Jonathan S. Gootenberg — accepted AI-conference papers

2026

Count Bridges enable Modeling and Deconvolving Transcriptomic Data

Nic Fishman, Gokul Gowri, Tanush Kumar, Jiaqi Lu, Valentin De Bortoli, Jonathan S. Gootenberg +1

ICLR 2026poster

Many modern biological assays, including RNA sequencing, yield integer-valued counts that reflect the number of molecules detected. These measurements are often not at the desired resolution: while the unit of interest is typically a single cell, many measurement technologies produce counts aggregat…

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2025

Generative Distribution Embeddings

Nic Fishman, Gokul Gowri, Peng Yin, Jonathan S. Gootenberg, Omar Abudayyeh

NeurIPS 2025poster

Many real-world problems require reasoning across multiple scales, demanding models which operate not on single data points, but on entire distributions. We introduce generative distribution embeddings (GDE), a framework that lifts autoencoders to the space of distributions. In GDEs, an encoder acts…

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