Demo Data from EDBT 2026 / reviewers in the wild / expert
Qiuyang Ding
dblp:322/3712
· DBLP profile ↗
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
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Natural language and speech › Language models and text generation › neural language model
protein language model |
0.6 | 1 | 2022 | Exploring evolution-aware & -free protein language models as protein function predictors · NeurIPS 2022 |
Bioinformatics and computational biology
protein function prediction |
0.6 | 1 | 2022 | 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 |
0.6 | 1 | 2022 | Exploring evolution-aware & -free protein language models as protein function predictors · NeurIPS 2022 |
Machine learning › Graph learning
protein structure prediction |
0.2 | 1 | 2022 | 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
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2022 | Exploring evolution-aware & -free protein language models as protein function predictorsabstractLarge-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 |
NeurIPS | 8 |