Related papers: A decoupled alignment kernel for peptide membrane …

Gaussian Process (GP) models are widely utilized as surrogate models in scientific and engineering fields. However, standard GP models are limited to continuous variables due to the difficulties in establishing correlation structures for…

Gaussian processes (GPs) are nonparametric priors over functions. Fitting a GP implies computing a posterior distribution of functions consistent with the observed data. Similarly, deep Gaussian processes (DGPs) should allow us to compute a…

The Molecular Distance Geometry Problem (MDGP) is essential in structural biology, as it seeks to determine three-dimensional protein structures from partial interatomic distances. Its discretizable subclass (DMDGP) admits an exact…

Deep learning-based approaches, particularly graph neural networks (GNNs), have gained prominence in simulating flexible deformations and contacts of solids, due to their ability to handle unstructured physical fields and nonlinear…

Multi-kernel learning has been well explored in the recent past and has exhibited promising outcomes for multi-class classification and regression tasks. In this paper, we present a multiple kernel learning approach for the One-class…

Gaussian processes (GPs) are Bayesian non-parametric models popular in a variety of applications due to their accuracy and native uncertainty quantification (UQ). Tuning GP hyperparameters is critical to ensure the validity of prediction…

In this paper, we propose a novel supervised learning method that is called Deep Embedding Kernel (DEK). DEK combines the advantages of deep learning and kernel methods in a unified framework. More specifically, DEK is a learnable kernel…

Generative models coupled with reinforcement learning (RL), such as REINVENT and PepINVENT, have emerged as a powerful framework for de novo molecular design. During the ideation process these generative frameworks utilize various…

We introduce a novel kernel that models input-dependent couplings across multiple latent processes. The pairwise joint kernel measures covariance along inputs and across different latent signals in a mutually-dependent fashion. A latent…

Accurate interpretation of electrocardiogram (ECG) signals is crucial for diagnosing cardiovascular diseases. Recent multimodal approaches that integrate ECGs with accompanying clinical reports show strong potential, but they still face two…

Molecular conformation generation (MCG) is a fundamental and important problem in drug discovery. Many traditional methods have been developed to solve the MCG problem, such as systematic searching, model-building, random searching,…

We consider unsupervised cell nuclei segmentation in this paper. Exploiting the recently-proposed unpaired image-to-image translation between cell nuclei images and randomly synthetic masks, existing approaches, e.g., CycleGAN, have…

The recent development of high-throughput sequencing creates a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating…

In decision-making systems, it is important to have classifiers that have calibrated uncertainties, with an optimisation objective that can be used for automated model selection and training. Gaussian processes (GPs) provide uncertainty…

We present a theoretically grounded Gaussian process framework that leverages neural feature maps to construct expressive kernels. We show that the learned feature map can be interpreted as an optimal low-rank approximation to a Gram matrix…

Motivation: Peptide-protein interactions (PepPIs) are central to cellular regulation and peptide therapeutics, but experimental characterization remains too slow for large-scale screening. Existing methods usually emphasize either…

This paper proposes a novel parameter selection strategy for kernel-based gradient descent (KGD) algorithms, integrating bias-variance analysis with the splitting method. We introduce the concept of empirical effective dimension to quantify…

Deep Gaussian processes (DGPs) are popular surrogate models for complex nonstationary computer experiments. DGPs use one or more latent Gaussian processes (GPs) to warp the input space into a plausibly stationary regime, then use typical GP…

We provide a definition and explicit expressions for $n$-body Gaussian Process (GP) kernels which can learn any interatomic interaction occurring in a physical system, up to $n$-body contributions, for any value of $n$. The series is…

Bayesian model updating based on Gaussian Process (GP) models has received attention in recent years, which incorporates kernel-based GPs to provide enhanced fidelity response predictions. Although most kernel functions provide high fitting…