Automatic Discovery of Shared Interest
Minimum Spanning Trees
Displaying Semantic Similarity
Włodzisław Duch & Co
Department of Informatics, Nicolaus Copernicus University,
Torun, Poland, & School of Computer Engineering, Nanyang
Technological University, Singapore
Google: Duch
The Vision

Vannevar Bush imagined in 1945 linked text/film information, a
kind of Wikipedia, his Memex was first hypertext systems.

Ted Nelson in “Computer Lib and Dream Machines” (1974)
extended this vision to all kinds of information integrated in
project Xanadu, a project founded in 1960. In essence:
unbreakable two-way links, connected to origin of info, facilitating
incremental publishing, deep version management & comparison.

WWW is not yet Xanadu, no links to origin of information, little
maintenance, searches are frequently tedious, and linking
information about any given subject is done in manual way.

Xanadu vision is not sufficient; all knowledge should be organized
in form of ideas supported by evidence, with links between
related pieces of information automatically created (QED project).

If only computes could analyze and present it in coherent way,
linking major ideas to papers, data, software, experiments ...
The Problem

Finding all people who share similar interests in large
organizations or worldwide is difficult (NTU experience).
Find who is related to me and in which way?

Each individual may have many different interests so the search
process should be topic-oriented, not people-oriented.

The process should be automatic – use info on people’s
homepages and their lists of publications.

Visualize relations using graphs with individuals as nodes and
different type of relations as edges.

The structure of the graphical representation depends strongly
on the selection of key entities of the nodes – text should be
projected first on domain ontology.
Steps

WWW spiders used to collect documents from some domain
(NTU home pages have been used for tests).

Convert html documents to text, clean using stop-words, apply
stemming etc.

Final filtering & dimensionality reduction to obtain vector
representation of the term-document matrix.

Cluster info in some way (try Clusty, Vivisimo or Carrot2).

Visualize related nodes that represent individual homepages,
link them by estimates of similarity of shared interest: see
Websom and its applications in digital lib, astro VizieR etc.
This goes beyond visualization of Google link analysis or
“the brain interface” use in Britannica BrainStormer.
Implementation and Design
Collection of
htmls documents
from NTU domain
“spider”
to crawl
and
retrieve
Data Pre
Processing
Keyword List
Parse documents
Porter’s Algorithm
Stop-words list
Stemming
Parse each
document
Remove
stopwords
Compare
document
vectors
Pearson Coefficient
Construct
Term
Document
Matrix
Compare
matrix
Cosine Similarity
Produce XML
ouput
Touchgraph
Visualization
Document-word matrix



Document1:
word1 word2 word3. word4 word3 word5.
Document2:
word1 word3 word5. word1 word3 word6.
The matrix: documents x word frequencies
W1
W2
W3
W4
W5 W6
Document 1
1 1 2 1 1 0 
F

2
0
2
0
1
1


Document 2
First shot: methods used

Inverse document frequency and term weighting.

Simple selection of relevant terms or

Latent Semantic Analysis (LSA) for dimensionality
reduction – standard method in info retrieval.

Minimum Spanning Trees for visual representation.

TouchGraph XML visualization of MST trees.
Data Preparation

Normalize columns of F dividing by highest word
frequencies:
tfij  fij / max fij
i

Among n documents, term j occurs dj times;
inverse document frequency idfj measures
uniqueness of term j:
idf j  log 2  n / d j   1, d j  0

tf x idf term weights:
wij  tfij  idf j
Simple selection

Take wij weights above certain threshold, binarize
and remove zero rows:
hij    wij   j 

Calculate similarity using cosine measure (takes
care of the vector length normalization):
sij 
h h
k 1
ik
jk
2

2 
h
h
  ik   jk 
 k 1
 k 1

Similarity using cosine measure
Using the same vectors, V1 ,V2 ,V3
V1  3 1 2 0 18 0 0
V2   2 1 5 4 4 0 0
V3  6 0 4 2 0 2 1
sij 
h h
k 1
ik
jk
2

2 
  hik   h jk 
 k 1
 k 1

Similarity of vector 1 and vector 2 is S12=0.615, and S13=0.1811.
Document 1 and Document 2 are more likely to be related.
For visualization a threshold value (ex. Sij > 0.3) which will
determine which links to show is used.
Dimensionality reduction

Latent Semantic Analysis (LSA): use Singular Value
Decomposition on weight matrix W
W  UΛV T
with U = eigenvectors of WWT and V of WTW.
Remove small eigenvalues from L, recreate
reduced W and calculate similarity:
sij 
Wi  W j
Wi  W j
Kruskal’s MST Algorithm and Top - Down
Clusterization
Minimum spanning tree = weighted graph with minimum total
cost, created by a simple greedy algorithm.
Cluster identification during MST
construction.
Some experiments:

Reuters-215785 datasets, with 5 categories and
1 – 176 elements per category, 600 documents:
can we see categories?

124 Personal Web Pages of the School of Electrical
and Electronic Engineering (EEE) of the Nanyang
Technological University (NTU) in Singapore.

5 department names may be used as categories:
control, microelectronics, information, circuit, power,
with 14 – 41 documents per category.
Can we discover department structure?
Reuters results
For 600 documents W rank in SVD is Wrank= 595
Method
No dim red.
LSA dim red. 0.8 (476)
LSA dim red. 0.6 (357)
Simple Selection
topics clusters accuracy
41
41
41
41
129
124
127
130
78.2%
76.2%
75.2%
78.5%
0.8 means 0.8*Wrank eigenvectors retained
Results for EEE NTU Web pages
Method
No dim red.
LSA dim red. 0.8 (467)
LSA dim red. 0.6 (350)
Simple Selection
topics clusters accuracy
10
10
10
10
142
129
137
145
84.7%
84.7%
82.8%
85.5%
Examples




Live demo http://www.neuron.m4u.pl/search
EEE full
EEE Selected
EEE Selected small clusters
Limitations

Keywords have been derived from what we find on web
pages only, too many, too sparse matrices.

Synonymous concepts should be treated as a single
feature, producing larger frequency counts.

People working on “architecture in mechanical design”
who are interested in “computer art” are associated with
someone in “computer architecture”.

Web pages contain many irrelevant information.

Abbreviations of all sorts are used.

No topics, therefore only a single category used.
Adding ontologies

Select relevant terms using engineering ontologies
(from keywords used in library classification)

Add medical concepts (ULMS) and use MetaMap to
discover these concepts in text.

Processing: Term weighting, stemming etc

Simple selection of relevant terms.

TouchGraph XML visualization
EEE: Simple Word-Doc Vector Space
EEE: Transformed Concept Vector Space
Med: Simple Word-Doc Vector Space
Med: Meta-Map Concept Vector Space
Med: after Metamap transformation
Results for Summary Discharges
New experiments on medical texts.
Short (~ half page) hospital summary discharges.
10 classes and 10 documents per class = main disease
treated.



Plain Doc-Word matrix ≈ 23%
Stop-List, TW-IDF, S.S. ≈ 64%
Metamap Transformation ≈ 93%
Summary



In real application knowledge-based approach is needed to
select relevant concepts and to parse web pages but problems
with acronyms, abbreviations, synonyms etc should be solved.
Other visualization and clusterization methods should be
explored.
People have many interests and thus may belong to several
topic groups – topics are related to concepts that should be
high in ontology, but have no simple description.

Could be a very useful tool to create new shared interest
groups for social networks in the Internet.

Could point out to potential collaborators or interesting
research from individual point of view.
Similar attempts
Flink is presentation of the scientific work and social
connectivity of Semantic Web reseachers, displaying
homepages of experts who have contributed to the
International Semantic Web Conference (ISWC) series.
 http://flink.semanticweb.org
Kartoo is a metasearch engine that displays topic
maps:
 http://www.kartoo.com
Related work in my group

Neural basis of language: creation of network of
concepts instead of vector models.

Medical text analysis using UMLS ontologies.

Instead of clustering formulate minimum number of
questions to define more precise search.

Creativity – inventing new names.
Words in the brain
The cell assembly model of language has strong experimental
support; F. Pulvermuller (2003) The Neuroscience of Language.
On Brain Circuits of Words and Serial Order. Cambridge University Press.
Acoustic signal => phonemes => words => semantic concepts.
Semantic activations are seen 90 ms after phonological in N200 ERPs.
Perception/action
networks, results
from ERP & fMRI.
Phonological density of words = # words that sound similar to a given word,
that is create similar activations in phonological areas.
Semantic density of words = # words that have similar meaning, or similar
extended activation network.
Words: simple model
Goals:
• make the simplest testable model of creativity;
• create interesting novel words that capture some features of products;
• understand new words that cannot be found in the dictionary.
Model inspired by the putative brain processes when new words are being
invented. Start from keywords priming auditory cortex.
Phonemes (allophones) are resonances, ordered activation of phonemes
will activate both known words as well as their combinations; context +
inhibition in the winner-takes-most leaves one or a few words.
Creativity = imagination (fluctuations) + filtering (competition)
Imagination: many chains of phonemes activate in parallel both words and
non-words reps, depending on the strength of synaptic connections.
Filtering: associations, emotions, phonological/semantic density.
Beyond ontologies
Neurocognitive approach to language understanding: use recognition,
semantic and episodic memory models, create graphs of consistent
concepts for interpretation, use spreading activation and inhibition to
simulate effect of semantic priming, annotate and disambiguate text.
For medical texts ULMS has >2M concepts, 15M relations …
See: Unambiguous Concept Mapping in a Medical Domain,
Thursday 11:45 (Matykiewicz, Duch, Pestian).
Query
Semantic memory
Applications, eg.
20 questions game
Humanized interface
Store
Part of speech tagger
& phrase extractor
verification
On line dictionaries
Manual
Parser
DREAM modules
Web/text/
databases interface
NLP
functions
Natural input
modules
Cognitive
functions
Text to
speech
Behavior
control
Talking
head
Control of
devices
Affective
functions
Specialized
agents
DREAM project is focused on perception (visual, auditory, text inputs), cognitive
functions (reasoning based on perceptions), natural language communication in
well defined contexts, real time control of the simulated/physical head.
Thank
you
for
lending
your
ears
...
Google: Duch => Papers