Related papers: PyPhi: A toolbox for integrated information theory
Covalent Organic Frameworks (COFs) have gained significant popularity in recent years due to their unique ability to provide a high surface area and customizable pore geometry and chemistry. These traits make COFs a highly promising choice…
The integration of artificial intelligence (AI) into pathology is advancing precision medicine by improving diagnosis, treatment planning, and patient outcomes. Digitised whole-slide images (WSIs) capture rich spatial and morphological…
Algorithmic fairness has received considerable attention due to the failures of various predictive AI systems that have been found to be unfairly biased against subgroups of the population. Many approaches have been proposed to mitigate…
A major trend in academia and data science is the rapid adoption of Bayesian statistics for data analysis and modeling, leading to the development of probabilistic programming languages (PPL). A PPL provides a framework that allows users to…
Mechanistic models are important tools to describe and understand biological processes. However, they typically rely on unknown parameters, the estimation of which can be challenging for large and complex systems. We present pyPESTO, a…
We introduce Diddy, a collection of Python scripts for analyzing infinite discrete dynamical systems. The main focus is on generalized multidimensional shifts of finite type (SFTs). We show how Diddy can be used to easily define SFTs and…
diffpy$.$morph addresses a need to gain scientific insights from 1D scientific spectra in model independent ways. A powerful approach for this is to take differences between pairs of spectra and look for meaningful changes that might…
Electronic-structure theory is the foundation of the description of materials including multiscale modeling of their properties and functions. Obviously, without sufficient accuracy at the base, reliable predictions are unlikely at any…
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Whether by deep learning or classical algorithms, image analysis pipelines then produce single-cell features. To…
PyRoss is an open-source Python library that offers an integrated platform for inference, prediction and optimisation of NPIs in age- and contact-structured epidemiological compartment models. This report outlines the rationale and…
Motivated by the possible applications that a better understanding of consciousness might bring, we follow Tononi's idea and calculate analytically a complexity index for two systems of Ising spins with parallel update dynamics, the…
We introduce GenAI-Powered Inference (GPI), a statistical framework for both causal and predictive inference using unstructured data, including text and images. GPI leverages open-source Generative Artificial Intelligence (GenAI) models --…
Explaining and reasoning about processes which underlie observed black-box phenomena enables the discovery of causal mechanisms, derivation of suitable abstract representations and the formulation of more robust predictions. We propose to…
This paper introduces a novel physics-informed impact identification (Phy-ID) framework. The proposed method integrates observational, inductive, and learning biases to combine physical knowledge with data-driven inference in a unified…
Mathematical modeling is a powerful tool in rheology, and we present pyRheo, an open-source package for Python designed to streamline the analysis of creep, stress relaxation, oscillation, and rotation tests. pyRheo contains a comprehensive…
Haydi (http://haydi.readthedocs.io) is a framework for generating discrete structures. It provides a way to define a structure from basic building blocks and then enumerate all elements, all non-isomorphic elements, or generate random…
A Materials Project based open-source Python tool, MPInterfaces, has been developed to automate the high-throughput computational screening and study of interfacial systems. The framework encompasses creation and manipulation of interface…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
This paper presents an open-source Python toolbox called Ensemble Feature Importance (EFI) to provide machine learning (ML) researchers, domain experts, and decision makers with robust and accurate feature importance quantification and more…
PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding…