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Jiawei Guan

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3 papers

2 author rows

ICML Conference 2025 Conference Paper

P(all-atom) Is Unlocking New Path For Protein Design

Wei Qu
Jiawei Guan
Rui Ma
Ke Zhai 0008
Weikun Wu
Haobo Wang

We introduce Pallatom, an innovative protein generation model capable of producing protein structures with all-atom coordinates. Pallatom directly learns and models the joint distribution $P(\textit{structure}, \textit{seq})$ by focusing on $P(\textit{all-atom})$, effectively addressing the interdependence between sequence and structure in protein generation. To achieve this, we propose a novel network architecture specifically designed for all-atom protein generation. Our model employs a dual-track framework that tokenizes proteins into token-level and atomic-level representations, integrating them through a multi-layer decoding process with "traversing" representations and recycling mechanism. We also introduce the $\texttt{atom14}$ representation method, which unifies the description of unknown side-chain coordinates, ensuring high fidelity between the generated all-atom conformation and its physical structure. Experimental results demonstrate that Pallatom excels in key metrics of protein design, including designability, diversity, and novelty, showing significant improvements across the board. Our model not only enhances the accuracy of protein generation but also exhibits excellent sampling efficiency, paving the way for future applications in larger and more complex systems.

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NeurIPS Conference 2024 Conference Paper

UQ-Guided Hyperparameter Optimization for Iterative Learners

Jiesong Liu
Feng Zhang
Jiawei Guan
Xipeng Shen

Hyperparameter Optimization (HPO) plays a pivotal role in unleashing the potential of iterative machine learning models. This paper addresses a crucial aspect that has largely been overlooked in HPO: the impact of uncertainty in ML model training. The paper introduces the concept of uncertainty-aware HPO and presents a novel approach called the UQ-guided scheme for quantifying uncertainty. This scheme offers a principled and versatile method to empower HPO techniques in handling model uncertainty during their exploration of the candidate space. By constructing a probabilistic model and implementing probability-driven candidate selection and budget allocation, this approach enhances the quality of the resulting model hyperparameters. It achieves a notable performance improvement of over 50\% in terms of accuracy regret and exploration time.

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NeurIPS Conference 2022 Conference Paper

TREC: Transient Redundancy Elimination-based Convolution

Jiawei Guan
Feng Zhang
Jiesong Liu
Hsin-Hsuan Sung
Ruofan Wu
Xiaoyong Du
Xipeng Shen

The intensive computations in convolutional neural networks (CNNs) pose challenges for resource-constrained devices; eliminating redundant computations from convolution is essential. This paper gives a principled method to detect and avoid transient redundancy, a type of redundancy existing in input data or activation maps and hence changing across inferences. By introducing a new form of convolution (TREC), this new method makes transient redundancy detection and avoidance an inherent part of the CNN architecture, and the determination of the best configurations for redundancy elimination part of CNN backward propagation. We provide a rigorous proof of the robustness and convergence of TREC-equipped CNNs. TREC removes over 96% computations and achieves 3. 51x average speedups on microcontrollers with minimal (about 0. 7%) accuracy loss.

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