114 citations · 347 across the 17 of their papers we have counts for
18 papers
Multi-Scale Representation Learning for Protein Fitness Prediction
Zuobai Zhang, Pascal Notin, Yining Huang +5
Designing novel functional proteins crucially depends on accurately modeling their fitness landscape. Given the limited availability of functional annotations from wet-lab experime…
Cell-ontology guided transcriptome foundation model
Xinyu Yuan, Zhihao Zhan, Zuobai Zhang +5
Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale s…
Fusing Neural and Physical: Augment Protein Conformation Sampling with Tractable Simulations
Jiarui Lu, Zuobai Zhang, Bozitao Zhong +2
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations…
ProtIR: Iterative Refinement between Retrievers and Predictors for Protein Function Annotation
Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan +3
Protein function annotation is an important yet challenging task in biology. Recent deep learning advancements show significant potential for accurate function prediction by learni…
Structure-Informed Protein Language Model
Zuobai Zhang, Jiarui Lu, Vijil Chenthamarakshan +3
Protein language models are a powerful tool for learning protein representations through pre-training on vast protein sequence datasets. However, traditional protein language model…
PDB-Struct: A Comprehensive Benchmark for Structure-based Protein Design
Chuanrui Wang, Bozitao Zhong, Zuobai Zhang +3
Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has…
Str2Str: A Score-based Framework for Zero-shot Protein Conformation Sampling
Jiarui Lu, Bozitao Zhong, Zuobai Zhang +1
The dynamic nature of proteins is crucial for determining their biological functions and properties, for which Monte Carlo (MC) and molecular dynamics (MD) simulations stand as pre…
DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing
Yangtian Zhang, Zuobai Zhang, Bozitao Zhong +2
Proteins play a critical role in carrying out biological functions, and their 3D structures are essential in determining their functions. Accurately predicting the conformation of…
A Systematic Study of Joint Representation Learning on Protein Sequences and Structures
Zuobai Zhang, Chuanrui Wang, Minghao Xu +4
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based…
Pre-Training Protein Encoder via Siamese Sequence-Structure Diffusion Trajectory Prediction
Zuobai Zhang, Minghao Xu, Aurélie Lozano +3
Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences or structures, neglecting the exploration…
FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning
Songtao Liu, Zhengkai Tu, Minkai Xu +6
Retrosynthetic planning aims to devise a complete multi-step synthetic route from starting materials to a target molecule. Current strategies use a decoupled approach of single-ste…
PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding
Minghao Xu, Zuobai Zhang, Jiarui Lu +5
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 th…
Neural-Symbolic Models for Logical Queries on Knowledge Graphs
Zhaocheng Zhu, Mikhail Galkin, Zuobai Zhang +1
Answering complex first-order logic (FOL) queries on knowledge graphs is a fundamental task for multi-hop reasoning. Traditional symbolic methods traverse a complete knowledge grap…
A Roadmap for Big Model
Sha Yuan, Hanyu Zhao, Shuai Zhao +97
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 c…
Protein Representation Learning by Geometric Structure Pretraining
Zuobai Zhang, Minghao Xu, Arian Jamasb +4
Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein function or structure. Existing approaches usually pretrain prote…
Structured Multi-task Learning for Molecular Property Prediction
Shengchao Liu, Meng Qu, Zuobai Zhang +2
Multi-task learning for molecular property prediction is becoming increasingly important in drug discovery. However, in contrast to other domains, the performance of multi-task lea…
TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery
Zhaocheng Zhu, Chence Shi, Zuobai Zhang +12
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., wh…
Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction
Zhaocheng Zhu, Zuobai Zhang, Louis-Pascal Xhonneux +1
Link prediction is a very fundamental task on graphs. Inspired by traditional path-based methods, in this paper we propose a general and flexible representation learning framework…