Aman Patel

Eric Nguyen, Michael Poli, Marjan Faizi et al.

Genomic (DNA) sequences encode an enormous amount of information for gene regulation and protein synthesis. Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers or fixed k-mers to aggregate meaningful DNA units, losing single nucleotide resolution where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity. Leveraging Hyena's new long-range capabilities, we present HyenaDNA, a genomic foundation model pretrained on the human reference genome with context lengths of up to 1 million tokens at the single nucleotide-level - an up to 500x increase over previous dense attention-based models. HyenaDNA scales sub-quadratically in sequence length (training up to 160x faster than Transformer), uses single nucleotide tokens, and has full global context at each layer. We explore what longer context enables - including the first use of in-context learning in genomics. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 18 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on 7 of 8 datasets on average by +10 accuracy points. Code at https://github.com/HazyResearch/hyena-dna.

Michael Galarnyk, Siddharth Lohani, Vidhyakshaya Kannan et al.

An Initial Public Offering (IPO) filing is a document released when a private firm goes public, allowing individual (retail) investors to purchase its shares. These filings describe a firm's business, financials, and risks and are long, multimodal documents with narrative text and images. Despite their importance to financial markets, there is no large-scale, standardized dataset or benchmark for studying IPO filings with modern language and multimodal models. These documents pose significant challenges: filings frequently exceed 500,000 tokens and lack consistent structural organization. We introduce the IPO-Toolkit, an open-source framework for downloading and parsing IPO filings into standardized section-structured text and extracted images. The toolkit segments filings, extracts embedded images, and produces structured outputs that enable large-scale, reproducible analysis workflows over long, multimodal documents. Using this infrastructure, we construct the IPO-Dataset, a large, section-structured, multimodal dataset covering more than 109,000 IPO filings and amendments from 1994 to 2026 and containing over 76,000 images. We establish structured evaluation tasks over extracted financial charts, including chart quality and misleadingness assessment. Our experiments show that state-of-the-art multimodal models often diverge from expert human judgments on these tasks, exposing alignment challenges in multimodal reasoning over long, real-world regulatory documents. Beyond benchmarking, the IPO-Dataset enables large-scale analysis of section-level textual variation and cross-industry differences in visual and textual disclosure practices. Our code, dataset, and website are publicly available under CC-BY-4.0.

Aman Patel, Arpita Singhal, Austin Wang et al.

Recent advances in self-supervised models for natural language, vision, and protein sequences have inspired the development of large genomic DNA language models (DNALMs). These models aim to learn generalizable representations of diverse DNA elements, potentially enabling various genomic prediction, interpretation and design tasks. Despite their potential, existing benchmarks do not adequately assess the capabilities of DNALMs on key downstream applications involving an important class of non-coding DNA elements critical for regulating gene activity. In this study, we introduce DART-Eval, a suite of representative benchmarks specifically focused on regulatory DNA to evaluate model performance across zero-shot, probed, and fine-tuned scenarios against contemporary ab initio models as baselines. Our benchmarks target biologically meaningful downstream tasks such as functional sequence feature discovery, predicting cell-type specific regulatory activity, and counterfactual prediction of the impacts of genetic variants. We find that current DNALMs exhibit inconsistent performance and do not offer compelling gains over alternative baseline models for most tasks, while requiring significantly more computational resources. We discuss potentially promising modeling, data curation, and evaluation strategies for the next generation of DNALMs. Our code is available at https://github.com/kundajelab/DART-Eval.