All Competitors

Alignment-free taxonomic classification of eukaryotic DNA in metagenomes. Reaches an F1 of 0.871 on 500 bp contigs, where k-mer tools falter.

Genome-anchored histopathology embeddings that predict molecular biomarkers, subtypes, and survival from whole-slide images alone at inference.

Bulk transcriptome foundation model, 150M parameters over ~20,000 protein-coding genes. Imputes masked expression at Pearson r = 0.954.

Multimodal viral foundation model over nucleotide and protein sequence, built for virus discovery, function annotation, and antibody design.

Multimodal large language model that writes free-form natural-language gene function descriptions directly from a nucleotide sequence and a prompt.

Domain-level language model treating Pfam protein domains as tokens to predict and design bacterial and fungal biosynthetic gene clusters.

Codon optimization model for heterologous expression in E. coli, fine-tuning ProtBert to label each residue with an expression-weighted codon.

DNA foundation model pretrained by supervised genomic profile prediction, using mixture-of-experts routing across species and assay types.

Open-source framework for building RNA and DNA foundation models, featuring WCED pretraining for transcriptomics and SNP-aware encoding for genomics.

Cross-modal co-embedding of biosynthetic gene clusters and natural products, enabling bidirectional retrieval between gene cluster and compound.

DNA-LLM reasoning model fusing genome foundation model embeddings with an LLM to produce step-by-step pathway and variant effect explanations.

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

Distribution-level representation learning that embeds whole cell populations, perturbation responses, and sequence sets, not individual data points.

Bidirectional DNA foundation model with a Mamba-attention-mixture-of-experts design, reading 1 million base pairs at single-nucleotide resolution.

Contrastive k-mer embedding model for sequencing reads whose latent space encodes genomic position, matching BWA-aln accuracy on ancient DNA mapping.

Transcriptomic perturbation prediction across unseen single and double gene knockdowns and unseen cell lines, driven by gene-gene knowledge graphs.

Single-cell chromatin accessibility foundation model with genome-aware tokenization, pretrained on 1.97 million scATAC-seq cells across 30 tissues.

Tri-modal pathology foundation model aligning whole-slide images, transcriptomes, and diagnostic reports, and running on any subset of the three.

Protein-DNA binding prediction and binder design from sequence, aligning protein and DNA language model embeddings instead of co-folding a complex.

Recombinant protein expression predictor scoring soluble E. coli production from construct sequence, with AUROC 0.83 on prospective constructs.

Genomic prediction model for plant and animal breeding, pretrained entirely on simulated populations and deployed with no training or tuning.

Single-cell foundation model inferring cis-regulatory relationships from scRNA-seq and scATAC-seq, pretrained on an atlas of 1.3 million cells.

Alignment-free biosynthetic gene cluster detection and annotation from ESM-2 gene embeddings in genomic context, up to 102x faster than antiSMASH.