4 papers
Circuit Tracing in Autoregressive Protein Language Models
Darin Tsui, William Deinzer, Daniel Saeedi +1
Protein language models (pLMs) can generate novel protein sequences with properties beyond those observed in nature, yet the mechanisms underlying protein generation remain poorly…
Protein Circuit Tracing via Cross-layer Transcoders
Darin Tsui, Kunal Talreja, Daniel Saeedi +1
Protein language models (pLMs) have emerged as powerful predictors of protein structure and function. However, the computational circuits underlying their predictions remain poorly…
cryoSENSE: Compressive Sensing Enables High-throughput Microscopy with Sparse and Generative Priors on the Protein Cryo-EM Image Manifold
Zain Shabeeb, Daniel Saeedi, Darin Tsui +2
Cryo-electron microscopy (cryo-EM) enables the atomic-resolution visualization of biomolecules; however, modern direct detectors generate data volumes that far exceed the available…
AstroAgents: A Multi-Agent AI for Hypothesis Generation from Mass Spectrometry Data
Daniel Saeedi, Denise Buckner, Jose C. Aponte +1
With upcoming sample return missions across the solar system and the increasing availability of mass spectrometry data, there is an urgent need for methods that analyze such data w…