2 citations · 6 across the 9 of their papers we have counts for
9 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…
SpecMER: Fast Protein Generation with K-mer Guided Speculative Decoding
Thomas Walton, Darin Tsui, Aryan Musharaf +1
Autoregressive models have transformed protein engineering by enabling the generation of novel protein sequences beyond those found in nature. However, their sequential inference i…
Sparse Autoencoders for Low- Protein Function Prediction and Design
Darin Tsui, Kunal Talreja, Amirali Aghazadeh
Predicting protein function from amino acid sequence remains a central challenge in data-scarce (low-) regimes, limiting machine learning-guided protein design when only small a…
Efficient Algorithm for Sparse Fourier Transform of Generalized -ary Functions
Darin Tsui, Kunal Talreja, Amirali Aghazadeh
Computing the Fourier transform of a -ary function , which maps -ary sequences to real numbers, is an important problem in mathemati…
SHAP zero Explains Biological Sequence Models with Near-zero Marginal Cost for Future Queries
Darin Tsui, Aryan Musharaf, Yigit Efe Erginbas +2
The growing adoption of machine learning models for biological sequences has intensified the need for interpretable predictions, with Shapley values emerging as a theoretically gro…
Online Mental Stress Detection Using Frontal-channel EEG Recordings in a Classroom Scenario
Chi-Yuan Chang, Chieh Hsu, Ying Choon Wu +3
Objective: To investigate the effects of different approaches to EEG preprocessing, channel montage selection, and model architecture on the performance of an online-capable stress…
On Recovering Higher-order Interactions from Protein Language Models
Darin Tsui, Amirali Aghazadeh
Protein language models leverage evolutionary information to perform state-of-the-art 3D structure and zero-shot variant prediction. Yet, extracting and explaining all the mutation…