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Darin Tsui

@darintsui.bsky.social
27 followers 270 following 22 posts

PhD candidate at Georgia Tech | ML for bioengineering | UC San Diego '23 darintsui.github.io

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Darin Tsui @darintsui.bsky.social · 15/07/2026
Finally, to facilitate adoption by the community, we provide an open-source Python package implementation of the eWHT! ⭐ Paper: www.biorxiv.org/content/10.6... ⭐ Package: github.com/amirgroup-co... P.S. special thanks to Kunal and my PI @amiralia.bsky.social!
biorxiv.org
Protein fitness landscapes are simpler under evolutionary distributions
Understanding how mutations combine to shape protein fitness remains a central challenge in biology, driven in part by the prevalence of highorder epistasis. Existing analyses of epistasis, however, i...
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Darin Tsui @darintsui.bsky.social · 15/07/2026
Notably, the epistatic interactions highlighted by the eWHT were highly interpretable! Across diverse fitness landscapes, the eWHT prioritized interactions that were structurally localized and present at contact regions. (5/n)
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Darin Tsui @darintsui.bsky.social · 15/07/2026
Using the eWHT, we consistently explained more phenotypic variation in evolutionary sequences using fewer spectral components, reduced apparent high-order interactions, and improved sparse recovery from limited experimental measurements. (4/n)
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Darin Tsui @darintsui.bsky.social · 15/07/2026
To fix this, we developed the evolutionary Walsh–Hadamard Transform (eWHT), a generalization of the Walsh–Hadamard transform that reweights the sequence space according to mutational probabilities, which can be estimated using MSAs or protein language models. (3/n)
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Darin Tsui @darintsui.bsky.social · 15/07/2026
The classic tool to analyze epistasis in fitness landscapes is the Walsh–Hadamard transform. However, it makes the flawed assumption that every mutation is equally likely to happen. In reality, natural selection biases which paths evolution actually takes. (2/n)
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Darin Tsui @darintsui.bsky.social · 15/07/2026
Protein fitness landscapes are simpler under evolutionary distributions! We show that much of the high-order epistasis observed in fitness landscapes is substantially diminished when analyzed under their natural evolutionary distributions. www.biorxiv.org/content/10.6... (1/n)
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Darin Tsui @darintsui.bsky.social · 14/05/2026
To democratize circuit tracing, we have open-sourced ProtoMech! Run ProtoMech through Colab and visualize your circuits on our website! We’re excited to see what the community discovers! (n/n) ⭐ Colab: colab.research.google.com/github/amirg... ⭐ Video tutorial: www.youtube.com/watch?v=wF6x...
colab.research.google.com
Google Colab
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Darin Tsui @darintsui.bsky.social · 14/05/2026
In our latest update, we have expanded ProtoMech to discover the computational mechanisms in ESM2-35M. You can check out the circuits on our website! (3/n) protmech.github.io
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Darin Tsui @darintsui.bsky.social · 14/05/2026
Brief recap: ProtoMech uses cross-layer transcoders to learn sparse representations jointly across the entire transformer. This enables ProtoMech to mimic the computation of pLMs, allowing us to discover the computational mechanisms governing their predictions. (2/n)
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Darin Tsui @darintsui.bsky.social · 14/05/2026
Can we learn how protein language models (pLMs) work? 👀 As a matter of fact, yes! I'm excited to shared that our paper, "Protein Circuit Tracing via Cross-layer Transcoders", has been accepted into ICML 2026! Check out our findings at protmech.github.io (1/n)
protmech.github.io
ProtoMech - Circuit tracing for proteins
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Darin Tsui @darintsui.bsky.social · 16/02/2026
We have developed a visualizer and release our code to facilitate novel applications of ProtoMech! (n/n) ⭐ Paper: arxiv.org/abs/2602.12026 ⭐ Code: github.com/amirgroup-co... ⭐ Website: protmech.github.io
arxiv.org
Protein Circuit Tracing via Cross-layer Transcoders
Protein language models (pLMs) have emerged as powerful predictors of protein structure and function. However, the computational circuits underlying their predictions remain poorly understood. Recent ...
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Darin Tsui @darintsui.bsky.social · 16/02/2026
ProtoMech circuits also align with biology. Analyzing circuits for kinase activity, NADP+ binding, and GB1 reveal known structural and functional motifs. (4/n)
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Darin Tsui @darintsui.bsky.social · 16/02/2026
We demonstrate that discovered circuits recover up to 79% of the original model's performance. Additionally, steering along these circuits identifies top-fitness variants in 71% of cases. (3/n)
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Darin Tsui @darintsui.bsky.social · 16/02/2026
ProtoMech uses cross-layer transcoders to learn sparse representations jointly across the entire transformer. This allows us to trace out the model’s full computational circuitry. (2/n)
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Darin Tsui @darintsui.bsky.social · 16/02/2026
🚨Excited to share ProtoMech: a framework for discovering the computational circuits inside protein language models (pLMs)! pLMs like ESM2 are powerful, but the computational mechanisms, or circuits, underlying their predictions remain poorly understood. (1/n)
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Darin Tsui @darintsui.bsky.social · 22/09/2025
We develop SHAP zero into a Python package, which opens the door for efficient, principled, and scalable interpretability of biological sequence models! ⭐ Paper: arxiv.org/abs/2410.19236 ⭐ Code: github.com/amirgroup-co...
arxiv.org
SHAP zero Explains Biological Sequence Models with Near-zero Marginal Cost for Future Queries
The growing adoption of machine learning models for biological sequences has intensified the need for interpretable predictions, with Shapley values emerging as a theoretically grounded standard for m...
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Darin Tsui @darintsui.bsky.social · 22/09/2025
We then moved to apply SHAP zero to extract epistatic interactions in protein language models. Despite the total feature space being larger than a trillion, SHAP zero ran up to 7x faster in amortized time and uncovered interactions associated with structural stability.
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Darin Tsui @darintsui.bsky.social · 22/09/2025
We demonstrate the power of SHAP zero by applying it to guide RNA and DNA repair models. SHAP zero uncovered high-order interactions at scale corresponding to known biological motifs, a task previously inaccessible due to the space of feature interactions.
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Darin Tsui @darintsui.bsky.social · 22/09/2025
Our secret? We connect the sparse Fourier transform of a model with Shapley explanations. If the model is "compressible" (which many biological sequence models are!), SHAP zero amortizes the computation of feature interactions up to 1000x faster than current methods.
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Darin Tsui @darintsui.bsky.social · 22/09/2025
Our core idea: instead of recomputing explanations for every new sequence from scratch, we pay a one-time cost to create a global sketch of the model. This enables SHAP zero to explain biological sequences from this sketch with near-zero marginal cost.
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Darin Tsui @darintsui.bsky.social · 22/09/2025
The success of biological sequence models has created an urgent need to explain their predictions. However, computing Shapley values, often the gold standard of explanations, over thousands of sequences to extract biological insight remains computationally prohibitive.
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Darin Tsui @darintsui.bsky.social · 22/09/2025
Excited to announce our paper, SHAP zero, has been accepted into NeurIPS 2025! SHAP zero takes the first steps toward extracting biological insights at scale from machine learning models by amortizing the cost of explanations across large-scale biological datasets.
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