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.

DySLIM: Dynamics Stable Learning by Invariant Measure for Chaotic Systems

Learning dynamics from dissipative chaotic systems is notoriously difficult due to their inherent instability, as formalized by their positive Lyapunov exponents, which exponentially amplify errors in the learned dynamics. However, many of these systems exhibit ergodicity and an attractor: a compact and highly complex manifold, to which trajectories converge in finite-time, that supports an invariant measure, i.e., a probability distribution that is invariant under the action of the dynamics, which dictates the long-term statistical behavior of the system. In this work, we leverage this structure to propose a new framework that targets learning the invariant measure as well as the dynamics, in contrast with typical methods that only target the misfit between trajectories, which often leads to divergence as the trajectories' length increases. We use our framework to propose a tractable and sample efficient objective that can be used with any existing learning objectives. Our Dynamics Stable Learning by Invariant Measures (DySLIM) objective enables model training that achieves better point-wise tracking and long-term statistical accuracy relative to other learning objectives. By targeting the distribution with a scalable regularization term, we hope that this approach can be extended to more complex systems exhibiting slowly-variant distributions, such as weather and climate models.

QuIP#: Even Better LLM Quantization with Hadamard Incoherence and Lattice Codebooks

Post-training quantization (PTQ) reduces the memory footprint of LLMs by quantizing their weights to low-precision. In this work, we introduce QuIP#, a weight-only PTQ method that achieves state-of-the-art results in extreme compression regimes ($\le$ 4 bits per weight) using three novel techniques. First, QuIP# improves the incoherence processing from QuIP by using the randomized Hadamard transform, which is faster and has better theoretical properties. Second, QuIP# uses vector quantization techniques to take advantage of the ball-shaped sub-Gaussian distribution that incoherent weights possess: specifically, we introduce a set of hardware-efficient codebooks based on the highly symmetric $E_8$ lattice, which achieves the optimal 8-dimension unit ball packing. Third, QuIP# uses fine-tuning to improve fidelity to the original model. Our experiments show that QuIP# outperforms existing PTQ methods, enables new behaviors in PTQ scaling, and supports fast inference.

Diffusion Variational Inference: Diffusion Models as Expressive Variational Posteriors

We propose denoising diffusion variational inference (DDVI), an approximate inference algorithm for latent variable models which relies on diffusion models as expressive variational posteriors. Our method augments variational posteriors with auxiliary latents, which yields an expressive class of models that perform diffusion in latent space by reversing a user-specified noising process. We fit these models by optimizing a novel lower bound on the marginal likelihood inspired by the wake-sleep algorithm. Our method is easy to implement (it fits a regularized extension of the ELBO), is compatible with black-box variational inference, and outperforms alternative classes of approximate posteriors based on normalizing flows or adversarial networks. When applied to deep latent variable models, our method yields the denoising diffusion VAE (DD-VAE) algorithm. We use this algorithm on a motivating task in biology -- inferring latent ancestry from human genomes -- outperforming strong baselines on the Thousand Genomes dataset.

Diffusion Models With Learned Adaptive Noise

Diffusion models have gained traction as powerful algorithms for synthesizing high-quality images. Central to these algorithms is the diffusion process, which maps data to noise according to equations inspired by thermodynamics and can significantly impact performance. A widely held assumption is that the ELBO objective of a diffusion model is invariant to the noise process (Kingma et al.,2021). In this work, we dispel this assumption -- we propose multivariate learned adaptive noise (MuLAN), a learned diffusion process that applies Gaussian noise at different rates across an image. Our method consists of three components -- a multivariate noise schedule, instance-conditional diffusion, and auxiliary variables -- which ensure that the learning objective is no longer invariant to the choice of the noise schedule as in previous works. Our work is grounded in Bayesian inference and casts the learned diffusion process as an approximate variational posterior that yields a tighter lower bound on marginal likelihood. Empirically, MuLAN sets a new state-of-the-art in density estimation on CIFAR-10 and ImageNet compared to classical diffusion. Code is available at https://github.com/s-sahoo/MuLAN

Active Preference Inference using Language Models and Probabilistic Reasoning

Actively inferring user preferences, for example by asking good questions, is important for any human-facing decision-making system. Active inference allows such systems to adapt and personalize themselves to nuanced individual preferences. To enable this ability for instruction-tuned large language models (LLMs), one may prompt them to ask users questions to infer their preferences, transforming the language models into more robust, interactive systems. However, out of the box, these models are not efficient at extracting preferences: the questions they generate are not informative, requiring a high number of user interactions and impeding the usability of the downstream system. In this work, we introduce an inference-time algorithm that helps LLMs quickly infer preferences by using more informative questions. Our algorithm uses a probabilistic model whose conditional distributions are defined by prompting an LLM, and returns questions that optimize expected entropy and expected model change. Results in a simplified interactive web shopping setting with real product items show that an LLM equipped with our entropy reduction algorithm outperforms baselines with the same underlying LLM on task performance while using fewer user interactions.

CommonCanvas: An Open Diffusion Model Trained with Creative-Commons Images

We assemble a dataset of Creative-Commons-licensed (CC) images, which we use to train a set of open diffusion models that are qualitatively competitive with Stable Diffusion 2 (SD2). This task presents two challenges: (1) high-resolution CC images lack the captions necessary to train text-to-image generative models; (2) CC images are relatively scarce. In turn, to address these challenges, we use an intuitive transfer learning technique to produce a set of high-quality synthetic captions paired with curated CC images. We then develop a data- and compute-efficient training recipe that requires as little as 3% of the LAION-2B data needed to train existing SD2 models, but obtains comparable quality. These results indicate that we have a sufficient number of CC images (~70 million) for training high-quality models. Our training recipe also implements a variety of optimizations that achieve ~3X training speed-ups, enabling rapid model iteration. We leverage this recipe to train several high-quality text-to-image models, which we dub the CommonCanvas family. Our largest model achieves comparable performance to SD2 on a human evaluation, despite being trained on our CC dataset that is significantly smaller than LAION and using synthetic captions for training. We release our models, data, and code at https://github.com/mosaicml/diffusion/blob/main/assets/common-canvas.md

Local Discovery by Partitioning: Polynomial-Time Causal Discovery Around Exposure-Outcome Pairs

This work addresses the problem of automated covariate selection under limited prior knowledge. Given an exposure-outcome pair {X,Y} and a variable set Z of unknown causal structure, the Local Discovery by Partitioning (LDP) algorithm partitions Z into subsets defined by their relation to {X,Y}. We enumerate eight exhaustive and mutually exclusive partitions of any arbitrary Z and leverage this taxonomy to differentiate confounders from other variable types. LDP is motivated by valid adjustment set identification, but avoids the pretreatment assumption commonly made by automated covariate selection methods. We provide theoretical guarantees that LDP returns a valid adjustment set for any Z that meets sufficient graphical conditions. Under stronger conditions, we prove that partition labels are asymptotically correct. Total independence tests is worst-case quadratic in |Z|, with sub-quadratic runtimes observed empirically. We numerically validate our theoretical guarantees on synthetic and semi-synthetic graphs. Adjustment sets from LDP yield less biased and more precise average treatment effect estimates than baselines, with LDP outperforming on confounder recall, test count, and runtime for valid adjustment set discovery.

Text Embeddings Reveal (Almost) As Much As Text

How much private information do text embeddings reveal about the original text? We investigate the problem of embedding \textit{inversion}, reconstructing the full text represented in dense text embeddings. We frame the problem as controlled generation: generating text that, when reembedded, is close to a fixed point in latent space. We find that although a na\"ive model conditioned on the embedding performs poorly, a multi-step method that iteratively corrects and re-embeds text is able to recover $92\%$ of $32\text{-token}$ text inputs exactly. We train our model to decode text embeddings from two state-of-the-art embedding models, and also show that our model can recover important personal information (full names) from a dataset of clinical notes. Our code is available on Github: \href{https://github.com/jxmorris12/vec2text}{github.com/jxmorris12/vec2text}.

ModuLoRA: Finetuning 3-Bit LLMs on Consumer GPUs by Integrating with Modular Quantizers

We propose a memory-efficient finetuning algorithm for large language models (LLMs) that supports finetuning LLMs with 65B parameters in 3-bit or 4-bit precision on as little as one 48GB GPU. Our method, modular low-rank adaptation (ModuLoRA), integrates any user-specified weight quantizer with finetuning via low-rank adapters (LoRAs). Our approach relies on a simple quantization-agnostic backward pass that adaptively materializes low-precision LLM weights from a custom black-box quantization module. This approach enables finetuning 3-bit LLMs for the first time--leveraging state-of-the-art 3-bit OPTQ quantization often outperforms finetuning that relies on less sophisticated 4-bit and 8-bit methods. In our experiments, ModuLoRA attains competitive performance on text classification, natural language infernece, and instruction following tasks using significantly less memory than existing approaches, and we also surpass the state-of-the-art ROUGE score on a popular summarization task. We release ModuLoRA together with a series of low-precision models--including the first family of 3-bit instruction following Alpaca LLMs--as part of LLMTOOLS, a user-friendly library for quantizing, running, and finetuning LLMs on consumer GPUs.