Related papers: Lie-RMSD: A Gradient-Based Framework for Protein S…

This paper proposes a sign gradient descent (SGD) algorithm for predicting the three-dimensional folded protein molecule structures under the kinetostatic compliance method (KCM). In the KCM framework, which can be used to simulate the…

Symmetry-adapted variational quantum eigensolvers (VQE) based on the Unitary Coupled-Cluster ansatz (SymUCCSD) effectively reduce the parameter count for Abelian molecular point groups. For non-Abelian groups, they systematically fail,…

Elliptic Partial Differential Equations (PDEs) play a central role in computing the equilibrium conditions of physical problems (heat, gravitation, electrostatics, etc.). Efficient solutions to elliptic PDEs are also relevant to computer…

Recent advancements in machine learning techniques for protein folding motivate better results in its inverse problem -- protein design. In this work we introduce a new graph mimetic neural network, MimNet, and show that it is possible to…

We initiate the study of numerical linear algebra in the sliding window model, where only the most recent $W$ updates in a stream form the underlying data set. We first introduce a unified row-sampling based framework that gives randomized…

The calibration of CALPHAD (CALculation of PHAse Diagrams) models involves the solution of a very challenging high-dimensional multiobjective optimization problem. Traditional approaches to parameter fitting predominantly rely on…

Learned image compression (LIC) using deep learning architectures has seen significant advancements, yet standard rate-distortion (R-D) optimization often encounters imbalanced updates due to diverse gradients of the rate and distortion…

This work presents a novel Bayesian framework for unsupervised domain adaptation (UDA) in medical image segmentation. While prior works have explored this clinically significant task using various strategies of domain alignment, they often…

Stochastic Gradient Descent (SGD) is arguably the most important single algorithm in modern machine learning. Although SGD with unbiased gradient estimators has been studied extensively over at least half a century, SGD variants relying on…

Stochastic lattice models (sLMs) are computational tools for simulating spatiotemporal dynamics in physics, computational biology, chemistry, ecology, and other fields. Despite their widespread use, it is challenging to fit sLMs to data, as…

Adaptive stochastic gradient methods such as AdaGrad have gained popularity in particular for training deep neural networks. The most commonly used and studied variant maintains a diagonal matrix approximation to second order information by…

High perceptual quality and low distortion degree are two important goals in image restoration tasks such as super-resolution (SR). Most of the existing SR methods aim to achieve these goals by minimizing the corresponding yet conflicting…

The ``differentiability gap'' presents a primary bottleneck in Earth system deep learning: since models cannot be trained directly on non-differentiable scientific metrics and must rely on smooth proxies (e.g., MSE), they often fail to…

We review our recently developed electronic structure calculation methods used for the dynamics of large-scale solids or liquids with an efficient algorithm for large scale simultaneous linear equations. The electronic structure calculation…

For low-dimensional data sets with a large amount of data points, standard kernel methods are usually not feasible for regression anymore. Besides simple linear models or involved heuristic deep learning models, grid-based discretizations…

Analyzing the structure of proteins is a key part of understanding their functions and thus their role in biology at the molecular level. In addition, design new proteins in a methodical way is a major engineering challenge. In this work,…

Polynomial reconstruction on Cartesian grids is fundamental in many scientific and engineering applications, yet it is still an open problem how to construct for a finite subset $K$ of $\mathbb{Z}^{\textsf{D}}$ a lattice $\mathcal{T}\subset…

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with…

This paper proposes a learning aided gradient descent (LAGD) algorithm to solve the weighted sum rate (WSR) maximization problem for multiple-input single-output (MISO) beamforming. The proposed LAGD algorithm directly optimizes the…

We study the problem of finding the best linear model that can minimize least-squares loss given a data-set. While this problem is trivial in the low dimensional regime, it becomes more interesting in high dimensions where the population…