3.1k citations
- Janelia Research CampusUS53 papers
- Rockefeller UniversityUS28 papers
- Harvard UniversityUS27 papers
- University of California, BerkeleyUS26 papers
- Princeton UniversityUS20 papers
- Northwestern UniversityUS17 papers
- California Institute of TechnologyUS16 papers
- Massachusetts Institute of TechnologyUS16 papers
- Stanford UniversityUS14 papers
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- University of ChicagoUS13 papers
- Centre National de la Recherche ScientifiqueFR12 papers
242 papers
Inference of germinal center evolutionary dynamics via simulation-based deep learning
Duncan K Ralph, Athanasios G Bakis, Jared Galloway +6
B cells and the antibodies they produce are vital to health and survival, motivating research on the details of the mutational and evolutionary processes in the germinal centers (G…
FILM: Mapping organellar metabolism by mid-infrared photothermal modulated fluorescence
Jianpeng Ao, Jiaze Yin, Haonan Lin +10
Metabolism unfolds within specific organelles in eukaryotic cells. Lysosomes are highly metabolically active organelles, and their metabolic states dynamically influence signal tra…
Lyra: An Efficient and Expressive Subquadratic Architecture for Modeling Biological Sequences
Krithik Ramesh, Sameed M. Siddiqui, Albert Gu +2
Deep learning architectures such as convolutional neural networks and Transformers have revolutionized biological sequence modeling, with recent advances driven by scaling up found…
Fourier-Based 3D Multistage Transformer for Aberration Correction in Multicellular Specimens
Thayer Alshaabi, Daniel E. Milkie, Gaoxiang Liu +17
High-resolution tissue imaging is often compromised by sample-induced optical aberrations that degrade resolution and contrast. While wavefront sensor-based adaptive optics (AO) ca…
A ghost mechanism: An analytical model of abrupt learning in recurrent networks
Fatih Dinc, Ege Cirakman, Bariscan Kurtkaya +4
Abrupt learning is a common phenomenon in recurrent neural networks (RNNs) trained on working memory tasks. In such cases, the networks develop transient slow regions in state spac…
Finding high posterior density phylogenies by systematically extending a directed acyclic graph
Chris Jennings-Shaffer, David H Rich, Matthew Macaulay +7
Bayesian phylogenetics typically estimates a posterior distribution, or aspects thereof, using Markov chain Monte Carlo methods. These methods integrate over tree space by applying…