Journal 

of Engineering, Computers & Applied Sciences (JEC&AS)                 ISSN No: 2319‐5606                  
 
Volume 2, No.4, April 2013 
_________________________________________________________________________________ 
 

To Identify Disease Treatment Relationship in Short Text

Using Machine Learning & Natural Language Processing 
Khan Razik, Student, Computer Department, Sinhgad Institute of Technology, Lonavala
Dhande Mayur, Student, Computer Department, Sinhgad Institute of Technology, Lonavala
Patil Aniket, Student, Computer Department, Sinhgad Institute of Technology, Lonavala
Gaikwad Namrata, Student, Computer Department, Sinhgad Institute of Technology, Lonavala
ABSTRACT
Due to advancements in medical domain automatic learning has gained popularity in the fields of medical
decision support, extraction of medical knowledge and complete health management. Using Machine
Learning(hereafter, ML) and Natural language Processing(hereafter, NLP) we can make the healthcare field
more efficient and reliable. This paper describes how ML and NLP can be used for extracting knowledge from
published medical papers. It extracts the sentences that mention diseases and treatments and identifies the
relationship between them
Kewwords: Automatic Learning, Medical Decision Support, Machine Learning, Natural Language processing,
Healthcare.

identify and eliminate uninformative sentences and

Introduction
People are more concerned about their health than
ever before. In spite of their busy schedules they
want each and everything to go in a good flow.
People want Fast access to reliable information and
in a manner that is suitable to their habits and
workflow. Medical field has grown to such an
extent that the people practicing medicine should
not only have experience but also information
about latest discoveries. Electronic Health
Record(hereafter, EHR) is becoming a standard in
healthcare domain. Websites such as Google
Health[9] and Microsoft Health Vault[10] make
people to care deeply about their health. Having an
EHR has the following benefits[11]:
1. Rapid access to information that is focused on
certain topics such as immunizations, drugs
etc.
2. To have quality medical data for taking proper
medical decisions. For this purpose we need a
better, more efficient and reliable access to
information.
According to researches people are searching the
web in order to be informed regularly about their
health. In medical domain the most used source of
information is MEDLINE[12]. MEDLINE is
database where all the research discoveries come
and enter at a high rate. Due to the busy schedules
the experts don't get time to read millions of
articles therefore there is a need to build a tool that
will suffice the purpose.
Our objective is to work with ML and NLP is
that the task of identifying and disseminating
reliable healthcare information becomes easy and
beneficial for the people. A hierarchical approach is
used for performing the two tasks: The first is to
then second is to classify the rest of the sentences
by the relation of interest. By this a substantial
improvement is shown getting the information
2 Related Work
Entity recognition for Diseases and Treatments--
The most relevant work is done by Rosario and
Hearst[2].It uses Hidden Markov Models and
maximum entropy models to perform both the task
of entity recognition and the relation
discrimination. Their representation techniques are
based on words in context, part of speech
information, phrases, and a medical lexical
ontology—Mesh terms[13].The task of relation
extraction or relation identification is previously
done by (Craven, [3])with a focus on biomedical
taks, gene disorder association(Ray and Craven,
[4]) and diseases and drugs(Shrinivasan and
Rindflesch, [5]).
Rule-based approaches
It has been widely used for solving relation
extraction tasks. The main sources of information
used by this technique are either syntactic: part-of-
speech (POS) and syntactic structures; or semantic
information in the form of fixed patterns that
contain words that trigger a certain relation. The
best rule-based systems are the ones that use rules
constructed manually or semi automatically—
extracted automatically and refined manually. A
positive aspect of rule-based systems is the fact that
they obtain good precision results, while the recall
levels tend to be low. They tend to require more
human-expert effort than data-driven methods
(though human effort is needed in data-driven
methods too, to label the data).

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Journal off Engineering,, Computers &
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5606                  
 
Volume 2,, No.4, April 2
2013 
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Syntacttic rule-basedd relation exttraction system ms
are compplex systems based
b on addittional tools ussed
to assignn POS tags or o to extract syntactic parrse
trees. It iis known thatt in the biommedical literatuure
such toolls are not yet at the state-off-the-art level as
they are for general English textss, and therefoore
their perrformance on sentences is not always the t
best(Bunnescu et al. [6]).
annd Side Efffect, becausee these are of most
immportance. Appplying task1 first followedd by task2
giives far bettter results thhan applying machine
leearning directtly to the conntent.This appproach is
beetter becau use uninform mative data can be
coonsidered as potential
p data if
i not filtered((task1).

3 Prop
posed Apprroach
3.1 Tassk
The workk that we preesent in this paper
p is focussed
on two ttasks: automaatically identiifying sentencces
publishedd in medical abstracts (Medline) as
containinng or not infoformation aboout diseases and a
treatmentts, and autommatically identtifying semanntic Fig 1.Architecture Of th
he Proposed System
S
relations that existt between diseases and a
treatmentts, as expressed in these teexts. The secoond 3..2 Algorithms
A U
UsedAs classsification
task is foocused on thrree semantic R Relations: Cuure, allgorithms, wee use a set of six repreesentative
Prevent, and Side Effeect. m
models: decisiion-based mo odels (Decisioon trees),
The prroblems addressed in this paper form the t prrobabilistic models
m (Naı¨¨ve Bayes (NB) ( and
building blocks of a frramework thatt can be used by Complement Naı¨ve N Bayees (CNB), which w is
healthcarre providers (ee.g., private cllinics, hospitaals, addapted for text withh imbalanceed class
medical ddoctors, etc.), or laypeople who want to be diistribution), adaptive
a learnning (Ada- B Boost), a
in chargee of their heaalth by readinng the latest lifel linnear classifieer (support vector machinne (SVM)
science published
p articcles related too their interessts. w
with polynomial kernel), and a classsifier that
The finall product cann be envisioneed as a browsser allways predictss the majorityy class in thee training
plug-in or a desk ktop applicattion that will w daata (used as a baseline). We W decided to use these
automaticcally find annd extract thee latest mediccal cllassifiers becaause they are representativve for the
discoveriies related too disease-treaatment relatioons leearning algorithms in thee literature and a were
and preseent them to thet user. The product can be shhown to work k well on bothh short and loong texts.
developeed and sold by y companies thatt do researrch D
Decision trees are
a decision-b based models similar to
in Heallthcare Inforrmatics, Nattural Languaage thhe rule-based models that are a used in haandcrafted
Processinng, and Mach hine Learning,, and companies syystems, and are suitabble for shoort texts.
that develop tools liike Microsoftt Health Vauult. Prrobabilistic models,
m especially the ones based on
Consumeers are looking to buy or use u products thhat thhe Naı¨ve Bayyes theory, aree the state of the art in
satisfy ttheir needs and gain their t trust and
a teext classificatiion and in almmost any autom matic text
confidencce. Healthcarre products arre probably the t cllassification task.
t Adaptivve learning algorithms
a
most sennsitive to th he trust and confidence of arre the ones th hat focus on hard-to-learn
h concepts,
consumers. Compannies that want w to sell
s ussually undeerrepresented in the data, a
informatiion technolo ogy healthcaare frameworrks chharacteristic that
t appears in i our short texts and
need to bbuild tools thhat allow them m to extract and
a immbalanced daata sets. SV VM-based moodels are
mine auutomatically the wealth of publish hed accknowledged state-of-th
he-art classsification
research. The first task (task 1 or sentennce teechniques on text.
t All classsifiers are partt of a tool
selectionn) identifies sentences from Medliine caalled Weka[14 4].(Oana Frunnza et al. [1]).
publishedd abstracts thhat talk abouut diseases and a
treatmentts. The taskk is similar to a scan of 3..2.1 Bag-of-w words Repressentation
sentencess contained inn the abstract of an article in Thhe bag-of-w words (BOW W) representtation is
order to present to thee user-only seentences that are a coommonly usedd
identifiedd as contaiining relevannt informatiion foor text classifiication tasks. It
I is a represeentation in
(disease treatment infformation). The T second taask w
which features are chosen am mong the wordds that are
(task 2 or relation identification)
i ) has a deepper prresent in the training
t data. Because we deal with
semantic dimension an nd it is focuseed on identifyiing shhort texts wiith an averaage of 20 w words per
disease-trreatment relattions in the seentences alreaady seentence, the difference
d beetween a binary value
selected as
a being inforrmative (e.g., task
t 1 is appliied reepresentation and
a a frequency value repreesentation
first). We focus on thhree relations:: Cure, Preveent, is not large. Inn our case, we w chose a ffrequency
vaalue representtation. This haas the advantaage that if

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Journal of Engineering, Computers & Applied Sciences (JEC&AS)                 ISSN No: 2319‐5606
Volume 2, No.4, April 2013 
_________________________________________________________________________________
a feature appears more than once in a sentence, this
means that it is important and the frequency value
representation will capture this—the feature’s value
will be greater than that of other features. We keep
only the words that appeared at least three times in
the training collection, contain at least one
alphanumeric character, are not part of an English
list of stop words[15] and are longer than three
characters. Words that have length of two or one
character are not considered as features because of
two other reasons: possible incorrect tokenization
and problems with very short acronyms in the
medical domain that could be highly ambiguous
(could be an acronym or an abbreviation of a
common word).
3.2.2 NLP Representation
The second type of representation is based on
syntactic information. In order to extract this type
of information we used the Stanford pos-tagger[8]
tool. The tagger analyzes English sentences and
outputs the base forms, part-of-speech tags, chunk
tags, and named entity tags.
The following preprocessing steps are applied in
order to identify the final set of features to be used
for classification: removing features that contain
only punctuation, removing
stop words (using the same list of words as for our
BOW representation), and considering valid
features only the lemma-based forms. We chose to
use lemmas because there are a lot of inflected
forms (e.g., plural forms) for the same word and
the lemmatized form (the base form of a word) will
give us the same base form for all of them.
4 Evaluation Measures
The most common used evaluation measures in the
ML settings are: accuracy, precision, recall, and F-
measure. All these measures are computed form a
confusion matrix (Kohavi and Provost [7]) that
contains information about the actual classes, the
true classes and the classes predicted
by the classifier. The test set on which the models
are evaluated contain the true classes and the
evaluation tries to identify how many of the true
classes were predicted by the model classifier. In
the ML settings, special attention needs to be
directed to the evaluation measures that are used.
For data sets that are highly imbalanced (one class
is overrepresented in comparison with another),
standard evaluation measures like accuracy are not
suitable. Because our data sets are imbalanced, we
chose to report in addition to accuracy, the
macroaveraged F-measure. We decided to report
macro and not microaveraged F-measure because
the
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macromeasure is not influenced by the majority
class, as the micromeasure is. The macromeasure
better focuses on the performance the classifier has
on the minority classes. The formulas for the
evaluation measures are: Accuracy ¼ the total
number of correctly classified instances; Recall ¼
the ratio of correctly classified positive instances to
the total number of positives. This evaluation
measure is known to the medical research
community as
sensitivity. Precision ¼ the ratio of correctly
classified positive instances to the total number of
classified as positive. F-measure ¼ the harmonic
mean between precision and recall(Oana Frunza et
al. [1]).
5 Conclusion
This approach is very useful for everyone as it
gives information only of the area of interest. The
task is divided into two tasks The first task that we
tackle in this paper is a task that has applications in
information retrieval, information extraction, and
text summarization. We identify potential
improvements in results when more information is
brought in the representation technique for the task
of classifying short medical texts.
The second task that we address can be viewed as
a task that could benefit from solving the first task
first. In this study, we have focused on three
semantic relations between diseases and treatments.
Our work shows that the best results are obtained
when the classifier is not overwhelmed by
sentences that are not related to the task.
This study is related to a particular field but the
future scope of the paper lies in the fact that this
can be extended to the information on the web.
Identifying and classifying medical-related
information on the web is a challenge that can
bring valuable information to the research
community and also to the end user. We also
consider as potential future work ways in which the
framework’s capabilities can be used in a
commercial recommender system and in
integration in a new EHR system.
6 Acknowledgement
We express our sincere gratitude towards co-
operative department who has provided us with
valuable assistance and requirements for the
development. We hereby take this opportunity to
record our sincere thanks and heartily gratitude to
our guide Prof. M. Galphade for her useful
guidance and making us available her intimate
knowledge and experience.
 
Journal of Engineering, Computers & Applied Sciences (JEC&AS)                 ISSN No: 2319‐5606                  
 
Volume 2, No.4, April 2013 
_________________________________________________________________________________ 
 

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