SHAKEN: Knowledge Base (KB) Authoring Environment for Subject ...

SHAKEN: Knowledge Base (KB) Authoring Environment for Subject ...

Technologies to Enable Biologists to Build Large Knowledge Bases on Human Anatomy and Physiology Bruce Porter Ken Barker Art Souther Department of Computer Science University of Texas at Austin Vinay Chaudhri AI Center, Stanford Research Institute

Peter Clark Math and Computing Research Center, Boeing Whats in an Ontology? lexicon to aid communication both for people and computers cataloging system to organize a library a library of multi-media objects meta-level schema for integrating databases so queries can be answered across databases

hierarchy of classes and instances supporting inheritance of general information knowledge base for autonomous reasoning Whats in an Ontology? lexicon to aid communication both for people and computers catalog system to organize a library library contains multi-media objects

strong AI meta-level schema for integrating databases so queries can be answered across databases hierarchy of classes and instances supporting inheritance of general information knowledge base for autonomous reasoning What is Autonomous Reasoning

Good for? answering questions that are unanticipated when the knowledge base is built why and what-if questions answers tailored to users interest and background superhuman performance finding gaps and inconsistencies in the knowledge base raising good questions Knowledge Base Evolution

from expert systems to multifunctional knowledge bases: Mycin and Guidon broadening both the task and the domain Large Multi-functional KB's can be Built e.g. the Botany Knowledge Base 10 year construction effort by full-time domain expert and tools developers contains 40,000 concepts and 160,000 facts much more information available via inheritance and rules

performance goal: robust, expert-level ability to answer questions with good explanations and they can work well: e.g., for the task of generating descriptions Q: What happens during embryo sac formation? A: Embryo sac formation is a kind of female gametophyte formation. During embryo sac formation, the embryo sac is formed from the megaspore mother cell. Embryo sac formation occurs in the ovule. Embryo sac formation is a step of angiosperm sexual reproduction. It consists of megasporogenesis and

embryo sac generation. During megasporogenesis, the megaspore mother cell divides in the nucellus to form 4 megaspores. During embryo sac generation, the embryo sac is generated from the megaspore. and they can work well: e.g., for the task of generating descriptions Q: What happens during embryo sac formation? A: Embryo sac formation is a kind of female gametophyte formation. During embryo sac formation, the embryo sac is formed from the megaspore mother cell. Embryo sac formation occurs in the ovule.

Embryo sac formation is a step of angiosperm sexual reproduction. It consists of megasporogenesis and embryo sac generation. During megasporogenesis, the megaspore mother cell divides in the nucellus to form 4 megaspores. During embryo sac generation, the embryo sac is generated from the megaspore. but we need a better process Enabling Domain Experts to Build Knowledge Bases Why not use knowledge engineers instead?

they are less concerned with the fidelity of the representations they lack the knowledge to simplify and abstract the knowledge thoughtfully they operate with sentence-level facts rather than domain-level theories We envision extensive knowledge bases built by the distributed community of active scientists, and maintained by organizations like NSF, NIH, NLM. Enabling Domain Experts to Build

Knowledge Bases Why not use knowledge engineers instead? they are less concerned with the fidelity of the representations they lack the knowledge to simplify and abstract the knowledge thoughtfully they operate with sentence-level facts rather than domain-level theories We envision extensive knowledge bases built by the distributed community of active scientists, and maintained by organizations like NSF, NIH, NLM.

This will only work if domain experts can work with familiar concepts and without writing axioms! Our Approach Building knowledge bases is a joint effort: knowledge engineers build a library consisting of a small hierarchy of reusable, composable, domainindependent knowledge units (components) a small vocabulary of relations to connect them

knowledge engineers develop generic question answering methods, such as simulation domain specialists build representations of fundamental concepts (pump priming) domain experts build a KB through the instantiation and composition of components supported by DARPAs Rapid Knowledge Formation project

ll a m s A Library of Components easy to learn and use broad semantic distinctions (easy to choose) allows detailed pre-engineering of declarative executable models (Paul Cohen, Umass) drawn from related work

ontology design/knowledge engineering linguistics semantic primitives case theory, discourse analysis, semantics English lexical resources dictionaries, thesauri, word lists WordNet, Roget, LDOCE, corpora, etc. Library Contents

actions things that happen, change states Breach,Enter, Copy, Replace, Transfer, etc. states relatively temporally stable events

Be-Closed, Be-Attached-To, Be-Confined, etc. entities things that are Substance, Place, Object, etc. roles things that are, but only in the context of things that happen

Catalyst,Container, Template, Vehicle, etc. Library Contents relations between events, entities, roles

agent, object, recipient, result, etc. content, part, material, possession, etc. causes, defeats, enables, prevents, etc. purpose, plays, etc. properties between events/entities and values

rate, frequency, intensity, direction, etc. size, color, integrity, shape, etc. Access browsing the hierarchy top-down semantic search

all components have hooks to WordNet climb the WordNet hypernym tree with search terms assemble: Attach, Come-Together mend: Repair infiltrate: Enter, Traverse, Penetrate, Move-Into gum-up: Block, Obstruct busted: Be-Broken, Be-Ruined

A Small Example The software system is called SHAKEN mRNA-Transport: mRNA is transported out of the cell nucleus into the cytoplasm unify location

Real KBs are Significantly Larger Heres part of the representation of mRNAProcessing built by a biologist (Art) Knowledge Types Taxonomic: RNA Capping is-a-kind-of Attach Partonomic: Eucaryotic Cell has-parts Nucleus, Mitochondrion

Causal: RNA Capping enables mRNA Export Subevents: mRNA processing has-subevents RNA Capping, Polyadenylation, mRNA Splicing . . . Temporal: RNA Capping occurs-before mRNA Export Knowledge Types

Qualitative Influences: RNA Capping inhibits mRNA Degradation Spatial Information: Eucaryotic Primary RNA Transcript has-region 5-prime UTR Structural: Nuclear Envelope encloses mRNA Telic: RNA polymerase has-purpose to be a Catalyst in

Polyadenylation Imagery: graphics and animation Evaluation Can Domain Experts learn to use the library to encode domain knowledge? Can sophisticated knowledge be captured through composition of components? Methodology

train biologists (4 graduate students) for six days have them encode knowledge from a college textbook, Essential Cell Biology by Bruce Alberts supply end-of-the-chapter-style Biology questions have the biologists pose the questions to their knowledge bases and record the answers have another biologist evaluate the answers on a scale of 0-3 qualitatively evaluate their KBs Some Example Questions What nucleotide base pairs with adenine in RNA?

How is uracil in RNA like thymine in DNA? What is the relationship between thymine and uracil? For a given bacterial gene, how are bacterial RNA and DNA molecules different? Describe RNA as a kind of polymer. What are the four bases/nucleotides of RNA? What is the relationship between a DNA gene and its RNA transcription product? Evaluation Question Answering Evaluation Productivity

Axioms 1000 2.5 2.0 1.5 Structural Implication Total 1.0

0.5 0.0 6/25 7/2 7/9 7/16 7/23

7/30 Summary Multi-functional knowledge bases can be built by domain experts, almost and they will be, with or without sound principles of ontological engineering and ontologists can significantly improve the results Summary Multi-functional knowledge bases can be built

by domain experts, almost and they will be, with or without sound principles of ontological engineering and ontologists can significantly improve the results Art and I would love to give you a demo! Ask us how you can get a PC version of SHAKEN for research use

Recently Viewed Presentations

  •   .      5  2013 1 : 1.  : ,

    . 5 2013 1 : 1. : ,

    Во ова предавање тие поимно се разграничуваат. Глаголскиот вид (Aktionsart) е лексичко-семантичка (објективна) категорија што ги изразува текот и степените на дејството (Левандовски 1990: 37).
  • ANL Talk

    ANL Talk

    Mass threshold Total Angular Momentum Orbital Angular Momentum Spin Angular Momentum Means: Quark Spin=1 (3 = 2 x 1 + 1) Quark Orbital Ang. Mom. = 0 Total J/y Spin = 1 Means: Total J/y Spin = 1 Parity is...
  • Povijesni razvij računala

    Povijesni razvij računala

    Nijemac Wilhelm Gottfried Leibniz izradio je stroj koji je izvodio 4 osnovne matematičke operacije (zbrajanje, oduzimanje, množenje i dijeljenje). Proučavao binarni brojevni sustav koji je osnova današnjih računala. ... (Electronic Numerical Integrator and Calculator), prvo računalo na ...
  • Apresentação do PowerPoint - WordPress.com

    Apresentação do PowerPoint - WordPress.com

    formaÇÃo continuada para professores da educaÇÃo bÁsica na Área de educaÇÃo do campo - moodle. formaÇÃo continuada para professores de matemÁtica no moodle. auxiliar de cozinha. certific camareira. certific pedreiro. instituto federal de roraima campus de amajari. amajari. operador de...
  • E-safety and what you need to know - Primary school

    E-safety and what you need to know - Primary school

    Don't give anyone your address! This is super dangerous! You don't know who is behind the screen! Don't mention your full name! Before getting any social media make sure to ask your parents permission and make sure have a private...
  • The MEP Recruiter - FL

    The MEP Recruiter - FL

    Self-starter. Knows local roads and has a good sense of direction. Knows local agricultural and fishing production and processing activities. Module 2 Level 1. National ID&R Curriculum, Funded by the U.S. Department of Education, V 2.0
  • The Mutual Reward Theory - University of Idaho

    The Mutual Reward Theory - University of Idaho

    The Mutual Reward Theory A manager cannot become a leader without helping employees become followers Employees that become followers do so voluntarily. There must be an element of trust and a strong belief that life will be better as a...
  • Open Geography as a Concept: - conference-service.com

    Open Geography as a Concept: - conference-service.com

    Open Geography is a combination of user needs, data, products, and dissemination. The portals are the primary means of disseminating geography data. The design of them is informed by user feedback and requirements.