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Due to the great potential in facilitating software development, code generation has attracted increasing attention recently. Generally, dominant models are Seq2Tree models, which convert the input natural language description into a…

The controllable generation of diffusion models aims to steer the model to generate samples that optimize some given objective functions. It is desirable for a variety of applications including image generation, molecule generation, and…

Recent deep learning approaches seek to automate CAD creation by representing a model as a sequence of discrete commands and parameters, and then generating them using autoregressive models or continuous diffusion operating in Euclidean…

Generative models have achieved remarkable success in image, video, and text domains. Inspired by this, researchers have explored utilizing generative models to generate neural network parameters. However, these efforts have been limited by…

Past work on story generation has demonstrated the usefulness of conditioning on a generation plan to generate coherent stories. However, these approaches have used heuristics or off-the-shelf models to first tag training stories with the…

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from…

Generating molecular graphs is crucial in drug design and discovery but remains challenging due to the complex interdependencies between nodes and edges. While diffusion models have demonstrated their potentiality in molecular graph design,…

Score-based diffusion models have emerged as effective approaches for both conditional and unconditional generation. Still conditional generation is based on either a specific training of a conditional model or classifier guidance, which…

The design of novel molecules with desired properties is a key challenge in drug discovery and materials science. Traditional methods rely on trial-and-error, while recent deep learning approaches have accelerated molecular generation.…

Causal representation learning seeks to uncover causal relationships among high-level latent variables from low-level, entangled, and noisy observations. Existing approaches often either rely on deep neural networks, which lack…

The discovery of patterns that accurately discriminate one class label from another remains a challenging data mining task. Subgroup discovery (SD) is one of the frameworks that enables to elicit such interesting hypotheses from labeled…

Despite substantial efforts, deep learning has not yet delivered a transformative impact on elucidating regulatory biology, particularly in the realm of predicting gene expression profiles. Here, we argue that genuine "foundation models" of…

Generative methods for graphs need to be sufficiently flexible to model complex dependencies between sets of nodes. At the same time, the generated graphs need to satisfy domain-dependent feasibility conditions, that is, they should not…

We introduce simple models of genetic regulatory networks and we proceed to the mathematical analysis of their dynamics. The models are discrete time dynamical systems generated by piecewise affine contracting mappings whose variables…

A common objective in the analysis of tabular data is estimating the conditional distribution (in contrast to only producing predictions) of a set of "outcome" variables given a set of "covariates", which is sometimes referred to as the…

Class-labeled datasets, particularly those common in scientific domains, are rife with internal structure, yet current class-conditional diffusion models ignore these relationships and implicitly diffuse on all classes in a flat fashion. To…

Conventional generative models for materials discovery are predominantly trained and validated using data from Density Functional Theory (DFT) with approximate exchange-correlation functionals. This creates a fundamental bottleneck: these…

Reaction networks are often used to model interacting species in fields such as biochemistry and ecology. When the counts of the species are sufficiently large, the dynamics of their concentrations are typically modeled via a system of…

Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…

To fully leverage the capabilities of diffusion models, we are often interested in optimizing downstream reward functions during inference. While numerous algorithms for reward-guided generation have been recently proposed due to their…