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Fusong Ju

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NeurIPS Conference 2022 Conference Paper

Exploring evolution-aware & -free protein language models as protein function predictors

  • Mingyang Hu
  • Fajie Yuan
  • Kevin Yang
  • Fusong Ju
  • Jin Su
  • Hui Wang
  • Fei Yang
  • Qiuyang Ding

Large-scale Protein Language Models (PLMs) have improved performance in protein prediction tasks, ranging from 3D structure prediction to various function predictions. In particular, AlphaFold, a ground-breaking AI system, could potentially reshape structural biology. However, the utility of the PLM module in AlphaFold, Evoformer, has not been explored beyond structure prediction. In this paper, we investigate the representation ability of three popular PLMs: ESM-1b (single sequence), MSA-Transformer (multiple sequence alignment), and Evoformer (structural), with a special focus on Evoformer. Specifically, we aim to answer the following key questions: (1) Does the Evoformer trained as part of AlphaFold produce representations amenable to predicting protein function? (2) If yes, can Evoformer replace ESM-1b and MSA-Transformer? (3) How much do these PLMs rely on evolution-related protein data? In this regard, are they complementary to each other? We compare these models by empirical study along with new insights and conclusions. All code and datasets for reproducibility are available at https: //github. com/elttaes/Revisiting-PLMs.

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NeurIPS Conference 2021 Conference Paper

Co-evolution Transformer for Protein Contact Prediction

  • He Zhang
  • Fusong Ju
  • Jianwei Zhu
  • Liang He
  • Bin Shao
  • Nanning Zheng
  • Tie-Yan Liu

Proteins are the main machinery of life and protein functions are largely determined by their 3D structures. The measurement of the pairwise proximity between amino acids of a protein, known as inter-residue contact map, well characterizes the structural information of a protein. Protein contact prediction (PCP) is an essential building block of many protein structure related applications. The prevalent approach to contact prediction is based on estimating the inter-residue contacts using hand-crafted coevolutionary features derived from multiple sequence alignments (MSAs). To mitigate the information loss caused by hand-crafted features, some recently proposed methods try to learn residue co-evolutions directly from MSAs. 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. Moreover, non-homologous residues and gaps commonly exist in MSAs. By aggregating features from all homologs equally, the non-homologous information may cause misestimation of the residue co-evolutions. To overcome these issues, we propose an attention-based architecture, Co-evolution Transformer (CoT), for PCP. CoT jointly considers the information from all homologous sequences in the MSA to better capture global coevolutionary patterns. To mitigate the influence of the non-homologous information, CoT selectively aggregates the features from different homologs by assigning smaller weights to non-homologous sequences or residue pairs. Extensive experiments on two rigorous benchmark datasets demonstrate the effectiveness of CoT. In particular, CoT achieves a $51. 6\%$ top-L long-range precision score for the Free Modeling (FM) domains on the CASP14 benchmark, which outperforms the winner group of CASP14 contact prediction challenge by $9. 8\%$.

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