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Standardized Descriptions of Taxa in

Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Application of Text Mining in Developing Standardized Descriptions of Taxa in

Paleontology: A Framework

Francisca E. Oboh-Ikuenobe, Geological Science & Engineering, ikuenobe@umr.edu

Wen-Bin (Vincent) Yu, Information Science & Technology, yuwen@umr.edu

Bih-Ru Lea, Business Administration, leabi@umr.edu

University of Missouri – Rolla

Rolla, MO 65401, USA

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Problems In PalynomorphClassifications And Interpretations

Description #2: Large proximate, cyst with irregular perforated crests, well developed paratabulation.

Description #1: Proximate, acavate cyst, large (75-95 µm) with irregular perforated parasuturalcrests, well developed paratabulation (including parasulcal paraplates), and precingular archaeopyle.

40 µm

2

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Text mining or Information Retrieval?Google Search/ online article database– Key word search (existing knowledge)

Web Mining/ Semantic Web – Structured ontology for Information Extraction

Text mining– A special case of data mining – Discover new knowledge by finding interesting and

non-trivial patterns in textural documents – Usually starts with clustering similar documents

and extracting key terms associated with each cluster

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Framework

Sample Database

CHRONOS

Text preprocessing

& Pattern Identification

Module

Clustering Module

Data Sources Text Mining

Model Creation Module

Model Selection Module

Data Mining

Model Evaluation

ModuleDescriptive

Model

Predictive Model

Variable Reduction

ModuleUser Input

…

Standardized Taxon

Recommendation Modeling Module

DinoSys

Data Mining/ Software Agent

3

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Framework- Text Mining Process

Sample Database

CHRONOS

Text preprocessing

& Pattern Identification

Module

Clustering Module

Data Sources Text Mining

Model Creation Module

Model Selection Module

Data Mining

Model Evaluation

ModuleDescriptive

Model

Predictive Model

Variable Reduction

ModuleUser Input

…

Standardized Taxon

Recommendation Modeling Module

DinoSys

Data Mining/ Software Agent

Text Mining is to find hidden patterns for textual documents by grouping similar descriptions

… portable and mobile video services could be ported to other locations, other devices or other media…. [IPTV, WiMAX get star billing at Supercomm 2005]

Data (Documents) Cleansing Text processing

– Parsing.– Stop words and start words.– Parts of speech– Stemming – Synonyms, Jargons, Abbreviations

Term Frequency MatrixWeighting Scheme

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Text mining process IITerm Frequency Matrix – Represent each document with selected terms– A note on Discriminating power: Terms with

the most discriminating power are those that occur frequently, but only in a few documents.

– Determine Term weights and Frequency weights

0111Doc 3

1100Doc 2

1011Doc 1

Term 4:id

Term 3:voice

Term 2:web

Term 1:process

4

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Framework- Text Mining Process

Sample Database

CHRONOS

Text preprocessing

& Pattern Identification

Module

Clustering Module

Data Sources Text Mining

Model Creation Module

Model Selection Module

Data Mining

Model Evaluation

ModuleDescriptive

Model

Predictive Model

Variable Reduction

ModuleUser Input

…

Standardized Taxon

Recommendation Modeling Module

DinoSys

Data Mining/ Software Agent

Text Mining is to find hidden patterns for textual documents by grouping similar descriptions

… portable and mobile video services could be ported to other locations, other devices or other media…. [IPTV, WiMAX get star billing at Supercomm 2005]

Data (Documents) Cleansing Text processing

– Parsing.– Stop words and start words.– Parts of speech– Stemming – Synonyms, Jargons, Abbreviations

Term Frequency MatrixWeighting Scheme

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Term Weights: Entropy MethodTerm weight (Gij)=

where – pij = aij / gi– aij: frequency that term i appears in document j. – gi: frequency that term i appears in document

collection.,– n: number of documents in the collection

Weighted Frequency Lij = log2(aij+1)

∑+=j

ijijj n

ppG

)(log)(log

12

2

5

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Framework- Text Mining Process

Sample Database

CHRONOS

Text preprocessing

& Pattern Identification

Module

Clustering Module

Data Sources Text Mining

Model Creation Module

Model Selection Module

Data Mining

Model Evaluation

ModuleDescriptive

Model

Predictive Model

Variable Reduction

ModuleUser Input

…

Standardized Taxon

Recommendation Modeling Module

DinoSys

Data Mining/ Software Agent

Text Mining is to find hidden patterns for textual documents by grouping similar descriptions

… portable and mobile video services could be ported to other locations, other devices or other media…. [IPTV, WiMAX get star billing at Supercomm 2005]

Data (Documents) Cleansing Text processing

– Parsing.– Stop words and start words.– Parts of speech– Stemming – Synonyms, Jargons, Abbreviations

Term Frequency MatrixWeighting Scheme

Variable Reduction & Transformation

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Text mining process IIIVariable reduction (Transformations)– SVD (Singular Value Decomposition)

• Principal components decomposition.

– Roll Up Term• use the n terms with the largest term weights.

Application in Data analysis – Cluster analysis– Classification– Predictions

6

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Text Mining Process – Example 1

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Framework- Text Mining Process

Sample Database

CHRONOS

Text preprocessing

& Pattern Identification

Module

Clustering Module

Data Sources Text Mining

Model Creation Module

Model Selection Module

Data Mining

Model Evaluation

ModuleDescriptive

Model

Predictive Model

Variable Reduction

ModuleUser Input

…

Standardized Taxon

Recommendation Modeling Module

DinoSys

Data Mining/ Software Agent

Clustering

Text Mining is to find hidden patterns for textual documents by grouping similar descriptions

… portable and mobile video services could be ported to other locations, other devices or other media…. [IPTV, WiMAX get star billing at Supercomm 2005]

Data (Documents) Cleansing Text processing

– Parsing.– Stop words and start words.– Parts of speech– Stemming – Synonyms, Jargons, Abbreviations

Term Frequency MatrixWeighting Scheme

Variable Reduction & Transformation

7

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Clusters with SVD 1

40 µm

Four different descriptions for the same dinocyst

* COL1, COL2 & COL3 represent the principle components (SVD variables) of the descriptive terms

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Clusters with SVD 2

8

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Text Mining Process – Example 2

Ifecysta sp. 2 Ifecysta sp. 1

Achomosphaera sp.Diphyes sp.

Ifecysta sp. 1

Ifecysta sp. 2

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Framework- Data Mining Process

Sample Database

CHRONOS

Text preprocessing

& Pattern Identification

Module

Clustering Module

Data Sources Text Mining

Model Creation Module

Model Selection Module

Data Mining

Model Evaluation

ModuleDescriptive

Model

Predictive Model

Variable Reduction

ModuleUser Input

…

Standardized Taxon

Recommendation Modeling Module

DinoSys

Data Mining/ Software Agent

Input (independent variable): – the SVD variables

output (dependent variable): – clusters

Descriptive models – Regression– Neural network– decision tree

Model EvaluationModel Selection

9

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Modelling: ANN

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Modelling: Regression

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By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Modelling: Decision Tree

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Dinocyst Description Modeling

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By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Model Evaluation

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Framework – Descriptive Model

Sample Database

CHRONOS

Text preprocessing

& Pattern Identification

Module

Clustering Module

Data Sources Text Mining

Model Creation Module

Model Selection Module

Data Mining

Model Evaluation

ModuleDescriptive

Model

Predictive Model

Variable Reduction

ModuleUser Input

…

Standardized Taxon

Recommendation Modeling Module

DinoSys

Data Mining/ Software Agent

12

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Scoring Dinocyst DescriptionAssume regression model is selected in the model selection process

Classification is proposed

A description is entered, analyzed by text mining process, and feed into the selected model (i.e., regression in this example)

Standardized Taxon

Recommendation Modeling Module

Standardized description is proposed

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

User/Human Interaction

Sample Database

CHRONOS

Text preprocessing

& Pattern Identification

Module

Clustering Module

Data Sources Text Mining

Model Creation Module

Model Selection Module

Data Mining

Model Evaluation

ModuleDescriptive

Model

Predictive Model

Variable Reduction

ModuleUser Input

…

Standardized Taxon

Recommendation Modeling Module

DinoSys

Data Mining/ Software Agent

the number of clustersthe validity of key termspossible start/stop words list…

13

By

Bih-Ru Lea

Standardized Descriptions of

Taxa in Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

Adoptive Model

Sample Database

CHRONOS

Text preprocessing

& Pattern Identification

Module

Clustering Module

Data Sources Text Mining

Model Creation Module

Model Selection Module

Data Mining

Model Evaluation

ModuleDescriptive

Model

Predictive Model

Variable Reduction

ModuleUser Input

…

Standardized Taxon

Recommendation Modeling Module

DinoSys

Data Mining/ Software Agent

Dinocyst descriptions collected and mined periodically to update model

Standardized Descriptions of Taxa in

Paleontology

ByVincent YuFrancisca

Oboh-Ikuenobe

Bih-Ru Lea

The End