University of Chinese Academy of Sciences

Single-cell foundation model that predicts latent representations of graph-connected gene blocks instead of reconstructing individual gene counts.

RNA and single-stranded DNA 3D structure prediction from sequence alone, with no MSA or language-model inputs and roughly 100x cheaper inference.

Vision-guided model that builds virtual 3D organoid surrogates from brightfield microscopy to predict chemical perturbation responses without omics.

Multi-view single-cell foundation model at 12B parameters, aligning expression and perception views with an LLM-JEPA joint-embedding objective.

Diffusion-based generative RNA model for de novo sequence design, conditioned on function, RNA family, structure, or binding proteins.

Generative antibody and nanobody design model that co-designs CDR sequences and antigen-bound structures for de novo design and affinity maturation.

Influenza genomic language model adapting DNABERT-2 to ~900,000 viral genomes, identifying subtypes, segments, and pathogenicity from sequence.

Species-conditioned codon language model that jointly reads 5'UTRs, coding sequence, and RNA secondary structure to design native-like genes.

Protein foundation model built on Bayesian Flow Networks, prompted with MSA profiles for structure- and function-preserving sequence design.

Cross-species brain spatial transcriptomics foundation model pretrained on 133M cells from human, macaque, marmoset, and mouse whole brains.

Multimodal drug-response model coupling cell and molecule foundation models, pretrained on 1.8M perturbation RNA-seq profiles over 22,000 compounds.

Relative protein-ligand binding affinity prediction from docked complexes, matching Schrodinger FEP+ ranking accuracy zero-shot on the FEP benchmark.

Compact 1.1M-parameter DNA language model distilled from Nucleotide Transformer v2, outperforming its 500M teacher on 11 of 18 benchmark tasks.

Cyclic peptide design conditioned on target protein structure, generating all four cyclization types via all-atom, all-bond harmonic SDE modeling.

Molecular conformation description language encoding 3D geometry as SMILES plus internal-coordinate tokens, turning 3D modeling into a sequence task.

All-atom generative model for protein complexes that designs multi-chain binders from scratch and performs multimer folding and inverse folding.

Single-cell multi-omics foundation model with a Mamba backbone, pretrained on 2.7 million paired scRNA-seq and scATAC-seq profiles.

De novo peptide sequencing from mirror-protease mass spectra, reading paired complementary spectra to recover near-complete fragment ion coverage.

Full-atom flow matching model that generates a ligand and the induced-fit holo pocket together, starting from an apo binding site.

Secondary metabolite structure prediction from microbial biosynthetic gene clusters, generating SMILES strings from Pfam functional-domain tokens.

Ternary complex structure predictor for PROTACs and molecular glues, placing E3 ligase, degrader, and target protein in one SE(3)-equivariant pass.

Translates whole-brain imaging phenotypes between humans and mice through a shared latent space built from transcriptomics and connectivity.

Molecular docking framework that poses several ligands sharing one protein pocket at once, using their consistency to sharpen each prediction.