arXiv subjects

Zuobai Zhang

Publications and source records attributed to Zuobai Zhang.

29 records · Page 2Linked to original sources

arXiv2023

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

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.

cs.LG↗

arXiv2023

FusionRetro: Molecule Representation Fusion via In-Context Learning for Retrosynthetic Planning

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-step retrosynthesis models and search algorithms, taking only the product as the input to predict the reactants for each planning step and ignoring valuable context information along the synthetic route. In this work, we propose a novel framework that utilizes context information for improved retrosynthetic planning. We view synthetic routes as reaction graphs and propose to incorporate context through three principled steps: encode molecules into embeddings, aggregate information over routes, and readout to predict reactants. Our approach is the first attempt to utilize in-context learning for retrosynthesis prediction in retrosynthetic planning. The entire framework can be efficiently optimized in an end-to-end fashion and produce more practical and accurate predictions. Comprehensive experiments demonstrate that by fusing in the context information over routes, our model significantly improves the performance of retrosynthetic planning over baselines that are not context-aware, especially for long synthetic routes. Code is available at https://github.com/SongtaoLiu0823/FusionRetro.

cs.LG↗

arXiv2023

Protein Representation Learning by Geometric Structure Pretraining

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.

cs.LG↗

arXiv2022

Structured Multi-task Learning for Molecular Property Prediction

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 learning in drug discovery is still not satisfying as the number of labeled data for each task is too limited, which calls for additional data to complement the data scarcity. In this paper, we study multi-task learning for molecular property prediction in a novel setting, where a relation graph between tasks is available. We first construct a dataset (ChEMBL-STRING) including around 400 tasks as well as a task relation graph. Then to better utilize such relation graph, we propose a method called SGNN-EBM to systematically investigate the structured task modeling from two perspectives. (1) In the \emph{latent} space, we model the task representations by applying a state graph neural network (SGNN) on the relation graph. (2) In the \emph{output} space, we employ structured prediction with the energy-based model (EBM), which can be efficiently trained through noise-contrastive estimation (NCE) approach. Empirical results justify the effectiveness of SGNN-EBM. Code is available on https://github.com/chao1224/SGNN-EBM.

q-bio.BM↗

arXiv2022

PEER: A Comprehensive and Multi-Task Benchmark for Protein Sequence Understanding

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

cs.LG↗

arXiv2022

Neural-Symbolic Models for Logical Queries on Knowledge Graphs

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 graph to extract the answers, which provides good interpretation for each step. Recent neural methods learn geometric embeddings for complex queries. These methods can generalize to incomplete knowledge graphs, but their reasoning process is hard to interpret. In this paper, we propose Graph Neural Network Query Executor (GNN-QE), a neural-symbolic model that enjoys the advantages of both worlds. GNN-QE decomposes a complex FOL query into relation projections and logical operations over fuzzy sets, which provides interpretability for intermediate variables. To reason about the missing links, GNN-QE adapts a graph neural network from knowledge graph completion to execute the relation projections, and models the logical operations with product fuzzy logic. Experiments on 3 datasets show that GNN-QE significantly improves over previous state-of-the-art models in answering FOL queries. Meanwhile, GNN-QE can predict the number of answers without explicit supervision, and provide visualizations for intermediate variables.

cs.AI↗

arXiv2022

Effects of Stubbornness on Opinion Dynamics

As an important factor governing opinion dynamics, stubbornness strongly affects various aspects of opinion formation. However, a systematically theoretical study about the influences of heterogeneous stubbornness on opinion dynamics is still lacking. In this paper, we study a popular opinion model in the presence of inhomogeneous stubbornness. We show analytically that heterogeneous stubbornness has a great impact on convergence time, expressed opinion of every node, and the overall expressed opinion. We provide an explanation of the expressed opinion in terms of stubbornness-dependent spanning diverging forests. We propose quantitative indicators to quantify some social concepts, including conflict, disagreement, and polarization by incorporating heterogeneous stubbornness, and develop a nearly linear time algorithm to approximate these quantities, which has a proved theoretical guarantee for the error of each quantity. To demonstrate the performance of our algorithm, we perform extensive experiments on a large set of real networks, which indicate that our algorithm is both efficient and effective, scalable to large networks with millions of nodes.

cs.SI↗

arXiv2022

A Roadmap for Big Model

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.

cs.LG↗

arXiv2022

TorchDrug: A Powerful and Flexible Machine Learning Platform for Drug Discovery

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.

cs.LG↗

arXiv2022

Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction

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 based on paths for link prediction. Specifically, we define the representation of a pair of nodes as the generalized sum of all path representations, with each path representation as the generalized product of the edge representations in the path. Motivated by the Bellman-Ford algorithm for solving the shortest path problem, we show that the proposed path formulation can be efficiently solved by the generalized Bellman-Ford algorithm. To further improve the capacity of the path formulation, we propose the Neural Bellman-Ford Network (NBFNet), a general graph neural network framework that solves the path formulation with learned operators in the generalized Bellman-Ford algorithm. The NBFNet parameterizes the generalized Bellman-Ford algorithm with 3 neural components, namely INDICATOR, MESSAGE and AGGREGATE functions, which corresponds to the boundary condition, multiplication operator, and summation operator respectively. The NBFNet is very general, covers many traditional path-based methods, and can be applied to both homogeneous graphs and multi-relational graphs (e.g., knowledge graphs) in both transductive and inductive settings. Experiments on both homogeneous graphs and knowledge graphs show that the proposed NBFNet outperforms existing methods by a large margin in both transductive and inductive settings, achieving new state-of-the-art results.

cs.LG↗

arXiv2021

Coherence Scaling of Noisy Second-Order Scale-Free Consensus Networks

A striking discovery in the field of network science is that the majority of real networked systems have some universal structural properties. In generally, they are simultaneously sparse, scale-free, small-world, and loopy. In this paper, we investigate the second-order consensus of dynamic networks with such universal structures subject to white noise at vertices. We focus on the network coherence $H_{\rm SO}$ characterized in terms of the $\mathcal{H}_2$-norm of the vertex systems, which measures the mean deviation of vertex states from their average value. We first study numerically the coherence of some representative real-world networks. We find that their coherence $H_{\rm SO}$ scales sublinearly with the vertex number $N$. We then study analytically $H_{\rm SO}$ for a class of iteratively growing networks -- pseudofractal scale-free webs (PSFWs), and obtain an exact solution to $H_{\rm SO}$, which also increases sublinearly in $N$, with an exponent much smaller than 1. To explain the reasons for this sublinear behavior, we finally study $H_{\rm SO}$ for Sierpinśki gaskets, for which $H_{\rm SO}$ grows superlinearly in $N$, with a power exponent much larger than 1. Sierpinśki gaskets have the same number of vertices and edges as the PSFWs, but do not display the scale-free and small-world properties. We thus conclude that the scale-free and small-world, and loopy topologies are jointly responsible for the observed sublinear scaling of $H_{\rm SO}$.

math.NA↗