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Qiuyang Ding

dblp:322/3712 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2022
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%
Artificial intelligence
1 paper
Language models and text generation · 77% Graph learning · 23%

Topics — the 4 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Natural language and speech › Language models and text generation › neural language model
protein language model
0.612022
Exploring evolution-aware & -free protein language models as protein function predictors · NeurIPS 2022
Bioinformatics and computational biology
protein function prediction
0.612022
Exploring evolution-aware & -free protein language models as protein function predictors · NeurIPS 2022
Bioinformatics and computational biology › protein analysis › protein bioinformatics › protein representation learning
protein language model embedding
0.612022
Exploring evolution-aware & -free protein language models as protein function predictors · NeurIPS 2022
Machine learning › Graph learning
protein structure prediction
0.212022
Exploring evolution-aware & -free protein language models as protein function predictors · NeurIPS 2022

Methods — techniques the papers use, named apart from their topics

protein language model · 1.1multiple sequence alignment · 1.1
YearPublicationVenuePosition
2022 Exploring evolution-aware & -free protein language models as protein function predictors
abstract
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 .
Mingyang Hu, Fajie Yuan, Kevin Yang, Fusong Ju, Jin Su, Qiuyang Ding
NeurIPS8