I am a Machine Learning Research Scientist at Altos Labs. Altos aims to understand why healthy cells are able to resist disease and how we can reprogram cells to restore this resilience. At Altos, I build machine learning systems that discover biologically significant cell and tissue states from multiscale, multimodal experimental data (e.g. spatial transcriptomics, scRNA-seq, histology, IF, IHC).
I am broadly interested in machine learning and computer vision, with an emphasis on developing machine learning systems that enable scientific discoveries. I have worked in many domains, including molecular biology, ecology, oceanography, remote sensing, acoustics, power systems, optics, and medicine.
I received a Ph.D. from the Computing and Mathematical Sciences department at Caltech where I was advised by Pietro Perona and supported by an NSF Graduate Research Fellowship. During my Ph.D. I completed internships at Google Research, Microsoft Research, and the U.S. Air Force Research Laboratory. Before that, I received a B.S.E. from Duke University with a double major in electrical engineering and mathematics. I am grateful to my passionate public school teachers in Utah (Grantsville, Sandy, Salt Lake City), Nebraska (Omaha), and Texas (San Antonio).
From Coarse to Fine-Grained Open-Set Recognition
Nico Lang, Vésteinn Snæbjarnarson, Elijah Cole, Oisin Mac Aodha, Christian Igel, Serge Belongie
CVPR 2024
TLDR: Revealing the factors that make open-set recognition easy or difficult, with new benchmarks.
[paper] [website]
Active Learning-Based Species Range Estimation
Christian Lange, Elijah Cole, Grant Van Horn, Oisin Mac Aodha
NeurIPS 2023
TLDR: An active learning approach to rapidly estimate the spatial distribution of a novel species.
[paper]
Spatial Implicit Neural Representations for Global-Scale Species Mapping
Elijah Cole, Grant Van Horn, Christian Lange, Alexander Shepard, Patrick Leary, Pietro Perona, Scott Loarie, Oisin Mac Aodha
ICML 2023
TLDR: Implicit neural representations for jointly estimating the spatial range of thousands of species from sparse data, with new benchmarks.
[paper]
[website]
[demo]
[code+data]
[blog]
On Label Granularity and Object Localization
Elijah Cole, Kimberly Wilber, Grant Van Horn, Xuan Yang, Marco Fornoni, Pietro Perona, Serge Belongie, Andrew Howard, Oisin Mac Aodha
ECCV 2022
TLDR: Increasing the accuracy and data efficiency of weakly supervised object localization by using coarse-grained labels.
[paper]
[website]
Benchmarking Representation Learning for Natural World Image Collections
Grant Van Horn, Elijah Cole, Sara Beery, Kimberly Wilber, Serge Belongie, Oisin Mac Aodha
CVPR 2021 (Oral)
TLDR: New benchmarks for self-supervised learning grounded in realistic fine-grained ecology tasks.
[paper]
[code+data]
[video]
Species Distribution Modeling for Machine Learning Practitioners: A Review
Sara Beery*, Elijah Cole*, Joseph Parker, Pietro Perona, Kevin Winner
ACM COMPASS 2021
TLDR: A review paper to help ML researchers learn about one of the most important problems in ecology and conservation.
[paper]