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Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley http://biotext.berkeley.edu Supported by NSF DBI-0317510 and a gift from Genentech

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Page 1: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Semantic Relation Detection

in Bioscience Text

Marti HearstSIMS, UC Berkeley

http://biotext.berkeley.eduSupported by NSF DBI-0317510 and a gift from Genentech

Page 2: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

BioText Project Goals

Provide flexible, intelligent access to information for use in biosciences applications.

Focus on Textual Information from Journal Articles Tightly integrated with other resources

Ontologies Record-based databases

Page 3: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Project Team

Project Leaders: PI: Marti Hearst Co-PI: Adam Arkin

Computational Linguistics Barbara Rosario Presley Nakov

Database Research Ariel Schwartz Gaurav Bhalotia (graduated)

Supported primarily by NSF DBI-0317510

and a gift from Genentech

User Interface / IR Adam Newberger Dr. Emilia Stoica

Bioscience Dr. TingTing Zhang Janice Hamerja

Page 4: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

BioText Architecture

Sophisticated Text Analysis

Annotations inDatabase

ImprovedSearch Interface

Page 5: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

The Nature of Bioscience Text

Claim: Bioscience semantics are simultaneously

easier and harder than general text.

Fewer subtletiesFewer ambiguities

“Systematic” meanings

Enormous terminologyComplex sentence structure

easier harder

Page 6: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Sample Sentence

“Recent research, in proliferating cells,

has demonstrated that interaction of E2F1 with the p53 pathway could involve transcriptional up-regulation of E2F1 target genes such as p14/p19ARF, which affect p53 accumulation [67,68], E2F1-induced phosphorylation of p53 [69], or direct E2F1-p53 complex formation [70].”

Page 7: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

BioScience Researchers

Read A LOT! Cite A LOT! Curate A LOT! Are interested in specific relations,

e.g.: What is the role of this protein in that

pathway? Show me articles in which a comparison

between two values is significant.

Page 8: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

This Talk

Discovering semantic relations Between nouns in noun compounds Between entities in sentences

Acquiring labeled data: Idea: use text surrounding citations to

documents to identify paraphrases A new direction; preliminary work only

Page 9: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Noun CompoundRelation Recognition

Page 10: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Noun Compounds (NCs)

Technical text is rich with NCs

Open-labeled long-term study of the subcutaneous sumatriptan efficacy and tolerability in acute migraine treatment.

NC is any sequence of nouns that itself functions as a noun asthma hospitalizations health care personnel hand wash

Page 11: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

NCs: 3 computational tasks

Identification Syntactic analysis (attachments)

[Baseline [headache frequency]] [[Tension headache] patient]

Our Goal: Semantic analysis Headache treatment treatment for

headache Corticosteroid treatment treatment that uses

corticosteroid

Page 12: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Descent of Hierarchy

Idea: Use the top levels of a lexical

hierarchy to identify semantic relations

Hypothesis: A particular semantic relation holds

between all 2-word NCs that can be categorized by a lexical category pair.

Page 13: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Related work (Semantic analysis of NCs)

Rule-based Finin (1980)

Detailed AI analysis, hand-coded Vanderwende (1994)

automatically extracts semantic information from an on-line dictionary, manipulates a set of handwritten rules. 13 classes, 52% accuracy

Probabilistic Lauer (1995):

probabilistic model, 8 classes, 47% accuracy Lapata (2000)

classifies nominalizations into subject/object. 2 classes, 80% accuracy

Page 14: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Related work (Semantic analysis of NCs)

Lexical Hierarchy Barrett et al. (2001)

WordNet, heuristics to classify a NC given the similarity to a known NC

Rosario and Hearst (2001) Relations pre-defined MeSH, Neural Network. 18 classes, 60% accuracy

Page 15: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Linguistic MotivationCan cast NC into head-modifier relation, and assume head noun has an argument and qualia structure.

(used-in): kitchen knife (made-of): steel knife (instrument-for): carving knife (used-on): putty knife (used-by): butcher’s knife

Page 16: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

The lexical Hierarchy: MeSH

1. Anatomy [A] 2. Organisms [B] 3. Diseases [C] 4. Chemicals and Drugs [D] 5. Analytical, Diagnostic and Therapeutic Techniques and Equipment [E] 6. Psychiatry and Psychology [F] 7. Biological Sciences [G] 8. Physical Sciences [H] 9. Anthropology, Education, Sociology and Social Phenomena [I] 10. Technology and Food and Beverages [J] 11. Humanities [K] 12. Information Science [L] 13. Persons [M] 14. Health Care [N] 15. Geographic Locations [Z]

Page 17: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

The lexical Hierarchy: MeSH

1. Anatomy [A] Body Regions [A01] 2. [B] Musculoskeletal System [A02] 3. [C] Digestive System [A03] 4. [D] Respiratory System [A04] 5. [E] Urogenital System [A05] 6. [F] …… 7. [G] 8. Physical Sciences [H] 9. [I] 10. [J] 11. [K] 12. [L] 13. [M]

Page 18: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Descending the Hierarchy 1. Anatomy [A] Body Regions [A01] Abdomen

[A01.047] 2. [B] Musculoskeletal System [A02] Back [A01.176] 3. [C] Digestive System [A03] Breast [A01.236] 4. [D] Respiratory System [A04] Extremities

[A01.378] 5. [E] Urogenital System [A05] Head [A01.456] 6. [F] …… Neck [A01.598] 7. [G] …. 8. Physical Sciences [H] 9. [I] 10. [J] 11. [K] 12. [L] 13. [M]

Page 19: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Descending the Hierarchy 1. Anatomy [A] Body Regions [A01] Abdomen

[A01.047] 2. [B] Musculoskeletal System [A02] Back [A01.176] 3. [C] Digestive System [A03] Breast [A01.236] 4. [D] Respiratory System [A04] Extremities

[A01.378] 5. [E] Urogenital System [A05] Head [A01.456] 6. [F] …… Neck [A01.598] 7. [G] …. 8. Physical Sciences [H] Electronics 9. [I] Astronomy 10. [J] Nature 11. [K] Time 12. [L] Weights and Measures 13. [M] ….

Page 20: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Descending the Hierarchy 1. Anatomy [A] Body Regions [A01] Abdomen

[A01.047] 2. [B] Musculoskeletal System [A02] Back [A01.176] 3. [C] Digestive System [A03] Breast [A01.236] 4. [D] Respiratory System [A04] Extremities

[A01.378] 5. [E] Urogenital System [A05] Head [A01.456] 6. [F] …… Neck [A01.598] 7. [G] …. 8. Physical Sciences [H] Electronics Amplifiers 9. [I] Astronomy Electronics, Medical 10. [J] Nature Transducers 11. [K] Time 12. [L] Weights and Measures 13. [M] ….

Page 21: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Descending the Hierarchy 1. Anatomy [A] Body Regions [A01] Abdomen

[A01.047] 2. [B] Musculoskeletal System [A02] Back [A01.176] 3. [C] Digestive System [A03] Breast [A01.236] 4. [D] Respiratory System [A04] Extremities

[A01.378] 5. [E] Urogenital System [A05] Head [A01.456] 6. [F] …… Neck [A01.598] 7. [G] …. 8. Physical Sciences [H] Electronics Amplifiers 9. [I] Astronomy Electronics, Medical 10. [J] Nature Transducers 11. [K] Time 12. [L] Weights and Measures Calibration 13. [M] …. Metric System Reference

Standard

Page 22: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Descending the Hierarchy 1. Anatomy [A] Body Regions [A01] Abdomen

[A01.047] 2. [B] Musculoskeletal System [A02] Back [A01.176] 3. [C] Digestive System [A03] Breast [A01.236] 4. [D] Respiratory System [A04] Extremities

[A01.378] 5. [E] Urogenital System [A05] Head [A01.456] 6. [F] …… Neck [A01.598] 7. [G] …. 8. Physical Sciences [H] Electronics Amplifiers 9. [I] Astronomy Electronics, Medical 10. [J] Nature Transducers 11. [K] Time 12. [L] Weights and Measures Calibration 13. [M] …. Metric System Reference

Standard

Homogeneous

Heterogeneous

Page 23: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Mapping Nouns to MeSH Concepts

headache recurrence C23.888.592.612.441 C23.550.291.937

headache painC23.888.592.612.441 G11.561.796.444

Page 24: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Levels of Description

headache pain

Level 0: C.23 G.11 Level 1: C23.888 G11.561 Level 1: C23.888.592 G11.561.796 … Original: C23.888.592.612.441 G11.561.796.444

Page 25: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Descent of Hierarchy

Idea: Words falling in homogeneous MeSH

subhierarchies behave “similarly” with respect to relation assignment

Hypothesis: A particular semantic relation holds

between all 2-word NCs that can be categorized by a MeSH category pairs

Page 26: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Grouping the NCs CP: A02 C04 (Musculoskeletal System,

Neoplasms) skull tumors, bone cysts, bone metastases, skull

osteosarcoma… CP: C04 M01 (Neoplasms, Person)

leukemia survivor, lymphoma patients, cancer physician, cancer nurses…

Page 27: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Distribution of Category Pairs

Page 28: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Collection ~70,000 NCs extracted from titles and

abstracts of Medline 2,627 CPs at level 0 (with at least 10 unique

NCs) We analyzed

250 CPs with Anatomy (A) 21 CPs with Natural Science (H01) 3 CPs with Neoplasm (C04)

This represents 10% of total CPs and 20% of total NCs

Page 29: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

For each CP

Divide its NCs into “training-testing” sets

“Training”: inspect NCs by hand Start from level 0 0 While NCs are not all similar

descend one level of the hierarchy Repeat until all NCs for that CP are similar

Classification Method

Page 30: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Classification Decisions A02 C04 B06 B06 C04 M01

C04 M01.643 C04 M01.526

A01 H01 A01 H01.770 A01 H01.671

A01 H01.671.538 A01 H01.671.868

A01 M01 A01 M01.643 A01 M01.526 A01 M01.898

Page 31: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Classification Decisions + Relations

A02 C04 Location of Disease B06 B06 Kind of Plants C04 M01

C04 M01.643 Person afflicted by Disease C04 M01.526 Person who treats Disease

A01 H01 A01 H01.770 A01 H01.671

A01 H01.671.538 A01 H01.671.868

A01 M01 A01 M01.643 A01 M01.526 A01 M01.898

Page 32: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Classification Decisions + Relations

A02 C04 Location of Disease B06 B06 Kind of Plants C04 M01

C04 M01.643 Person afflicted by Disease C04 M01.526 Person who treats Disease

A01 H01 A01 H01.770 A01 H01.671

A01 H01.671.538 A01 H01.671.868

A01 M01 A01 M01.643 Person afflicted by Disease A01 M01.526 A01 M01.898

Page 33: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Classification Decision Levels Anatomy: 250 CPs

187 (75%) remain first level 56 (22%) descend one level 7 (3%) descend two levels

Natural Science (H01): 21 CPs 1 ( 4%) remain first level 8 (39%) descend one level 12 (57%) descend two levels

Neoplasms (C04) 3 CPs: 3 (100%) descend one level

Page 34: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Evaluation Test the decisions on “testing” set Count how many NCs that fall in the groups

defined in the classification decisions are similar to each other

Accuracy (for 2nd noun): Anatomy: 91% Natural Science: 79% Neoplasm: 100%

Total Accuracy : 90.8% Generalization: our 415 classification

decisions cover ~ 46,000 possible CP pairs

Page 35: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Ambiguity – Two Types

Lexical ambiguity: mortality

state of being mortal death rate

Relationship ambiguity: bacteria mortality

death of bacteria death caused by bacteria

Page 36: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Four CasesSingle MeSH senses Multiple MeSH senses

Only one possible relationship: abdomen radiography, aciclovir treatment

Multiple relationships: hospital databases, education efforts, kidney metabolism

Only one possible relationship: alcoholism treatment

Ambiguity of relationship

Multiple relationships bacteria mortality

Page 37: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Four CasesSingle MeSH senses Multiple MeSH senses

Only one possible relationship: abdomen radiography, aciclovir treatment

Multiple relationships: hospital databases, education efforts, kidney metabolism

Only one possible relationship: alcoholism treatment

Ambiguity of relationship

Multiple relationships bacteria mortality

Most problematic cases

… but rare!

Page 38: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Conclusions on NN Relation Classification

Very simple method for assigning semantic relations to two-word technical NCs 90.8% accuracy

Lexical resource (MeSH) useful for this task

Probably works because of the relative lack of ambiguity in this kind of technical text.

Page 39: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Entity-EntityRelation Recognition

Page 40: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Problem: Which relations hold between 2 entities?

Treatment Disease

Cure?

Prevent?

Side Effect?

Page 41: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Hepatitis Examples

Cure These results suggest that con A-induced

hepatitis was ameliorated by pretreatment with TJ-135.

Prevent A two-dose combined hepatitis A and B

vaccine would facilitate immunization programs

Vague Effect of interferon on hepatitis B

Page 42: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Two tasks

Relationship Extraction: Identify the several semantic relations

that can occur between the entities disease and treatment in bioscience text

Entity extraction: Related problem: identify such entities

Page 43: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

The Approach

Data: MEDLINE abstracts and titles Graphical models

Combine in one framework both relation and entity extraction

Both static and dynamic models Simple discriminative approach:

Neural network Lexical, syntactic and semantic

features

Page 44: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Related Work We allow several DIFFERENT relations between

the same entities Thus differs from the problem statement of other

work on relations Many find one relation which holds between

two entities (many based on ACE) Agichtein and Gravano (2000), lexical patterns for location of Zelenko et al. (2002) SVM for person affiliation and

organization-location Hasegawa et al. (ACL 2004) Person-Organization -> President

“relation” Craven (1999, 2001) HMM for subcellular-location and

disorder-association Doesn’t identify the actual relation

Page 45: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Related work: Bioscience

Many hand-built rules Feldman et al. (2002), Friedman et al. (2001) Pustejovsky et al. (2002) Saric et al.; this conference

Page 46: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Data and Relations

MEDLINE, abstracts and titles 3662 sentences labeled

Relevant: 1724 Irrelevant: 1771

e.g., “Patients were followed up for 6 months” 2 types of Entities, many instances

treatment and disease 7 Relationships between these entities

Page 47: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Semantic Relationships 810: Cure

Intravenous immune globulin for recurrent spontaneous abortion

616: Only Disease Social ties and susceptibility to the common

cold 166: Only Treatment

Flucticasone propionate is safe in recommended doses

63: Prevent Statins for prevention of stroke

Page 48: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Semantic Relationships 36: Vague

Phenylbutazone and leukemia 29: Side Effect

Malignant mesodermal mixed tumor of the uterus following irradiation

4: Does NOT cure Evidence for double resistance to

permethrin and malathion in head lice

Page 49: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Features Word Part of speech Phrase constituent Orthographic features

‘is number’, ‘all letters are capitalized’, ‘first letter is capitalized’ …

MeSH (semantic features) Replace words, or sequences of words, with

generalizations via MeSH categories Peritoneum -> Abdomen

Page 50: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Models

2 static generative models 3 dynamic generative models 1 discriminative model (neural

network)

Page 51: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Static Graphical Models S1: observations dependent on Role

but independent from Relation given roles

S2: observations dependent on both Relation and Role

S1 S2

Page 52: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Dynamic Graphical Models

D1, D2 as in S1, S2

D3: only one observation per state isdependent on both the relation and the role

D1

D2

D3

Page 53: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Graphical Models Relation node:

Semantic relation (cure, prevent, none..) expressed in the sentence

Page 54: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Graphical Models

Role nodes: 3 choices: treatment, disease, or

none

Page 55: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Graphical Models

Feature nodes (observed): word, POS, MeSH…

Page 56: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Graphical Models

For Dynamic Model D1: Joint probability distribution over relation,

roles and features nodes

Parameters estimated with maximum likelihood and absolute discounting smoothing

) Role | P(f, Rela) | RoleP(Role

Rela)|oleP(Rela)P(R)f,..f,RoleleP(Rela, Ro

t

T

1t

n

j

jtt-1t

0nTT0

1

10 , ,..,

Page 57: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Neural Network

Feed-forward network (MATLAB) Training with conjugate gradient

descent One hidden layer (hyperbolic tangent

function) Logistic sigmoid function for the output

layer representing the relationships Same features Discriminative approach

Page 58: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Role extraction

Results in terms of F-measure Graphical models

Junction tree algorithm (BNT) Relation hidden and marginalized over

Neural Net Couldn’t run it (features vectors too large)

(Graphical models can do role extraction and relationship classification simultaneously)

Page 59: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Role Extraction: Results

F-measuresD1 best when no smoothing

Page 60: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Role Extraction: ResultsF-measuresD2 best with smoothing, but doesn’t boost

scores as much as in relation classification

Page 61: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Role Extraction: ResultsStatic models better than Dynamic for

Note: No Neural Networks

Page 62: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Relation classification: Results

With Smoothing and Roles, D1 best GM

Page 63: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Features impact: Role Extraction

Most important features: 1)Word, 2)MeSH

Models D1 D2 All features 0.67 0.71 No word 0.58 0.61

-13.4% -14.1% No MeSH 0.63 0.65

-5.9% -8.4%

(rel. + irrel.)

Page 64: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Most important features: Roles

Accuracy: D1 D2 NN All feat. + roles 91.6 82.0 96.9 All feat. – roles 68.9 74.9 79.6

-24.7% -8.7% -17.8% All feat. + roles – Word 91.6 79.8 96.4

0% -2.8% -0.5% All feat. + roles – MeSH 91.6 84.6 97.3

0% 3.1% 0.4%

Features impact: Relation classification

(rel. + irrel.)

Page 65: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Relation extraction Results in terms of classification accuracy

(with and without irrelevant sentences) 2 cases:

Roles hidden Roles given

Graphical models

NN: simple classification problem

)f,..,f,,...,RoleRole,P(RelaRela nTTkRela

^

k

argmax 100

Page 66: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Relation classification: Results

Neural Net always best

Page 67: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Relation classification: Results

With Smoothing and No Roles, D2 best GM

Page 68: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Relation classification: Results

Dynamic models always outperform Static

Page 69: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Relation classification: Results

With no smoothing, D1 best Graphical Model

Page 70: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Relation classification: Confusion Matrix

Computed for the model D2, “rel + irrel.”, “only features”

Page 71: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Features impact: Relation classification

Most realistic case: Roles not known Most important features: 1) Mesh 2) Word for D1

and NN (but vice versa for D2)

Accuracy: D1 D2 NN All feat. – roles 68.9 74.9 79.6 All feat. - roles – Word 66.7 66.1 76.2

-3.3% -11.8% -4.3% All feat. - roles – MeSH 62.7 72.5 74.1

-9.1% -3.2% -6.9% (rel. + irrel.)

Page 72: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Relation Recognition: Conclusions

Classification of subtle semantic relations in bioscience text Discriminative model (neural network) achieves

high classification accuracy Graphical models for the simultaneous extraction

of entities and relationships Importance of lexical hierarchy

Next Step: Different entities/relations Semi-supervised learning to discover relation types

Page 73: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Acquiring Labeled Data using Citances

Page 74: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

A discovery is made …

A paper is written …

Page 75: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

That paper is cited …

and cited …

and cited …

… as the evidence for some fact(s) F.

Page 76: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Each of these in turn are cited for some fact(s) …

… until it is the case that all important facts in the field can be found in citationsentences alone!

Page 77: Semantic Relation Detection in Bioscience Text Marti Hearst SIMS, UC Berkeley  Supported by NSF DBI-0317510 and a gift from

Citances Nearly every statement in a bioscience journal article

is backed up with a cite. It is quite common for papers to be cited 30-100

times. The text around the citation tends to state biological

facts. (Call these citances.)

Different citances will state the same facts in different ways …

… so can we use these for creating models of language expressing semantic relations?

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Using Citances Potential uses of citation sentences (citances)

creation of training and testing data for semantic analysis,

synonym set creation, database curation, document summarization, and information retrieval generally.

Some preliminary results: Citances to a document align well with a hand-built

curation. Citances are good candidates for paraphrase creation.

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Citances for Acquiring Examples of Semantic Relations

A relationship type R between entities of type A and B can be expressed in many ways.

Use citances to build a model the different ways to express the relationship:

Seed learning algorithms with examples that mention A and B, for which relation R holds.

Train a model to recognize R when the relation is not known.

Results may extend to sentences that are not citances as well.

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Issues for Processing Citances

Text span Identification of the appropriate phrase, clause,

or sentence that constructs a citance. Correct mapping of citations when shown as lists

or groups (e.g., “[22-25]”). Grouping citances by topic

Citances that cite the same document should be grouped by the facts they state.

Normalizing or paraphrasing citances For IR, summarization, learning synonyms,

relation extraction, question answering, and machine translation.

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Related Work Traditional citation analysis dates back to the

1960’s (Garfield). Includes: Citation categorization, Context analysis, Citer motivation.

Citation indexing systems, such as ISI’s SCI, and CiteSeer. Mercer and Di Marco (2004) propose to improve

citation indexing using citation types. Bradshaw (2003) introduces Reference Directed

Indexing (RDI), which indexes documents using the terms in the citances citing them.

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Related Work (cont.)

Teufel and Moens (2002) identify citances to improve summarization of the citing paper..

Nanba et. al. (2000) use citances as features for classifying papers into topics.

Related field to citation indexing is the use of link structure and anchor text of Web pages. Applications include: IR, classification, Web

crawlers, and summarization.

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Example: protein-protein

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Early results:Paraphrase Creation from Citances

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Sample Sentences NGF withdrawal from sympathetic neurons

induces Bim, which then contributes to death.

Nerve growth factor withdrawal induces the expression of Bim and mediates Bax dependent cytochrome c release and apoptosis.

The proapoptotic Bcl-2 family member Bim is strongly induced in sympathetic neurons in response to NGF withdrawal.

In neurons, the BH3 only Bcl2 member, Bim, and JNK are both implicated in apoptosis caused by nerve growth factor deprivation.

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Their Paraphrases NGF withdrawal induces Bim. Nerve growth factor withdrawal induces the

expression of Bim. Bim has been shown to be upregulated

following nerve growth factor withdrawal. Bim implicated in apoptosis caused by

nerve growth factor deprivation.

They all paraphrase: Bim is induced after NGF withdrawal.

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Paraphrase Creation Algorithm1. Extract the sentences that cite the target.

2. Mark the NEs of interest (genes/proteins, MeSH terms)

and normalize.3. Dependency parse (MiniPar).4. For each parse

For each pair of NEs of interesti. Extract the path between them.ii. Create a paraphrase from the path.

5. Rank the candidates for a given pair of NEs.6. Select only the ones above a threshold.7. Generalize.

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Creating a Paraphrase

Given the path from the dependency parse:Restore the original word order. Add words to improve grammaticality.

• Bim … shown … be … following nerve growth factor withdrawal.

• Bim [has] [been] shown [to] be [upregulated] following nerve growth factor withdrawal.

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2-word Heuristic Demonstration

NGF withdrawal induces Bim. Nerve growth factor withdrawal induces

[the] expression of Bim. Bim [has] [been] shown [to] be

[upregulated] following nerve growth factor withdrawal.

Bim [is] induced in [sympathetic] neurons in response to NGF withdrawal.

member Bim implicated in apoptosis caused by nerve growth factor deprivation.

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Evaluation (1) An influential journal paper from Neuron:

J. Whitfield, S. Neame, L. Paquet, O. Bernard, and J. Ham. Dominantnegative c-jun promotes neuronal survival by reducing bim expression and inhibiting mitochondrial cytochrome c release. Neuron, 29:629–643, 2001.

99 journal papers citing it 203 citances in total 36 different types of important biological

factoids But we concentrated on one model sentence:

“Bim is induced after NGF withdrawal.”

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Evaluation (2) Set 1: 67 citances pointing to the target

paper and manually found to contain a good or acceptable paraphrase (do not necessarily contain Bim or NGF); (Ideal conditions)

Set 2: 65 citances pointing to the target paper and containing both Bim and NGF;

Set 3: 102 sentences from the 99 texts, containing both Bim and NGF (Do citances do better than arbitrarily chosen

sentences?)

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Correctness (Judgments) Bad (0.0), if:

different relation (often phosphorylation aspect); opposite meaning; vagueness (wording not clear enough).

Acceptable (0.5), If it was not Bad and: contains additional terms (e.g., DP5 protein) or

topics (e.g., PPs like in sympathetic neurons); the relation was suggested but not definitely.

Else Good (1.0)

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Results Obtained 55, 65 and 102 paraphrases for

sets 1, 2 and 3 Only one paraphrase from each sentence

comparison of the dependency path to that of the model sentence

% - good (1.0) or acceptable (0.5)

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Correctness (Recall) Calculated on Set 1 60 paraphrases (out of 67 citances) 5 citances produced 2 paraphrases system recall: 55/67, i.e. 82.09% 10 of the 67 relevant in Set 1 initially

missed by the human annotator 8 good, 2 acceptable.

human recall is 57/67, i.e. 85.07%

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Misses Sample system miss (no NGF):

Growth factor withdrawal was shown to cause increased Bim expression in various populations of neuronal cell types.

Sample human miss: The precise targets of c-Jun necessary for the

induction of apoptosis have been the subject of intense interest and recently, Bim and Dp5, both “BH3-domain only” family members, have been identified as pro-apoptotic genes induced in a c-Jun-dependent manner in both sympathetic neurons subjected to NGF withdrawal and in cerebellar granule cells deprived of KCl.

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Grammaticality Missing coordinating “and”:

“Hrk/DP5 Bim [have] [been] found [to] be upregulated after NGF withdrawal”

Verb subcategorization “caused by NGF role for Bim”

Extra subject words member Bim implicated in apoptosis caused

by NGF deprivation sentence: “In neurons, the BH3-only Bcl2

member, Bim, and JNK are both implicated in apoptosis caused by NGF deprivation.”

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Related Work Word-level paraphrases. Grefenstette uses a

semantic parser to compare the distributional similarity of local contexts for synonyms extraction.

Phrase-level paraphrases. Barzilay&McKeown use POS information from the local context and co-training.

Template paraphrases. Lin&Pantel apply the idea of Grefenstette to dependency tree paths. Later refined by Shinyama&al.

Sentence-level paraphrases. Barzilay&Lee use multiple sequence alignment. Pang&al. merge parse trees into a transducer.

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Relevant Papers Citances: Citation Sentences for Semantic

Analysis of Bioscience Text, Preslav Nakov, Ariel Schwartz, and Marti Hearst, in the SIGIR'04 workshop on Search and Discovery in Bioinformatics.  

Classifying Semantic Relations in Bioscience Text, Barbara Rosario and Marti Hearst, in ACL 2004.  

The Descent of Hierarchy, and Selection in Relational Semantics, Barbara Rosario, Marti Hearst, and Charles Fillmore, in ACL 2002.

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Thank you!

Marti HearstSIMS, UC Berkeley

http://biotext.berkeley.edu

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Additional slides

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Our D1

Thompson et al. 2003Frame classification and role

labeling for FrameNet sentencesTarget word must be observed

More relations and roles

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Smoothing: absolute discounting

Lower the probability of seen events by subtracting a constant from their count (ML estimate: )

The remaining probability is evenly divided by the unseen events

e

MLec

eceP

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0)( if

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ML

MLMLad

events)seen (

events)seen (

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F-measures for role extraction in function of smoothing factors

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Relation accuracies in function of smoothing factors