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Daniel Diaz

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3 papers

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NeurIPS Conference 2025 Conference Paper

Ambient Proteins - Training Diffusion Models on Noisy Structures

Giannis Daras
Jeffrey Ouyang-Zhang
Krithika Ravishankar
Constantinos Daskalakis
Adam Klivans
Daniel Diaz

We present Ambient Protein Diffusion, a framework for training protein diffusion models that generates structures with unprecedented diversity and quality. State-of-the-art generative models are trained on computationally derived structures from AlphaFold2 (AF), as experimentally determined structures are relatively scarce. The resulting models are therefore limited by the quality of synthetic datasets. Since the accuracy of AF predictions degrades with increasing protein length and complexity, de novo generation of long, complex proteins remains challenging. Ambient Protein Diffusion overcomes this problem by treating low-confidence AF structures as corrupted data. Rather than simply filtering out low-quality AF structures, our method adjusts the diffusion objective for each structure based on its corruption level, allowing the model to learn from both high and low quality structures. Empirically, ambient protein diffusion yields major improvements: on proteins with 700 residues, diversity increases from 45% to 85% from the previous state-of-the-art, and designability improves from 70% to 88%.

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NeurIPS Conference 2023 Conference Paper

Predicting a Protein's Stability under a Million Mutations

Jeffrey Ouyang-Zhang
Daniel Diaz
Adam Klivans
Philipp Kraehenbuehl

Stabilizing proteins is a foundational step in protein engineering. However, the evolutionary pressure of all extant proteins makes identifying the scarce number of mutations that will improve thermodynamic stability challenging. Deep learning has recently emerged as a powerful tool for identifying promising mutations. Existing approaches, however, are computationally expensive, as the number of model inferences scales with the number of mutations queried. Our main contribution is a simple, parallel decoding algorithm. Mutate Everything is capable of predicting the effect of all single and double mutations in one forward pass. It is even versatile enough to predict higher-order mutations with minimal computational overhead. We build Mutate Everything on top of ESM2 and AlphaFold, neither of which were trained to predict thermodynamic stability. We trained on the Mega-Scale cDNA proteolysis dataset and achieved state-of-the-art performance on single and higher-order mutations on S669, ProTherm, and ProteinGym datasets. Our code is available at https: //github. com/jozhang97/MutateEverything.

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AAAI Conference 2015 Conference Paper

Solving Hard Stable Matching Problems via Local Search and Cooperative Parallelization

Danny Munera
Daniel Diaz
Salvador Abreu
Francesca Rossi
Vijay Saraswat
Philippe Codognet

Stable matching problems have several practical applications. If preference lists are truncated and contain ties, finding a stable matching with maximal size is computationally difficult. We address this problem using a local search technique, based on Adaptive Search and present experimental evidence that this approach is much more efficient than state-of-the-art exact and approximate methods. Moreover, parallel versions (particularly versions with communication) improve performance so much that very large and hard instances can be solved quickly.

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