diff --git a/readme.md b/readme.md
index dea9fb32e8328974df97d0450af1b8f917e5a101..ddbef5203cb5e584a3d29963f645159daa405989 100644
--- a/readme.md
+++ b/readme.md
@@ -1,13 +1,14 @@
the ncd source repo
all work (c) andrew r. cohen and paul m. b. vitanyi
-andrew.r.cohen@drexel.edu
+
+contact: andrew.r.cohen@drexel.edu
unless otherwise specified, source license is GPL
refer to :
-A.R. Cohen and P.M.B. Vitányi, The Cluster Structure Function, in preparation.
+A.R. Cohen and P.M.B. Vitányi, The Cluster Structure Function, in review and arXiv ().
A.R. Cohen and P.M.B. Vitányi, Web Similarity in Sets of Search Terms Using Database Queries, SN Computer Science, 1, 161 (2020). https://doi.org/10.1007/s42979-020-00148-5. Also arXiv 1502.05957 (pdf).
@@ -16,3 +17,17 @@ A.R.Cohen and P.M.B. Vitányi, Normalized Compression Distance of Multisets with
A.R. Cohen, F. Gomes, B. Roysam, and M. Cayouette, Computational prediction of neural progenitor cell fates. Nature Methods, 2010. 7(3): p. 213 – 218.
A.R. Cohen, C. Bjornsson, S. Temple, G. Banker and B. Roysam, Automatic Summarization of Changes in Biological Image Sequences using Algorithmic Information Theory. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2009. 31(8): pp. 1386-1403.
+
+**usage tips**
+
+The NCD code includes both bzip and FLIF in-memory compression, and works on Windows and Linux OS. MacOS support pending.
+
+Key functions include:
+
+- src/MATLAB/ncdSample.m : demonstrates NCD with and without symbolization for numeric data
+- src/MATLAB/NCD/NCD.m : bzip NCD
+- src/MATLAB/NCD/imNCDM : FLIF multiset NCD for image data (tested with NIST digits dataset)
+- src/MATLAB/Cluster.SpectralCluster : Spectral clustering based on NCD distance matrix
+- src/MATLAB/NWD/NWD.m : uses pubmed or reddit (note: free api keys required for these two), or wikipedia to compute web distance
+
+
diff --git a/src/MATLAB/+Cluster/esym2d.m b/src/MATLAB/+Cluster/esym2d.m
index 07630b7824f361e52fbe49247867dd081d227cb3..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391 100644
--- a/src/MATLAB/+Cluster/esym2d.m
+++ b/src/MATLAB/+Cluster/esym2d.m
@@ -1,71 +0,0 @@
-%
-%
-% /******************************************************************************
-%
-% This program, "NCDM", the associated MATLAB scripts and all
-% provided data, are copyright (C) 2014 Andrew R. Cohen, All rights reserved.
-%
-% This program uses bzip2 compressor as a static library.
-% A built version for windows 64 is included. for other platforms, see
-% the files in the bzlib project on https://git-bioimage.coe.drexel.edu
-%
-% This software may be referenced as:
-%
-% A.R. Cohen, C. Bjornsson, S. Temple, G. Banker, and B. Roysam,
-% "Automatic Summarization of Changes in Biological Image Sequences
-% using Algorithmic Information Theory". IEEE Transactions on Pattern
-% Analysis and Machine Intelligence, 2009. 31(8): p. 1386-1403.
-%
-% Redistribution and use in source and binary forms, with or without
-% modification, are permitted provided that the following conditions
-% are met:
-%
-% 1. Redistributions of source code must retain the above copyright
-% notice, this list of conditions and the following disclaimer.
-%
-% 2. The origin of this software must not be misrepresented; you must
-% not claim that you wrote the original software. If you use this
-% software in a product, an acknowledgment in the product
-% documentation would be appreciated but is not required.
-%
-% 3. Altered source versions must be plainly marked as such, and must
-% not be misrepresented as being the original software.
-%
-% 4. The name of the author may not be used to endorse or promote
-% products derived from this software without specific prior written
-% permission.
-%
-% THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
-% OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-% WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
-% ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
-% DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-% DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
-% GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
-% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
-% WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
-% NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
-% SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-%
-% Andrew R. Cohen acohen@coe.drexel.edu
-% GapSpectral version 1.0 (release) November 2014
-%
-% ******************************************************************************/
-
-% this function is used for quantizing time sequence data
-function sData=esym2d(N,c2,mu,s1,Data)
-
-sData=[];
-
-for i=1:size(Data,1)
- rcv=Data(i,:);
- if isinf(rcv)
- sData{i,1}=char(10);
- else
- z=(rcv-mu)*s1*(rcv-mu)';
- zs=sum(z>c2,2);
- sData{i,1}=[char('a'+zs)];
- end
-end
-
-
diff --git a/src/MATLAB/+Cluster/symbolize.m b/src/MATLAB/+Cluster/symbolize.m
deleted file mode 100644
index 3b6fd5b75fbc24db7e05ffd9be019d2d88fa31dd..0000000000000000000000000000000000000000
--- a/src/MATLAB/+Cluster/symbolize.m
+++ /dev/null
@@ -1,17 +0,0 @@
-% quantize input matrix m to N symbols ('a'...'a'+N)
-function s=symbolize(m,N)
-
-if size(m,1)==1
- m=m';
-end
-
-s=[];
-mu=mean(m);
-sig=cov(m);
-s1=sig^-1;
-bps=[1/N:1/N:1-1/N];
-c2 = chi2inv(bps,size(m,2));
-for i= 1: size(m,1)
- iq=esym2d(N,c2,mu,s1,m(i,:));
- s=[s iq{:}];
-end
diff --git a/src/MATLAB/+NCD/symbolize.m b/src/MATLAB/+NCD/symbolize.m
new file mode 100644
index 0000000000000000000000000000000000000000..c328234a1ff1abbd162e1d78417945f786341bbf
--- /dev/null
+++ b/src/MATLAB/+NCD/symbolize.m
@@ -0,0 +1,35 @@
+% quantize input matrix m to N symbols ('a'...'a'+N)
+function s=symbolize(m,N)
+
+if size(m,1)==1
+ m=m';
+end
+
+s=[];
+mu=mean(m);
+sig=cov(m);
+s1=sig^-1;
+bps=[1/N:1/N:1-1/N];
+c2 = chi2inv(bps,size(m,2));
+for i= 1: size(m,1)
+ iq=esym2d(c2,mu,s1,m(i,:));
+ s=[s iq{:}];
+end
+
+function sData=esym2d(c2,mu,s1,Data)
+
+sData=[];
+
+for i=1:size(Data,1)
+ rcv=Data(i,:);
+ if isinf(rcv)
+ sData{i,1}=char(10);
+ else
+ z=(rcv-mu)*s1*(rcv-mu)';
+ zs=sum(z>c2,2);
+ sData{i,1}=[char('a'+zs)];
+ end
+end
+
+
+
diff --git a/src/MATLAB/ncdSample.m b/src/MATLAB/ncdSample.m
new file mode 100644
index 0000000000000000000000000000000000000000..f49af5275036bf41f1c062cf39f58bc7e65da5ed
--- /dev/null
+++ b/src/MATLAB/ncdSample.m
@@ -0,0 +1,26 @@
+% NCD sample scripts
+
+% NCD.NCD will use an in-memory version of bzip
+%
+% random vectors
+v1 = rand(1000,1);
+v2 = rand(1000,1);
+% less random vector
+v3 = v1 + 0.01*rand(1000,1);
+
+% NCD can work with numeric values, but compressor may struggle
+d1 = NCD.NCD(v1,v2);
+d2 = NCD.NCD(v1,v3);
+d3 = NCD.NCD(v2,v3);
+
+[d1, d2, d3]
+% symbolize the data for more precise numerical relations
+s1 = NCD.symbolize(v1,10);
+s2 = NCD.symbolize(v2,10);
+s3 = NCD.symbolize(v3,10);
+
+ds1 = NCD.NCD(s1,s2);
+ds2 = NCD.NCD(s1,s3);
+ds3 = NCD.NCD(s2,s3);
+
+[ds1, ds2, ds3]