Modeling Protein Using Large-scale Pretrain Language Model
Published in Pretrain@KDD 2021, 2021
The early research on Protein Language Models featured the largest Protein Language Model at the time.
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Rethinking the Setting of Semi-supervised Learning on Graphs
Published in IJCAI 2022, 2022
We highlight the issue of over-tuning in GNNs on the validation set.
Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN
Published in Nature Methods 2024, 2024
Double-ended synthesis planning with goal-constrained bidirectional search
Published in NeurIPS 2024, 2024
Rewiring protein sequence and structure generative models to enhance protein stability prediction
Published in RECOMB 2025, 2025
RECOMB version of the SPURS.
Deconvolving mutation effects on protein stability and function with disentangled protein language models
Published in RECOMB 2026, 2026
DETANGO disentangles functional and stability constraints in protein function modeling by integrating evolutionary and thermodynamic predictors, and evaluates this relationship following the SPURS functional site identification task.
Generalizable and scalable protein stability prediction with rewired protein generative models
Published in Nature Communications 2026, 2026
We developed SPURS (stability prediction using a rewired strategy), the SOTA protein stability predictor, to benefit protein function understanding, such as functional site discovery, fitness prediction, and pathogenicity.