HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution

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 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 Hyenas 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 for simple adaptation to novel tasks without updating pretrained model weights. On fine-tuned benchmarks from the Nucleotide Transformer, HyenaDNA reaches state-of-the-art (SotA) on 12 of 17 datasets using a model with orders of magnitude less parameters and pretraining data. On the GenomicBenchmarks, HyenaDNA surpasses SotA on all 8 datasets on average by +9 accuracy points.

SequenceMatch: Imitation Learning for Autoregressive Sequence Modelling with Backtracking

In many domains, autoregressive models can attain high likelihood on the task of predicting the next observation. However, this maximum-likelihood (MLE) objective does not necessarily match a downstream use-case of autoregressively generating high-quality sequences. The MLE objective weights sequences proportionally to their frequency under the data distribution, with no guidance for the model's behaviour out of distribution (OOD): leading to compounding error during autoregressive generation. In order to address this compounding error problem, we formulate sequence generation as an imitation learning (IL) problem. This allows us to minimize a variety of divergences between the distribution of sequences generated by an autoregressive model and sequences from a dataset, including divergences with weight on OOD generated sequences. The IL framework also allows us to incorporate backtracking by introducing a backspace action into the generation process. This further mitigates the compounding error problem by allowing the model to revert a sampled token if it takes the sequence OOD. Our resulting method, SequenceMatch, can be implemented without adversarial training or major architectural changes. We identify the SequenceMatch-$\chi^2$ divergence as a more suitable training objective for autoregressive models which are used for generation. We show that empirically, SequenceMatch training leads to improvements over MLE on text generation with language models.

Parallel Sampling of Diffusion Models

Diffusion models are powerful generative models but suffer from slow sampling, often taking 1000 sequential denoising steps for one sample. As a result, considerable efforts have been directed toward reducing the number of denoising steps, but these methods hurt sample quality. Instead of reducing the number of denoising steps (trading quality for speed), in this paper we explore an orthogonal approach: can we run the denoising steps in parallel (trading compute for speed)? In spite of the sequential nature of the denoising steps, we show that surprisingly it is possible to parallelize sampling via Picard iterations, by guessing the solution of future denoising steps and iteratively refining until convergence. With this insight, we present ParaDiGMS, a novel method to accelerate the sampling of pretrained diffusion models by denoising multiple steps in parallel. ParaDiGMS is the first diffusion sampling method that enables trading compute for speed and is even compatible with existing fast sampling techniques such as DDIM and DPMSolver. Using ParaDiGMS, we improve sampling speed by 2-4x across a range of robotics and image generation models, giving state-of-the-art sampling speeds of 0.2s on 100-step DiffusionPolicy and 16s on 1000-step StableDiffusion-v2 with no measurable degradation of task reward, FID score, or CLIP score.

GEO-Bench: Toward Foundation Models for Earth Monitoring

Recent progress in self-supervision has shown that pre-training large neural networks on vast amounts of unsupervised data can lead to substantial increases in generalization to downstream tasks. Such models, recently coined foundation models, have been transformational to the field of natural language processing. Variants have also been proposed for image data, but their applicability to remote sensing tasks is limited. To stimulate the development of foundation models for Earth monitoring, we propose a benchmark comprised of six classification and six segmentation tasks, which were carefully curated and adapted to be both relevant to the field and well-suited for model evaluation. We accompany this benchmark with a robust methodology for evaluating models and reporting aggregated results to enable a reliable assessment of progress. Finally, we report results for 20 baselines to gain information about the performance of existing models. We believe that this benchmark will be a driver of progress across a variety of Earth monitoring tasks.

On the Equivalence of Consistency-Type Models: Consistency Models, Consistent Diffusion Models, and Fokker-Planck Regularization

The emergence of various notions of ``consistency'' in diffusion models has garnered considerable attention and helped achieve improved sample quality, likelihood estimation, and accelerated sampling. Although similar concepts have been proposed in the literature, the precise relationships among them remain unclear. In this study, we establish theoretical connections between three recent ``consistency'' notions designed to enhance diffusion models for distinct objectives. Our insights offer the potential for a more comprehensive and encompassing framework for consistency-type models.

Direct Preference Optimization: Your Language Model is Secretly a Reward Model

While large-scale unsupervised language models (LMs) learn broad world knowledge and some reasoning skills, achieving precise control of their behavior is difficult due to the completely unsupervised nature of their training. Existing methods for gaining such steerability collect human labels of the relative quality of model generations and fine-tune the unsupervised LM to align with these preferences, often with reinforcement learning from human feedback (RLHF). However, RLHF is a complex and often unstable procedure, first fitting a reward model that reflects the human preferences, and then fine-tuning the large unsupervised LM using reinforcement learning to maximize this estimated reward without drifting too far from the original model. In this paper, we leverage a mapping between reward functions and optimal policies to show that this constrained reward maximization problem can be optimized exactly with a single stage of policy training, essentially solving a classification problem on the human preference data. The resulting algorithm, which we call Direct Preference Optimization (DPO), is stable, performant and computationally lightweight, eliminating the need for fitting a reward model, sampling from the LM during fine-tuning, or performing significant hyperparameter tuning. Our experiments show that DPO can fine-tune LMs to align with human preferences as well as or better than existing methods. Notably, fine-tuning with DPO exceeds RLHF's ability to control sentiment of generations and improves response quality in summarization and single-turn dialogue while being substantially simpler to implement and train.

MADiff: Offline Multi-agent Learning with Diffusion Models

Diffusion model (DM), as a powerful generative model, recently achieved huge success in various scenarios including offline reinforcement learning, where the policy learns to conduct planning by generating trajectory in the online evaluation. However, despite the effectiveness shown for single-agent learning, it remains unclear how DMs can operate in multi-agent problems, where agents can hardly complete teamwork without good coordination by independently modeling each agent's trajectories. In this paper, we propose MADiff, a novel generative multi-agent learning framework to tackle this problem. MADiff is realized with an attention-based diffusion model to model the complex coordination among behaviors of multiple diffusion agents. To the best of our knowledge, MADiff is the first diffusion-based multi-agent offline RL framework, which behaves as both a decentralized policy and a centralized controller, which includes opponent modeling and can be used for multi-agent trajectory prediction. MADiff takes advantage of the powerful generative ability of diffusion while well-suited in modeling complex multi-agent interactions. Our experiments show the superior performance of MADiff compared to baseline algorithms in a range of multi-agent learning tasks.

UniControl: A Unified Diffusion Model for Controllable Visual Generation In the Wild

Achieving machine autonomy and human control often represent divergent objectives in the design of interactive AI systems. Visual generative foundation models such as Stable Diffusion show promise in navigating these goals, especially when prompted with arbitrary languages. However, they often fall short in generating images with spatial, structural, or geometric controls. The integration of such controls, which can accommodate various visual conditions in a single unified model, remains an unaddressed challenge. In response, we introduce UniControl, a new generative foundation model that consolidates a wide array of controllable condition-to-image (C2I) tasks within a singular framework, while still allowing for arbitrary language prompts. UniControl enables pixel-level-precise image generation, where visual conditions primarily influence the generated structures and language prompts guide the style and context. To equip UniControl with the capacity to handle diverse visual conditions, we augment pretrained text-to-image diffusion models and introduce a task-aware HyperNet to modulate the diffusion models, enabling the adaptation to different C2I tasks simultaneously. Trained on nine unique C2I tasks, UniControl demonstrates impressive zero-shot generation abilities with unseen visual conditions. Experimental results show that UniControl often surpasses the performance of single-task-controlled methods of comparable model sizes. This control versatility positions UniControl as a significant advancement in the realm of controllable visual generation.

CSP: Self-Supervised Contrastive Spatial Pre-Training for Geospatial-Visual Representations

Geo-tagged images are publicly available in large quantities, whereas labels such as object classes are rather scarce and expensive to collect. Meanwhile, contrastive learning has achieved tremendous success in various natural image and language tasks with limited labeled data. However, existing methods fail to fully leverage geospatial information, which can be paramount to distinguishing objects that are visually similar. To directly leverage the abundant geospatial information associated with images in pre-training, fine-tuning, and inference stages, we present Contrastive Spatial Pre-Training (CSP), a self-supervised learning framework for geo-tagged images. We use a dual-encoder to separately encode the images and their corresponding geo-locations, and use contrastive objectives to learn effective location representations from images, which can be transferred to downstream supervised tasks such as image classification. Experiments show that CSP can improve model performance on both iNat2018 and fMoW datasets. Especially, on iNat2018, CSP significantly boosts the model performance with 10-34% relative improvement with various labeled training data sampling ratios.

Geometric Latent Diffusion Models for 3D Molecule Generation

Generative models, especially diffusion models (DMs), have achieved promising results for generating feature-rich geometries and advancing foundational science problems such as molecule design. Inspired by the recent huge success of Stable (latent) Diffusion models, we propose a novel and principled method for 3D molecule generation named Geometric Latent Diffusion Models (GeoLDM). GeoLDM is the first latent DM model for the molecular geometry domain, composed of autoencoders encoding structures into continuous latent codes and DMs operating in the latent space. Our key innovation is that for modeling the 3D molecular geometries, we capture its critical roto-translational equivariance constraints by building a point-structured latent space with both invariant scalars and equivariant tensors. Extensive experiments demonstrate that GeoLDM can consistently achieve better performance on multiple molecule generation benchmarks, with up to 7\% improvement for the valid percentage of large biomolecules. Results also demonstrate GeoLDM's higher capacity for controllable generation thanks to the latent modeling. Code is provided at \url{https://github.com/MinkaiXu/GeoLDM}.