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Employment (2)

University of Southern California: Los Angeles, CA, US

Associate Research Professor (Computer Science)
Employment
Source: Self-asserted source
Jose Luis Ambite

Information Sciences Institute: Marina Del Rey, CA, US

1999-01 to present | Research Team Leader
Employment
Source: Self-asserted source
Jose Luis Ambite

Education and qualifications (1)

University of Southern California: Los Angeles, CA, US

1998-12 | Ph.D. (Computer Science)
Education
Source: Self-asserted source
Jose Luis Ambite

Works (50 of 118)

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Synthetic Diffusion Tensor Imaging Maps Generated by 2D and 3D Probabilistic Diffusion Models: Evaluation and Applications

2025-02-25 | Preprint
Contributors: Tamoghna Chattopadhyay; Chirag Jagad; Rudransh Kush; Vraj Dharmesh Desai; Sophia I. Thomopoulos; Julio E. Villalón-Reina; Jose Luis Ambite; Greg Ver Steeg; Paul M. Thompson
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A federated learning architecture for secure and private neuroimaging analysis

Patterns
2024-08 | Journal article
Part of ISSN: 2666-3899
Contributors: DIMITRIS STRIPELIS; Umang Gupta; Hamza Saleem; Nikhil Dhinagar; Tanmay Ghai; Chrysovalantis Anastasiou; Rafael Sánchez; Greg Ver Steeg; Srivatsan Ravi; Muhammad Naveed et al.
Source: Self-asserted source
Jose Luis Ambite
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Comparison of deep learning architectures for predicting amyloid positivity in Alzheimer’s disease, mild cognitive impairment, and healthy aging, from T1-weighted brain structural MRI

Frontiers in Neuroscience
2024-07-02 | Journal article
Part of ISSN: 1662-453X
Contributors: Tamoghna Chattopadhyay; Saket S. Ozarkar; Ketaki Buwa; Neha Ann Joshy; Dheeraj Komandur; Jayati Naik; Sophia I. Thomopoulos; Greg Ver Steeg; Jose Luis Ambite; Paul M. Thompson
Source: Self-asserted source
Jose Luis Ambite
grade
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q-Diffusion leverages the full dimensionality of gene coexpression in single-cell transcriptomics

Communications Biology
2024-04-02 | Journal article
Contributors: Myrl G. Marmarelis; Russell Littman; Francesca Battaglin; Donna Niedzwiecki; Alan Venook; Jose-Luis Ambite; Aram Galstyan; Heinz-Josef Lenz; Greg Ver Steeg
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Federated Learning over Harmonized Data Silos

Studies in Computational Intelligence
2023 | Book chapter
Part of ISBN: 9783031369377
Part of ISBN: 9783031369384
Part of ISSN: 1860-949X
Part of ISSN: 1860-9503
Contributors: Dimitris Stripelis; José Luis Ambite
Source: Self-asserted source
Jose Luis Ambite
grade
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NeuroBridge ontology: computable provenance metadata to give the long tail of neuroimaging data a FAIR chance for secondary use

Frontiers in Neuroinformatics
2023 | Journal article
Part of ISSN: 1662-5196
Contributors: Sahoo, Satya S.; Turner, Matthew D.; Wang, Lei; Ambite, Jose Luis; Appaji, Abhishek; Rajasekar, Arcot; Lander, Howard M.; Wang, Yue; Turner, Jessica A.
Source: Self-asserted source
Jose Luis Ambite

MetisFL: An Embarrassingly Parallelized Controller for Scalable & Efficient Federated Learning Workflows

Proceedings of the 4th International Workshop on Distributed Machine Learning
2023-12 | Conference paper
Part of ISBN: 9798400704475
Contributors: Stripelis, Dimitris; Anastasiou, Chrysovalantis; Toral, Patrick; Asghar, Armaghan; Ambite, José Luis
Source: Self-asserted source
Jose Luis Ambite

NeuroBridge: a prototype platform for discovery of the long-tail neuroimaging data

Frontiers in Neuroinformatics
2023-01 | Journal article
Part of ISSN: 1662-5196
Contributors: Wang, Lei; Ambite, José Luis; Appaji, Abhishek; Bijsterbosch, Janine; Dockes, Jerome; Herrick, Rick; Kogan, Alex; Lander, Howard; Marcus, Daniel; Moore, Stephen M et al.
Source: Self-asserted source
Jose Luis Ambite

Alzheimer’s Disease Detection with a 3D Convolutional Neural Network using Gray Matter Maps from T1-weighted Brain MRI

Alzheimer's & Dementia
2022 | Journal article
Part of ISSN: 1552-5279
Contributors: Dhinagar, Nikhil J; Thomopoulos, Sophia I; Owens-Walton, Conor; Stripelis, Dimitris; Ambite, José Luis; Steeg, Greg Ver; Thompson, Paul M
Source: Self-asserted source
Jose Luis Ambite

Enabling Scientific Reproducibility through FAIR Data Management: An Ontology-driven Deep Learning Approach in the NeuroBridge Project

American Medical Informatics Association (AMIA) 2022 Annual Symposium
2022 | Conference paper
Contributors: Xiaochen Wang; Yue Wang; José Luis Ambite; Abhishek Appaji; Howard Lander; Stephen M. Moore; Arcot K. Rajasekar; Jessica A. Turner; Matthew D. Turner; Lei Wang et al.
Source: Self-asserted source
Jose Luis Ambite

Federated Deep Learning for Detecting Alzheimer’s Disease in Multi-Cohort Brain MRI

Alzheimer's Association International Conference
2022 | Conference paper
Part of ISSN: 1552-5279
Contributors: Stripelis, Dimitris; Dhinagar, Nikhil J; Sanchez Romero, Rafael V.; Thomopoulos, Sophia I; Thompson, Paul M; Ambite, José Luis
Source: Self-asserted source
Jose Luis Ambite
grade
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Federated Progressive Sparsification (Purge-Merge-Tune)+

Workshop on Federated Learning: Recent Advances and New Challenges (in Conjunction with NeurIPS 2022)
2022 | Conference paper
Contributors: Dimitris Stripelis; Umang Gupta; Greg Ver Steeg; Jose Luis Ambite
Source: Self-asserted source
Jose Luis Ambite

Performance Weighting for Robust Federated Learning Against Corrupted Sources

arXiv:2205.01184
2022 | Journal article
Contributors: Stripelis, Dimitris; Abram, Marcin; Ambite, Jose Luis
Source: Self-asserted source
Jose Luis Ambite

Predicted gene expression in ancestrally diverse populations leads to discovery of susceptibility loci for lifestyle and cardiometabolic traits

American Journal of Human Genetics
2022 | Journal article
Contributors: Heather M Highland; Genevieve L Wojcik; Mariaelisa Graff; Katherine K Nishimura; Chani J Hodonsky; Antoine R Baldassari; Alanna C Cote; Iona Cheng; Christopher R Gignoux; Ran Tao et al.
Source: Self-asserted source
Jose Luis Ambite

Shared genetics drive mate selection

Annual Meeting of the American Society of Human Genetics
2022 | Conference paper
Contributors: Keith Burghardt; Thalida Em Arpawong; José Luis Ambite
Source: Self-asserted source
Jose Luis Ambite

Towards Sparsified Federated Neuroimaging Models via Weight Pruning

Distributed, Collaborative, and Federated Learning, and Affordable AI and Healthcare for Resource Diverse Global Health - Third MICCAI Workshop, DeCaF 2022, and Second MICCAI Workshop, FAIR 2022, Held in Conjunction with Medical Image Computing and Computer Assisted Intervention Society MICCAI Conference 2022, Singapore, September 18 and 22, 2022, Proceedings
2022 | Conference paper
Contributors: Dimitris Stripelis and Umang Gupta and Nikhil Dhinagar and Greg Ver Steeg and Paul M. Thompson and José Luis Ambite; Shadi Albarqouni and Spyridon Bakas and Sophia Bano and M. Jorge Cardoso and Bishesh Khanal and Bennett A. Landman and Xiaoxiao Li and Chen Qin and Islem Rekik and Nicola Rieke and Holger Roth and Debdoot Sheet and Daguang Xu
Source: Self-asserted source
Jose Luis Ambite

Selecting Clustering Algorithms for Identity-By-Descent Mapping

Biocomputing 2023, Proceedings of the Pacific Symposium
2022-11 | Conference paper
Part of ISBN: 9789811270604
Contributors: Shemirani, Ruhollah; Belbin, Gillian M; Burghardt, Keith; Lerman, Kristina; Avery, Christy L; Kenny, Eimear E; Gignoux, Christopher R; Ambite, José Luis
Source: Self-asserted source
Jose Luis Ambite

Semi-Synchronous Federated Learning for Energy-Efficient Training and Accelerated Convergence in Cross-Silo Settings

ACM Transactions on Intelligent Systems and Technology
2022-10-31 | Journal article
Contributors: Dimitris Stripelis; Paul M. Thompson; José Luis Ambite
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Evaluation of Transfer Learning Methods for Detecting Alzheimer’s Disease with Brain MRI

2022-08-25 | Preprint
Contributors: Nikhil J. Dhinagar; Sophia I. Thomopoulos; Priya Rajagopalan; Dimitris Stripelis; Jose Luis Ambite; Greg Ver Steeg; Paul M. Thompson
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3D Convolutional Neural Networks for Classification of Alzheimer's and Parkinson's Disease with T1-Weighted Brain MRI

17th International Symposium on Medical Information Processing and Analysis (SIPAIM)
2021 | Conference paper
Contributors: Nikhil J. Dhinagar; Sophia I. Thomopoulos; Conor Owens-Walton; Dimitris Stripelis; José Luis Ambite; Greg Ver Steeg; Daniel Weintraub; Philip Cook; Corey McMillan; Paul M. Thompson
Source: Self-asserted source
Jose Luis Ambite

iCURL: Refining Estimated Identical-by-Descent Segments Via Community Detection

Annual Meeting of the American Society of Human Genetics
2021 | Conference paper
Contributors: Ruhollah Shemirani; Christopher Gignoux; Noah Zaitlen; Christy Avery; Eimear Kenny; Gillian Belbin; José Luis Ambite
Source: Self-asserted source
Jose Luis Ambite

Membership Inference Attacks on Deep Regression Models for Neuroimaging

Medical Imaging with Deep Learning (MIDL)
2021 | Conference paper
Contributors: Umang Gupta; Dimitris Stripelis; Pradeep K. Lam; Paul M. Thompson; José Luis Ambite; Greg Ver Steeg
Source: Self-asserted source
Jose Luis Ambite

Secure Neuroimaging Analysis using Federated Learning with Homomorphic Encryption

17th International Symposium on Medical Information Processing and Analysis (SIPAIM)
2021 | Conference paper
Contributors: Dimitris Stripelis; Hamza Saleem; Tanmay Ghai; Nikhil Dhinagar; Umang Gupta; Chrysovalantis Anastasiou; Greg Ver Steeg; Srivatsan Ravi; Muhammad Naveed; Paul M.Thompson et al.
Source: Self-asserted source
Jose Luis Ambite

Using Dynamic Time Warping Self-Organizing Maps to Characterize Diurnal Patterns in Environmental Exposures

Scientific Reports
2021 | Journal article
Contributors: Kenan Li; Katherine Sward; Huiyu Deng; John Morrison; Rima Habre; Meredith Franklin; Yao-Yi Chiang; Jose-Luis Ambite; John P. Wilson; Sandrah P. Eckel
Source: Self-asserted source
Jose Luis Ambite

NERO: a biomedical named-entity (recognition) ontology with a large, annotated corpus reveals meaningful associations through text embedding

npj Systems Biology and Applications
2021-10 | Journal article
Contributors: Wang, Kanix; Stevens, Robert; Alachram, Halima; Li, Yu; Soldatova, Larisa; King, Ross; Ananiadou, Sophia; Schoene, Annika M.; Li, Maolin; Christopoulou, Fenia et al.
Source: Self-asserted source
Jose Luis Ambite

W-TSS: A Wavelet-Based Algorithm for Discovering Time Series Shapelets

Sensors
2021-08-28 | Journal article
Contributors: Kenan Li; Huiyu Deng; John Morrison; Rima Habre; Meredith Franklin; Yao-Yi Chiang; Katherine Sward; Frank D. Gilliland; José Luis Ambite; Sandrah P. Eckel
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Selecting Clustering Algorithms for IBD Mapping

2021-08-12 | Other
Contributors: Ruhollah Shemirani; Gillian M Belbin; Keith Burghardt; Kristina Lerman; Christy L Avery; Eimear E Kenny; Christopher R Gignoux; José Luis Ambite
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Crossref

3D Convolutional Neural Networks for Classification of Alzheimer’s and Parkinson’s Disease with T1-Weighted Brain MRI

2021-07-27 | Other
Contributors: 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
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BD2K Training Coordinating Center's ERuDIte: The Educational Resource Discovery Index for Data Science

IEEE Transactions on Emerging Topics in Computing
2021-01-01 | Journal article
Contributors: Jose Luis Ambite; Lily Fierro; Jonathan Gordon; Gully A. P. C. Burns; Florian Geigl; Kristina Lerman; John D. Van Horn
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Crossref

A phenome-wide association study (PheWAS) in the Population Architecture using Genomics and Epidemiology (PAGE) study reveals potential pleiotropy in African Americans

PLOS ONE
2019-12-31 | Journal article
Contributors: Sarah A. Pendergrass; Gregory P. Copenhaver; Steven Buyske; Janina M. Jeff; Alex Frase; Scott Dudek; Yuki Bradford; Jose-Luis Ambite; Christy L. Avery; Petra Buzkova et al.
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Rapid detection of identity-by-descent tracts for mega-scale datasets

2019-09-08 | Other
Contributors: Ruhollah Shemirani; Gillian M. Belbin; Christy L. Avery; Eimear E. Kenny; Christopher R. Gignoux; José Luis Ambite
Source: check_circle
Crossref
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Genetic analyses of diverse populations improves discovery for complex traits

Nature
2019-06 | Journal article
Part of ISSN: 0028-0836
Part of ISSN: 1476-4687
Contributors: Genevieve L. Wojcik; Mariaelisa Graff; Katherine K. Nishimura; Ran Tao; Jeffrey Haessler; Christopher R. Gignoux; Heather M. Highland; Yesha M. Patel; Elena P. Sorokin; Christy L. Avery et al.
Source: Self-asserted source
Jose Luis Ambite

Advancing the international data science workforce through shared training and education

F1000Research
2019-03-04 | Journal article
Contributors: John Van Horn; Sumiko Abe; José Luis Ambite; Teresa K. Attwood; Niall Beard; Louisa Bellis; Avnish Bhattrai; Alex Bui; Gully Burns; Lily Fierro et al.
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Applying Multivariate Segmentation Methods to Human Activity Recognition From Wearable Sensors’ Data

JMIR mHealth and uHealth
2019-02-07 | Journal article
Contributors: Kenan Li; Rima Habre; Huiyu Deng; Robert Urman; John Morrison; Frank D Gilliland; José Luis Ambite; Dimitris Stripelis; Yao-Yi Chiang; Yijun Lin et al.
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Crossref

Democratizing data science through data science training

Pacific Symposium on Biocomputing, 2018
2018 | Conference paper
EID:

2-s2.0-85048474383

Contributors: Van Horn, J.D.; Fierro, L.; Kamdar, J.; Gordon, J.; Stewart, C.; Bhattrai, A.; Abe, S.; Lei, X.; O’Driscoll, C.; Sinha, A. et al.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Discovery, fine-mapping, and conditional analyses of genetic variants associated with C-reactive protein in multiethnic populations using the Metabochip in the Population Architecture using Genomics and Epidemiology (PAGE) study

Human Molecular Genetics
2018 | Journal article
EID:

2-s2.0-85054997249

Contributors: Kocarnik, J.M.; Richard, M.; Graff, M.; Haessler, J.; Bien, S.; Carlson, C.; Carty, C.L.; Reiner, A.P.; Avery, C.L.; Ballantyne, C.M. et al.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

The genetic underpinnings of variation in ages at menarche and natural menopause among women from the multi-ethnic Population Architecture using Genomics and Epidemiology (PAGE) Study: A trans-ethnic meta-analysis

PLoS ONE
2018 | Journal article
EID:

2-s2.0-85050732362

Contributors: Fernández-Rhodes, L.; Malinowski, J.R.; Wang, Y.; Tao, R.; Pankratz, N.; Jeff, J.M.; Yoneyama, S.; Carty, C.L.; Setiawan, V.W.; Le Marchand, L. et al.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Applying Multivariate Segmentation Methods to Human Activity Recognition From Wearable Sensors’ Data (Preprint)

2018-06-01 | Other
Contributors: Kenan Li; Rima Habre; Huiyu Deng; Robert Urman; John Morrison; Frank D Gilliland; José Luis Ambite; Dimitris Stripelis; Yao-Yi Chiang; Yijun Lin et al.
Source: check_circle
Crossref

A scalable data integration and analysis architecture for sensor data of pediatric asthma

Proceedings - International Conference on Data Engineering
2017 | Conference paper
EID:

2-s2.0-85021195619

Contributors: Stripelis, D.; Ambite, J.L.; Chiang, Y.-Y.; Eckel, S.P.; Habre, R.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Mining Public Datasets for Modeling Intra-City PM<inf>2.5</inf> Concentrations at a Fine Spatial Resolution

GIS: Proceedings of the ACM International Symposium on Advances in Geographic Information Systems
2017 | Conference paper
EID:

2-s2.0-85041009930

Contributors: Lin, Y.; Stripelis, D.; Chiang, Y.-Y.; Ambite, J.L.; Habre, R.; Pan, F.; Eckel, S.P.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Abstract meaning representations as linked data

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2016 | Book
EID:

2-s2.0-84992597297

Contributors: Burns, G.A.; Hermjakob, U.; Ambite, J.L.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Fine-mapping of lipid regions in global populations discovers ethnic-specific signals and refines previously identified lipid loci

Human Molecular Genetics
2016 | Journal article
EID:

2-s2.0-85016010547

Contributors: Zubair, N.; Graff, M.; Ambite, J.L.; Bush, W.S.; Kichaev, G.; Lu, Y.; Manichaikul, A.; Sheu, W.H.-H.; Absher, D.; Assimes, T.L. et al.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Learning the semantics of structured data sources

Journal of Web Semantics
2016 | Journal article
EID:

2-s2.0-84955264843

Contributors: Taheriyan, M.; Knoblock, C.A.; Szekely, P.; Ambite, J.L.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Leveraging linked data to discover semantic relations within data sources

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2016 | Book
EID:

2-s2.0-84992603308

Contributors: Taheriyan, M.; Knoblock, C.A.; Szekely, P.; Ambite, J.L.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Northwestern University schizophrenia data sharing for SchizConnect: A longitudinal dataset for large-scale integration

NeuroImage
2016 | Journal article
EID:

2-s2.0-84949316673

Contributors: Kogan, A.; Alpert, K.; Ambite, J.L.; Marcus, D.S.; Wang, L.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

SchizConnect: Mediating neuroimaging databases on schizophrenia and related disorders for large-scale integration

NeuroImage
2016 | Journal article
EID:

2-s2.0-84949318348

Contributors: Wang, L.; Alpert, K.I.; Calhoun, V.D.; Cobia, D.J.; Keator, D.B.; King, M.D.; Kogan, A.; Landis, D.; Tallis, M.; Turner, M.D. et al.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Data integration in the life sciences: 11th International Conference, DILS 2015 Los Angeles, CA, USA, July 9-10, 2015 Proceedings

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2015 | Book
EID:

2-s2.0-84947273019

Contributors: Ashish, N.; Ambite, J.-L.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Finding concept coverings in aligning ontologies of linked data

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2015 | Book
EID:

2-s2.0-84942567490

Contributors: Parundekar, R.; Knoblock, C.A.; Ambite, J.L.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier
grade
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GEM: The GAAIN entity mapper

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
2015 | Book
EID:

2-s2.0-84947234208

Contributors: Ashish, N.; Dewan, P.; Ambite, J.-L.; Toga, A.W.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier

Leveraging linked data to infer semantic relations within structured sources

CEUR Workshop Proceedings
2015 | Conference paper
EID:

2-s2.0-84948657327

Contributors: Taheriyan, M.; Knoblock, C.A.; Szekely, P.; Ambite, J.L.; Chen, Y.
Source: Self-asserted source
Jose Luis Ambite via Scopus - Elsevier
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