From 8d0d64a09411f7e29b0da679fe1bd65c9b7e1e4d Mon Sep 17 00:00:00 2001
From: g-pica <giuseppe.pica@iit.it>
Date: Mon, 27 Nov 2017 00:23:50 +0100
Subject: [PATCH] Extend documentation to intersection information

---
 README.md | 23 ++++++++++++++++++++---
 1 file changed, 20 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index 9dcb0d6..8babf46 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,27 @@
-# SubPID - Subatomic Partial Information Decomposition
+# Intersection information and SubPID (Subatomic Partial Information Decomposition)
 
 [![DOI](https://zenodo.org/badge/61385385.svg)](https://zenodo.org/badge/latestdoi/61385385)
 
-This package is composed by two parts:
+This package is composed by four parts:
 
 - A MATLAB implementation of the partial information decomposition
   (PID) for distributions over three random variables using the
   definitions from Bertschinger, N., Rauh, J., Olbrich, E., Jost, J.,
   and Ay, N. *Quantifying unique information.*. Entropy 2014,
   16(4):2161–2183.
+- Two MATLAB implementations of the intersection information I_{II}(S;R;C)
+  that, in perceptual discrimination experiments, quantifies the sensory 
+  information in the recorded neural response R that is relevant to behavior.
+  This measure is defined and described in Pica, G., Piasini, E., Safaai, H., 
+  Runyan, C.A., Diamond, M.E., Fellin, T., Kayser, C., Harvey, C.D., Panzeri, S.,
+  *Quantifying how much sensory information in a neural code is 
+  relevant for behavior*, Advances in neural information processing 2017, 3687-3697.
+  The first implementation, "src/matlab/intersection information.m", evaluates 
+  I_{II}(S;R;C) starting from the empirical joint probability distribution p(s,r,c).
+  The second implementation, "src/matlab/intersection information_from_binned_response.m", 
+  evaluates I_{II}(S;R;C) starting from vectors containing the stimulus s, the response r, 
+  and the choice c, corresponding to each trial. Here, the response is discretized into equipopulated
+  bins for a conservative estimate of I_{II}(S;R;C).
 - A MATLAB numerical implementation of the subatomic partial
   information decomposition proposed in Pica, G., Piasini, E.,
   Chicharro, D., and Panzeri, S. *Invariant Components of Synergy,
@@ -18,11 +31,15 @@ This package is composed by two parts:
 
 ## Requirements
 
-`SubPID` requires [glpkmex](https://github.com/blegat/glpkmex) to be
+`Intersection information and SubPID` requires [glpkmex](https://github.com/blegat/glpkmex) to be
 installed on your system.
 
 ## Usage
 
+The intersection information can be estimated from raw response data
+with "src/matlab/intersection information_from_binned_response.m", 
+while the more general "src/matlab/intersection information.m" should 
+be used if the user has already estimated p(s,r,c) from the experimental dataset.
 The PID and the subatomic PID are implemented by `src/matlab/pid.m`
 and `src/matlab/subatomic_pid.m`, respectively. See the function
 descriptions for details.