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Weian Mao

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5 papers

1 author row

ICLR Conference 2025 Conference Paper

Boltzmann-Aligned Inverse Folding Model as a Predictor of Mutational Effects on Protein-Protein Interactions

Xiaoran Jiao
Weian Mao
Wengong Jin
Peiyuan Yang
Hao Chen 0012
Chunhua Shen

Predicting the change in binding free energy ($\Delta \Delta G$) is crucial for understanding and modulating protein-protein interactions, which are critical in drug design. Due to the scarcity of experimental $\Delta\Delta G$ data, existing methods focus on pre-training, while neglecting the importance of alignment. In this work, we propose Boltzmann Alignment technique to transfer knowledge from pre-trained inverse folding models to prediction of $\Delta\Delta G$. We begin by analyzing the thermodynamic definition of $\Delta\Delta G$ and introducing the Boltzmann distribution to connect energy to the protein conformational distribution. However, the protein conformational distribution is intractable. Therefore, we employ Bayes’ theorem to circumvent direct estimation and instead utilize the log-likelihood provided by protein inverse folding models for the estimation of $\Delta\Delta G$. Compared to previous methods based on inverse folding, our method explicitly accounts for the unbound state of the protein complex in the $\Delta \Delta G$ thermodynamic cycle, introducing a physical inductive bias and achieving supervised and unsupervised state-of-the-art (SoTA) performance. Experimental results on SKEMPI v2 indicate that our method achieves Spearman coefficients of 0.3201 (unsupervised) and 0.5134 (supervised) on SKEMPI v2, significantly surpassing the previously reported %SoTA values SoTA results of 0.2632 and 0.4324, respectively. Furthermore, we demonstrate the capability of our method in binding energy prediction, protein-protein docking, and antibody optimization tasks. Code is available at [https://github.com/aim-uofa/BA-DDG](https://github.com/aim-uofa/BA-DDG)

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ICLR Conference 2025 Conference Paper

Revisiting Convolution Architecture in the Realm of DNA Foundation Models

Yu Bo
Weian Mao
Yanjun Shao
Weiqiang Bai
Peng Ye 0006
Xinzhu Ma
Junbo Zhao
Hao Chen 0041

In recent years, A variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there is a lack of comparison between these recent approaches and the classical architecture—convolutional networks (CNNs)—on foundation model benchmarks. This raises the question: are CNNs truly being surpassed by these recent approaches based on transformer and SSM architectures? In this paper, we develop a simple but well-designed CNN-based method, termed ConvNova. ConvNova identifies and proposes three effective designs: 1) dilated convolutions, 2) gated convolutions, and 3) a dual-branch framework for gating mechanisms. Through extensive empirical experiments, we demonstrate that ConvNova significantly outperforms recent methods on more than half of the tasks across several foundation model benchmarks. For example, in histone-related tasks, ConvNova exceeds the second-best method by an average of 5.8\%, while generally utilizing fewer parameters and enabling faster computation. In addition, the experiments observed findings that may be related to biological characteristics. This indicates that CNNs are still a strong competitor compared to Transformers and SSMs. We anticipate that this work will spark renewed interest in CNN-based methods for DNA foundation models.

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ICLR Conference 2024 Conference Paper

De novo Protein Design Using Geometric Vector Field Networks

Weian Mao
Muzhi Zhu
Zheng Sun
Shuaike Shen
Lin Yuanbo Wu
Hao Chen 0041
Chunhua Shen

Advances like protein diffusion have marked revolutionary progress in $\textit{de novo}$ protein design, a central topic in life science. These methods typically depend on protein structure encoders to model residue backbone frames, where atoms do not exist. Most prior encoders rely on atom-wise features, such as angles and distances between atoms, which are not available in this context. Only a few basic encoders, like IPA, have been proposed for this scenario, exposing the frame modeling as a bottleneck. In this work, we introduce the Vector Field Network (VFN), that enables network layers to perform learnable vector computations between coordinates of frame-anchored virtual atoms, thus achieving a higher capability for modeling frames. The vector computation operates in a manner similar to a linear layer, with each input channel receiving 3D virtual atom coordinates instead of scalar values. The multiple feature vectors output by the vector computation are then used to update the residue representations and virtual atom coordinates via attention aggregation. Remarkably, VFN also excels in modeling both frames and atoms, as the real atoms can be treated as the virtual atoms for modeling, positioning VFN as a potential $\textit{universal encoder}$. In protein diffusion (frame modeling), VFN exhibits a impressive performance advantage over IPA, excelling in terms of both designability ($\textbf{67.04}$\% vs. 53.58\%) and diversity ($\textbf{66.54}$\% vs. 51.98\%). In inverse folding(frame and atom modeling), VFN outperforms the previous SoTA model, PiFold ($\textbf{54.7}$\% vs. 51.66\%), on sequence recovery rate; we also propose a method of equipping VFN with the ESM model, which significantly surpasses the previous ESM-based SoTA ($\textbf{62.67}$\% vs. 55.65\%), LM-Design, by a substantial margin. Code is available at https://github.com/aim-uofa/VFN

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ICML Conference 2024 Conference Paper

Floating Anchor Diffusion Model for Multi-motif Scaffolding

Ke Liu 0012
Weian Mao
Shuaike Shen
Xiaoran Jiao
Zheng Sun
Hao Cheng 0012
Chunhua Shen

Motif scaffolding seeks to design scaffold structures for constructing proteins with functions derived from the desired motif, which is crucial for the design of vaccines and enzymes. Previous works approach the problem by inpainting or conditional generation. Both of them can only scaffold motifs with fixed positions, and the conditional generation cannot guarantee the presence of motifs. However, prior knowledge of the relative motif positions in a protein is not readily available, and constructing a protein with multiple functions in one protein is more general and significant because of the synergies between functions. We propose a Floating Anchor Diffusion (FADiff) model. FADiff allows motifs to float rigidly and independently in the process of diffusion, which guarantees the presence of motifs and automates the motif position design. Our experiments demonstrate the efficacy of FADiff with high success rates and designable novel scaffolds. To the best of our knowledge, FADiff is the first work to tackle the challenge of scaffolding multiple motifs without relying on the expertise of relative motif positions in the protein. Code is available at https: //github. com/aim-uofa/FADiff.

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ICML Conference 2024 Conference Paper

Generative Active Learning for Long-tailed Instance Segmentation

Muzhi Zhu
Chengxiang Fan
Hao Chen 0041
Yang Liu 0357
Weian Mao
Xiaogang Xu 0002
Chunhua Shen

Recently, large-scale language-image generative models have gained widespread attention and many works have utilized generated data from these models to further enhance the performance of perception tasks. However, not all generated data can positively impact downstream models, and these methods do not thoroughly explore how to better select and utilize generated data. On the other hand, there is still a lack of research oriented towards active learning on generated data. In this paper, we explore how to perform active learning specifically for generated data in the long-tailed instance segmentation task. Subsequently, we propose BSGAL, a new algorithm that estimates the contribution of the current batch-generated data based on gradient cache. BSGAL is meticulously designed to cater for unlimited generated data and complex downstream segmentation tasks. BSGAL outperforms the baseline approach and effectually improves the performance of long-tailed segmentation.

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