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We present a new Python package called "motives", a symbolic manipulation package based on SymPy capable of handling and simplifying motivic expressions in the Grothendieck ring of Chow motives and other types of $\lambda$-rings. The…
Recent advances in self-supervised deep learning have improved our ability to quantify cellular morphological changes in high-throughput microscopy screens, a process known as morphological profiling. However, most current methods only…
We present an extension to the DynAlloy tool to navigate DynAlloy counterexamples: the DynAlloy Visualizer. The user interface mimics the functionality of a programming language debugger. Without this tool, a DynAlloy user is forced to deal…
The (py)LIon package is a set of tools to simulate the classical trajectories of ensembles of ions in electrodynamic traps. Molecular dynamics simulations are performed using LAMMPS, an efficient and feature-rich program. (py)LIon has been…
We introduce MOS, a software application designed to facilitate the deployment, integration, management, and analysis of mathematical optimization models. MOS approaches mathematical optimization at a higher level of abstraction than…
The Simulation Environment for Atomistic and Molecular Modeling (SEAMM) is an open-source software package written in Python that provides a graphical interface for setting up, executing, and analyzing molecular and materials simulations.…
Pre-trained on extensive text and image corpora, current Multi-Modal Large Language Models (MLLM) have shown strong capabilities in general visual reasoning tasks. However, their performance is still lacking in physical domains that require…
We introduce the \prog{Mathematica} package \prog{MT} which can be used to compute, both analytically and numerically, convolutions involving harmonic polylogarithms, polynomials or generalized functions. As applications contributions to…
Retrosynthesis prediction is fundamental to drug discovery and chemical synthesis, requiring the identification of reactants that can produce a target molecule. Current template-free methods struggle to capture the structural invariance…
Molecular dynamics simulations provide detailed trajectories at the atomic level, but extracting interpretable and robust insights from these high-dimensional data remains challenging. In practice, analyses typically rely on a single…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
The availability of open-source molecular simulation software packages allows scientists and engineers to focus on running and analyzing simulations without having to write, parallelize, and validate their own simulation software. While…
This paper describes a novel Python package, named causalgraph, for modeling and saving causal graphs embedded in knowledge graphs. The package has been designed to provide an interface between causal disciplines such as causal discovery…
Multimodal Small-to-Medium sized Language Models (MSLMs) have demonstrated strong capabilities in integrating visual and textual information but still face significant limitations in visual comprehension and mathematical reasoning,…
Molecular representation learning plays a crucial role in various downstream tasks, such as molecular property prediction and drug design. To accurately represent molecules, Graph Neural Networks (GNNs) and Graph Transformers (GTs) have…
A code package, BlurRing, is developed as a method to allow for multi-dimensional likelihood visualisation. From the BlurRing visualisation additional information about the likelihood can be extracted. The spread in any direction of the…
We present the graph-based molecule software Molassembler for building organic and inorganic molecules. Molassembler provides algorithms for the construction of molecules built from any set of elements from the periodic table. In…
Pore forming toxins (PFTs) are virulent proteins released by several species, including many strains of bacteria, to attack and kill host cells. In this article, we focus on the utility of molecular dynamics (MD) simulations and the…
For organic molecules adsorbed as well-oriented ultra-thin films on metallic surfaces, angle-resolved photoemission spectroscopy has evolved into a technique called photoemission tomography (PT). By approximating the final state of the…
We provide a visualization model that targets the visualization of Protein-Protein Interactions(PPI) and combines it with a super view based on publications and methods to extract interactions. Although there are several existing tools, our…