Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI...
Transcript of Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI...
![Page 1: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/1.jpg)
KENI Pilot
Status Report
![Page 2: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/2.jpg)
Contents
1. Intro and Overview – 3 min. - Joe
2. KENI Architecture – 5 min. – Joe
3. Ontology – 5 min. – Nathan
4. Quant Modeling – 5 min. – Krishna
5. Pilot Model – 7 min – Joe and Krishna
6. Q&A – 5 min.
![Page 3: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/3.jpg)
KENI Pilot Overview
• Purpose - leverage successful representation and computation
methods from an array of disciplines, integrating them into an
interdisciplinary informatics intelligence solution
• Organization - three core components:
– KENI Architecture
– Ontology
– Quant Modeling
• Pilot team - Jessica Adamick (project manager),
Nathan Baker, Brian Davis, Joe Glick (pilot lead), Liz
Hahn-Dantona, Neil Jacobson, Fred Klaessig, Phil
Lippel, Krishna Rajan and Dennis Thomas
![Page 4: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/4.jpg)
Differentiation - Comparison of KENI Initiative with
Wolfram Alpha, Large Knowledge Collider and IBM Watson
IBM Watson KENI - CCR LarKC Wolfram Alpha
Computes Answer Relevance Selected process
outputs
Answer
Approach - Statistical
match
- Computing
power (85,000
watts)
- Contextual parsing
- Concept
quantification
- Relationship
discovery
- Massive,
distributed and
incomplete
reasoning lab
- Linguistic parsing
- Curating
computable
knowledge
User
Systems Custodian
Systems
KENI Engine
Data Sources
Minimum
Information
Requirements
Quant
Formalisms
![Page 5: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/5.jpg)
KENI Components Overview
KENI Architecture Ontology Quant Modeling
Lead Joe Glick Nathan Baker Krishna Rajan
Inputs - existing models
- pilot content
sources
- pilot data & rules
- literature
abstracts
- ontologies
- taxonomies
- candidate data
- computation
methods &
theories
Deliverables - Prototype model
- Computable
Context
Representation
(CCR)
- Sample
content
- Subsumption
architecture
- Sample data,
rules
- Computational
use cases
![Page 6: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/6.jpg)
KENI Architecture - Status
• Initial Content– NPO
– Internano Taxonomy
– ISO Nano Terminology
– USPTO Class 977 Taxonomy & Abstracts
– caNanoLab Publications Abstracts
– (Krishna’s Data)
• Initial Prototype Functionality– Dynamic multi-factor analysis
– Discovery of relationships and common factors
– Multidimensional quantitative exploration
![Page 7: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/7.jpg)
KENI Architecture - Future
• Next Stage Content– NIH Thesaurus
– Biomedical Knowledge Bases
– Materials Science Knowledge Bases
• Computational Approaches:
XXScenario Automation
XXX
Conceptual
Rationalization
XXXCognitive Architectures
XXXXXInteraction Simulation
XXXXRelevance Inference
XXRule Inference
XXXNeural Modeling
UncertaintyComplexitySilosOpaquenessChaosMitigation Strategies
XXScenario Automation
XXX
Conceptual
Rationalization
XXXCognitive Architectures
XXXXXInteraction Simulation
XXXXRelevance Inference
XXRule Inference
XXXNeural Modeling
UncertaintyComplexitySilosOpaquenessChaosMitigation Strategies
![Page 8: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/8.jpg)
KENI project
Meta-ontology subgroup
Jessica Adamick, Nathan Baker, Brian Davis, Joe Glick, Liz Hahn-
Dantona, Fred Klaessig, Phil Lippel, Dennis Thomas
![Page 9: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/9.jpg)
Long-term objectives
• Develop a “consistent” vocabulary for
nanotechnology across its numerous
domains
• Provide structure for integrating existing
terminologies
• Support machine learning, semantic
search, and related informatics
applications
![Page 10: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/10.jpg)
Aim 1: Inventory vocabularies• Collect, identify, and describe the different
taxonomies/terminologies/etc. that are currently available for Nanotechnology
• Possible terminologies– NCImt (NPO, NCIt, HUGO, ChEBI)
– InterNano NanoManufacturing taxonomy
– USPTO Class 977 hierarchical terminology (taxonomy-ish)
– Standards (ISO TC229, ASTM E56, OECD, IEEE)• What is our relationship to these?
• Who are our advocates?
– Other vocabularies?
• How do we deal with proprietary information in this domain (standards copyright, materials genome, etc.)?– Identification of proprietary info through KENI
– Discriminate between things that are business-sensitive and things that are not free
![Page 11: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/11.jpg)
Aim 2: Describe use cases• Describing the use cases for Nanotechnology ontology in the
KENI project (and beyond)
• Identify communities– What are the primary applications and objectives for each
community?• Develop prioritized requirements and use cases
– Variables• Roles (Researcher, program manager, policy maker, infrastructure
provider, clinician, student, worker, …)
• Environments (Regulatory, manufacturing, safety, clinical, research, …)
– Your feedback is needed
• Identify use cases and requirements– Search (semantic capability, resolving synonomy problems,
searching across resources)
– Machine learning (descriptors for QSAR-like studies)
– Annotation (meta-data for deposited information, nano-TAB, journal articles, etc.)
– Reasoning (logical and probabilistic inference)
– Others?
![Page 12: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/12.jpg)
Aim 3: Develop plan of action
• Develop a plan of action for the “meta-ontology” that “combines” the most relevant terminologies
• Terminology alignment/comparison– Semi-automatic
• NLP-based probabilistic approaches
• Ontology-based logical alignment approaches
– Human curation
– How should the output be presented to end-users?
• Deployment– Versioning
– Description language
– Integration with KENI infrastructure/architecture
• Application– What are the first use-case-based demonstrations?
![Page 13: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/13.jpg)
KENI project
Quant Modeling subgroup
Jessica Adamick, Joe Glick,
Phil Lippel, Krishna Rajan
![Page 14: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/14.jpg)
Targeted
Property(s)
“materials genes”
Challenge:
To construct Robust Correlations
between materials properties to features/ characteristics
Methods:
Data Manifold Representations
Dimensionality Reduction
Machine/Statistical Learning
Uncertainty Quantification
Mapping Materials Discovery= F ( x1 , x2 , x3 , x4 , x5 , x6 , x7 , x8 …)
Materials Genome Mapping
![Page 15: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/15.jpg)
Krishna Rajan
Pilot ModelMaterials Science “Cartography
![Page 16: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/16.jpg)
Initial KENI Prototype
• Reminder: we are prototyping the design
and functionality of the KENI engine, not
interfaces for end users, which is the
responsibility of implementation owners
• The KENI platform is a repository for the
integration and rationalization of multi-
disciplinary knowledge and methods for
nanoinformatics research and discovery
![Page 17: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/17.jpg)
Sample data
![Page 18: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/18.jpg)
Prototype Materials Genome Map
Targeted
Property(s)
“materials genes”
Structure
Assumptions
Context Uncertainty, etc.Predictors,
Provenance
Quant
Method
Compound Property
Targeted
Structure(s)
Site
![Page 19: Nanoinformatics Workshop | Nanoinformatics - …nanoinformatics.org/nidocuments/download/KENI Pilot.pdfContents 1. Intro and Overview –3 min. - Joe 2. KENI Architecture –5 min.](https://reader034.fdocuments.net/reader034/viewer/2022050311/5f73167fe644cf1b4d346d09/html5/thumbnails/19.jpg)
Prototype Demo
Q & A