edges and nodes.
If you want to see numerical values for the rankings, hit the results list icon on the bottom left of the ranking panel. You can see numerical ranking values for both nodes and edges as shown in Figures 8 and 9.
Figure 8: Node ranking (see left of figure)
Figure 9: Edge ranking
It is easy to see from the figure that documents 21 and 29 are the most similar in terms of cosine ranking. This makes sense, they are pieces in which I have ranted about the current state of enterprise architecture – the first article is about EA in general and the other about the TOGAF framework. If you have a quick skim through, you’ll see that they have a fair bit in common.
Finally, it would be nice if we could adjust node size to reflect the connectedness of the associated document. You can do this via the “gem” symbol on the top right of the ranking panel. Select appropriate min and max sizes (I chose defaults) and hit apply. The node size is now reflective of the connectivity of the node – i.e. the number of other documents to which it is cosine similar to varying degrees. The thickness of the edges reflect the degree of similarity. See Figure 10.
Figure 10: Node sizes reflecting connectedness
Now that looks good enough to export. To do this, hit the preview tab on main panel and make following adjustments to the default settings:
Under Node Labels:
1. Check Show Labels
2. Uncheck proportional size
3. Adjust font to required size
Under Edges:
1. Change thickness to 10
2. Check rescale weight
Hit refresh after making the above adjustments. You should get something like Fig 11.
Figure 11: Export preview
All that remains now is to do the deed: hit export SVG/PDF/PNG to export the diagram. My output is displayed in Figure 12. It clearly shows the relationships between the different documents (nodes) in the corpus. The nodes with the highest connectivity are indicated via node size and colour (purple for high, green for low) and strength of similarity is indicated by edge thickness.
Figure 12: Gephi network graph of document corpus
…which brings us to the end of this journey.
Wrapping up
The techniques of text analysis enable us to quantify relationships between documents. Document similarity is one such relationship. Numerical measures are good, but the comprehensibility of these can be further enhanced through meaningful visualisations. Indeed, although my stated objective in this article was to provide an introduction to creating network graphs using Gephi and R (which I hope I’ve succeeded in doing), a secondary aim was to show how document similarity can be quantified and visualised. I sincerely hope you’ve found the discussion interesting and useful.
Many thanks for reading! As always, your feedback would be greatly appreciated.
Eight to Late 