We introduce the use of latent subspaces in the exponential parameter space of product manifolds of categorial distributions, as a tool for learning generative models of discrete data. The low-dimensional latent space encodes statistical dependencies and removes redundant degrees of freedom among the categorial variables. We equip the parameter domain with a Riemannian geometry such that the spaces and distances are related by isometries which enables consistent flow matching. In particular, geodesics become straight lines which makes model training by flow matching effective. Empirical results demonstrate that reduced latent dimensions suffice to represent data for generative modeling.

Generative modeling over discrete data has recently seen numerous success stories, with applications spanning language modeling, biological sequence design, and graph-structured molecular data. The predominant generative modeling paradigm for discrete data is still autoregressive, with more recent alternatives based on diffusion or flow-matching falling short of their impressive performance in continuous data settings, such as image or video generation. In this work, we introduce Fisher-Flow, a novel flow-matching model for discrete data. Fisher-Flow takes a manifestly geometric perspectiveby considering categorical distributions over discrete data as points residing on a statistical manifold equipped with its natural Riemannian metric: the \emph{Fisher-Rao metric}. As a result, we demonstrate discrete data itself can be continuously reparameterised to points on the positive orthant of the $d$-hypersphere $\mathbb{S}^d_+$, which allows us to define flows that map any source distribution to target in a principled manner by transporting mass along (closed-form) geodesics of $\mathbb{S}^d_+$. Furthermore, the learned flows in Fisher-Flow can be further bootstrapped by leveraging Riemannian optimal transport leading to improved training dynamics. We prove that the gradient flow induced by Fisher-FLow is optimal in reducing the forward KL divergence. We evaluate Fisher-Flow on an array of synthetic and diverse real-world benchmarks, including designing DNA Promoter, and DNA Enhancer sequences. Empirically, we find that Fisher-Flow improves over prior diffusion and flow-matching models on these benchmarks.

Despite Flow Matching and diffusion models having emerged as powerful generative paradigms for continuous variables such as images and videos, their application to high-dimensional discrete data, such as language, is still limited. In this work, we present Discrete Flow Matching, a novel discrete flow paradigm designed specifically for generating discrete data. Discrete Flow Matching offers several key contributions: (i) it works with a general family of probability paths interpolating between source and target distributions; (ii) it allows for a generic formula for sampling from these probability paths using learned posteriors such as the probability denoiser ($x$-prediction) and noise-prediction ($\epsilon$-prediction); (iii) practically, focusing on specific probability paths defined with different schedulers improves generative perplexity compared to previous discrete diffusion and flow models; and (iv) by scaling Discrete Flow Matching models up to 1.7B parameters, we reach 6.7% Pass@1 and 13.4% Pass@10 on HumanEval and 6.7% Pass@1 and 20.6% Pass@10 on 1-shot MBPP coding benchmarks. Our approach is capable of generating high-quality discrete data in a non-autoregressive fashion, significantly closing the gap between autoregressive models and discrete flow models.

Bayesian optimization is a powerful method for optimizing black-box functions with limited function evaluations. Recent works have shown that optimization in a latent space through deep generative models such as variational autoencoders leads to effective and efficient Bayesian optimization for structured or discrete data. However, as the optimization does not take place in the input space, it leads to an inherent gap that results in potentially suboptimal solutions. To alleviate the discrepancy, we propose Correlated latent space Bayesian Optimization (CoBO), which focuses on learning correlated latent spaces characterized by a strong correlation between the distances in the latent space and the distances within the objective function. Specifically, our method introduces Lipschitz regularization, loss weighting, and trust region recoordination to minimize the inherent gap around the promising areas. We demonstrate the effectiveness of our approach on several optimization tasks in discrete data, such as molecule design and arithmetic expression fitting, and achieve high performance within a small budget.

We provide the first complete continuous time framework for denoising diffusion models of discrete data. This is achieved by formulating the forward noising process and corresponding reverse time generative process as Continuous Time Markov Chains (CTMCs). The model can be efficiently trained using a continuous time version of the ELBO. We simulate the high dimensional CTMC using techniques developed in chemical physics and exploit our continuous time framework to derive high performance samplers that we show can outperform discrete time methods for discrete data. The continuous time treatment also enables us to derive a novel theoretical result bounding the error between the generated sample distribution and the true data distribution.

Unobserved discrete data are ubiquitous in many scientific disciplines, and how to learn the causal structure of these latent variables is crucial for uncovering data patterns. Most studies focus on the linear latent variable model or impose strict constraints on latent structures, which fail to address cases in discrete data involving non-linear relationships or complex latent structures. To achieve this, we explore a tensor rank condition on contingency tables for an observed variable set $\mathbf{X}_p$, showing that the rank is determined by the minimum support of a specific conditional set (not necessary in $\mathbf{X}_p$) that d-separates all variables in $\mathbf{X}_p$. By this, one can locate the latent variable through probing the rank on different observed variables set, and further identify the latent causal structure under some structure assumptions. We present the corresponding identification algorithm and conduct simulated experiments to verify the effectiveness of our method. In general, our results elegantly extend the identification boundary for causal discovery with discrete latent variables and expand the application scope of causal discovery with latent variables.

In fact, the additive noise model assumes that all categories of the variables are placed in the "right" order; furthermore, if

We observe that our approach obtains improved performance to comparable discrete diffusion and flow matching methods of Austin et al. [8], Stark et al. [68].

We answer major comments from each reviewer below; we'll fix the minor ones. REVIEWER 1: "This paper ranks high in novelty...The experimental results are strong, especially on T ext Some important details are unclear . E.g. what is the base distribution for sampling? REVIEWER 2: "Originality: This paper is the first demonstration of flow-based models to discrete data. As such, the work is fairly novel....That being said, the main technical contribution amounts to...on top of the We agree about simplicity being a benefit.

In fact, the additive noise model assumes that all categories of the variables are placed in the "right" order; furthermore, if