Minghao Xu

Minghao Xu, Zuobai Zhang, Jiarui Lu et al.

We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose such a benchmark called PEER, a comprehensive and multi-task benchmark for Protein sEquence undERstanding. PEER provides a set of diverse protein understanding tasks including protein function prediction, protein localization prediction, protein structure prediction, protein-protein interaction prediction, and protein-ligand interaction prediction. We evaluate different types of sequence-based methods for each task including traditional feature engineering approaches, different sequence encoding methods as well as large-scale pre-trained protein language models. In addition, we also investigate the performance of these methods under the multi-task learning setting. Experimental results show that large-scale pre-trained protein language models achieve the best performance for most individual tasks, and jointly training multiple tasks further boosts the performance. The datasets and source codes of this benchmark are all available at https://github.com/DeepGraphLearning/PEER_Benchmark

Zuobai Zhang, Minghao Xu, Arian Jamasb et al.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain protein language models on a large number of unlabeled amino acid sequences and then finetune the models with some labeled data in downstream tasks. Despite the effectiveness of sequence-based approaches, the power of pretraining on known protein structures, which are available in smaller numbers only, has not been explored for protein property prediction, though protein structures are known to be determinants of protein function. In this paper, we propose to pretrain protein representations according to their 3D structures. We first present a simple yet effective encoder to learn the geometric features of a protein. We pretrain the protein graph encoder by leveraging multiview contrastive learning and different self-prediction tasks. Experimental results on both function prediction and fold classification tasks show that our proposed pretraining methods outperform or are on par with the state-of-the-art sequence-based methods, while using much less pretraining data. Our implementation is available at https://github.com/DeepGraphLearning/GearNet.

Zuobai Zhang, Chuanrui Wang, Minghao Xu et al.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

Sha Yuan, Hanyu Zhao, Shuai Zhao et al. · bytedance, pku

With the rapid development of deep learning, training Big Models (BMs) for multiple downstream tasks becomes a popular paradigm. Researchers have achieved various outcomes in the construction of BMs and the BM application in many fields. At present, there is a lack of research work that sorts out the overall progress of BMs and guides the follow-up research. In this paper, we cover not only the BM technologies themselves but also the prerequisites for BM training and applications with BMs, dividing the BM review into four parts: Resource, Models, Key Technologies and Application. We introduce 16 specific BM-related topics in those four parts, they are Data, Knowledge, Computing System, Parallel Training System, Language Model, Vision Model, Multi-modal Model, Theory&Interpretability, Commonsense Reasoning, Reliability&Security, Governance, Evaluation, Machine Translation, Text Generation, Dialogue and Protein Research. In each topic, we summarize clearly the current studies and propose some future research directions. At the end of this paper, we conclude the further development of BMs in a more general view.

Zuobai Zhang, Minghao Xu, Aurélie Lozano et al.

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. Our implementation is available at https://github.com/DeepGraphLearning/SiamDiff.

Minghao Xu, Yuanfan Guo, Yi Xu et al.

Modeling spatial relationship in the data remains critical across many different tasks, such as image classification, semantic segmentation and protein structure understanding. Previous works often use a unified solution like relative positional encoding. However, there exists different kinds of spatial relations, including short-range, medium-range and long-range relations, and modeling them separately can better capture the focus of different tasks on the multi-range relations (e.g., short-range relations can be important in instance segmentation, while long-range relations should be upweighted for semantic segmentation). In this work, we introduce the EurNet for Efficient multi-range relational modeling. EurNet constructs the multi-relational graph, where each type of edge corresponds to short-, medium- or long-range spatial interactions. In the constructed graph, EurNet adopts a novel modeling layer, called gated relational message passing (GRMP), to propagate multi-relational information across the data. GRMP captures multiple relations within the data with little extra computational cost. We study EurNets in two important domains for image and protein structure modeling. Extensive experiments on ImageNet classification, COCO object detection and ADE20K semantic segmentation verify the gains of EurNet over the previous SoTA FocalNet. On the EC and GO protein function prediction benchmarks, EurNet consistently surpasses the previous SoTA GearNet. Our results demonstrate the strength of EurNets on modeling spatial multi-relational data from various domains. The implementations of EurNet for image modeling are available at https://github.com/hirl-team/EurNet-Image . The implementations for other applied domains/tasks will be released soon.

Minghao Xu, Xinyu Yuan, Santiago Miret et al.

Current protein language models (PLMs) learn protein representations mainly based on their sequences, thereby well capturing co-evolutionary information, but they are unable to explicitly acquire protein functions, which is the end goal of protein representation learning. Fortunately, for many proteins, their textual property descriptions are available, where their various functions are also described. Motivated by this fact, we first build the ProtDescribe dataset to augment protein sequences with text descriptions of their functions and other important properties. Based on this dataset, we propose the ProtST framework to enhance Protein Sequence pre-training and understanding by biomedical Texts. During pre-training, we design three types of tasks, i.e., unimodal mask prediction, multimodal representation alignment and multimodal mask prediction, to enhance a PLM with protein property information with different granularities and, at the same time, preserve the PLM's original representation power. On downstream tasks, ProtST enables both supervised learning and zero-shot prediction. We verify the superiority of ProtST-induced PLMs over previous ones on diverse representation learning benchmarks. Under the zero-shot setting, we show the effectiveness of ProtST on zero-shot protein classification, and ProtST also enables functional protein retrieval from a large-scale database without any function annotation.

Minghao Xu, Jiaze Song, Keming Wu et al.

Understanding the various properties of glycans with machine learning has shown some preliminary promise. However, previous methods mainly focused on modeling the backbone structure of glycans as graphs of monosaccharides (i.e., sugar units), while they neglected the atomic structures underlying each monosaccharide, which are actually important indicators of glycan properties. We fill this blank by introducing the GlycanAA model for All-Atom-wise Glycan modeling. GlycanAA models a glycan as a heterogeneous graph with monosaccharide nodes representing its global backbone structure and atom nodes representing its local atomic-level structures. Based on such a graph, GlycanAA performs hierarchical message passing to capture from local atomic-level interactions to global monosaccharide-level interactions. To further enhance model capability, we pre-train GlycanAA on a high-quality unlabeled glycan dataset, deriving the PreGlycanAA model. We design a multi-scale mask prediction algorithm to endow the model about different levels of dependencies in a glycan. Extensive benchmark results show the superiority of GlycanAA over existing glycan encoders and verify the further improvements achieved by PreGlycanAA. We maintain all resources at https://github.com/kasawa1234/GlycanAA

Zhaocheng Zhu, Chence Shi, Zuobai Zhang et al.

Machine learning has huge potential to revolutionize the field of drug discovery and is attracting increasing attention in recent years. However, lacking domain knowledge (e.g., which tasks to work on), standard benchmarks and data preprocessing pipelines are the main obstacles for machine learning researchers to work in this domain. To facilitate the progress of machine learning for drug discovery, we develop TorchDrug, a powerful and flexible machine learning platform for drug discovery built on top of PyTorch. TorchDrug benchmarks a variety of important tasks in drug discovery, including molecular property prediction, pretrained molecular representations, de novo molecular design and optimization, retrosynthsis prediction, and biomedical knowledge graph reasoning. State-of-the-art techniques based on geometric deep learning (or graph machine learning), deep generative models, reinforcement learning and knowledge graph reasoning are implemented for these tasks. TorchDrug features a hierarchical interface that facilitates customization from both novices and experts in this domain. Tutorials, benchmark results and documentation are available at https://torchdrug.ai. Code is released under Apache License 2.0.