AGI's Lab (Alex G. Ioannidis)

We develop state-of-the-art computational AI/ML methods for genomics, large-scale biobanks, and precision health.

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AI-sandbox GitHub newest releases:

Point Cloud Local Ancestry Inference (PCLAI) is a deep learning-based approach for inferring continuous population genetic structure along the genome.
ADAMIXTURE is an unsupervised global ancestry inference method that scales the ADMIXTURE model to biobank-sized datasets.
iLTM is a foundation model for tabular data that integrates tree-derived embeddings, dimensionality-agnostic representations, a meta-trained hypernetwork, MLP neural networks, and retrieval.
snputils is a Python package designed to ease the processing and analysis of genomic datasets.
Gnomix is a fast, scalable, and accurate local ancestry method.

Bio

Alexander Ioannidis, Ph.D., M.Phil, is Assistant Professor (Research) in the Department of Biomedical Data Science and the Department of Genetics at Stanford Medical School. He graduated summa cum laude in Chemistry and Physics from Harvard, completed an M.Phil in Computational Biology at the University of Cambridge, earned a Ph.D. in Computational & Mathematical Engineering at Stanford, and an M.S. in Management Science & Engineering (Numerical Optimization).

Prior to academia he worked on superconducting computing logic and quantum computing at Northrop Grumman's Advanced Technology Lab.

People

Current

Alexander Ioannidis, Ph.D., M.Phil

Principal Investigator

Daniel Mas Montserrat, Ph.D.

Chief Researcher

NeurIPS 2023, ICASSP 2020

Contributing:
Nature Comp. Sci. 2023

Javier Blanco-Portillo, Ph.D.

Postdoc

Nature 2021, Nature 2020

Margarita Geleta

Ph.D. Student

Genome Research 2026, ICASSP 2026

Contributing:
NeurIPS 2023

David Bonet

Ph.D. Student

SIGKDD 2025, AAAI 2024, PSB 2024

Contributing:
Human Genomics 2025

Samuel Sacco

Ph.D. Student

Contributing:
Nature 2025, Nature 2024, Nature 2023

Cole Shanks

Ph.D. Student

Contributing:
Nature 2025

Peter Gerlach

Ph.D. Student

Contributing:
Nature Metabolism 2024

Míriam Barrabés

Research Staff

NeurIPS 2023

Contributing:
Human Genomics 2025, Human Genomics 2024

Christophe Thomassin

Research Staff

Qudsi Aljabiri

M.S. Student

Jason Vu

Undergraduate Student

Sarah Alegre

Undergraduate Student

Ray Verma

Undergraduate Student

AAAI 2026

Pau Mateo Bernadó

Undergraduate student

Anna Fomitchev

Undergraduate Student

Trisha Moorkoth

Undergraduate Student

Anastasia Geleta

Undergraduate Student

Ainel Jaras

Research Affiliate

Marçal Comajoan Cara

Research Affiliate

PSB 2024

Naga Vyjayanthi

Research Affiliate

Riccardo Smeriglio

Visiting Student

Alumni

Petria Russell

Engineer, California Resources Board - Prev. Graduate Student (2026)

Òscar Molina Sedano

Research Eng. at Barcelona Supercomputing Center - Prev. Undergraduate Student (2025)

Joan Saurina

Research Intern at EMBL-EBI Cambridge - Prev. Undergraduate Student (2025)

Edward C. Huang

Fullbright Research Scholar at Max-Planck Institute - Prev. M.S. Student (2025)

Thomas Gillespie

Medical Student, University of Oxford - Prev. Graduate Student (2025)

Juan Esteban Rodriguez Rodriguez

Prev. M.S. student (2025)

Phi. Trans. B 2022

Contributing:
Nature 2021, Nature 2020

May Levin

Ph.D. Student at Cambridge University - Prev. M.S. Student (2024)

Contributing:
PSB 2024

Maria Perera

Data Scientist at Aily Labs - Prev. M.S. student (2024)

IEEE EMBC 2024

Contributing:
SIGKDD 2025

Alex Meléndez

Ph.D. Student at Imperial College - Prev. Undergraduate Student (2023)

IEEE BIBM 2023

Feng Liu

Prev. M.S. Student (2023)

Mark Penjueli

M.S. Student at MBZAI University, Abu Dhabi - Prev. Undergraduate Student (2023)

Benet Oriol Sabat

Ph.D. Student at UCLA - Prev. M.S. Student (2022)

Bioinformatics 2022

Aigerim Rymbekova

Ph.D. at University of Vienna - Prev. M.S. Student (2022)

Contributing:
IEEE EMBC 2022

Albert Dominguez Mantes

Ph.D. student at EPFL - Prev. Undergraduate Student (2022)

Nature Com. Sci. 2023

Contributing:
PLoS Computational Biology 2022

Richa Rastogi

Ph.D. Student at Cornell University - Prev. M.S. Student (2021)

Jan Sokol, M.D.

Boston University Medical School - Prev. M.S. Student (2021)

Arvind Kumar

Illumina, Prev. NVIDIA - Prev. M.S. Student (2021)

ICLR 2020

Helgi Hilmarsson

Zoom - Prev. M.S. Student (2021)

Julia Gimbernat Mayol

Microsoft AI, InstaDeep - Prev. M.S. Student (2021)

PLoS Computational Biology 2022

Khaled Aounallah

Boston Consulting Group - Prev. M.S. Student (2020)

Devang Agrawal

Data Scientist at Cequence Security - Prev. M.S. student (2020)

Illustration of lab members — Lab at the Meteora monasteries, a UNESCO World Heritage site, in Greece after HUGO HGM conference (2026)