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Commit 17258d6c authored by Andrew Cohen's avatar Andrew Cohen
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removed spare parts

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spareParts/GapSpectral.m deleted 100644 → 0
+ 0
− 65
View file @ 0bf58d85
function [kGap Gap S idx] = GapSpectral(DistanceMatrix,nMaxClusters,bAlgorithmicInformationDistance)
if nargin<3
bAlgorithmicInformationDistance=1;
end
B = 50; % size of Monte Carlo distribution
if nMaxClusters>size(DistanceMatrix,1)
nMaxClusters = size(DistanceMatrix,1)-1;
end
D = Regularize(DistanceMatrix);
bound=D;
for i=1: size(bound,1)
bound(i,i)=NaN;
end
a = min(min(bound));%;
b = max(max(bound));
UV = a + (b-a)*rand(size (D,1),size (D,2),B); % uniform distribution
for k=1:nMaxClusters
if (1==k) %
% one happy cluster
idx = ones(size (D,1),1);
else
idx = SpectralCluster(D,k);
end
W(k)=WkSpectral(k,idx,D);
for ib =1:B
uni = UV(:,:,ib);
uni = Regularize(uni); % make uni a valid distance matrix
if (1==k) %
% one happy cluster
idx = ones(size (D,1),1);
else
idx = SpectralCluster(uni,k);
end
Wb(ib,k)=WkSpectral(k,idx,uni);;
end
Wkb = Wb(:,k);
lkb = log(Wkb);
if bAlgorithmicInformationDistance
Gap(k) = 1/B*sum(Wkb) - W(k);
sdk = std(Wkb,1);
else
Gap(k) = 1/B*sum(lkb) - log(W(k));
sdk = std(lkb,1);
end
S(k)=sdk * sqrt(1+1/B);
% Gap
% S
end
% figure
% errorbar( [1:nMaxClusters],Gap,S)
% set(gca,'XTick',[1:nMaxClusters])
k=1;
while ((k<nMaxClusters) && (Gap(k) < Gap(k+1)-S(k+1)))
k=k+1;
end
kGap=k;
if (kGap>1)
idx = SpectralCluster(D,kGap);
else
idx = ones(size (D,1),1);
end
spareParts/GetCount.m deleted 100644 → 0
+ 0
− 58
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function f = GetCount(words,strServer)
if ~exist('strServer','var')
strServer='wikipedia'
end
term=[ words{1} ];
for i=2:length(words)
term=[ term '+' words{i}];
end
idx=strfind(term,' ');
term(idx)='+';
if strcmp(strServer,'pubmed')
f=Count.pubmed(term);
elseif strcmp(strServer,'amazon')
f=doQueryAmazon(term);
elseif strcmp(strServer,'google')
f=GetCountGoogle(term);
elseif strcmp(strServer,'reddit')
f=Count.reddit(term);
else
f=Count.wikipedia(term);
end
% f=max(f,1); % no zero counts - sends nwd to NaN
f=f+1;
end
% amazon no longer returning search totals as of 1/2019...
% function f=doQueryAmazon(term)
%
% URL=['http://www.amazon.com/s/ref=nb_sb_noss?url=search-alias%3Daps&field-keywords=' term '&rh=i%3Aaps%2Ck%3A' term];
% for i=1:5
%
% str = urlread(URL);
% try
% %amazon
% idx=strfind(str,'results for <span>');
% idx=idx(1)-2;
% idxStart=idx;
% chPrev = str(idxStart-1);
% while(isNumeric(chPrev))
% idxStart=idxStart-1;
% chPrev = str(idxStart-1);
% end
% nx=str(idxStart:idx);
% f=str2double(nx);
% break;
% catch
% f=0;
% pause(1);
% end
% end
%
% end
spareParts/GetSynthesizedCount.m deleted 100644 → 0
+ 0
− 19
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function fX=GetSynthesizedCount(words)
k=length(words);
fX=0;
for i=1:2^k-1
binary=decimalToBinaryVector(i,k,'LSBFirst');
idx=find(binary);
if 0==mod(length(idx),2)
bAdd=-1;
% fprintf('-');
else
bAdd=1;
% fprintf('+')
end
% fprintf('%s',mat2str(idx));
fX=fX+bAdd*GetCount(words(idx),0);
end
% fprintf('\n');
spareParts/Regularize.m deleted 100644 → 0
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− 26
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function [D,degenerate] = Regularize(DistanceMatrix)
% turn output from NCD into well behaved distance matrix
D=DistanceMatrix;
% b = max(max(D));
% D=D/b;
for i=1:size (D,1)
for j= 1:i-1
D(i,j)= D(j,i);
end
D(i,i)=0;
end
bound=D;
for i=1: size(bound,1)
bound(i,i)=NaN;
end
a = min(min(bound));
if 0==a
degenerate=1;
else
degenerate=0;
end
spareParts/WkSpectral.m deleted 100644 → 0
+ 0
− 17
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function w=WkSpectral(k,idx,DistanceMatrix)
% called by GapSpectral
for r =1:k
% find points in cluster r
pr = find(idx==r);
D(r) = 0;
for i=1:size(pr,1)
for j=i:size(pr,1)
D(r) = D(r)+DistanceMatrix(pr(i),pr(j));
end
end
D(r) = D(r)/(2*size(pr,1)); %(2) in paper
end
w = sum(D);
spareParts/goAmazon.m deleted 100644 → 0
+ 0
− 40
View file @ 0bf58d85
tic
% goNWD
%
%
global strServer
strServer='amazon'
global QueryCache
if isempty(QueryCache)
QueryCache.Queries={};
QueryCache.Count=[];
end
global nQueryCount nCacheCount
nQueryCount=0;
nCacheCount=0;
words1={'Macbeth','The Tempest','Othello','King Lear','Hamlet'...
'The Merchant of Venice','A Midsummer Nights Dream',...
'Much Ado About Nothing', 'Taming of the Shrew','Twelfth Night' }
words2={'Carrie','Salems Lot','The Shining','The Stand','The Dead Zone',...
'Firestarter','Cujo'}
words3={'Adventures of Huckleberry Finn','A Connecticut Yankee in King Arthurs Court','Life on the Mississippi'...
'Puddnhead Wilson'}
words4 = {'The Old Man and The Sea','The Sun Also Rises','For Whom the Bell Tolls','A Farewell To Arms'}
words5={'Anna Karenina','War and Peace','The Death of Ivan Ilyich'}
idxKey = [ones(1,length(words1)) 2*ones(1,length(words2)) 3*ones(1,length(words3)) 4*ones(1,length(words4)) 5*ones(1,length(words5))]
GetCount(words1)
GetCount(words2)
%
[d]=GetDistances([words1,words2,words3,words4,words5],idxKey);
idx=getDistancesPairs([words1,words2,words3,words4,words5],idxKey);
spareParts/goNWD.m deleted 100644 → 0
+ 0
− 32
View file @ 0bf58d85
tic
% goNWD
%
%
strServer='wikipedia'
words1={'red','orange','yellow','green','blue','indigo'}
words2={'lion','tiger','bear','monkey','zebra','elephant','aardvark','lamb','fox','ape','dog'}
idxKey = [ones(1,length(words1)) 2*ones(1,length(words2))]
d=GetDistances([words1,words2],idxKey);
idx=getDistancesPairs([words1,words2],idxKey);
words1={'red','orange','yellow','green','blue','indigo','violet','purple','cyan','white'}
words2={'square','circle','rectangle','ellipse','triangle','rhombus'}
idxKey = [ones(1,length(words1)) 2*ones(1,length(words2))]
d=GetDistances([words1,words2],idxKey);
idx=getDistancesPairs([words1,words2],idxKey);
words1={'Barack Obama','Hillary Clinton','John Edwards','Joe Biden','Chris Dodd','Mike Gravel'}
words2={'John McCain','Mitt Romney','Mike Huckabee','Ron Paul','Fred Thompson','Alan Keyes'}
idxKey = [ones(1,length(words1)) 2*ones(1,length(words2))]
d=GetDistances([words1,words2],idxKey);
idx=getDistancesPairs([words1,words2],idxKey);
%
% words1={'Labidochromis caeruleus','Sciaenochromis fryeri','Betta splendens','Carassius auratus','Melanochromis cyaneorhabdos'}
% words2={'Ecsenius bicolor','Pictichromis paccagnellae','Amphiprion ocellaris ','Paracanthurus hepatus','Chromis viridis'}
% [d1,d2]=GetDistances(words1,words2);
% idx=getDistancesPairs(words1,words2);
toc
spareParts/goPubMed.m deleted 100644 → 0
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− 71
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global strServer
strServer='pubmed'
%http://www.nature.com/nature/journal/v511/n7510/full/nature13595.html
% supp table 2, in ranked order
shizophrenia = {'rs1702294','rs11191419','rs2007044','rs4129585',...
'rs35518360'};
% http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3250464/
% table 1
leukemia = {'rs17483466','rs13397985','rs757978','rs2456449','rs735665',...
'rs783540','rs305061','rs391525','rs1036935','rs11083846'};
%alzheimers
% http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3365264/
% table 1
% http://www.nature.com/tp/journal/v2/n5/fig_tab/tp201245t1.html#figure-title
alzheimers={'rs4420638','rs7561528','rs17817600','rs3748140','rs12808148','rs6856768','rs11738335','rs1357692'};
% obesity
% http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2858696/
% table 1
obesity={'rs10926984','rs12145833','rs2783963','rs11127485','rs17150703','rs13278851'};
%
% % neuroblastoma
% % http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3716226/
% % table 3
% neuroblastoma={'rs6939340','rs4712653','rs6435862','rs3768716','rs7585356'};
% neuroblastoma 2
% http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2742373/table/T1/
neuroblastoma = {'rs6939340','rs4712653','rs9295536','rs3790171','rs7272481'};
% parkinsons
% http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3305333/
% table 2, rs entries, by pvalue
% now trying http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852568/table/tbl03/
% p<.1% in 2/3
% parkinsons={'rs356219','rs10847864','rs1491942','rs947211','rs2390669'}
parkinsons={'rs356219','rs10847864','rs2942168','rs11724635'}
% http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839234/
% http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3839234/table/T1/
als = {'rs2303565','rs1344642','rs2814707','rs3849942','rs2453556', 'rs1971791', 'rs8056742'};
words={ alzheimers;parkinsons;als;shizophrenia;leukemia;obesity;neuroblastoma}
global QueryCache
if isempty(QueryCache)
QueryCache.Queries={};
QueryCache.Count=[];
end
global nQueryCount nCacheCount
nQueryCount=0;
nCacheCount=0;
d=[];
for i=1:length(words)
for j=1:length(words)
d(i,j)=NWD( [words{i},words{j}]);
end
end
dx=[];
for i=1:length(words)
for j=1:length(words)
dx(i,j)=d(i,j)-d(i,i);
end
end
xlswrite('rr.xls',[d dx])
spareParts/goTypical.m deleted 100644 → 0
+ 0
− 28
View file @ 0bf58d85
path(path,'..\Gap')
% goTypical
global QueryCache
if isempty(QueryCache)
QueryCache.Queries={};
QueryCache.Count=[];
end
global nQueryCount nCacheCount
nQueryCount=0;
nCacheCount=0;
% words1={'red','orange','yellow','green','blue','vermilion','chartreuse'}
% words1={'red','orange','yellow','green','blue','indigo','violet'}
words1={'red','orange','yellow','green','blue'}
% words1={'red','orange','yellow','green','blue','indigo','texas'}
dx=NWD(words1)
d=[];
for i=1:length(words1)
wordsX=words1;
wordsX(i)=[];
d(i)=NWD(wordsX);
end
warning off all
d=dx-d';
[K Gap S idx] = GapKM(d,length(words1)-1);
spareParts/goWikiFamous.m deleted 100644 → 0
+ 0
− 23
View file @ 0bf58d85
tic
global QueryCache
if isempty(QueryCache)
QueryCache.Queries={};
QueryCache.Count=[];
end
global nQueryCount nCacheCount
nQueryCount=0;
nCacheCount=0;
nobels2014={'Isamu Akasaki', 'Hiroshi Amano', 'Shuji Nakamura','Eric Betzig', 'Stefan W. Hell', 'William E. Moerner','John O''Keefe', 'May-Britt Moser', 'Edvard I. Moser' }
physics={'Albert Einstein','Isaac Newton','Stephen Hawking','Nils Bohr','James Maxwell'}
chemistry={'Amedeo Avogadro','Louis Pasteur','Linus Pauling','Robert Boyle'}
medicine={'Elizabeth Blackwell','William Harvey','Carl Jung','Richard Lister'}
idxKey = [ones(1,length(nobels2014)) 2*ones(1,length(physics)) 2*ones(1,length(chemistry))...
2*ones(1,length(medicine))]
[d]=GetDistances([nobels2014,physics,chemistry,medicine],idxKey);
idx=getDistancesPairs([nobels2014,physics,chemistry,medicine],idxKey)
spareParts/goWikiScientists.m deleted 100644 → 0
+ 0
− 28
View file @ 0bf58d85
tic
global QueryCache
if isempty(QueryCache)
QueryCache.Queries={};
QueryCache.Count=[];
end
global nQueryCount nCacheCount
nQueryCount=0;
nCacheCount=0;
words1={'Kolmogorov','Fermat','Hilbert', 'Godel', 'Riemann','Gauss'} % mathematicians
words2={'Einstein','Newton','Hawking','Bohr','Maxwell','Boltzmann',} %physicists
words3={'Freud','Pavlov','Skinner','Jung'} %psychologists
words4={'Turing','Lovelace','Knuth','Hopper'} % computer scientists
words5={'Darwin','Lamarck','Linnaeus','Mendel'} % biology
idxKey = [ones(1,length(words1)) 2*ones(1,length(words2)) 3*ones(1,length(words3)) 4*ones(1,length(words4)) 5*ones(1,length(words5))]
[d]=GetDistances([words1,words2,words3,words4,words5],idxKey);
idx=getDistancesPairs([words1,words2,words3,words4,words5],idxKey);
spareParts/pubmed gwas results.pdf deleted 100644 → 0
+ 0
− 0
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File deleted
spareParts/pubmed gwas results.xlsx deleted 100644 → 0
+ 0
− 0
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File deleted
spareParts/results.txt.orig deleted 100644 → 0
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− 546
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-------------------------
GetDistances::(multiples) NW=5
2014 5 1 16 51 5.961
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,nQueryCount=49, nCacheCount=335
[6 0;0 6]
-------------------------
GetDistances::(pairs)
2014 5 1 16 51 57.306
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,kGap=2
nQueryCount=66, nCacheCount=198
nCorrect=11
-------------------------
GetDistances::(multiples) NW=5
2014 5 1 16 52 14.308
red,orange,yellow,green,blue,indigo,square,circle,rectangle,ellipse,triangle,rhombus,nQueryCount=30, nCacheCount=354
[6 0;0 6]
-------------------------
GetDistances::(pairs)
2014 5 1 16 52 53.707
red,orange,yellow,green,blue,indigo,square,circle,rectangle,ellipse,triangle,rhombus,kGap=2
nQueryCount=51, nCacheCount=213
nCorrect=12
-------------------------
GetDistances::(multiples) NW=5
2014 5 1 16 53 30.481
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,nQueryCount=48, nCacheCount=336
[6 0;0 6]
-------------------------
GetDistances::(pairs)
2014 5 1 16 54 30.869
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,kGap=2
nQueryCount=66, nCacheCount=198
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 5 1 16 54 55.778
Labidochromis caeruleus,Sciaenochromis fryeri,Betta splendens,Carassius auratus,Melanochromis cyaneorhabdos,Ecsenius bicolor,Pictichromis paccagnellae,Amphiprion ocellaris ,Paracanthurus hepatus,Chromis viridis,nQueryCount=40, nCacheCount=240
[0 5;0 5]
-------------------------
GetDistances::(multiples) NW=5
2014 5 26 17 48 59.115
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,nQueryCount=49, nCacheCount=335
[6 0;0 6]
-------------------------
GetDistances::(pairs)
2014 5 26 17 49 47.104
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,kGap=2
nQueryCount=66, nCacheCount=198
nCorrect=11
-------------------------
GetDistances::(multiples) NW=5
2014 5 26 17 50 3.128
red,orange,yellow,green,blue,indigo,square,circle,rectangle,ellipse,triangle,rhombus,nQueryCount=30, nCacheCount=354
[6 0;0 6]
-------------------------
GetDistances::(pairs)
2014 5 26 17 50 38.946
red,orange,yellow,green,blue,indigo,square,circle,rectangle,ellipse,triangle,rhombus,kGap=2
nQueryCount=51, nCacheCount=213
nCorrect=12
-------------------------
GetDistances::(multiples) NW=5
2014 5 26 17 51 15.729
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,nQueryCount=48, nCacheCount=336
[6 0;0 6]
-------------------------
GetDistances::(pairs)
2014 5 26 17 52 16.695
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,kGap=2
nQueryCount=66, nCacheCount=198
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 5 26 17 52 38.784
Labidochromis caeruleus,Sciaenochromis fryeri,Betta splendens,Carassius auratus,Melanochromis cyaneorhabdos,Ecsenius bicolor,Pictichromis paccagnellae,Amphiprion ocellaris ,Paracanthurus hepatus,Chromis viridis,nQueryCount=40, nCacheCount=240
[0 5;0 5]
-------------------------
GetDistances::(multiples) NW=5
2014 5 26 18 9 46.311
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,nQueryCount=150, nCacheCount=474
[0 6;6 0]
-------------------------
GetDistances::(pairs)
2014 5 26 18 9 48.012
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,kGap=4
nQueryCount=0, nCacheCount=330
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 5 26 18 10 50.192
red,orange,yellow,green,blue,indigo,square,circle,rectangle,ellipse,triangle,rhombus,nQueryCount=111, nCacheCount=513
[0 6;4 2]
-------------------------
GetDistances::(pairs)
2014 5 26 18 10 51.87
red,orange,yellow,green,blue,indigo,square,circle,rectangle,ellipse,triangle,rhombus,kGap=3
nQueryCount=0, nCacheCount=330
nCorrect=6
-------------------------
GetDistances::(multiples) NW=5
2014 5 26 18 12 44.564
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,nQueryCount=150, nCacheCount=474
[1 5;6 0]
-------------------------
GetDistances::(pairs)
2014 5 26 18 12 46.22
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,kGap=2
nQueryCount=0, nCacheCount=330
nCorrect=8
-------------------------
GetDistances::(multiples) NW=5
2014 5 26 18 13 46.902
Labidochromis caeruleus,Sciaenochromis fryeri,Betta splendens,Carassius auratus,Melanochromis cyaneorhabdos,Ecsenius bicolor,Pictichromis paccagnellae,Amphiprion ocellaris ,Paracanthurus hepatus,Chromis viridis,nQueryCount=100, nCacheCount=340
[0 5;0 5]
-------------------------
GetDistances::(pairs)
2014 5 26 18 13 48.428
Labidochromis caeruleus,Sciaenochromis fryeri,Betta splendens,Carassius auratus,Melanochromis cyaneorhabdos,Ecsenius bicolor,Pictichromis paccagnellae,Amphiprion ocellaris ,Paracanthurus hepatus,Chromis viridis,kGap=3
nQueryCount=0, nCacheCount=225
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 5 27 11 29 56.627
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,nQueryCount=0, nCacheCount=672
[6 0;3 3]
-------------------------
GetDistances::(pairs)
2014 5 27 11 29 58.3
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,kGap=1
nQueryCount=0, nCacheCount=396
nCorrect=10
-------------------------
GetDistances::(multiples) NW=5
2014 5 27 11 29 58.339
red,orange,yellow,green,blue,indigo,square,circle,rectangle,ellipse,triangle,rhombus,nQueryCount=0, nCacheCount=672
[6 0;2 4]
-------------------------
GetDistances::(pairs)
2014 5 27 11 30 0.027
red,orange,yellow,green,blue,indigo,square,circle,rectangle,ellipse,triangle,rhombus,kGap=2
nQueryCount=0, nCacheCount=396
nCorrect=9
-------------------------
GetDistances::(multiples) NW=5
2014 5 27 11 30 0.066
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,nQueryCount=0, nCacheCount=672
[6 0;0 6]
-------------------------
GetDistances::(pairs)
2014 5 27 11 30 1.765
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,kGap=2
nQueryCount=0, nCacheCount=396
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 5 27 11 30 1.794
Labidochromis caeruleus,Sciaenochromis fryeri,Betta splendens,Carassius auratus,Melanochromis cyaneorhabdos,Ecsenius bicolor,Pictichromis paccagnellae,Amphiprion ocellaris ,Paracanthurus hepatus,Chromis viridis,nQueryCount=0, nCacheCount=480
[0 5;0 5]
-------------------------
GetDistances::(multiples) NW=5
2014 7 2 12 52 27.35
WHSC1,NSD1,ASH1l,SETD2,MLL5,CREBBP,EP300,MLL,PHIP(2),BRWD3(2),nQueryCount=141, nCacheCount=339
[0 5;0 5]
-------------------------
GetDistances::(multiples) NW=5
2014 7 2 13 3 7.572
WHSC1,NSD1,ASH1l,SETD2,MLL5,CREBBP,EP300,MLL,PHIP(2),BRWD3(2),nQueryCount=130, nCacheCount=350
[2 3;0 5]
-------------------------
GetDistances::(pairs)
2014 7 2 13 3 23.862
WHSC1,NSD1,ASH1l,SETD2,MLL5,CREBBP,EP300,MLL,PHIP(2),BRWD3(2),kGap=1
nQueryCount=45, nCacheCount=225
nCorrect=9
-------------------------
GetDistances::(multiples) NW=5
2014 7 2 13 9 10.186
ELP3,KAT2B,MYST4,KAT5,HAT1,CREBBP,EP300,MLL,PHIP(2),BRWD3(2),nQueryCount=100, nCacheCount=380
[4 1;2 3]
-------------------------
GetDistances::(pairs)
2014 7 2 13 9 24.264
ELP3,KAT2B,MYST4,KAT5,HAT1,CREBBP,EP300,MLL,PHIP(2),BRWD3(2),kGap=1
nQueryCount=35, nCacheCount=235
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 7 2 15 0 45.002
ELP3,KAT2B,MYST4,KAT5,HAT1,CREBBP,EP300,MLL,PHIP,BRWD3,nQueryCount=141, nCacheCount=339
[3 2;2 3]
-------------------------
GetDistances::(pairs)
2014 7 2 15 1 0.536
ELP3,KAT2B,MYST4,KAT5,HAT1,CREBBP,EP300,MLL,PHIP,BRWD3,kGap=1
nQueryCount=45, nCacheCount=225
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 7 2 15 4 42.089
PPRV,CDV,RPV,MeV,hPIV2,SV41,PIV5,MuV,PorPV,MprPV,nQueryCount=141, nCacheCount=339
[2 2;4 2]
-------------------------
GetDistances::(pairs)
2014 7 2 15 4 53.022
PPRV,CDV,RPV,MeV,hPIV2,SV41,PIV5,MuV,PorPV,MprPV,kGap=1
nQueryCount=39, nCacheCount=231
nCorrect=5
-------------------------
GetDistances::(multiples) NW=5
2014 7 2 15 25 40.952
ONAC001,ONAC003,ONAC005,ONAC014,ONAC028,ONAC010,ONAC016,ONAC024,ONAC058,ONAC088,nQueryCount=141, nCacheCount=339
[0 5;0 5]
-------------------------
GetDistances::(multiples) NW=5
2014 7 2 15 31 4.826
SwObihiro92,Leningrad91,Stockholm90,Yamagata89,SwNebraska92,SwStHyacinthe91,SwQuebec90,SwIowa88,nQueryCount=92, nCacheCount=228
[0 4;0 4]
-------------------------
GetDistances::(multiples) NW=5
<<<<<<< HEAD
2014 8 12 11 31 57.976
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,aardvark,lamb,fox,ape,dog,nQueryCount=389, nCacheCount=903
[6 0;0 11]
=======
2014 7 7 15 3 13.02
brm,CG17652,BRWD3,Hem,br,velo,E2f,Dp,ctp,nQueryCount=116, nCacheCount=280
[2 2;0 5]
>>>>>>> bef2f507c6358a5ceee1c070702fd6d9ada135b7
-------------------------
GetDistances::(pairs)
<<<<<<< HEAD
2014 8 12 11 33 12.318
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,aardvark,lamb,fox,ape,dog,kGap=2
nQueryCount=136, nCacheCount=680
nCorrect=17
=======
2014 7 7 15 3 24.91
brm,CG17652,BRWD3,Hem,br,velo,E2f,Dp,ctp,kGap=1
nQueryCount=30, nCacheCount=186
nCorrect=6
>>>>>>> bef2f507c6358a5ceee1c070702fd6d9ada135b7
-------------------------
GetDistances::(multiples) NW=5
<<<<<<< HEAD
2014 8 12 11 36 37.787
red,orange,yellow,green,blue,indigo,violet,purple,tan,white,square,circle,rectangle,ellipse,triangle,rhombus,nQueryCount=342, nCacheCount=810
[9 1;0 6]
=======
2014 7 7 15 4 40.842
Cap-G,aub,vas,neb,br,velo,E2f,Dp,ctp,nQueryCount=75, nCacheCount=321
[1 3;1 4]
>>>>>>> bef2f507c6358a5ceee1c070702fd6d9ada135b7
-------------------------
GetDistances::(pairs)
<<<<<<< HEAD
2014 8 12 11 37 33.886
red,orange,yellow,green,blue,indigo,violet,purple,tan,white,square,circle,rectangle,ellipse,triangle,rhombus,kGap=2
nQueryCount=105, nCacheCount=615
nCorrect=16
=======
2014 7 7 15 4 48.483
Cap-G,aub,vas,neb,br,velo,E2f,Dp,ctp,kGap=1
nQueryCount=20, nCacheCount=196
nCorrect=5
>>>>>>> bef2f507c6358a5ceee1c070702fd6d9ada135b7
-------------------------
GetDistances::(multiples) NW=5
<<<<<<< HEAD
2014 8 12 11 39 45.674
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,nQueryCount=198, nCacheCount=474
[6 0;0 6]
=======
2014 7 25 6 22 5.7
Actin,Arp2/3,Coronin,Dystrophin,FtsZ,Keratin,Cadherin,Ependymin,Integrin,NCAM,Selectin,nQueryCount=168, nCacheCount=404
[4 2;3 2]
>>>>>>> bef2f507c6358a5ceee1c070702fd6d9ada135b7
-------------------------
GetDistances::(pairs)
<<<<<<< HEAD
2014 8 12 11 40 28.955
Barack Obama,Hillary Clinton,John Edwards,Joe Biden,Chris Dodd,Mike Gravel,John McCain,Mitt Romney,Mike Huckabee,Ron Paul,Fred Thompson,Alan Keyes,kGap=2
nQueryCount=66, nCacheCount=330
nCorrect=7
=======
2014 7 25 6 22 36.598
Actin,Arp2/3,Coronin,Dystrophin,FtsZ,Keratin,Cadherin,Ependymin,Integrin,NCAM,Selectin,kGap=1
nQueryCount=55, nCacheCount=275
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 7 25 6 24 12.565
Actin,Arp2/3,Coronin,Dystrophin,FtsZ,Keratin,Cadherin,Ependymin,Integrin,NCAM,Selectin,nQueryCount=0, nCacheCount=572
[4 2;3 2]
-------------------------
GetDistances::(pairs)
2014 7 25 6 24 14.609
Actin,Arp2/3,Coronin,Dystrophin,FtsZ,Keratin,Cadherin,Ependymin,Integrin,NCAM,Selectin,kGap=1
nQueryCount=0, nCacheCount=330
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 7 25 6 59 53.568
cytoskeleton,Actin,Arp2/3,Coronin,Dystrophin,FtsZ,Keratin,adhesion,Cadherin,Ependymin,Integrin,NCAM,Selectin,nQueryCount=232, nCacheCount=548
[5 2;4 2]
-------------------------
GetDistances::(pairs)
2014 7 25 7 0 26.173
cytoskeleton,Actin,Arp2/3,Coronin,Dystrophin,FtsZ,Keratin,adhesion,Cadherin,Ependymin,Integrin,NCAM,Selectin,kGap=1
nQueryCount=78, nCacheCount=390
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 7 25 11 26 29.498
DRD2,GRM3,GRIN2A,SRR,SNCA,LRRK2,PINK1,ATP13A2,nQueryCount=87, nCacheCount=233
[3 1;4 0]
-------------------------
GetDistances::(pairs)
2014 7 25 11 26 36.154
DRD2,GRM3,GRIN2A,SRR,SNCA,LRRK2,PINK1,ATP13A2,kGap=1
nQueryCount=16, nCacheCount=152
nCorrect=7
-------------------------
GetDistances::(pairs)
2014 7 25 11 28 39.277
DRD2,GRM3,GRIN2A,SRR,SNCA,LRRK2,PINK1,ATP13A2,kGap=1
nQueryCount=6, nCacheCount=196
nCorrect=7
-------------------------
GetDistances::(multiples) NW=5
2014 7 25 11 35 8.274
Schizophrenia,DRD2,GRM3,GRIN2A,SRR,Parkinsons,LRRK2,PINK1,ATP13A2,MAPT,nQueryCount=105, nCacheCount=375
[5 0;2 3]
-------------------------
GetDistances::(multiples) NW=5
2014 7 25 11 52 50.767
Schizophrenia,DRD2,GRM3,GRIN2A,SRR,CACNA1I,RIMS1,KCTD13,Parkinsons,LRRK2,PINK1,ATP13A2,MAPT,SNCA,HLA-DRB5,BST1,GAK,nQueryCount=376, nCacheCount=916
[8 0;1 8]
-------------------------
GetDistances::(multiples) NW=5
2014 7 25 11 55 21.349
DRD2,GRM3,GRIN2A,SRR,CACNA1I,RIMS1,KCTD13,LRRK2,PINK1,ATP13A2,MAPT,SNCA,HLA-DRB5,BST1,GAK,nQueryCount=244, nCacheCount=776
[4 3;5 3]
-------------------------
GetDistances::(multiples) NW=5
2014 7 25 15 19 39.235
DRD2,GRM3,GRIN2A,SRR,CACNA1I,RIMS1,KCTD13,LRRK2,PINK1,ATP13A2,MAPT,SNCA,HLA-DRB5,BST1,GAK,ACMSD,STK39,MCCC1/LAMP3,SYT11,CCDC62/HIP1R,nQueryCount=390, nCacheCount=1370
[3 4;8 5]
-------------------------
GetDistances::(multiples) NW=5
2014 8 4 16 2 31.248
rs17483466,rs13397985,rs757978,rs872071,rs2456449,rs735665,rs6939340,rs4712653,rs3768716,rs7585356,rs2070094,rs2229571,nQueryCount=199, nCacheCount=473
[6 0;2 4]
-------------------------
GetDistances::(multiples) NW=5
2014 8 4 16 23 16.536
rs17483466,rs13397985,rs757978,rs872071,rs2456449,rs735665,rs4420638,rs7561528,rs17817600,rs3748140,rs12808148,rs6856768,rs11738335,rs1357692,nQueryCount=161, nCacheCount=735
[3 3;5 3]
-------------------------
GetDistances::(multiples) NW=5
2014 8 4 16 41 56.569
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,nQueryCount=199, nCacheCount=473
[0 6;0 6]
-------------------------
GetDistances::(multiples) NW=5
2014 8 4 16 42 20.597
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,nQueryCount=0, nCacheCount=672
[0 6;0 6]
-------------------------
GetDistances::(multiples) NW=5
2014 8 4 17 2 36.636
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,nQueryCount=191, nCacheCount=481
[6 0;1 5]
-------------------------
GetDistances::(pairs)
2014 8 4 17 5 6.979
red,orange,yellow,green,blue,indigo,lion,tiger,bear,monkey,zebra,elephant,kGap=2
nQueryCount=66, nCacheCount=330
nCorrect=9
>>>>>>> bef2f507c6358a5ceee1c070702fd6d9ada135b7
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% wikiScientistsGoRDK.m
% load wiki_scientists_9_12_18.mat
words1={'Kolmogorov','Fermat','Hilbert', 'Godel', 'Riemann','Gauss'} % mathematicians
words2={'Einstein','Newton','Hawking','Bohr','Maxwell','Boltzmann',} %physicists
words3={'Freud','Pavlov','Skinner','Jung'} %psychologists
words4={'Turing','Lovelace','Knuth','Hopper'} % computer scientists
words5={'Darwin','Lamarck','Linnaeus','Mendel'} % biology
idxKey = [ones(1,length(words1)) 2*ones(1,length(words2)) 3*ones(1,length(words3)) 4*ones(1,length(words4)) 5*ones(1,length(words5))]
words=[words1,words2,words3,words4,words5];
dx=[];
for i=1:length(words)
for j=i+1:length(words)
dx(i,j)=NWD([words(i),words(j)]);
end
end
% ack! pad d
dx(length(words),:)=0;
dx=Regularize(dx);
path(path,'../Gap');
hk=[];
for KK=1:15
idxSpectral=SpectralCluster(dx,KK);
hki=[];
ni=[];
% go through each cluster, compute the NWD for that cluster
for i=1:KK
idxi=find(idxSpectral==i);
ni(i)=length(idxi);
if length(idxi)<2
% singleton
hki(i)=NaN;
break;
end
hki(i)=NWD(words(idxi));
end
fprintf(1,'KK=%d : h=%0.3f, hki=%s, ni=%s\n',KK,max(hki),mat2str(hki,2),mat2str(ni,2));
ek=[];
for k=1:KK
idxk=find(idxSpectral==k);
fprintf(1,' %s\n',mat2str([idxKey(idxk)]));
idxTrueI=idxKey(idxk);
pred=mode(idxTrueI);
ek(k)=length(find(idxTrueI~=pred));
if 1==length(idxk)
ek(k)=NaN;
end
end
errorK(KK)=sum(ek);
fprintf(1,'errorK(%d)=%0.2f\n',KK,errorK(KK)/length(words));
hk(KK)=max(hki);
end
x=[1:length(hk)]'
hkn=hk
hkn(isnan(hk))=[]
x(isnan(hk))=[]
hkn=hkn'
p=polyfit(x,hkn,1);
hkd=hkn-(p(1).*x+p(2))
hkd=diff(hkd);
figure(1);clf;plot(hk,'-*')
title('average per cluster NWD')
figure(2);clf;plot(errorK./length(tx),'-+');
title('error rate')
figure(3);clf;plot(hkd,'-^')
title('1st derivative of de-biased average per cluster NWD')
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