Search Results for author: Bin Shao

Found 15 papers, 3 papers with code

Self-Consistency Training for Hamiltonian Prediction

no code implementations14 Mar 2024 He Zhang, Chang Liu, Zun Wang, Xinran Wei, Siyuan Liu, Nanning Zheng, Bin Shao, Tie-Yan Liu

This merit addresses the data scarcity difficulty, and distinguishes the task from other property prediction formulations with unique benefits: (1) self-consistency training enables the model to be trained on a large amount of unlabeled data, hence substantially enhances generalization; (2) self-consistency training is more efficient than labeling data with DFT for supervised training, since it is an amortization of DFT calculation over a set of molecular structures.

Property Prediction

Overcoming the Barrier of Orbital-Free Density Functional Theory for Molecular Systems Using Deep Learning

no code implementations28 Sep 2023 He Zhang, Siyuan Liu, Jiacheng You, Chang Liu, Shuxin Zheng, Ziheng Lu, Tong Wang, Nanning Zheng, Bin Shao

Orbital-free density functional theory (OFDFT) is a quantum chemistry formulation that has a lower cost scaling than the prevailing Kohn-Sham DFT, which is increasingly desired for contemporary molecular research.

PIDRo: Parallel Isomeric Attention with Dynamic Routing for Text-Video Retrieval

no code implementations ICCV 2023 Peiyan Guan, Renjing Pei, Bin Shao, Jianzhuang Liu, Weimian Li, Jiaxi Gu, Hang Xu, Songcen Xu, Youliang Yan, Edmund Y. Lam

The parallel isomeric attention module is used as the video encoder, which consists of two parallel branches modeling the spatial-temporal information of videos from both patch and frame levels.

Representation Learning Retrieval +3

Multi-View Substructure Learning for Drug-Drug Interaction Prediction

no code implementations28 Mar 2022 Zimeng Li, Shichao Zhu, Bin Shao, Tie-Yan Liu, Xiangxiang Zeng, Tong Wang

Drug-drug interaction (DDI) prediction provides a drug combination strategy for systemically effective treatment.

Co-evolution Transformer for Protein Contact Prediction

1 code implementation NeurIPS 2021 He Zhang, Fusong Ju, Jianwei Zhu, Liang He, Bin Shao, Nanning Zheng, Tie-Yan Liu

These methods generally derive coevolutionary features by aggregating the learned residue representations from individual sequences with equal weights, which is inconsistent with the premise that residue co-evolutions are a reflection of collective covariation patterns of numerous homologous proteins.

Pre-training Co-evolutionary Protein Representation via A Pairwise Masked Language Model

no code implementations29 Oct 2021 Liang He, Shizhuo Zhang, Lijun Wu, Huanhuan Xia, Fusong Ju, He Zhang, Siyuan Liu, Yingce Xia, Jianwei Zhu, Pan Deng, Bin Shao, Tao Qin, Tie-Yan Liu

The key problem in the protein sequence representation learning is to capture the co-evolutionary information reflected by the inter-residue co-variation in the sequences.

Language Modelling Multiple Sequence Alignment +1

SE(3) Equivariant Graph Neural Networks with Complete Local Frames

1 code implementation26 Oct 2021 Weitao Du, He Zhang, Yuanqi Du, Qi Meng, Wei Chen, Bin Shao, Tie-Yan Liu

In this paper, we propose a framework to construct SE(3) equivariant graph neural networks that can approximate the geometric quantities efficiently.

Computational Efficiency

Improved Drug-target Interaction Prediction with Intermolecular Graph Transformer

no code implementations14 Oct 2021 Siyuan Liu, Yusong Wang, Tong Wang, Yifan Deng, Liang He, Bin Shao, Jian Yin, Nanning Zheng, Tie-Yan Liu

The identification of active binding drugs for target proteins (termed as drug-target interaction prediction) is the key challenge in virtual screening, which plays an essential role in drug discovery.

Drug Discovery Molecular Docking +1

Defending Model Inversion and Membership Inference Attacks via Prediction Purification

no code implementations8 May 2020 Ziqi Yang, Bin Shao, Bohan Xuan, Ee-Chien Chang, Fan Zhang

Neural networks are susceptible to data inference attacks such as the model inversion attack and the membership inference attack, where the attacker could infer the reconstruction and the membership of a data sample from the confidence scores predicted by the target classifier.

Inference Attack Membership Inference Attack

SEEK: Segmented Embedding of Knowledge Graphs

1 code implementation ACL 2020 Wentao Xu, Shun Zheng, Liang He, Bin Shao, Jian Yin, Tie-Yan Liu

In recent years, knowledge graph embedding becomes a pretty hot research topic of artificial intelligence and plays increasingly vital roles in various downstream applications, such as recommendation and question answering.

Knowledge Graph Embedding Knowledge Graphs +2

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