From 6a2211563872d6e7b1718b77c2e005194efcabe4 Mon Sep 17 00:00:00 2001
From: Tenzin Chan <tenzin_chan@mymail.sutd.edu.sg>
Date: Wed, 15 May 2024 11:11:32 -0700
Subject: [PATCH] Updated README

---
 README.md | 46 +++++++++++++++++++++++++++++++---------------
 1 file changed, 31 insertions(+), 15 deletions(-)

diff --git a/README.md b/README.md
index f9e09b6..ed58892 100644
--- a/README.md
+++ b/README.md
@@ -1,15 +1,6 @@
 # NeuralMaxEnt
 
-## Data
-I have used this data for initial analysis [pvc3 data](https://crcns.org/data-sets/vc/pvc-3/about)
-
-## Experiments and analysis
-To run experiments on the above dataset, run the `blanch_expt.jl` file with the following command:
-```julia blanche_expt.jl <binsz> <maxiter> <numsplt> <dev> <batchsize>```
-
-For these experiments, `binsz` ranged from 500 to 5000 (in microseconds), `maxiter` was set to 100, `numsplit` was set to 10, `dev` is just the device ID for different runs and `batchsize` was set to 10000.
-
-
+## DrWatson install instructions
 This code base is using the [Julia Language](https://julialang.org/) and
 [DrWatson](https://juliadynamics.github.io/DrWatson.jl/stable/)
 to make a reproducible scientific project named
@@ -30,10 +21,35 @@ To (locally) reproduce this project, do the following:
 This will install all necessary packages for you to be able to run the scripts and
 everything should work out of the box, including correctly finding local paths.
 
-You may notice that most scripts start with the commands:
-```julia
-using DrWatson
-@quickactivate "NeuralMaxEnt"
+## Estimating entropy with CDM in octave
+First install [octave](https://octave.org/download).
+Then, start octave and innstall `statistics`, `struct` and `parallel` with
 ```
-which auto-activate the project and enable local path handling from DrWatson.
+pkg install -forge statistics
+pkg install -forge struct
+pkg install -forge parallel
+```
+
+## Data
+I have used these two datasets for my experiments: [pvc3](https://crcns.org/data-sets/vc/pvc-3/about)
+and [this one from Lamberti](https://datadryad.org/stash/dataset/doi:10.5061/dryad.p5hqbzkqj).
+
+## Experiments and analysis
+To run experiments on the above datasets, place their files into a `data/exp_raw` directory and
+run the `blanch_expt.jl` file with the following command:
+```julia blanche_expt.jl <binsz> <maxiter> <numsplit> <dev> <batchsize>```
+
+### Heatmaps
+For these experiments, `binsz` ranged from 500 to 6000 (in microseconds), `maxiter` was set to 100,
+`numsplit` was set to 1, `dev` is the device ID and `batchsize` was set to 10000.
+If GPU runs out of memory, please lower the `batchsize` variable or use smaller window sizes.
+
+### Entropy vs window size
+We chose a fixed `binsz` and varied `winsz` from 1 to some large value (typically up to
+a timescale that we're interested in based on the chosen bin size).
+
+## Citations
+Blanche, Tim (2009): Multi-neuron recordings in primary visual cortex. CRCNS.org.
+http://dx.doi.org/10.6080/K0MW2F2J
+Lamberti, M., Hess, M., Dias, I. et al. Maximum entropy models provide functional connectivity estimates in neural networks. Sci Rep 12, 9656 (2022). https://doi.org/10.1038/s41598-022-13674-4