Learning Ensembles ofFirst-Order Clauses for Recall-Precision Curves

A Case Study inBiomedical Information Extraction

Mark Goadrich, Louis Oliphant and Jude ShavlikDepartment of Computer Sciences

University of Wisconsin – Madison USA19 Sept 2004

Talk Outline Inductive Logic Programming Biomedical Information Extraction Our Gleaner Approach Aleph Ensembles Evaluation and Results Future Work

Inductive Logic Programming Machine Learning

Classify data into categories Divide data into train and test sets Generate hypotheses on train set and then

measure performance on test set

In ILP, data are Objects … person, block, molecule, word, phrase, …

and Relations between them grandfather, has_bond, is_member, …

Learning daughter(A,B) Positive

daughter(mary, ann) daughter(eve, tom)

Negative daughter(tom, ann) daughter(eve, ann) daughter(ian, tom) daughter(ian, ann) …

Background Knowledge mother(ann, mary) mother(ann, tom) father(tom, eve) father(tom, ian) female(ann) female(mary) female(eve) male(tom) male(ian)

Ann

IanEve

MaryTom

Possible Rules daughter(A,B) :- true. daughter(A,B) :- female(A). daughter(A,B) :- female(A), male(B). daughter(A,B) :- female(A), father(B,A). daughter(A,B) :- female(A), mother(B,A). …

Father Father

Mother Mother

ILP Domains Object Learning

Trains, Carcinogenesis

Link Learning Binary predicates

Biomedical Information Extraction

*image courtesy of National Human Genome Research Institute

Yeast Protein Database

Biomedical Information Extraction Given: Medical Journal abstracts tagged

with protein localization relations Do: Construct system to extract protein

localization phrases from unseen text

NPL3 encodes a nuclear protein with an RNA recognition motif and similarities to a family of proteins involved in RNA metabolism.

Biomedical Information Extraction

NPL3 encodes a nuclear protein with …

verbnoun article adj noun prep

sentence

prepphrase

…verb

phrasenoun

phrasenoun

phrase

alphanumeric marked location

nounphrase

nounphrase

Sample Extraction Structure

Find structures using ILP

S

C B

Aarticle

containsalphanumeric

containsalphanumeric

Pnoun

Lnoun

containsmarkedlocation

contains nobetween halfX verb

Protein Localization Extraction Hand-labeled dataset (Ray & Craven ’01)

7,245 sentences from 871 abstracts Examples are phrase-phrase combinations

1,810 positive & 279,154 negative

1.6 GB of background knowledge Structural, Statistical, Lexical and Ontological In total, 200+ distinct background predicates

Our Generate-and-Test Approach

rel(Prot, Loc) rel(Prot, Loc)

rel(Prot, Loc)

rel(Prot, Loc) rel(Prot, Loc) rel(Prot,

Loc)

rel(Prot, Loc) rel(Prot, Loc) rel(Prot,

Loc)

Parsed sentence (NP’s non-blue)

Candidates generated

NPL3 encodes a nuclear protein with …

Some Ranking Predicates High-scoring words in protein phrases

repressor, ypt1p, nucleoporin

High-scoring words in location phrases cytoskeleton, inner, predominately

High-scoring BETWEEN prot & loc cofraction, mainly, primarily, …, locate

Stemming seemed to hurt here … Warning: must do PER fold

Some Biomedical Predicates On-Line Medical Dictionary

natural source for semantic classes eg, word occurs in category ‘cell biology’

Medical Subject Headings (MeSH) canonized method for indexing biomedical articles ISA hierarchy of words and subcategories

Gene Ontology (GO) another ISA hierarchy of biological knowledge

Some More Predicates Look-ahead Phrase Predicates

few_POS_in_phrase(Phrase, POS) phrase_contains_specific_word_triple(Phrase, W1, W2, W3) phrase_contains_some_marked_up_arg(Phrase, Arg#, Word, Fold)

Relative Location of Phrases protein_before_location(ExampleID) word_pair_in_between_target_phrases(ExampleID, W1, W2)

Link Learning Large skew toward negatives

500 relational objects 5000 positive links means 245,000 negative links

Difficult to measure success Always negative classifier is 98% accurate ROC curves look overly optimistic

Enormous quantity of data 4,285,199,774 web pages indexed by Google PubMed includes over 15 million citations

Our Approach Develop fast ensemble algorithms focused

on recall and precision evaluation Key Ideas of Gleaner

Keep wide range of clauses Create separate theories for different recall ranges

Evaluation Area Under Recall Precision Curve (AURPC) Time = Number of clauses considered

Gleaner - Background Prediction vs Actual

Positive or Negative True or False

Focus on positive examples Recall =

Precision =

FNTP

TP

FPTP

TP

TP

FP FN

TN

actu

al

prediction

Gleaner - Background Seed Example

A positive example that our clause must cover

Bottom Clause All predicates which are true about seed example

Rapid Random Restart (Zelezny et al ILP 2002) Stochastic selection of starting clause Time-limited local heuristic search We store variety of clauses (based on recall)

Gleaner - LearningP

reci

sion

Recall

Create B Bins Generate Clauses Record Best Repeat for K seeds

Gleaner - Combining Combine K clauses per bin

If at least L of K clauses match, call example positive

How to choose L ? L=1 then high recall, low  precision L=K then low  recall, high precision

Our method Choose L such that ensemble recall matches bin b Bin b’s precision should be higher than any clause in it

We should now have set of high precision rule sets spanning space of recall levels

How to use GleanerP

reci

sion

Recall

Generate Curve User Selects Recall Bin Return Classifications

With Precision Confidence

Recall = 0.50Precision = 0.70

Aleph - Learning Aleph learns theories of clauses

(Srinivasan, v4, 2003) Pick positive seed example, find bottom clause Use heuristic search to find best clause Pick new seed from uncovered positives

and repeat until threshold of positives covered

Theory produces one recall-precision point Learning complete theories is time-consuming Can produce ranking with ensembles

Aleph Ensembles We compare to ensembles of theories Algorithm (Dutra et al ILP 2002)

Use K different initial seeds Learn K theories containing C clauses Rank examples by the number of theories

Need to balance C for high performance Small C leads to low recall Large C leads to converging theories

Aleph Ensembles (100 theories)

0 . 0 0

0 . 1 0

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N u m b e r o f C l a u s e s U s e d P e r T h e o r y

Te

sts

et

AU

RP

C

Evaluation Metrics Area Under Recall-

Precision Curve (AURPC) All curves standardized

to cover full recall range Averaged AURPC

over 5 folds Number of clauses

considered Rough estimate of time Both are “stop anytime”

parallel algorithms Recall

Pre

cisi

on

1.0

1.0

AURPC Interpolation Convex interpolation in RP space?

Precision interpolation is counterintuitive Example: 1000 positive & 9000 negative

TP FP TP Rate FP Rate Recall Prec

500 500 0.50 0.06 0.50 0.50

1000 9000 1.00 1.00 1.00 0.10

Example Counts RP CurvesROC Curves

750 4750 0.75 0.53 0.75 0.14

AURPC Interpolation

0.0

0.2

0.4

0.6

0.8

1.0

0.0 0.2 0.4 0.6 0.8 1.0

Recall

Pre

cis

ion

Correct Interpolation Incorrect Interpolation

Experimental Methodology Performed five-fold cross-validation Variation of parameters

Gleaner (20 recall bins) # seeds = {25, 50, 75, 100} # clauses = {1K, 10K, 25K, 50K, 100K, 250K, 500K}

Ensembles (0.75 minacc, 35,000 nodes) # theories = {10, 25, 50, 75, 100} # clauses per theory = {1, 5, 10, 15, 20, 25, 50}

Results: Testfold 5 at 1,000,000 clauses

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0 . 0 0 . 1 0 . 2 0 . 3 0 . 4 0 . 5 0 . 6 0 . 7 0 . 8 0 . 9 1 . 0

R e c a l l

Pre

cis

ion

Ensembles

Gleaner

Results: Gleaner vs Aleph Ensembles

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0 . 0 5

0 . 1 0

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1 0 , 0 0 0 1 0 0 , 0 0 0 1 , 0 0 0 , 0 0 0 1 0 , 0 0 0 , 0 0 0 1 0 0 , 0 0 0 , 0 0 0

N u m b e r o f C la u s e s G e n e r a t e d ( L o g a r i t h m ic S c a le )

Te

sts

et

AU

RP

C

G le a n e r A le p h E n s e m b le s

Further Results

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1 0 , 0 0 0 1 0 0 , 0 0 0 1 , 0 0 0 , 0 0 0 1 0 , 0 0 0 , 0 0 0 1 0 0 , 0 0 0 , 0 0 0

N u m b e r o f C la u s e s G e n e r a t e d ( L o g a r it h m ic S c a le )

Te

sts

et

AU

RP

C

G le a n e r A le p h E n s e m b le s E n s e m b le s 1 K

Conclusions Gleaner

Focuses on recall and precision Keeps wide spectrum of clauses Good results in few cpu cycles

Aleph ensembles ‘Early stopping’ helpful Require more cpu cycles

AURPC Useful metric for comparison Interpolation unintuitive

Future Work Improve Gleaner performance over time Explore alternate clause combinations Better understanding of AURPC Search for clauses that optimize AURPC Examine more ILP link-learning datasets Use Gleaner with other ML algorithms

Acknowledgements USA NLM Grant 5T15LM007359-02 USA NLM Grant 1R01LM07050-01 USA DARPA Grant F30602-01-2-0571 USA Air Force Grant F30602-01-2-0571 Condor Group David Page Vitor Santos Costa, Ines Dutra Soumya Ray, Marios Skounakis, Mark Craven

Dataset available at (URL in proceedings)ftp://ftp.cs.wisc.edu/machine-learning/shavlik-group/datasets/IE-protein-location

Deleted Scenes Clause Weighting Gleaner Algorithm

Director Commentaryon off

Take-Home Message Definition of Gleaner

One who gathers grain left behind by reapers

Gleaner and ILP Many clauses constructed and evaluated in ILP

hypothesis search We need to make better use of those that aren’t

the highest scoring ones

Thanks, Questions?

Clause Weighting Single Theory Ensemble

rank by how many clauses cover examples

Weight clauses using tuneset statistics CN2 (average precision of matching clauses) Lowest False Positive Rate Score Cumulative

F1 score Recall Precision Diversity

Clause Weighting

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P r e c i s i o n E q u a l R a n k e d L i s t C N 2W e ig h t in g S c h e m e s

AU

RP

C

Gleaner Algorithm Create B equal-sized recall bins For K different seeds

Generate rules using Rapid Random Restart Record best rule (precision x recall)

found for each bin For each recall bin B

Find threshold L of K clauses such thatrecall of “at least L of K clauses match examples”= recall for this bin

Find recall and precision on testset using each bin’s “at least L of K” decision process