José Luis Ambite
- Principal Scientist
- Information Sciences Institute
- University of Southern California
-
4676 Admiralty Way, Suite 1001
- Marina del Rey, CA 90292
- Email:
- Phone: +1-310-448-8472
- Fax: +1-310-822-0751
- Research Associate Professor
- Computer Science Department
- University of Southern California
- Senior Research Scientist
- Digital Government Research Center
- University of Southern California
Research
My core expertise is on information integration, including query rewriting under
constrains, learning schema mappings, and entity linkage. I have research interests
in databases, knowledge representation, semantic web, scientific workflows,
federated learning, biomedical informatics, and genetics.
I'm a member of the USC/ISI Information Integration
Research Group and the USC Computer Science Database Group.
Current Projects
-
DARPA Cooperative Secure Learning
SHELFI: Secure Heterogeneous Learning Federation with Information-Theoretic Guarantees.
There are situations where data relevant to a machine learning problem
are distributed among multiple locations that cannot share the data
due to regulatory, competitiveness, security, or privacy reasons. for
example, medical records at different hospitals. A recent promising
approach is Federated Learning that can learn deep neural networks
from data silos by aggregating locally-computed model
updates. However, the current state of the art in Federated Learning
suffers from slow convergence rates, and learning performance degrades
in heterogeneous environments where each site has different amounts of
data, target class distributions, or computational capabilities.
To address the multiple challenges of privacy, security, efficient
learning, and heterogeneous data and computational environments, we
propose a novel approach to secure heterogeneous federated learning
with information-theoretic guarantees that can learn a joint complex
neural network model over all the available data without any data
sharing, while providing faster convergence, minimizing information
data leakage, and performing well in heterogeneous environments.
We applying our architecture to the high-profile neuroscience
datasets, such as the ENIGMA
Consortium, and the neuroimgaing subset of the UK
Biobank.
-
NIH-NIBIB
Pediatric Research using Integrated Sensor Monitoring Systems
(PRISMS): Data and Software Coordination and Integration Center
(DSCIC)
The major goals of the PRISMS-DSCIC are (1) to integrate
environmental, physiological, and behavioral data produced by the
sensor-based health monitoring systems funded under PRISMS and data
from relevant external sources, and (2) facilitate access, analysis,
and dissemination of such data and software generated by PRISMS
program. Program
description at NIBIB.
USC News item on PRISMS:
USC, UCLA to develop children's asthma prediction app.
-
BigDataU: the NIH Big Data to Knowledge (BD2K) Biomedical Data Science Training
Coordination Center
(RFA)
The goal of BigDataU is to develop an online education platform to
automatically identify, describe, organize, and personalize web-based
open training materials in biomedical data science.
USC News items on BigDataU:
-
NIMH
SchizConnect
This project integrates schizophrenia neuroimaging-related data from
disparate, heterogeneous databases. This gives you access to
multi-site, multi-dimensional, multi-modal data all in one place.
ISI News item on SchizConnect:
A Beautiful Find: Facilitating Schizophrenia Research.
-
DARPA
Big Mechanism
L2K2R2: Learn to Read to Know, Know to Learn to Read
This project reads the cancer literature to automatically
extract relevant pathway knowledge and causal models.
-
NHGRI
Population Architecture
using Genomics and Epidemiology (PAGE) Coordinating Center
The Coordinating Center provides data integration and grid computing
infrastructure for the investigation, in well-characterized population
studies, of genetic variants identified as potentially causally
associated with complex diseases in genome-wide association and other
genetic studies.
-
NIMH
Repository and Genomics
Resource (aka Center for Collaborative Genomic Studies of Mental Disorders)
We provide data integration and grid computing infrastructure to support
the NIMH Center for Collaborative Genetic Studies of Mental Disorders,
which is investigating the inherited (genetic), environmental and
physiologic causes of mental disorders, such as schizophrenia, bipolar
disorder, depression, and autism.
Past Projects
-
NIH-NHLBI
PhenoExplorer
The goal of this project is to automatically discover related
phenotypes across multiple studies. This is a common problem in many
biomedical domains, and especially needed in gentics studies, such
as those deposited at
dbGaP. We use a
combination of machine-learning, record-linkage and information retrieval
techniques to construct a semantic similarity metric between the
definitions of phenotypic variables. This project is
funded under NHLBI's
pFINDR program.
-
NIH-NIGMS
Biomedical Informatics Research
Network (BIRN)
The major goal of this project is to develop a federated and
distributed infrastructure for the storage, retrieval, analysis, and
documentation of biomedical data for the NCRR Biomedical Informatics
Research Network. My major focus within BIRN is on the developement
of the BIRN mediator, a data integration system.
-
Southern California Clinical and
Translational Science Institute (SC-CTSI) Center for Biomedical
Informatics Sciences (CBIS)
The SC-CSTI CBIS's vision is to create a shared, common informatics infrastructure to serve as the cornerstone for information acquisition, management, integration, and analysis of needs across the CTSI.
-
Argos focused on
automatic web service composition, applied to a transportation
planning domain.
-
The Center for Health Informatics aimed to provide a secure,
seamless, global computing platform for creating and exchanging
health information between the public, private and academic sectors.
- EntityBases developed techniques to extract, link, and
integrate massive amounts of data from numerous heterogeneous sources.
-
CALO (Cognitive Assistant that
Learns and Organizes): facilitating information integration by learning source models.
- Heracles is an
interactive data-driven constraint-based hierarchical planner.
- SIMS and Ariadne are mediator architectures that integrate
information from distributed and heterogeneous data sources.
- The DGRC Energy Data
Collection (EDC) project integrates information from government
databases and extends the integration framework of SIMS by leveraging
large ontologies such as SENSUS (now OMEGA
) and natural language processing techniques.
-
Proteus focuses on
web service composition and execution.
Courses
-
Spring 2019: CSCI 648, Advanced Information Integration
(Syllabus)
Instructors:
Jose Luis Ambite,
Shobeir Fakhraei
-
Spring 2019: CSCI 548, Information Integration on the Web
(Syllabus)
Instructors:
Jose Luis Ambite,
Shobeir Fakhraei
-
Fall 2016: CSCI 548, Information Integration on the Web
(Syllabus)
Instructors:
Jose Luis Ambite,
Mayank Kejriwal
-
Spring 2015: CSCI 548, Information Integration on the Web
(Syllabus)
Instructors:
Jose Luis Ambite,
Craig Knoblock
-
Spring 2014: CSCI 548, Information Integration on the Web
(Syllabus)
Instructors:
Jose Luis Ambite,
Pedro Szekely
-
Fall 2013: CSCI 599, Foundations of Databases, Knowledge Representation,
Data Integration and Data Exchange
(Syllabus)
Instructors:
Jose Luis Ambite,
George Konstantinidis
-
Spring 2013: CSCI 548, Information Integration on the Web
(Syllabus)
Instructors:
Jose Luis Ambite,
Pedro Szekely
-
Spring 2012: CSCI 548, Information Integration on the Web
(Syllabus)
Instructors:
Craig Knoblock,
Pedro Szekely,
Jose Luis Ambite
-
Spring 2011: CSCI 548, Information Integration on the Web
(Syllabus)
Instructors:
Kristina Lerman,
Jose Luis Ambite
-
ICAPS 2004
Tutorial on Planning on the Web
Whistler, British Columbia, Canada, 3 June 2004
Craig Knoblock and
Jose Luis Ambite
-
Fall 2003: CS 541,
Artificial Intelligence Planning
Instructors:
Jim Blythe,
Jose Luis Ambite
and
Yolanda Gil.
Workshops
-
The 4th International Workshop on AI for Service Composition
in conjunction with
The 17th European Conference on Artificial Intelligence
(ECAI 2006)
Riva del Garda, Trento, Italy, 28 August 2006
Organizing Committee:
Jose Luis Ambite,
Jim Blythe,
Jana Koehler,
Sheila McIlraith,
Marco Pistore,
Biplav Srivastava.
-
AAAI 2005
Workshop on Exploring Planning and Scheduling for Web Services, Grid and Autonomic Computing
Pittsburgh, Pennsylvania, 9-10 July 2005
Organizing Committee:
Biplav Srivastava (co-chair),
Jim Blythe (co-chair),
Jose Luis Ambite,
Yun-Heh (Jessica)
Chen-Burger,
Subbarao Kambhampati,
Sheila McIlraith,
Paolo Traverso.
-
ICAPS 2004
Workshop on Planning and Scheduling for Web and Grid Services
Whistler, British Columbia, Canada, 4 June 2004
Organizing Committee:
Jim Blythe (co-chair),
Jose Luis Ambite (co-chair),
Derek Long,
Drew McDermott,
Sheila McIlraith,
Biplav Srivastava, and
Paolo Traverso.
-
ICAPS 2003
Workshop on Planning for Web Services
Trento, Italy, 10 June 2003
Organizing Committee:
Jose Luis Ambite,
Craig Knoblock,
Sheila McIlraith,
Mike P. Papazoglou,
Biplav Srivastava, and
Paolo Traverso.
Publications
-
My Publications in
PubMed,
Google
Scholar,
DBLP
-
Semi-Synchronous Federated Learning for Energy-Efficient Training and Accelerated Convergence in Cross-Silo Settings.,
Dimitris Stripelis, Paul M. Thompson, and Jose Luis Ambite
ACM Transactions on Intelligent Systems and Technology13(5). 2022.
-
Rapid
detection of identity-by-descent tracts for mega-scale datasets,
Ruhollah Shemirani, Gillian M. Belbin, Christy L. Avery, Eimear
E. Kenny, Christopher R. Gignoux, Jose Luis Ambite.
Nature Communications 12, 3546. 2021.
-
Genetic
analyses of diverse populations improves discovery for complex
traits. Wojcik et al.
Nature. 2019 Jun; 570(7762):514-518. doi:10.1038/s41586-019-1310-4. Epub 2019 Jun 19.
-
Secure neuroimaging analysis using federated learning with homomorphic encryption.
Dimitris Stripelis, Hamza Saleem, Tanmay Ghai, Nikhil Dhinagar, Umang
Gupta, Chrysovalantis Anastasiou, Greg Ver Steeg, Srivatsan Ravi, Muhammad
Naveed, Paul M.Thompson, and Jose Luis Ambite.
17th International Symposium on Medical Information Processing and Analysis (SIPAIM),
Campinas, Brazil, 2021.
-
3D Convolutional Neural Networks for Classification of Alzheimer's and Parkinson's Disease with T1-Weighted Brain MRI
.
Nikhil J. Dhinagar, Sophia I. Thomopoulos, Conor Owens-Walton, Dimitris Stripelis, Jose Luis Ambite, Greg Ver Steeg, Daniel Weintraub, Philip Cook, Corey McMillan, Paul M. Thompson.
17th International Symposium on Medical Information Processing and Analysis (SIPAIM),
Campinas, Brazil, 2021.
-
Scaling
Neuroscience Research using Federated Learning.
Dimitris Stripelis, Jose Luis Ambite, Pradeep Lam, and Paul Thompson.
International Symposium on Biomedical Imaging (ISBI). Nice, France,
2021.
-
Membership inference attacks on deep regression models for neuroimaging.
Umang Gupta, Dimitris Stripelis, Pradeep K. Lam, Paul M. Thompson,
Jose Luis Ambite, and Greg Ver Steeg
Medical Imaging with Deep Learning (MIDL),
Zurich, Switzerland.
2021.
-
NSEEN: Neural Semantic Embedding for Entity Normalization.
Shobeir Fakhraei, Joel Mathew, and Jose Luis Ambite.
European Conference on Machine Learning and Principles and
Practice of Knowledge Discovery in Databases (ECML-PKDD-2019),Würzburg, Germany.
-
Finding Prerequisite Relations using the Wikipedia Clickstream.
Mohsen Sayyadiharikandeh, Jonathan Gordon, Jose Luis Ambite,
Kristina Lerman.
Wiki Workshop 2019. WWW'19 Companion, San Francisco, CA, USA.
-
Linking educational resources on data science.
Jose Luis Ambite, Jonathan Gordon, Lily Fierro, Gully Burns, Joel Mathew.
Proceedings of the 31st Innovative Applications of Artificial Intelligence Conference (IAAI).
Honolulu, Hawaii, 2019.
-
Biomedical Named Entity Recognition via Reference-Set Augmented
Bootstrapping.
Joel Mathew, Shobeir Fakhraei, Jose Luis Ambite
ICML Workshop on Computational Biology, Long Beach, CA, 2019
-
BD2K Training Coordinating Center's ERuDIte: the Educational Resource Discovery Index for Data Science.
Jose Luis Ambite, Lily Fierro, Jonathan Gordon, Gully A. Burns, Florian Geigl, Kristina Lerman, John D. Van Horn
IEEE Transactions on Emerging Topics in Computing 9 (1), 316-328, 1 Jan.-March 2021, doi: 10.1109/TETC.2019.2903466.
-
Exploiting spatiotemporal patterns for accurate air quality forecasting using deep learning.
Yijun Lin, Nikhit Mago, Yu Gao, Yaguang Li, Yao-Yi Chiang, Cyrus Shahabi, Jose Luis Ambite.
Proceedings of the 26th ACM SIGSPATIAL International Conference
on Advances in Geographic Information Systems (SIGSPATIAL).
Seattle, WA, USA, 2018.
-
Democratizing data science through data science training.
JD Van Horn, L Fierro, J Kamdar, J Gordon, C Stewart, A Bhattrai,
S Abe, X Lei, C O'Driscoll, A Sinha, P Jain, G Burns, K Lerman, and
JL Ambite.
Biocomputing 2018, Proceedings of the Pacific Symposium.
Kohala Coast, HI, 2018.
-
Extending Apache Spark with a Mediation Layer.
Dimitris Stripelis, Chrysovalantis Anastasiou, Jose Luis Ambite.
International Semantic Big Data Workshop, SIGMOD
Houston, TX, 2018.
-
Genetic Diversity Turns a New PAGE in Our Understanding of Complex Traits.
G Wojick et al.
bioRxiv, 2017.
-
Ultra-rapid detection of identity-by-descent tracts for biobank-scale inference.
R. Shemirani, G.M. Belbin, E.E. Kenny, C.R. Gignoux, and J.L. Ambite.
67th Annual Meeting of the American Society of Human Genetics.
Orlando, FL, 2017.
-
A neural named entity recognition approach to biological entity identification.
Emily Sheng, Scott Miller, Jose Luis Ambite, and Prem Natarajan
BioCreative VI Challenge and Workshop.
Bethesda, MD, 2017.
-
Mining public datasets for modeling intra-city PM2:5 concentrations at a fine spatial resolution.
Yijun Lin, Fan Pan, Yao-Yi Chiang, Dimitris Stripelis, Jose Luis Ambite, Sandrah P. Eckel, and Rima Habre.
ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems.
Redondo Beach, CA, 2017.
-
The BD2K training coordinating centers data science education platform.
Jose Luis Ambite, Lily Fierro, Florian Geigl, Jonathan Gordon, Gully A.P.C. Burns, Kristina Lerman, Jeana Kamdar, Crystal Stewart, Avnish Bhattrai, Xiaoyu Lei, Sumiko Abe, and John Darrell Van Horn.
American Medical Informatics Association (AMIA) Annual Symposium (System Demonstration).
Washington, DC, 2017.
-
A Scalable Data Integration and Analysis Architecture for Sensor Data of Pediatric Asthma.
Dimitris Stripelis, Jose Luis Ambite, Yao-Yi Chiang, Sandrah P. Eckel, Rima Habre
IEEE International Conference on Data Engineering (ICDE).
San Diego, CA, 2017. Demonstration Paper.
-
BD2K ERuDIte: the Educational Resource Discovery Index for Data
Science.
Jose Luis Ambite, Kristina Lerman, Lily Fierro, Florian Geigl,
Jonathan Gordon, Gully A. Burns, John D. Van Horn
Proceedings of the 26th International Conference on World Wide Web. WWW'17 Companion. (The 4th WWW Workshop on Big Scholarly Data: Towards the Web of Scholars).
Perth, Australia, 2017.
doi:10.1145/3041021.3053060.BD2K
-
Leveraging Linked Data to Discover Semantic Relations within Data Sources.
Mohsen Taheriyan, Craig A. Knoblock, Pedro Szekely, Jose Luis Ambite
Proceedings of the 15th International Semantic Web Conference
(ISWC).
Kobe, Japan, 2016.
-
Abstract Meaning Representations as Linked Data.
Gully Burns, Ulf Hermjakob and Jose Luis Ambite
Proceedings of the 15th International Semantic Web Conference
(ISWC),
Kobe, Japan, 2016.
-
Learning the semantics of structured data sources.
Mohsen Taheriyan, Craig A. Knoblock, Pedro Szekely, Jose Luis Ambite
Web Semantics: Science, Services and Agents on the World Wide Web,
Volumes 37-38, Pages 152-169. March 2016.
-
SchizConnect: Virtual Data Integration in Neuroimaging.
Ambite, J.L., Tallis, M., Alpert, K., Keator, D., King, M., Landis, D.,
Konstantinidis, G., Calhoun, V., Potkin, S., Turner, J., Wang, L.
Data Integration in the Life Sciences (DILS). 2015.
-
GEM: The GAAIN Entity Mapper.
Naveen Ashish, Peehoo Dewan, Jose Luis Ambite, Arthur W. Toga.
Data Integration in the Life Sciences (DILS). 2015.
-
Terminology Development Towards Harmonizing Multiple Clinical
Neuroimaging Research Repositories.
Turner, J., Pasquerello, D., Turner, M., Keator, D., Alpert, K., King,
M., Landis, D., Calhoun, V., Potkin, S., Tallis, M., Ambite, J.L., Wang, L.
Data Integration in the Life Sciences (DILS). 2015.
-
Optimizing the Chase: Scalable Data Integration under Constraints.
George Konstantinidis and Jose Luis Ambite.
PVLDB 7(14):1869-1880. 2014.
-
A Scalable Approach to Learn Semantic Models of Structured Sources.
Taheriyan, M.; Knoblock, C. A.; Szekely, P.; and Ambite, J. L.
Proceedings of the 8th IEEE International Conference on Semantic Computing, 2014.
-
Phenome-Wide Association Study (PheWAS) for Detection of
Pleiotropy within the Population Architecture using Genomics and
Epidemiology (PAGE) Network.
Pendergrass SA, Brown-Gentry K, Dudek S, Frase A, Torstenson ES, Goodloe R, Ambite JL, Avery CL, Buyske S, Buzcova P, Deelman E, Fesinmeyer MD, Haiman CA, Heiss G, Hindorff LA, Hsu CN, Jackson RD, Kooperberg C, Le Marchand L, Lin Y, Matise TC, Monroe KR, Moreland L, Park SL, Reiner A, Wallace R, Wilkens LR, Crawford DC, Ritchie MD.
PLoS Genetics 9(1):e1003087, 2013. doi:10.1371/journal.pgen.1003087
-
Aligning Ontologies of Linked Data.
Rahul Parundekar, Craig Knoblock, and Jose Luis Ambite.
In Andreas Harth, Katja hose, and Ralf Schenkel (editors),
Linked Data Management: Principles and Techniques,
CRC Press, 2014.
-
A Graph-based Approach to Learn Semantic Descriptions of Data Sources.
Taheriyan, M.; Knoblock, C. A.; Szekely, P.; and Ambite, J. L.
Proceedings of the 12th International Semantic Web Conference (ISWC 2013),
Sydney, Australia, 2013.
-
Discovering Concept Coverings in Ontologies of Linked Data
Sources.
Rahul Parundekar, Craig Knoblock, and Jose Luis Ambite.
Proceedings of the 11th International Semantic Web Conference (ISWC 2012),
Boston, Massachusetts, 2012.
Best Research Paper Award.
-
Rapidly Integrating Services into the Linked Data Cloud.
Mohsen Taheriyan, Craig Knoblock, Pedro Szekely and Jose Luis Ambite.
Proceedings of the 11th International Semantic Web Conference (ISWC 2012),
Boston, Massachusetts, 2012.
-
Semi-Automatically Mapping Structured Sources into the
Semantic Web.
Craig Knoblock, Pedro Szekely, Jose Luis Ambite, Aman Goel,
Shubham Gupta, Kristina Lerman, Parag Mallick, Maria Muslea and Mohsen
Taheriyan.
Proceedings of the 9th Extended Semantic Web Conference (ESWC
2012),
Heraklion, Crete, Greece, 2012.
-
Optimizing Query Rewriting for Multiple Queries.
George Konstantinidis and Jose Luis Ambite.
Proceedings of the 9th Workshop on
Information Integration on the Web (IIWeb 2012).
Scottsdale, Arizona, 2012.
-
Consistent Directions of Effect for Established Type 2 Diabetes
Risk Variants Across Populations: The Population Architecture using
Genomics and Epidemiology (PAGE) Consortium.
Haiman CA, Fesinmeyer MD, Spencer KL, BuzkovC! P, Voruganti VS, Wan P,
Haessler J, Franceschini N, Monroe KR, Howard BV, Jackson RD, Florez
JC, Kolonel LN, Buyske S, Goodloe RJ, Liu S, Manson JE, Meigs JB,
Waters K, Mukamal KJ, Pendergrass SA, Shrader P, Wilkens LR, Hindorff
LA, Ambite JL, North KE, Peters U, Crawford DC, Le Marchand L, Pankow JS.
Diabetes 61(6), 2012. doi:10.2337/db11-1296
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A Phenomics-Based Strategy Identifies Loci on APOC1, BRAP, and
PLCG1 Associated with Metabolic Syndrome Phenotype Domains.
CL Avery, Q He, KE North, JL Ambite, E Boerwinkle, M Fornage, LA
Hindorff, C Kooperberg, JB Meigs, JS Pankow, SA Pendergrass, BM Psaty,
MD Ritchie, JI Rotter, KD Taylor, LR Wilkens, G Heiss, DY Lin
PLoS Genetics 7(10), 2012. doi:10.1371/journal.pgen.1002322
-
Evaluation of the Metabochip Genotyping Array in African Americans
and Implications for Fine Mapping of GWAS-Identified Loci: The PAGE Study.
S Buyske, Y Wu, CL Carty, I Cheng, TL Assimes, L Dumitrescu, LA Hindorff, S Mitchell,
JL Ambite, E Boerwinkle, P Buzkova, CS Carlson, B Cochran, D Duggan, CB Eaton,
MD Fesinmeyer, N Franceschini, J Haessler, N
Jenny, HM Kang, C Kooperberg, Y Lin, L Le
Marchand, TC Matise, JG Robinson, C
Rodriguez, FR Schumacher, BF Voight, A
Young, TA Manolio, KL Mohlke, CA Haiman, U Peters, DC Crawford, KE North
PLoS One 7(4),
2012. doi:10.1371/journal.pone.0035651
-
Exploring Label Dependency in Active Learning for Phenotype Mapping.
Shefali Sharma, Leslie Lange, Jose Luis Ambite, Yigal Arens, and Chun-Nan Hsu.
Proceedings of the 2012 Workshop on Biomedical Natural Language Processing (BioNLP-2012), Association for Computational
Linguistics, Montreal, Canada, 2012
-
Scalable Query Rewriting: A Graph-Based Approach.
George Konstantinidis and Jose Luis Ambite.
Proceedings of the ACM SIGMOD International Conference on Management of Data (SIGMOD 2011), Athens, Greece, 2011.
-
Learning phenotype mapping for integrating large genetic data.
Chun-Nan Hsu, Cheng-Ju Kuo, Congxing Cai, Sarah A. Pendergrass, Marylyn D. Ritchie, and Jose Luis Ambite.
Proceedings of BioNLP 2011 Workshop (BioNLP '11).
Association for Computational Linguistics, Stroudsburg, PA, USA, 2011.
-
Genetic Determinants of Lipid Traits in Diverse Populations from
the Population Architecture using Genomics and Epidemiology (PAGE)
Study
L Dumitrescu, CL Carty, K Taylor, FR Schumacher, LA Hindorff, JL Ambite, G
Anderson, LG Best, K Brown-Gentry, P Buzkova,
CS Carlson, B Cochran, SA Cole, RB Devereux, D Duggan, CB Eaton, M Fornage,
N Franceschini, J Haessler, BV Howard, KC Johnson, S Laston, LN Kolonel, ET Lee,
JW MacCluer, TA Manolio, SA Pendergrass, M
Quibrera, RV Shohet, LR Wilkens, CA Haiman, L Le Marchand, S Buyske, C Kooperberg, KE North, DC Crawford
PLoS Genetics 7(6), 2011.
doi:10.1371/journal.pgen.1002138
-
The use of phenome-wide association studies (PheWAS) for
exploration of novel genotype-phenotype relationships and pleiotropy
discovery.
Pendergrass SA, Brown-Gentry K, Dudek SM, Torstenson ES, Ambite JL,
Avery CL, Buyske S, Cai C, Fesinmeyer MD, Haiman C, Heiss G, Hindorff
LA, Hsu CN, Jackson RD, Kooperberg C, Le Marchand L, Lin Y, Matise TC,
Moreland L, Monroe K, Reiner AP, Wallace R, Wilkens LR, Crawford DC,
Ritchie MD.
Genetic Epidemiology 35(5):410-422, 2011.
doi:10.1002/gepi.20589
-
The Next PAGE in Understanding Complex Traits: Design for the Analysis of Population Architecture Using Genetics and Epidemiology (PAGE) Study.
Tara C. Matise, Jose Luis Ambite, Steven Buyske, Steven, Chris S. Carlson, Shelley A. Cole, Dana C. Crawford, Chris A. Haiman, Gerardo Heiss, Charles Kooperberg, Loic Le Marchand, Teri A. Manolio, Kari E. North, Ulrike Peters, Marylyn D. Ritchie, Lucia A. Hindorff, Jonathan L. Haines, for the PAGE Study
American Journal of Epidemiology 174 (7): 849-859, 2011. doi:10.1093/aje/kwr160
-
Enabling collaborative research using the Biomedical Informatics Research Network (BIRN).
Karl G Helmer, Jose Luis Ambite, Joseph Ames, Rachana Ananthakrishnan, Gully Burns, Ann L Chervenak, Ian Foster, Lee Liming, David Keator, Fabio Macciardi, Ravi Madduri, John-Paul Navarro, Steven Potkin, Bruce Rosen, Seth Ruffins, Robert Schuler, Jessica A Turner, Arthur Toga, Christina Williams, Carl Kesselman, for the Biomedical Informatics Research Network
Journal of the American Medical Informatics Association JAMIA 2011;18:416-422, 2011.
doi:10.1136/amiajnl-2010-000032
-
Neuroscience data integration through mediation: an (F)BIRN case study.
Naveen Ashish, Jose Luis Ambite, Maria Muslea and Jessica A. Turner.
Frontiers in Neuroinformatics 4:118, 2010.
doi: 10.3389/fninf.2010.00118
-
Linking and Building Ontologies of Linked Data.
Rahul Parundekar, Craig A. Knoblock and Jose Luis Ambite.
Proceedings of the 9th International Semantic Web Conference
(ISWC 2010), Shanghai, China, 2010.
-
Automatically
constructing semantic web services from online sources
Jose Luis Ambite, Sirish Darbha, Aman Goel,Craig A. Knoblock, Kristina
Lerman, Rahul Parundekar, and Thomas Russ.
Proceedings of the 8th International Semantic Web Conference
(ISWC 2009), Washington, D.C., 2009.
-
Interactive data integration through smart copy & paste.
Zachary G. Ives, Craig A. Knoblock, Steven Minton, Marie Jacob, Partha Pratim Talukdar, Rattapoom Tuchinda, Jose Luis Ambite, Maria Muslea, and Cenk Gazen.
Fourth Biennial Conference on Innovative Data Systems
Research (CIDR), Pacific Grove, CA, January 2009.
-
Discovering and learning semantic models of online sources for information integration.
Jose Luis Ambite, Bora Gazen, Craig A. Knoblock, Kristina
Lerman, and Thomas Russ
Proceedings of the IJCAI Workshop on Information Integration
on the Web, Pasadena, CA, 2009.
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Exploiting data semantics to discover, extract, and model web sources.
Jose Luis Ambite, Craig A. Knoblock, Kristina Lerman, Anon Plangprasopchok, Thomas Russ, Cenk Gazen, Steven Minton, and Mark Carman.
Proceedings of the First International Workshop on Semantic Aspects in Data Mining (SADM'08), 2008.
-
Beyond the Elves: Making Intelligent Agents Intelligent
Craig A. Knoblock, Jose Luis Ambite, Mark Carman,Matthew Michelson, Pedro Szekely and Rattapoom Tuchinda.
AI Magazine, 29(2). Summer 2008.
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Automatically Composing Data Workflows with Relational Descriptions and Shim Services
Jose Luis Ambite and Dipsy Kapoor.
Proceedings of the 6th International Semantic Web Conference (ISWC-2007), Busan, Korea, November 2007.
-
Quality-Driven Geospatial Data Integration
Snehal Thakkar, Craig A. Knoblock and Jose Luis Ambite.
Proceedings of the 15th ACM International Symposium on Advances in Geographic Information Systems (ACM GIS 2007), Seattle, WA, November 2007.
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EntityBases: Compiling, organizing and querying massive entity repositories.
Craig A. Knoblock, Jose Luis Ambite, Kavita Ganesan, Maria Muslea, Steven
Minton, Greg Barish, Evan Gamble, Claude Nanjo, Kane See, Cyrus Shahabi, ,
and Ching-Chien Chen.
Proceedings of the International Conference on Artificial Intelligence
(ICAI'07), Las Vegas, Nevada, USA, June 2007.
-
Automatic Generation of Data Processing Workflows for Transportation Modeling
Jose Luis Ambite and Dipsy Kapoor.
Proceedings of the 8th Annual International Conference on Digital
Government Research (dg.o2007), Philadelphia, PA, May 2007.
Best Paper Award.
-
Argos: A Framework for Automatically Generating Data Processing Workflows
Jose Luis Ambite and Dipsy Kapoor.
Proceedings of the 8th Annual National Conference on Digital
Government Research (dg.o2007), Philadelphia, PA, May 2007.
-
ARGOS: Dynamic Composition of Web Services for Goods Movement Analysis and Planning (Project Highlights 2007)
Jose Luis Ambite, Genevieve Giuliano and Peter Gordon.
Proceedings of the 8th Annual National Conference on Digital
Government Research (dg.o2007), Philadelphia, PA, May 2007.
-
Data Processing Workflows in the Social Sciences: Representation and Automatic Generation (Abstract)
Jose Luis Ambite, Dipsy Kapoor, and Mountu Jinwala.
Proceedings of the 7th Annual National Conference on Digital
Government Research (dg.o2006), San Diego, California, May 2006.
-
Design and implementation of the CALO query manager
Jose Luis Ambite, Vinay K. Chaudhri, Richard Fikes, Jessica Jenkins, Sunil
Mishra, Maria Muslea, Tomas Uribe, and Guizhen Yang.
Proceedings of the 18th Conference on Innovative Applications of Artificial Intelligence (IAAI-2006), Boston, Massachusetts, July 2006.
-
Composing, optimizing, and executing plans for bioinformatics web services
Snehal Thakkar, Jose Luis Ambite, and Craig A. Knoblock.
The VLDB Journal, 14(3): 330-353, 2005.
-
Conditional constraint networks for interleaved planning and information gathering
Jose Luis Ambite, Craig A. Knoblock, Maria Muslea, and Steve Minton.
IEEE Intelligent Systems, 20(2), March/April 2005.
A slightly longer version is here.
-
Automatic Composition of Aggregation Workflows for Transportation Modeling
Jose Luis Ambite and Matthew Weathers.
Proceedings of the 6th Annual National Conference on Digital
Government Research (dg.o2005), Atlanta, Georgia, May 2005.
-
Retrieving and Semantically Integrating Heterogeneous Data from the Web
Martin Michalowski, Jose Luis Ambite, Craig A. Knoblock, Steve Minton,
Snehal Thakkar, and Rattapoom Tuchinda
IEEE Intelligent Systems., Vol. 19, No. 3, 2004, pp. 72-79.
-
Plan Optimization by Plan Rewriting
Jose Luis Ambite, Craig A. Knoblock and Steve Minton
In Intelligent Techniques for Planning., Ioannis Vlahavas and Dimitris
Vrakas Eds., Idea Group Publishing, Hershey, PA, 2005.
This paper combines and summarizes the JAIR 2001 and ICAPS 2000 papers
below. A draft of the book chapter is here
-
A Data Integration Approach to Automatically Composing and Optimizing Web Services
Snehal Thakkar, Jose Luis Ambite and Craig A. Knoblock
In Proceeding of 2004 ICAPS Workshop on Planning and Scheduling
for Web and Grid Services , June 2004.
-
Argos: Dynamic Composition of Web Services for Goods Movement Analysis and Planning
Jose Luis Ambite, Genevieve Giuliano, Peter Gordon,
Andreas Harth, Karanbir Jassar, Qisheng Pan and LanLan Wang
Project Highlight at the National Conference on Digital
Government Research (dg.o 2004),
Seattle, Washington,
May 2004.
-
Argos: An Ontology and Web Service Composition Infrastructure for Goods Movement Analysis
Jose Luis Ambite, Genevieve Giuliano, Peter Gordon,
Andreas Harth, Karanbir Jassar, Qisheng Pan and LanLan Wang
System Demosntration at the National Conference on Digital
Government Research (dg.o 2004),
Seattle, Washington,
May 2004.
-
A View Integration Approach to Dynamic Composition of Web Services
Snehal Thakkar, Craig Knoblock and Jose Luis Ambite
Workshop on Planning for Web Services, The 13th
International Conference on Automated Planning & Scheduling (ICAPS 2003),
Trento, Italy, 2003.
-
Proteus: A System for Dynamically Composing and Intelligently Executing Web Services
Shahram Ghandeharizadeh, Craig A. Knoblock, Christos
Papadopoulos, Cyrus Shahabi, Esam Alwagait, Jose Luis Ambite, Min Cai,
Ching-Chien Chen, Parikshit Pol, Rolfe Schmidt, Saihong Song, Snehal
Thakkar, and Runfang Zhou.
In Proceedings of the First International Conference on Web Services (ICWS), Las Vegas, Nevada, June 2003.
-
Getting from Here to There: Interactive Planning and Agent Execution for Optimizing Travel
(ps.gz)
(slides)
Jose Luis Ambite, Greg Barish, Craig A. Knoblock, Maria Muslea,
Jean Oh, and Steven Minton
The Fourteenth Innovative Applications of Artificial
Intelligence Conference (IAAI),
Edmonton, Alberta, Canada, 2002.
-
Data integration and access: The Digital Government Research Center's Energy Data Collection (EDC) project.
Jose Luis Ambite, Yigal Arens, Walter Bourne, Steve Feiner, Luis
Gravano, Vasileios Hatzivassiloglou, Eduard Hovy, Judith Klavans,
Andrew Philpot, Usha Ramachandran, Kenneth Ross, Jay Sandhaus, Deniz
Sarioz, Rolfe R. Schmidt, Cyrus Shahabi, Anurag Singla, Surabhan
Temiyabutr, and Brian Whitman.
In Advances in Digital Government: Technology, Human Factors, and
Policy. William J.McIver and Ahmed K.Elmagarmid, Eds., Kluwer
Academic Publishers, 2002.
-
Dynamically Composing Web Services from On-line Sources
Snehal Thakkar, Craig A. Knoblock, Jose Luis Ambite, and Cyrus Shahabi
Workshop on Intelligent Service Integration,
The Eighteenth National Conference on Artificial Intelligence (AAAI),
Edmonton, Alberta, Canada, 2002.
-
Integrating Heterogeneous Sources for Better Freight Flow Analysis and Planning
Jose Luis Ambite, Genevieve Giuliano, Peter Gordon, Qisheng Pan,
and Sandipan Bharracharjee
Second National Conference on Digital Government Research
(dg.o 2002), Redondo Beach, California, May 2002.
A longer
version of this paper was presented at the Transportation
Research Board 82nd Annual Meeting, Washington, D.C., January 2003
-
DGRC AskCal: Natural Language Question Answering for Energy Time Series
Andrew Philpot, Jose Luis Ambite, and Eduard Hovy
Second National Conference on Digital Government Research
(dg.o 2002), Redondo Beach, California, May 2002.
-
A Portal for Access to Complex Distributed Information about Energy
Jose Luis Ambite, Yigal Arens, Walter Bourne, Peter T. Davis,
Steven Feiner, Eduard H. Hovy, Judith L. Klavans, Andrew Philpot,
Samuel Popper, Ken Ross, Ju-Ling Shih, Peter Sommer, Surabhan (Nick)
Temiyabutr, and Laura Zadoff
Second National Conference on Digital Government Research
(dg.o 2002), Redondo Beach, California, May 2002.
-
Planning by Rewriting
(HTML)
(ps.Z)
Jose Luis Ambite and Craig A. Knoblock
Journal of Artificial Intelligence Research, 15, pp 207-261,
2001.
-
Mixed-Initiative, Multi-source Information Assistants
(HTML)
(ps.gz)
Craig A. Knoblock, Steve Minton, Jose Luis Ambite, Maria Muslea, Jean Oh, and Martin Frank
The Tenth International World Wide Web Conference (WWW10),
Hong Kong, 2001.
-
Efficiently Querying Moving Objects with Pre-defined Paths in a Distributed Environment
Cyrus Shahabi, Mohammad R. Kolahdouzan, Snehal Thakkar, Jose Luis Ambite, and Craig A. Knoblock.
The Ninth ACM International Symposium on Advances in Geographic Information Systems (ACM-GIS), Atlanta, Georgia, U.S.A., November 2001.
-
The WorldInfo Assistant: Spatio-Temporal Information Integration on the Web
Jose Luis Ambite, Craig A. Knoblock, Mohammad R. Kolahdouzan,
Maria Muslea, Cyrus Shahabi and Snehal Thakkar
Proceedings of the 27th International Conference on Very
Large Data Bases (System Demonstration), Rome, Italy, September
2001.
-
Fast Approximate Evaluation of OLAP Queries for Integrated Statistical Data
Jose Luis Ambite, Cyrus Shahabi, Rolfe R. Schmidt, and
Andrew Philpot.
Proceedings of the First National Conference on Digital
Government Research (dg.o 2001), Redondo Beach, May 2001.
-
Data Acquisition and Integration in the DGRC's Energy Data Collection Project
Eduard Hovy, Andrew Philpot, Jose Luis Ambite, Yigal Arens,
Judith Klavans, Walter Bourne, and Deniz Saroz.
Proceedings of the First National Conference on Digital
Government Research (dg.o 2001), Redondo Beach, May 2001.
-
Simplifying Data Access: The Energy Data Collection Project
Jose Luis Ambite, Yigal Arens, Eduard Hovy, Andrew Philpot, Luis
Gravano, Vasileios Hatzivassiloglou, and Judith Klavans.
IEEE Computer 34 (2), Special Issue on Digital Government,
February 2001.
-
Integrating the World: The WorldInfo Assistant
Craig A. Knoblock, Jose Luis Ambite, Steven Minton, Cyrus
Shahabi, Mohammad Kolahdouzan, Maria Muslea, Jean Oh, and Snehal
Thakkar.
International Conference on Artificial Intelligence (IC-AI),
Las Vegas, 2001.
-
Compiling Source Descriptions for Efficient and Flexible Information Integration
Jose Luis Ambite, Craig A. Knoblock, Ion Muslea, and Andrew Philpot.
Journal of Intelligent Information Systems,
16(2):149-187, 2001.
-
The Ariadne Approach to Web-based Information Integration ,
Craig A. Knoblock, Steven Minton, Jose Luis Ambite,
Naveen Ashish, Ion Muslea, Andrew G. Philpot, and Sheila Tejada.
International the Journal on Cooperative
Information Systems (IJCIS) 10 (1-2) Special Issue on Intelligent
Information Agents: Theory and Applications, pp 145-169, 2001.
-
Flexible and Scalable Cost-Based Query Planning in Mediators: A
Transformational Approach
(ps)
Jose Luis Ambite, Craig A. Knoblock.
Artificial Intelligence Journal, 118 (1-2), pp 115-161,
April 2000.
-
Learning Plan Rewriting Rules
(ps)
Jose Luis Ambite, Craig A. Knoblock, and Steven Minton.
Proceedings of the Fifth International Conference on
Artificial Intelligence Planning and Scheduling Systems,
Breckenridge, Colorado, 2000.
-
Planning by Rewriting
(ps.gz)
Jose Luis Ambite
Ph.D. Thesis.
University of Southern California,
1998.
-
Modeling Web Sources for Information Integration ,
(ps)
Craig A. Knoblock, Steven Minton, Jose Luis Ambite, Naveen
Ashish, Pragnesh Jay Modi, Ion Muslea, Andrew G. Philpot, and Sheila
Tejada.
Proceedings of the Fifteenth National Conference on
Artificial Intelligence, Madison, Wisconsin, 1998.
-
Flexible and scalable query planning in distributed and heterogeneous environments
(ps)
Jose Luis Ambite and Craig A. Knoblock.
Proceedings of the Fourth International Conference on Artificial
Intelligence Planning Systems, Pittsburgh, Pennsylvania, 1998.
-
ARIADNE: A System for Constructing Mediators for Internet Sources
Jose Luis Ambite, Naveen Ashish, Craig A. Knoblock, Steven
Minton, Pragnesh J. Modi, Ion Muslea, Andrew Philpot, and Sheila Tejada.
Proceedings of the ACM SIGMOD
International Conference on Management of Data (System Demonstration), Seattle, Washington,
1998
-
Planning by rewriting: Efficiently generating high-quality plans
,
(ps)
Jose Luis Ambite and Craig A. Knoblock.
Proceedings of the Fourteenth National Conference on
Artificial Intelligence, Providence, Rhode Island, 1997.
-
Agents for Information Gathering
(ps)
Craig A. Knoblock and Jose Luis Ambite.
In Software Agents, J. Bradshaw ed., AAAI/MIT Press, Menlo
Park, California, 1997.
-
Agents for Information Gathering
Jose Luis Ambite and Craig A. Knoblock.
IEEE Expert: Intelligent Systems and their applications.
September/October 1997.
-
Flexible and Scalable Query Access Planning using an AI Planner
(ps)
Jose Luis Ambite and Craig A. Knoblock.
Proceedings of the IEEE Knowledge and Data Engineering Exchange
Workshop , Newport Beach, California, 1997.
-
SIMS Manual (ps)
Jose Luis Ambite, Yigal Arens, Naveen Ashish, Chin Y. Chee,
Chun-Nan Hsu, Craig A. Knoblock Wei-Min Shen, and Sheila
Tejada.
University of Southern California, Information Sciences Institute,
December 1997.
-
Efficient Planning by Graph Rewriting
(ps)
Jose Luis Ambite and Craig A. Knoblock.
Student Abstract in Proceedings of the Thirteenth National Conference on
Artificial Intelligence, Portland, Oregon, 1996.
-
Reconciling Distributed Information Sources
(ps)
Jose Luis Ambite and Craig A. Knoblock.
Working Notes of the AAAI Spring Symposium on Information
Gathering in Distributed Heterogeneous Environments, Palo Alto,
California, 1995.
-
Reconciling Agents Models
Jose Luis Ambite and Craig Knoblock.
Workshop on Intelligent Information Agents of the Third
International Conference on Information and Knowledge Management
(IIA-CIKM'94), NIST, Gaithersburg, Maryland, November, 1994.
Master Kwon's Hapkido