Bo Wang

Sedigheh Eslami, Maksim Gaiduk, Markus Krimmel et al.

In this report, we introduce pplx-embed, a family of multilingual embedding models that employ multi-stage contrastive learning on a diffusion-pretrained language model backbone for web-scale retrieval. By leveraging bidirectional attention through diffusion-based pretraining, our models capture comprehensive bidirectional context within passages, enabling the use of mean pooling and a late chunking strategy to better preserve global context across long documents. We release two model types: pplx-embed-v1 for standard retrieval, and pplx-embed-context-v1 for contextualized embeddings that incorporate global document context into passage representations. pplx-embed-v1 achieves competitive performance on the MTEB(Multilingual, v2), MTEB(Code), MIRACL, BERGEN, and ToolRet retrieval benchmarks, while pplx-embed-context-v1 sets new records on the ConTEB benchmark. Beyond public benchmarks, pplx-embed-v1 demonstrates strong performance on our internal evaluation suite, which focuses on real-world, large-scale search scenarios over tens of millions of documents. These results validate the models' effectiveness in production environments where retrieval quality and efficiency are critical at scale.

Arnav Shah, Junzhe Li, Parsa Idehpour et al.

Genomic foundation models have the potential to decode DNA syntax, yet face a fundamental tradeoff in their input representation. Standard fixed-vocabulary tokenizers fragment biologically meaningful motifs such as codons and regulatory elements, while nucleotide-level models preserve biological coherence but incur prohibitive computational costs for long contexts. We introduce dnaHNet, a state-of-the-art tokenizer-free autoregressive model that segments and models genomic sequences end-to-end. Using a differentiable dynamic chunking mechanism, dnaHNet compresses raw nucleotides into latent tokens adaptively, balancing compression with predictive accuracy. Pretrained on prokaryotic genomes, dnaHNet outperforms leading architectures including StripedHyena2 in scaling and efficiency. This recursive chunking yields quadratic FLOP reductions, enabling $>3 \times$ inference speedup over Transformers. On zero-shot tasks, dnaHNet achieves superior performance in predicting protein variant fitness and gene essentiality, while automatically discovering hierarchical biological structures without supervision. These results establish dnaHNet as a scalable, interpretable framework for next-generation genomic modeling.