Soochow University

Variant effect and disease phosphosite prediction that fuses frozen ESM-2 embeddings with normal-mode protein dynamics over AlphaFold residue graphs.

Antibody-specific epitope prediction that replaces sequence-offset rotary attention with backbone local-frame 3D geometry. 0.410 MCC on AsEP.

Protein function prediction via compressed in-context learning on a sequence-structure language model, cutting 751-token demonstrations to under 16.

Single-cell diaPASEF proteomics search that scores coelution with a pretrained CNN and returns a protein matrix with no missing values.

Protein language model that tokenizes sequence, backbone structure, and text into one vocabulary for function prediction, design, and fold editing.

Goal-oriented de novo molecule design with an instruction-tuned LLM that honors property targets, substructure constraints, and numeric values.

Cell-free DNA methylation deconvolution at individual-read resolution, estimating cell-type proportions and condition-specific methylation profiles.

Protein question-answering model that fuses sequence and structure into an LLM prompt as virtual tokens, answering free-form questions about function.

Peptide identification for diaPASEF proteomics, scoring fragment coelution across retention time and ion mobility with a pretrained CNN.

Protein structure tokenizer that encodes all-atom folds as artificial amino acids and decodes them back to coordinates at TM-score above 0.96.