Intelligent Information Directory System for Clinical Documents Qinghua Zou 6/3/2005 Dr. Wesley W....
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Transcript of Intelligent Information Directory System for Clinical Documents Qinghua Zou 6/3/2005 Dr. Wesley W....
Intelligent Information Directory System for Clinical Documents
Qinghua Zou
6/3/2005
Dr. Wesley W. Chu (Advisor)
When searching clinical reports
Keyword Search Problems
Hard to compose good keywords
Lack an outlook of the content
Interchangeable words
Intelligent Directory System
1. Overview 2. Extracting Key Concepts 3. Mining Topics 4. Building Directories 5. Searching 6. Conclusion
2. Concept Extraction
2.1 Introduction 2.2 Our approach: IndexFinder
Index Phase (Offline) Search Phase (Real Time)
2.3 Experiments 2.4 Summary
2.1 Motivation Clinical texts are
valuable in medical practice Search relevant reports Search similar patients
What is key information? UMLS provides
key medical concepts Our Goal
Extract UMLS concepts from clinical texts
Clinical Texts
•Extract key info.•Standard terms
2.1 Previous Approaches
Free text
ip
dp i1
i0 vplambs
will v0
eat
dp
oats
NLP Parser
UMLS
Mapping
UMLS Concepts
Noun phrases
•lambs•oats
2.1 Problems of Previous Approaches
Concepts cannot be discovered if they are not in a single noun phrase. E.g. In “second, third, and fourth ribs”,
“Second rib” can not be discovered.
Difficult to scale to large text computing. Natural language processing requires
significant computing resources
2.2 Our Approach: IndexFinder
Free text
NLP Parser
Noun phrases
UMLS
Mapping Concepts
We would discard all words in the text except “lung” and “cancer”.
Our approach: UMLSfree text Previous: free textUMLS
Suppose UMLS contains only“Lung cancer”
Indexing
Index Data ~80MB
UMLS 2GB Index phase(offline)
conceptsFilteringExtracting
Free text Search phase(real time)
2.2 Our Approach: What’s New?
Knowledge-based approach Using the compact index data
without using any database system
Permuting words in a sentence to generate UMLS concept candidates.
Using filters to eliminate irrelevant concepts.
2.2 Concept Candidates GenerationAssumptions Knowledge base provides a
phrase table. Each phrase (concept) is a
set of words. An input text T is
represented as a set of words.
Goal Combining words in T to
generate concept candidates
Example T={D,E,F}
Answer: 5
2.2 Search Phase: FilteringUse filters to eliminate irrelevant
concepts Syntactic filter:
Word combination is limited within a sentence.
Semantic filter: Filter out irrelevant concepts using
semantic types (e.g. body part, disease, treatment, diagnose).
Filter out general concepts using the ISA relationship and keep the more specific ones.
2.3 Experiment Comparison with MetaMap [3]
Input: A small mass was found in the left hilum of the lung.
MetaMap
IndexFinder
2.4 Summary An efficient method that maps from UMLS
to free text for extracting concepts without using any database system.
Syntactic and semantic filters are used to eliminate irrelevant candidates.
IndexFinder is able to find more specific concepts than NLP approaches.
IndexFinder is scalable and can be operated in real time.
3. Mining Topics: SmartMiner
3.1 Introduction 3.2 Search Space 3.3 SmartMiner 3.4 Experiment 3.5 Summary
3.1 Introduction
A Topic (assumption) a set of concepts a frequent pattern
Finding topics by data mining Frequent patterns, or Maximal frequent patterns
Require efficient data mining
3.1 Data Mining Problem
1: a b c d e2: a b c d3: b c d4: b e5: c d e
id: item setDataset
MinSup=2
MFI abcd, be, cde
What itemsets are frequent itemsets (FI)?
a, b, c, d, e, ab, ac, ad, bc, bd, be, cd, ce, de, abc, abd, acd, bcd, cde,
abcd
Maximal frequent itemset(MFI): No superset is frequent.
3.1 Why MFI not FI? Mining FI is infeasible when there exists long FI. E.g, Suppose we have a 20-item frequent set a1 a2 … a20. All of its subset are frequent, i.e., 220=1,048,576
Mining MFI is fast and we can generate all the FI.
3.1 Previous work
Superset checking. A study shows that CPU spends 40% time for superset checking.
Search tree is too large A large number of support counting
Need more efficient method
3.2 Search spaceGiven 5 items: a, b, c, d, e. What is the search space?
Ø, a, b, c, d, e, ab, ac, ad, ae, bc, …, abcde
We use “head:tail” to denote the space as:
:abcdesimplify
Ø:abcde
What is the space of ? ab:cd
ab, abc, abd, abcd
3.2 Space decomposition
For a space :abcde, if abcg is frequent,
Then, the known space any subset of abc is frequent known space is :abc
The unknown space are: Any itemsets contain d or e. d:abce and e:abc
:abcde = d:abce + e:abc + :abc
3.3 The basic idea
(b) SmartMiner Strategy
SmartMiner takes advantages of the information from previous steps.
(a) Previous approach
B2
…
A1
B1 …
Creating B2 before exploring B1
Bn B’
…
A1
B1 …
Creating B’ after exploring B1
Using information from B to prune the space at B’
3.3 The tail information
For the space :abcde, if we know abcf, abcg and abfg are frequent, then we project them to the space. abcf abc. abcg abc. abfg ab.
Thus Tinf(abcf,abcg, abfg|:abcde)={abc}
3.4 Running time on Mushroom
0
1
10
100
1000
10 1 0.1 0.01 Minimum Support (%)
Total Time(sec)SmartMinerGenMaxMafia
3.5 Summary
SmartMiner uses tail information to guide the mining, efficient since A smaller search tree. No superset checking. Reduces the number of support counting.
4. Building Directories
4.1 Introduction 4.2 Knowledge Hierarchies 4.3 User Specification 4.4 Directory Generation 4.5 Integration various
directories 4.6 Summary
4.2 Knowledge Hierarchies UMLS concept hierarchies
PA: parent-child relationship RA: rather-than relationship
Problems A concept: several parents, different granularity
[lung cancer] [Neoplasms, Respiratory Tract] [lung cancer] [Neoplasms, Respiratory
System] A concept: hundreds of paths to roots
[lung cancer]: 233 different paths in UMLS by PA
4.2 Select Proper Hierarchies Set source preference order, e.g
[disease]: ICD9>SNOMED>MeSH [body part]: SNOMED>ICD9
Select proper granularity C: a set of concepts; n: a path node Score function for selecting the
node n S(n)=|{ci| cin, ci in C}|
Expert review
4.3 User Specifications A good directory ~ usage pattern User spec usage pattern User may have different specs A spec: a series of knowledge
names [disease] + [body part], or [body part] + [disease]
Build a directory for a spec by the ordering
4.4 Directory GenerationAn example
User spec 1: d + p [disease] + [body part]
User spec 2: p + d [body part] + [disease]
4.5 Integration various directories
For each Di, get all dir paths to Di
A Di is tree: XML Key words can
associate with tree nodes
Query: xpath Exist redundant
information
4.5 simplified model Keep only the
first level knowledge trees
For //d6//p6, we use XPath query
//doc[//d6 and //p6]
Size smaller, require some computation