Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance.

Griffin: Mixing Gated Linear Recurrences with Local Attention for Efficient Language Models

Recurrent neural networks (RNNs) have fast inference and scale efficiently on long sequences, but they are difficult to train and hard to scale. We propose Hawk, an RNN with gated linear recurrences, and Griffin, a hybrid model that mixes gated linear recurrences with local attention. Hawk exceeds the reported performance of Mamba on downstream tasks, while Griffin matches the performance of Llama-2 despite being trained on over 6 times fewer tokens. We also show that Griffin can extrapolate on sequences significantly longer than those seen during training. Our models match the hardware efficiency of Transformers during training, and during inference they have lower latency and significantly higher throughput. We scale Griffin up to 14B parameters, and explain how to shard our models for efficient distributed training.

Mamba: Linear-Time Sequence Modeling with Selective State Spaces

Foundation models, now powering most of the exciting applications in deep learning, are almost universally based on the Transformer architecture and its core attention module. Many subquadratic-time architectures such as linear attention, gated convolution and recurrent models, and structured state space models (SSMs) have been developed to address Transformers' computational inefficiency on long sequences, but they have not performed as well as attention on important modalities such as language. We identify that a key weakness of such models is their inability to perform content-based reasoning, and make several improvements. First, simply letting the SSM parameters be functions of the input addresses their weakness with discrete modalities, allowing the model to selectively propagate or forget information along the sequence length dimension depending on the current token. Second, even though this change prevents the use of efficient convolutions, we design a hardware-aware parallel algorithm in recurrent mode. We integrate these selective SSMs into a simplified end-to-end neural network architecture without attention or even MLP blocks (Mamba). Mamba enjoys fast inference (5$\times$ higher throughput than Transformers) and linear scaling in sequence length, and its performance improves on real data up to million-length sequences. As a general sequence model backbone, Mamba achieves state-of-the-art performance across several modalities such as language, audio, and genomics. On language modeling, our Mamba-3B model outperforms Transformers of the same size and matches Transformers twice its size, both in pretraining and downstream evaluation.

Augmenting conformers with structured state space models for online speech recognition

Online speech recognition, where the model only accesses context to the left, is an important and challenging use case for ASR systems. In this work, we investigate augmenting neural encoders for online ASR by incorporating structured state-space sequence models (S4), which are a family of models that provide a parameter-efficient way of accessing arbitrarily long left context. We perform systematic ablation studies to compare variants of S4 models and propose two novel approaches that combine them with convolutions. We find that the most effective design is to stack a small S4 using real-valued recurrent weights with a local convolution, allowing them to work complementarily. Our best model achieves WERs of 4.01%/8.53% on test sets from Librispeech, outperforming Conformers with extensively tuned convolution.

Resurrecting Recurrent Neural Networks for Long Sequences

Recurrent Neural Networks (RNNs) offer fast inference on long sequences but are hard to optimize and slow to train. Deep state-space models (SSMs) have recently been shown to perform remarkably well on long sequence modeling tasks, and have the added benefits of fast parallelizable training and RNN-like fast inference. However, while SSMs are superficially similar to RNNs, there are important differences that make it unclear where their performance boost over RNNs comes from. In this paper, we show that careful design of deep RNNs using standard signal propagation arguments can recover the impressive performance of deep SSMs on long-range reasoning tasks, while also matching their training speed. To achieve this, we analyze and ablate a series of changes to standard RNNs including linearizing and diagonalizing the recurrence, using better parameterizations and initializations, and ensuring proper normalization of the forward pass. Our results provide new insights on the origins of the impressive performance of deep SSMs, while also introducing an RNN block called the Linear Recurrent Unit that matches both their performance on the Long Range Arena benchmark and their computational efficiency.

Structured State Space Models for In-Context Reinforcement Learning

Structured state space sequence (S4) models have recently achieved state-of-the-art performance on long-range sequence modeling tasks. These models also have fast inference speeds and parallelisable training, making them potentially useful in many reinforcement learning settings. We propose a modification to a variant of S4 that enables us to initialise and reset the hidden state in parallel, allowing us to tackle reinforcement learning tasks. We show that our modified architecture runs asymptotically faster than Transformers and performs better than LSTM models on a simple memory-based task. Then, by leveraging the model's ability to handle long-range sequences, we achieve strong performance on a challenging meta-learning task in which the agent is given a randomly-sampled continuous control environment, combined with a randomly-sampled linear projection of the environment's observations and actions. Furthermore, we show the resulting model can adapt to out-of-distribution held-out tasks. Overall, the results presented in this paper suggest that the S4 models are a strong contender for the default architecture used for in-context reinforcement learning

Modelling Long Range Dependencies in N-D: From Task-Specific to a General Purpose CNN

Performant Convolutional Neural Network (CNN) architectures must be tailored to specific tasks in order to consider the length, resolution, and dimensionality of the input data. In this work, we tackle the need for problem-specific CNN architectures. We present the Continuous Convolutional Neural Network (CCNN): a single CNN able to process data of arbitrary resolution, dimensionality and length without any structural changes. Its key component are its continuous convolutional kernels which model long-range dependencies at every layer, and thus remove the need of current CNN architectures for task-dependent downsampling and depths. We showcase the generality of our method by using the same architecture for tasks on sequential ($1{\rm D}$), visual ($2{\rm D}$) and point-cloud ($3{\rm D}$) data. Our CCNN matches and often outperforms the current state-of-the-art across all tasks considered.

Pretraining Without Attention

Transformers have been essential to pretraining success in NLP. Other architectures have been used, but require attention layers to match benchmark accuracy. This work explores pretraining without attention. We test recently developed routing layers based on state-space models (SSM) and model architectures based on multiplicative gating. Used together these modeling choices have a large impact on pretraining accuracy. Empirically the proposed Bidirectional Gated SSM (BiGS) replicates BERT pretraining results without attention and can be extended to long-form pretraining of 4096 tokens without approximation.

S4ND: Modeling Images and Videos as Multidimensional Signals Using State Spaces

Visual data such as images and videos are typically modeled as discretizations of inherently continuous, multidimensional signals. Existing continuous-signal models attempt to exploit this fact by modeling the underlying signals of visual (e.g., image) data directly. However, these models have not yet been able to achieve competitive performance on practical vision tasks such as large-scale image and video classification. Building on a recent line of work on deep state space models (SSMs), we propose S4ND, a new multidimensional SSM layer that extends the continuous-signal modeling ability of SSMs to multidimensional data including images and videos. We show that S4ND can model large-scale visual data in $1$D, $2$D, and $3$D as continuous multidimensional signals and demonstrates strong performance by simply swapping Conv2D and self-attention layers with S4ND layers in existing state-of-the-art models. On ImageNet-1k, S4ND exceeds the performance of a Vision Transformer baseline by $1.5\%$ when training with a $1$D sequence of patches, and matches ConvNeXt when modeling images in $2$D. For videos, S4ND improves on an inflated $3$D ConvNeXt in activity classification on HMDB-51 by $4\%$. S4ND implicitly learns global, continuous convolutional kernels that are resolution invariant by construction, providing an inductive bias that enables generalization across multiple resolutions. By developing a simple bandlimiting modification to S4 to overcome aliasing, S4ND achieves strong zero-shot (unseen at training time) resolution performance, outperforming a baseline Conv2D by $40\%$ on CIFAR-10 when trained on $8 \times 8$ and tested on $32 \times 32$ images. When trained with progressive resizing, S4ND comes within $\sim 1\%$ of a high-resolution model while training $22\%$ faster.

How to Train Your HiPPO: State Space Models with Generalized Orthogonal Basis Projections

Linear time-invariant state space models (SSM) are a classical model from engineering and statistics, that have recently been shown to be very promising in machine learning through the Structured State Space sequence model (S4). A core component of S4 involves initializing the SSM state matrix to a particular matrix called a HiPPO matrix, which was empirically important for S4's ability to handle long sequences. However, the specific matrix that S4 uses was actually derived in previous work for a particular time-varying dynamical system, and the use of this matrix as a time-invariant SSM had no known mathematical interpretation. Consequently, the theoretical mechanism by which S4 models long-range dependencies actually remains unexplained. We derive a more general and intuitive formulation of the HiPPO framework, which provides a simple mathematical interpretation of S4 as a decomposition onto exponentially-warped Legendre polynomials, explaining its ability to capture long dependencies. Our generalization introduces a theoretically rich class of SSMs that also lets us derive more intuitive S4 variants for other bases such as the Fourier basis, and explains other aspects of training S4, such as how to initialize the important timescale parameter. These insights improve S4's performance to 86% on the Long Range Arena benchmark, with 96% on the most difficult Path-X task.