Related papers: libRoadRunner 2.0: A High-Performance SBML Simulat…
This paper presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models \ expressed using Systems Biology Markup Language (SBML). SBML is the most widely…
Motivation: Estimating model parameters from experimental observations is one of the key challenges in systems biology and can be computationally very expensive. While the Julia programming language was recently developed as a high-level…
Summary: The Systems Biology Markup Language (SBML) is an extensible standard format for exchanging biochemical models. One of the extensions for SBML is the SBML Layout and Render package. This allows modelers to describe a biochemical…
We present JDLL, an agile Java library that offers a comprehensive toolset/API to unify the development of high-end applications of DL for bioimage analysis and to streamline their installation and maintenance. JDLL provides all the…
Advances in bioengineering and biomedicine demand a deep understanding of the dynamic behavior of biological systems, ranging from protein pathways to complex cellular processes. Biological networks like gene regulatory networks and protein…
Motivation: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard…
We describe a web-based tool, MakeSBML (https://sys-bio.github.io/makesbml/), that provides an installation-free application for creating, editing, and searching the Biomodels repository for SBML-based models. MakeSBML is a client-based web…
The emergence of Multimodal Large Language Models ((M)LLMs) has ushered in new avenues in artificial intelligence, particularly for autonomous driving by offering enhanced understanding and reasoning capabilities. This paper introduces…
We present Ramulator 2.0, a highly modular and extensible DRAM simulator that enables rapid and agile implementation and evaluation of design changes in the memory controller and DRAM to meet the increasing research effort in improving the…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
In this technical report, we describe a new version of SimpleSBML which provides an easier to use interface to python-libSBML allowing users of Python to more easily construct, edit, and inspect SBML based models. The most commonly used…
The rapid advancement of large language models has unlocked remarkable capabilities across a diverse array of natural language processing tasks. However, the considerable differences among available LLMs-in terms of cost, performance, and…
LIBS2ML is a library based on scalable second order learning algorithms for solving large-scale problems, i.e., big data problems in machine learning. LIBS2ML has been developed using MEX files, i.e., C++ with MATLAB/Octave interface to…
Motivation: Building and iterating machine learning models is often a resource-intensive process. In biomedical research, scientific codebases can lack scalability and are not easily transferable to work beyond what they were intended.…
Building multiscale biological models requires integrating independently developed submodels, which involves sharing variables and coordinating execution. Most existing tools focus on isolated mechanisms and numerical methods, but rarely…
This paper presents LIBTwinSVM, a free, efficient, and open source library for Twin Support Vector Machines (TSVMs). Our library provides a set of useful functionalities such as fast TSVMs estimators, model selection, visualization, a…
Current-generation Large Language Models (LLMs) have stirred enormous interest in recent months, yielding great potential for accessibility and automation, while simultaneously posing significant challenges and risk of misuse. To facilitate…
To safely navigate intricate real-world scenarios, autonomous vehicles must be able to adapt to diverse road conditions and anticipate future events. World model (WM) based reinforcement learning (RL) has emerged as a promising approach by…
MIML library is a Java software tool to develop, test, and compare classification algorithms for multi-instance multi-label (MIML) learning. The library includes 43 algorithms and provides a specific format and facilities for data managing…
BLVRUN is a command line shell script designed to offer developers within the BLV community a succinct and insightful overview of traceback errors. Its primary function involves parsing errors and utilizing a refined large language model to…