Related papers: PyRigi -- a general-purpose Python package for the…
In the paper a recent enhancement to the open source package SfePy (Simple Finite Elements in Python, http://sfepy.org) is introduced, namely the addition of another numerical discretization scheme, the isogeometric analysis, to the…
In this paper we prove a recursive characterisation of generic rigidity for frameworks periodic with respect to a partially variable lattice. We follow the approach of modelling periodic frameworks as frameworks on a torus and use the…
This paper describes the algorithms, features and implementation of PyDEC, a Python library for computations related to the discretization of exterior calculus. PyDEC facilitates inquiry into both physical problems on manifolds as well as…
The Python robotics ecosystem faces a challenge: while many libraries exist for rigid body transformations, few are both lightweight and mathematically strict. This paper introduces SE3Kit, a lightweight Python library efficient operations…
Protein (receptor)--ligand interaction prediction is a critical component in computer-aided drug design, significantly influencing molecular docking and virtual screening processes. Despite the development of numerous scoring functions in…
HYPERTILING is a high-performance Python library for the generation and visualization of regular hyperbolic lattices embedded in the Poincar\'e disk model. Using highly optimized, efficient algorithms, hyperbolic tilings with millions of…
Probabilistic graphical models (PGMs) serve as a powerful framework for modeling complex systems with uncertainty and extracting valuable insights from data. However, users face challenges when applying PGMs to their problems in terms of…
Rigidity analysis using the "pebble game" can usefully be applied to protein crystal structures to obtain information on protein folding, assembly and the structure-function relationship. However, previous work using this technique has not…
The Random Geometric Graph (RGG) is a random graph model for network data with an underlying spatial representation. Geometry endows RGGs with a rich dependence structure and often leads to desirable properties of real-world networks such…
To enable heterogeneous computing systems with autonomous programming and optimization capabilities, we propose a unified, end-to-end, programmable graph representation learning (PGL) framework that is capable of mining the complexity of…
Python is one of the most popular programming languages; as such, projects written in Python involve an increasing number of diverse security vulnerabilities. However, existing state-of-the-art analysis tools for Python only support a few…
For scientific knowledge to be findable, accessible, interoperable, and reusable, it needs to be machine-readable. Moving forward from post-publication extraction of knowledge, we adopted a pre-publication approach to write research…
The PyProcar Python package plots the band structure and the Fermi surface as a function of site and/or s,p,d,f - projected wavefunctions obtained for each $k$-point in the Brillouin zone and band in an electronic structure calculation.…
In this work, we review the theory involved in the Bayesian calibration of complex computer models, with particular emphasis on their use for applications involving computationally expensive simulations and scarce experimental data. In the…
Graphs provide a powerful framework for modeling complex systems, but their structural variability poses significant challenges for analysis and classification. To address these challenges, we introduce GAUDI (Graph Autoencoder Uncovering…
We use algebraic geometry to study matrix rigidity, and more generally, the complexity of computing a matrix-vector product, continuing a study initiated by Kumar, et. al. We (i) exhibit many non-obvious equations testing for (border)…
A minimally rigid graph, also called Laman graph, models a planar framework which is rigid for a general choice of distances between its vertices. In other words, there are finitely many ways, up to isometries, to realize such a graph in…
It is well-known that there exist rigid frameworks whose physical models can snap between different realizations due to non-destructive elastic deformations of material. We present a method to measure this snapping capability based on the…
The Kieker observability framework is a tool that provides users with the means to design a custom observability pipeline for their application. Originally tailored for Java, supporting Python with Kieker is worthwhile. Python's popularity…
Models used for control design are, to some degree, uncertain. Model uncertainty must be accounted for to ensure the robustness of the closed-loop system. $\mu$-analysis and $\mu$-synthesis methods allow for the analysis and design of…