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PiML (read $\pi$-ML, /`pai`em`el/) is an integrated and open-access Python toolbox for interpretable machine learning model development and model diagnostics. It is designed with machine learning workflows in both low-code and high-code…
Agent-based models (ABMs) offer a powerful framework for understanding complex systems. However, their computational demands often become a significant barrier as the number of agents and complexity of the simulation increase. Traditional…
Deep learning has enabled major advances in the fields of computer vision, natural language processing, and multimedia among many others. Developing a deep learning system is arduous and complex, as it involves constructing neural network…
Simulation of non-adiabatic dynamics of a quantum system coupled to dissipative environments poses significant challenges. New sophisticated methods are regularly being developed with an eye towards moving to larger systems and more…
State of the art analyzers in the Logic Programming (LP) paradigm are nowadays mature and sophisticated. They allow inferring a wide variety of global properties including termination, bounds on resource consumption, etc. The aim of this…
This paper covers two major subjects: First, the presentation of a new open-source library called FMI.jl for integrating FMI into the Julia programming environment by providing the possibility to load, parameterize and simulate FMUs.…
Sequential sampling models (SSMs) are a widely used framework describing decision-making as a stochastic, dynamic process of evidence accumulation. SSMs popularity across cognitive science has driven the development of various software…
Rapid advances of hardware-based technologies during the past decades have opened up new possibilities for Life scientists to gather multimodal data in various application domains (e.g., Omics, Bioimaging, Medical Imaging, and…
The paper presents a parallel math library, dMath, that demonstrates leading scaling when using intranode, internode, and hybrid-parallelism for deep learning (DL). dMath provides easy-to-use distributed primitives and a variety of…
Building trustworthy clinical AI systems requires not only accurate predictions but also transparent, biologically grounded explanations. We present \texttt{DiagnoLLM}, a hybrid framework that integrates Bayesian deconvolution, eQTL-guided…
Here we report on a set of programs developed at the ZMBH Bio-Imaging Facility for tracking real-life images of cellular processes. These programs perform 1) automated tracking; 2) quantitative and comparative track analyses of different…
The D4M tool was developed to address many of today's data needs. This tool is used by hundreds of researchers to perform complex analytics on unstructured data. Over the past few years, the D4M toolbox has evolved to support connectivity…
The scaling of Large Language Models (LLMs) for retrieval-based tasks, particularly in Retrieval Augmented Generation (RAG), faces significant memory constraints, especially when fine-tuning extensive prompt sequences. Current open-source…
In this paper we present the development of an open-source simulation toolbox, PowerSimulationsDynamics.jl, to study the dynamic response of power systems, focusing on the requirements to model systems with high penetrations of…
We present DataDeps.jl: a julia package for the reproducible handling of static datasets to enhance the repeatability of scripts used in the data and computational sciences. It is used to automate the data setup part of running software…
fmeval is an open source library to evaluate large language models (LLMs) in a range of tasks. It helps practitioners evaluate their model for task performance and along multiple responsible AI dimensions. This paper presents the library…
PowerDynamics.jl is a Julia package for time-domain modeling of power grids that is specifically designed for the stability analysis of systems with high shares of renewable energies. It makes use of Julia's state-of-the-art differential…
We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implements S-system representations, a canonical power-law…
In this paper, we introduce ChainerRL, an open-source deep reinforcement learning (DRL) library built using Python and the Chainer deep learning framework. ChainerRL implements a comprehensive set of DRL algorithms and techniques drawn from…
We present QuantumToolbox$.$jl, an open-source Julia package for simulating open quantum systems. Designed with a syntax familiar to users of QuTiP (Quantum Toolbox in Python), it harnesses Julia's high-performance ecosystem to deliver fast…