Related papers: Python Unleashed on Systems Biology

Python has become the de-facto language for training deep neural networks, coupling a large suite of scientific computing libraries with efficient libraries for tensor computation such as PyTorch or TensorFlow. However, when models are used…

There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types -- such as disease names, cell types or chemicals -- that are used in metadata associated with…

Scalable learning for planning research generally involves juggling between different programming languages for handling learning and planning modules effectively. Interpreted languages such as Python are commonly used for learning routines…

We present pomegranate, an open source machine learning package for probabilistic modeling in Python. Probabilistic modeling encompasses a wide range of methods that explicitly describe uncertainty using probability distributions. Three…

PYSCF is a Python-based general-purpose electronic structure platform that both supports first-principles simulations of molecules and solids, as well as accelerates the development of new methodology and complex computational workflows.…

SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging…

Mathematical programming is widely employed across various sectors - such as logistics, energy, and workforce planning - to model and solve industrial optimisation problems, but its use requires substantial domain expertise. Large language…

Nowadays the analysis of dynamics of and on networks represents a hot topic in the Social Network Analysis playground. To support students, teachers, developers and researchers in this work we introduce a novel framework, namely NDlib, an…

In this paper, we present a new gas-grain chemical code for interstellar clouds written in pure Python (GGCHEMPY). By combining with the high-performance Python compiler Numba, GGCHEMPY is as efficient as the Fortran-based version. With the…

The rapid growth of scientific software has created practical barriers for bioinformatics research. Although powerful statistical, artificial intelligence (AI)-based methods are now widely available, their effective use is often hindered by…

We present nbodykit, an open-source, massively parallel Python toolkit for analyzing large-scale structure (LSS) data. Using Python bindings of the Message Passing Interface (MPI), we provide parallel implementations of many commonly used…

We present an object-oriented open-source framework for solving the dynamics of open quantum systems written in Python. Arbitrary Hamiltonians, including time-dependent systems, may be built up from operators and states defined by a quantum…

We introduce PyText - a deep learning based NLP modeling framework built on PyTorch. PyText addresses the often-conflicting requirements of enabling rapid experimentation and of serving models at scale. It achieves this by providing simple…

rigidPy is a Python package that provides a set of tools necessary for studying rigidity and mechanical response in spring networks. It also includes suitable modules for generating new realizations of networks with applications in glassy…

We introduce PyPulse, a Python package for imputation of biosignals in both clinical and wearable sensor settings. Missingness is commonplace in these settings and can arise from multiple causes, such as insecure sensor attachment or data…

We introduce TopoX, a Python software suite that provides reliable and user-friendly building blocks for computing and machine learning on topological domains that extend graphs: hypergraphs, simplicial, cellular, path and combinatorial…

Computer simulation has become one of the most important tools in scientific research in many disciplines. Benefiting from the dynamical trajectories regulated by versatile interatomic interactions, various material properties can be…

In recent years, there has been increasing interest in network diffusion models and related problems. The most popular of these are the independent cascade and linear threshold models. Much of the recent experimental work done on these…

Pyxel is a novel python tool for end-to-end detection chain simulation i.e. from detector optical effects to readout electronics effects. It is an easy-to-use framework to host and pipeline any detector effect model. It is suited for…

Graph representations of programs are commonly a central element of machine learning for code research. We introduce an open source Python library python_graphs that applies static analysis to construct graph representations of Python…