Predicting mutational effects on protein-protein binding via a side-chain diffusion probabilistic model

1 code implementation • NeurIPS 2023 • Shiwei Liu, Tian Zhu, Milong Ren, Chungong Yu, Dongbo Bu, Haicang Zhang

Many crucial biological processes rely on networks of protein-protein interactions.

Representation Learning

A Theory of Human-Like Few-Shot Learning

no code implementations • 3 Jan 2023 • Zhiying Jiang, Rui Wang, Dongbo Bu, Ming Li

We aim to bridge the gap between our common-sense few-sample human learning and large-data machine learning.

Common Sense Reasoning Few-Shot Learning

NIERT: Accurate Numerical Interpolation through Unifying Scattered Data Representations using Transformer Encoder

1 code implementation • 19 Sep 2022 • Shizhe Ding, Boyang xia, Milong Ren, Dongbo Bu

Interpolation for scattered data is a classical problem in numerical analysis, with a long history of theoretical and practical contributions.

Decoder Representation Learning

Seq-SetNet: Exploring Sequence Sets for Inferring Structures

no code implementations • 6 Jun 2019 • Fusong Ju, Jianwei Zhu, Guozheng Wei, Qi Zhang, Shiwei Sun, Dongbo Bu

Therefore, the traditional deep neural networks designed for image processing cannot be directly applied on sequence sets.

Multiple Sequence Alignment Protein Secondary Structure Prediction +1

Predicting protein inter-residue contacts using composite likelihood maximization and deep learning

1 code implementation • 31 Aug 2018 • Haicang Zhang, Qi Zhang, Fusong Ju, Jianwei Zhu, Yujuan Gao, Ziwei Xie, Minghua Deng, Shiwei Sun, Wei-Mou Zheng, Dongbo Bu

We further present successful application of the predicted contacts to accurately build tertiary structures for proteins in the PSICOV dataset.