I have a large sparse matrix which represents whether the action is happened or not. Each columns represent each action. Each row represents time. The data is collected for every 15min. Zero in the matrix represents the action doesn't happen or any number represents the action has happened that many times. I want to find how each action is dependent on another action

Now I have to find patterns in the happening of actions(say, where ever action-2 and action-4 occurs action-5 will more likely to occur)

Is there any algorithms available to solve this? How to approach this kinda problem using R? any packages available in R?


I would suggest you to model your problem as a graph. You could convert your nxm matrix (n actions over m time points) into a nxn similarity matrix for every pairwise linear correlation between the vector time-series representing your actions. When the time-series of two actions are highly correlated it means that these actions are highly synchronised, which I think is what you want.

Such similarity/correlation matrix can be easily constructed in R using:

Y = cor(X, method="pearson")

where X is your original matrix. At this point you have a similarity/correlation matrix which you can visualise as a heatmap in order to see how your actions correlate. You can further convert this correlation matrix Y into an adjacency/sparse matrix by setting a threshold value below which all slots in the matrix will take zero values:

Z = Y[Y>=0.8]

I used a random threshold value of 0.8 but you should set that value empirically by "spying" your matrix at different thresholds (see here how to do that in R). Z is now a binary adjacency/sparse matrix representing an unweighted undirected graph. A connection between two nodes in that graph implies the presence of a high co-expression between two actions. You could alternatively create a weighted graph by explicitly setting all values below your threshold to zero while keeping the values above your threshold to their original correlation values instead of converting to 1:

Z = Y

Z[Z<0.8] = 0

By now you have a graph where:

  • Every node represents an action
  • Every undirected edge (connection) between nodes i and j indicates that action i is synchronous/correlated/co-expressed with action j. This connection may or may not have a weight (that's up to you).

Once you have that setup you can basically perform any graph-related algorithm to gain insights on your data, e.g.:

  • manually isolate every node along with all its parent nodes (adjacent nodes pointing to that node). That would allow you to make up a set of rules based a node's number of parents and their corresponding weights.

  • Find all possible paths between every pair of nodes {i,j} and evaluate their lengths by adding up all weights composing them. That would give you a metric of strength of transition (or causality) between all actions (nodes) in your graph.

  • model your graph as a Bayesian network. That would require to normalise and convert your weights into transition probabilities between states (actions) and would offer you a probabilistic inferential graphical model of your data.

  • Use graph metrics (degree centrality, betweeness, etc.) along with graph clustering algorithms (e.g. community structure partition) in order to detect important actions and groups of actions.

For your generic network-graph theoretical needs as well as solution 1 and/or solution 2, I would recommend packages igraph, rgraphviz, or networkd3. For Bayesian networks I would suggest gRain.

I hope that helps.

  • $\begingroup$ Thanks! But my matrix is not square. It is 2lakh x 60 dimension. How can I interpret this as a graph? $\endgroup$ – Kavipriya Jul 28 '15 at 5:19
  • $\begingroup$ If it's not square then what do you have on the columns? How would you say that an action affects another action if it's not square? $\endgroup$ – Digio Jul 28 '15 at 5:26
  • $\begingroup$ Each columns represent each action. Each row represents time. The data is collected for every 15min. I want to find how each action is dependent on another action. $\endgroup$ – Kavipriya Jul 28 '15 at 5:48
  • $\begingroup$ Well that was important missing information. I'll need to update my answer, and by update I mean completely rewrite. $\endgroup$ – Digio Jul 28 '15 at 5:53
  • $\begingroup$ I updated my question itself. Sorry for that. It will be nice if you help. Thanks! $\endgroup$ – Kavipriya Jul 28 '15 at 6:45

Association Rule learning method is used for discovering interesting relations from large databases. Apriori and eclat algorithms are available.

"arules" package from R, has all association rules related functions.

  • 1
    $\begingroup$ The link doesn't work--and even if it can be made to, it's important that answers stand on their own without requiring readers to visit another site to understand them. Could you please explain what this method is and how it would be applied in this particular circumstance? Without such an explanation, this answer would appear to be of little direct use or interest. $\endgroup$ – whuber Sep 8 '15 at 18:39

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.