arXiv subjects

Hunter Nisonoff

Publications and source records attributed to Hunter Nisonoff.

5 recordsLinked to original sources

arXiv2026

Flexible Kernels for Protein Property Prediction

Despite its importance to applications in protein design, predicting protein properties like binding affinity and thermostability from sparse experimental data remains a significant challenge. Accordingly, we introduce a class of sequence kernels that exploit evolutionary substitution matrices as well as local linearity and demonstrate that the resulting Gaussian processes provide data-efficient models of protein property landscapes, frequently outperforming alternatives that rely on foundation model embeddings. Furthermore--by learning what are in effect structure-aware substitution matrices--we show that our kernels can readily incorporate structural information from foundation models. We demonstrate that these structure-conditioned kernels are well suited to multi-task learning across multiple protein property landscapes and can decisively outperform local supervised learning methods.

cs.LG↗

arXiv2025

ProteinGuide: On-the-fly property guidance for protein sequence generative models

Sequence generative models are transforming protein engineering. However, no principled framework exists for conditioning these models on auxiliary information, such as experimental data, without additional training of a generative model. Herein, we present ProteinGuide, a method for such "on-the-fly" conditioning, amenable to a broad class of protein generative models including Masked Language Models (e.g. ESM3), any-order auto-regressive models (e.g. ProteinMPNN) as well as diffusion and flow matching models (e.g. MultiFlow). ProteinGuide stems from our unifying view of these model classes under a single statistical framework. As proof of principle, we perform several in silico experiments. We first guide pre-trained generative models to design proteins with user-specified properties, such as higher stability or activity. Next, we design for optimizing two desired properties that are in tension with each other. Finally, we apply our method in the wet lab, using ProteinGuide to increase the editing activity of an adenine base editor in vivo with data from only a single pooled library of 2,000 variants. We find that a single round of ProteinGuide achieves a higher editing efficiency than was previously achieved using seven rounds of directed evolution.

cs.LG↗

arXiv2024

Unlocking Guidance for Discrete State-Space Diffusion and Flow Models

Generative models on discrete state-spaces have a wide range of potential applications, particularly in the domain of natural sciences. In continuous state-spaces, controllable and flexible generation of samples with desired properties has been realized using guidance on diffusion and flow models. However, these guidance approaches are not readily amenable to discrete state-space models. Consequently, we introduce a general and principled method for applying guidance on such models. Our method depends on leveraging continuous-time Markov processes on discrete state-spaces, which unlocks computational tractability for sampling from a desired guided distribution. We demonstrate the utility of our approach, Discrete Guidance, on a range of applications including guided generation of small-molecules, DNA sequences and protein sequences.

cs.LG↗

arXiv2022

Augmenting Neural Networks with Priors on Function Values

The need for function estimation in label-limited settings is common in the natural sciences. At the same time, prior knowledge of function values is often available in these domains. For example, data-free biophysics-based models can be informative on protein properties, while quantum-based computations can be informative on small molecule properties. How can we coherently leverage such prior knowledge to help improve a neural network model that is quite accurate in some regions of input space -- typically near the training data -- but wildly wrong in other regions? Bayesian neural networks (BNN) enable the user to specify prior information only on the neural network weights, not directly on the function values. Moreover, there is in general no clear mapping between these. Herein, we tackle this problem by developing an approach to augment BNNs with prior information on the function values themselves. Our probabilistic approach yields predictions that rely more heavily on the prior information when the epistemic uncertainty is large, and more heavily on the neural network when the epistemic uncertainty is small.

cs.LG↗

arXiv2020

A deep-learning view of chemical space designed to facilitate drug discovery

Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a particular drug discovery goal. The use of deep learning technologies could augment the typical practice of using human intuition in the design cycle, and thereby expedite drug discovery projects. Here we present DESMILES, a deep neural network model that advances the state of the art in machine learning approaches to molecular design. We applied DESMILES to a previously published benchmark that assesses the ability of a method to modify input molecules to inhibit the dopamine receptor D2, and DESMILES yielded a 77% lower failure rate compared to state-of-the-art models. To explain the ability of DESMILES to hone molecular properties, we visualize a layer of the DESMILES network, and further demonstrate this ability by using DESMILES to tailor the same molecules used in the D2 benchmark test to dock more potently against seven different receptors.

cs.LG↗