Related papers: A hybrid combinatorial-continuous strategy for sol…

Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring…

The gradient discretisation method (GDM) is a generic framework designed recently, as a discretise in spatial space, to partial differential equations. This paper aims to use the GDM to establish a first general error estimate for numerical…

In recent years, molecular graph representation learning (GRL) has drawn much more attention in molecular property prediction (MPP) problems. The existing graph methods have demonstrated that 3D geometric information is significant for…

This paper aims to present a fairly accessible generalization of several symmetric Gauss-Seidel decomposition based multi-block proximal alternating direction methods of multipliers (ADMMs) for convex composite optimization problems. The…

Denoising diffusion probabilistic models (DDPMs) have pioneered new state-of-the-art results in disciplines such as computer vision and computational biology for diverse tasks ranging from text-guided image generation to structure-guided…

This article presents a new and efficient alternative to well established algorithms for molecular geometry optimization. The new approach exploits the approximate decoupling of molecular energetics in a curvilinear internal coordinate…

In this work we propose to combine the advantages of learningbased and combinatorial formalisms for 3D shape matching. While learningbased methods lead to state-of-the-art matching performance, they do not ensure geometric consistency, so…

We present a geometric formulation of the Multiple Kernel Learning (MKL) problem. To do so, we reinterpret the problem of learning kernel weights as searching for a kernel that maximizes the minimum (kernel) distance between two convex…

Machine learning interatomic potentials (MLIPs) enables molecular dynamics (MD) simulations with ab initio accuracy and has been applied to various fields of physical science. However, the performance and transferability of MLIPs are…

Generalizing both mixed-integer linear optimization and convex optimization, mixed-integer convex optimization possesses broad modeling power but has seen relatively few advances in general-purpose solvers in recent years. In this paper, we…

In this work we study the interleaving distance between merge trees from a combinatorial point of view. We use a particular type of matching between trees to obtain a novel formulation of the distance. With such formulation, we tackle the…

Straight-forward conformation generation models, which generate 3-D structures directly from input molecular graphs, play an important role in various molecular tasks with machine learning, such as 3D-QSAR and virtual screening in drug…

This paper proposes a Riemannian Multiobjective Proximal Gradient Method (RMPGM) for composite optimization problems on manifolds. Unlike scalarization-based approaches, the proposed framework directly handles vector-valued objectives and…

Gaussian processes (GPs) can provide a principled approach to uncertainty quantification with easy-to-interpret kernel hyperparameters, such as the lengthscale, which controls the correlation distance of function values. However, selecting…

Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…

Multi-block separable convex problems recently received considerable attention. This class of optimization problems minimizes a separable convex objective function with linear constraints. The algorithmic challenges come from the fact that…

The Continuous p-Dispersion Problem (CpDP) with boundary constraints asks for the placement of a fixed number of points in a compact subset of Euclidean space such that the minimum distance between any two points, as well as the points and…

We propose a rigorous, conservative invariant-domain preserving (IDP) projection technique for hierarchical discretizations that enforces membership in physics-implied convex sets when mapping between solution spaces. When coupled with…

We present FilterDDP, a differential dynamic programming algorithm for solving discrete-time, optimal control problems (OCPs) with nonlinear equality constraints. Unlike prior methods based on merit functions or the augmented Lagrangian…

This paper considers a class of constrained stochastic composite optimization problems whose objective function is given by the summation of a differentiable (possibly nonconvex) component, together with a certain non-differentiable (but…