2 citations · 6 across the 9 of their papers we have counts for
5 papers · 1 filter
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…
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…
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…