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Aurelie C. Lozano

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2 papers

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NeurIPS Conference 2023 Conference Paper

Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction

Zuobai Zhang
Minghao Xu
Aurelie C. Lozano
Vijil Chenthamarakshan
Payel Das
Jian Tang

Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences or structures, neglecting the exploration of their joint distribution, which is crucial for a comprehensive understanding of protein functions by integrating co-evolutionary information and structural characteristics. In this work, inspired by the success of denoising diffusion models in generative tasks, we propose the DiffPreT approach to pre-train a protein encoder by sequence-structure joint diffusion modeling. DiffPreT guides the encoder to recover the native protein sequences and structures from the perturbed ones along the joint diffusion trajectory, which acquires the joint distribution of sequences and structures. Considering the essential protein conformational variations, we enhance DiffPreT by a method called Siamese Diffusion Trajectory Prediction (SiamDiff) to capture the correlation between different conformers of a protein. SiamDiff attains this goal by maximizing the mutual information between representations of diffusion trajectories of structurally-correlated conformers. We study the effectiveness of DiffPreT and SiamDiff on both atom- and residue-level structure-based protein understanding tasks. Experimental results show that the performance of DiffPreT is consistently competitive on all tasks, and SiamDiff achieves new state-of-the-art performance, considering the mean ranks on all tasks. Code will be released upon acceptance.

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NeurIPS Conference 2021 Conference Paper

Adaptive Proximal Gradient Methods for Structured Neural Networks

Jihun Yun
Aurelie C. Lozano
Eunho Yang

We consider the training of structured neural networks where the regularizer can be non-smooth and possibly non-convex. While popular machine learning libraries have resorted to stochastic (adaptive) subgradient approaches, the use of proximal gradient methods in the stochastic setting has been little explored and warrants further study, in particular regarding the incorporation of adaptivity. Towards this goal, we present a general framework of stochastic proximal gradient descent methods that allows for arbitrary positive preconditioners and lower semi-continuous regularizers. We derive two important instances of our framework: (i) the first proximal version of \textsc{Adam}, one of the most popular adaptive SGD algorithm, and (ii) a revised version of ProxQuant for quantization-specific regularizers, which improves upon the original approach by incorporating the effect of preconditioners in the proximal mapping computations. We provide convergence guarantees for our framework and show that adaptive gradient methods can have faster convergence in terms of constant than vanilla SGD for sparse data. Lastly, we demonstrate the superiority of stochastic proximal methods compared to subgradient-based approaches via extensive experiments. Interestingly, our results indicate that the benefit of proximal approaches over sub-gradient counterparts is more pronounced for non-convex regularizers than for convex ones.

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