相关论文: Python Unleashed on Systems Biology

Dynamically typed languages such as Python have become very popular. Among other strengths, Python's dynamic nature and its straightforward linking to native code have made it the de-facto language for many research areas such as Artificial…

This paper presents a lightweight, open-source and high-performance python package for solving peridynamics problems in solid mechanics. The development of this solver is motivated by the need for fast analysis tools to achieve the large…

Flaky tests obstruct software development, and studying and proposing mitigations against them has therefore become an important focus of software engineering research. To conduct sound investigations on test flakiness, it is crucial to…

Language Models (LLMs), such as transformer-based neural networks trained on billions of parameters, have become increasingly prevalent in software engineering (SE). These models, trained on extensive datasets that include code…

We introduce DisCoPy, an open source toolbox for computing with monoidal categories. The library provides an intuitive syntax for defining string diagrams and monoidal functors. Its modularity allows the efficient implementation of…

We introduce biomedical and clinical English model packages for the Stanza Python NLP library. These packages offer accurate syntactic analysis and named entity recognition capabilities for biomedical and clinical text, by combining…

Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…

PySCF is a general-purpose electronic structure platform designed from the ground up to emphasize code simplicity, both to aid new method development, as well as for flexibility in computational workflow. The package provides a wide range…

Understanding protein function at the molecular level requires connecting residue-level annotations with physical and structural properties. This can be cumbersome and error-prone when functional annotation, computation of physico-chemical…

Scientific applications that involve simulation ensembles can be accelerated greatly by using experiment design methods to select the best simulations to perform. Methods that use machine learning (ML) to create proxy models of simulations…

The scientific computing ecosystem in Python is largely confined to single-node parallelism, creating a gap between high-level prototyping in NumPy and high-performance execution on modern supercomputers. The increasing prevalence of…

The principles of automation and innovation serve as foundational elements for advancement in contemporary science and technology. Here, we introduce Pygen, an automation platform designed to empower researchers, technologists, and…

PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…

The Epiphany is a many-core, low power, low on-chip memory architecture and one can very cheaply gain access to a number of parallel cores which is beneficial for HPC education and prototyping. The very low power nature of these…

BioScape is a concurrent language motivated by the biological landscapes found at the interface of biology and biomaterials. It has been motivated by the need to model antibacterial surfaces, biofilm formation, and the effect of DNAse in…

We present PrismSSL, a Python library that unifies state-of-the-art self-supervised learning (SSL) methods across audio, vision, graphs, and cross-modal settings in a single, modular codebase. The goal of the demo is to show how researchers…

SparseChem provides fast and accurate machine learning models for biochemical applications. Especially, the package supports very high-dimensional sparse inputs, e.g., millions of features and millions of compounds. It is possible to train…

Biological neural networks are often modeled as systems of coupled, nonlinear, ordinary or partial differential equations. The number of differential equations used to model a network increases with the size of the network and the level of…

Parsl is a parallel programming library for Python that aims to make it easy to specify parallelism in programs and to realize that parallelism on arbitrary parallel and distributed computing systems. Parsl relies on developers annotating…

This article introduces SCALPEL3, a scalable open-source framework for studies involving Large Observational Databases (LODs). Its design eases medical observational studies thanks to abstractions allowing concept extraction, high-level…