Publications

Tissue Reassembly with Generative AI

Tingyang Yu, Chanakya Ekbote, Nikita Morozov, Jiashuo Fan, Pascal Frossard, Stéphane d’Ascoli, Maria Brbić
bioRxiv 2025

Large (Vision) Language Models Are Unsupervised In-Context Learners

Artyom Gadetsky*, Andrei Atanov*, Yulun Jiang*, Zhitong Gao, Ghazal Mighan, Amir Zamir, Maria Brbić
ICLR 2025

Let Go of Your Labels with Unsupervised Transfer

Artyom Gadetsky*, Yulun Jiang*, Maria Brbić
ICML 2024

Cross-Domain Open-World Discovery

Shuo Wen, Maria Brbić
ICML 2024

Fine-Grained Labels and How to Find Them

Matej Grcić*, Artyom Gadetsky*, Maria Brbić
ICML 2024

Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN

Yanay Rosen*, Maria Brbić*, Yusuf Roohani*, Kyle Swanson, Ziang, Li, Jure Leskovec
Nature Methods 2024

The Pursuit of Human Labeling: A New Perspective on Unsupervised Learning

Artyom Gadetsky, Maria Brbić
NeurIPS spotlight 2023

Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution

Tzu-Chiao Lu*, Maria Brbić*, Ye-Jin Park, Tyler Jackson, Jiaye Chen, Sai Saroja Kolluru, Yanyan Qi, Nadja Sandra Katheder, Xiaoyu Tracy Cai, Seungjae Lee, YenChung Chen, Niccole Auld, Doug Welsch, Samuel D’Souza , Angela Oliveira Pisco , Robert C. Jones , Jure Leskovec, Eric C. Lai, Hugo J. Bellen, Liqun Luo, Heinrich Jasper, Stephen R. Quake, Hongjie Li
Science 2023

Organization of the human intestine at single-cell resolution

John W. Hickey, Winston R. Becker, Stephanie A. Nevins, Aaron Horning, Almudena Espin Perez, Roxanne Chiu, Derek C. Chen, Daniel Cotter, Edward D. Esplin, Annika K. Weimer, Chiara Caraccio, Vishal Venkataraaman, Christian M. Schürch, Sarah Black, Maria Brbić, Kaidi Cao, Jure Leskovec, Zhengyan Zhang, Shin Lin, Teri Longacre, Sylvia K. Plevitis, Yiing Lin, Garry P. Nolan, William J. Greenleaf, Michael Snyder
Nature 2023

Annotation of Spatially Resolved Single-cell Data with STELLAR

Maria Brbić*, Kaidi Cao*, John W. Hickey*, Yuqi Tan, Michael Snyder, Garry P. Nolan, Jure Leskovec
Nature Methods 2022

Open-World Semi-Supervised Learning

Kaidi Cao*, Maria Brbić*, Jure Leskovec
ICLR 2022

Fly Cell Atlas: A Single-Cell Transcriptomic Atlas of the Adult Fruit Fly

Hongjie Li, Jasper Janssens, Maxime De Waegeneer, Sai Saroja Kolluru, Kristofer Davie, Vincent Gardeux, Wouter Saelens, Fabrice David, Maria Brbić, Katina Spanier, Jure Leskovec, Colleen N. McLaughlin, Qijing Xie, Robert C. Jones et al.
Science 2022

Chemoreceptor Co-Expression in Drosophila Olfactory Neurons

Darya Task, Chun-Chieh Lin, Alina Vulpe, Ali Afify, Sydney Ballou, Maria Brbić, Philipp Schlegel, Gregory S. X. E. Jefferis, Hongjie Li, Karen Menuz, Christopher J. Potter
eLife 2022

Concept Learners for Few-Shot Learning

Kaidi Cao*, Maria Brbić*, Jure Leskovec
ICLR 2021

Leveraging the Cell Ontology to Classify Unseen Cell Types

Sheng Wang, Angela Oliveira Pisco, Aaron McGeever, Maria Brbić, Marinka Zitnik, Spyros Darmanis, Jure Leskovec, Jim Karkanias, Russ B. Altman
Nature Communications 2021

Single-Cell Transcriptomes of Developing and Adult Olfactory Receptor Neurons in Drosophila

Colleen N. McLaughlin*, Maria Brbić*, Qijing Xie, Tongchao Li, Felix Horns, Sai Saroja Kolluru, Justus M. Kebschull, David Vacek, Anthony Xie, Jiefu Li, Robert Jones, Jure Leskovec, Stephen R. Quake, Liqun Luo, Hongjie Li
eLife 2021

Temporal evolution of Single-Cell Transcriptomes of Drosophila Olfactory Projection Neurons

Qijing Xie, Maria Brbić, Felix Horns, Sai Saroja Kolluru, Robert Jones, Jiefu Li, R. Reddy, Anay Xie, Sayeh Kohani, Zhuoran Li, Colleeen N. McLaughlin, Tongchao Li, Chuanyun Xu, David Vacek, David J. Luginbuhl, Jure Leskovec, Stephen R. Quake, Liqun Luo, Hongjie Li
eLife 2021

Publications

Tissue Reassembly with Generative AI

Large (Vision) Language Models Are Unsupervised In-Context Learners

Let Go of Your Labels with Unsupervised Transfer

Cross-Domain Open-World Discovery

Fine-Grained Labels and How to Find Them

Towards Universal Cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN

The Pursuit of Human Labeling: A New Perspective on Unsupervised Learning

Aging Fly Cell Atlas Identifies Exhaustive Aging Features at Cellular Resolution

Organization of the human intestine at single-cell resolution

Annotation of Spatially Resolved Single-cell Data with STELLAR

Open-World Semi-Supervised Learning

Fly Cell Atlas: A Single-Cell Transcriptomic Atlas of the Adult Fruit Fly

Chemoreceptor Co-Expression in Drosophila Olfactory Neurons

Concept Learners for Few-Shot Learning

Leveraging the Cell Ontology to Classify Unseen Cell Types

Single-Cell Transcriptomes of Developing and Adult Olfactory Receptor Neurons in Drosophila

Temporal evolution of Single-Cell Transcriptomes of Drosophila Olfactory Projection Neurons

MARS: Discovering Novel Cell Types across Heterogeneous Single-Cell Experiments

A Synthesis of Bacterial and Archaeal Phenotypic Trait Data

Model-Agnostic Graph Regularization for Few-Shot Learning

Selective Sampling-Based Scalable Sparse Subspace Clustering

ℓ₀-Motivated Low-Rank Sparse Subspace Clustering

Multi-View Low-Rank Sparse Subspace Clustering

Phenotype Inference from Text and Genomic Data

The Landscape of Microbial Phenotypic Traits and Associated Genes

Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled