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Rapid advance of experimental techniques provides an unprecedented in-depth view into complex developmental processes. Still, little is known on how the complexity of multicellular organisms evolved by elaborating developmental programs and…
Accurate protein structures are essential for understanding biological function, yet incorporating experimental data into protein generative models remains a major challenge. Most predictors of experimental observables are…
We explore the methodology and theory of reward-directed generation via conditional diffusion models. Directed generation aims to generate samples with desired properties as measured by a reward function, which has broad applications in…
One of the major applications of generative models for drug Discovery targets the lead-optimization phase. During the optimization of a lead series, it is common to have scaffold constraints imposed on the structure of the molecules…
We investigate a human-machine collaborative drawing environment in which an autonomous agent sketches images while optionally allowing a user to directly influence the agent's trajectory. We combine Monte Carlo Tree Search with image…
Advances in deep generative models shed light on de novo molecule generation with desired properties. However, molecule generation targeted for dual protein targets still faces formidable challenges including protein 3D structure data…
Data-driven generative models excel in language and vision, but diffusion models often fail in constrained planning and design tasks, exhibiting severe constraint violations in engineering inverse design, molecular generation, multi-robot…
We demonstrate how conditional generation from diffusion models can be used to tackle a variety of realistic tasks in the production of music in 44.1kHz stereo audio with sampling-time guidance. The scenarios we consider include…
Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes…
Recent papers have demonstrated the possibility of energy-based text generation by adapting gradient-based sampling algorithms, a paradigm of MCMC algorithms that promises fast convergence. However, as we show in this paper, previous…
Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while…
Generating novel and functional protein sequences is critical to a wide range of applications in biology. Recent advancements in conditional diffusion models have shown impressive empirical performance in protein generation tasks. However,…
Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph…
Discovering functional crystalline materials entails navigating an immense combinatorial design space. While recent advances in generative artificial intelligence have enabled the sampling of chemically plausible compositions and…
Conditional generation models for longitudinal sequences can produce new or modified trajectories given a conditioning input. However, they often lack control over when the condition should take effect (timing) and which variables it should…
Discrete diffusion models have emerged as powerful frameworks for generating structured categorical data. However, efficiently sampling from reward-tilted distributions remains a fundamental challenge. While Twisted Sequential Monte Carlo…
The structural design of functional molecules, also called molecular optimization, is an essential chemical science and engineering task with important applications, such as drug discovery. Deep generative models and combinatorial…
While plan-and-infill decoding in Masked Diffusion Models (MDMs) shows promise for mathematical and code reasoning, performance remains highly sensitive to slot infilling order, often yielding substantial output variance. We introduce…
Discrete diffusion models have recently shown significant progress in modeling complex data, such as natural languages and DNA sequences. However, unlike diffusion models for continuous data, which can generate high-quality samples in just…
Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To…