Related papers: Process Bigraphs and the Architecture of Compositi…
Open-source scientific software is a major driver of scientific progress, yet its development and reuse remain difficult in collaborative settings. Researchers repeatedly face four recurring challenges: discovering and reproducing existing…
Many disciplines of science and engineering deal with problems related to compositions, ranging from chemical compositions in materials science to portfolio compositions in economics. They exist in non-Euclidean simplex spaces, causing many…
Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent…
The growing complexity of decision-making in public health and health care has motivated an increasing use of mathematical modeling. An important line of health modeling is based on stock & flow diagrams. Such modeling elevates transparency…
Flow-matching generative models are increasingly used to simulate cell responses to biological perturbations. However, the design space for building such models is large and underexplored. We systematically analyse the design space of flow…
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…
Workflow management systems allow the users to develop complex applications at a higher level, by orchestrating functional components without handling the implementation details. Although a wide range of workflow engines are developed in…
Bio-inspired algorithms utilize natural processes such as evolution, swarm behavior, foraging, and plant growth to solve complex, nonlinear, high-dimensional optimization problems. However, a plethora of these algorithms require a more…
Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale…
The behavior of complex systems is determined not only by the topological organization of their interconnections but also by the dynamical processes taking place among their constituents. A faithful modeling of the dynamics is essential…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
This paper introduces a novel toolbox named BIDEAL for the generation of biclusters, their analysis, visualization, and validation. The objective is to facilitate researchers to use forefront biclustering algorithms embedded on a single…
We present a topology grounded, multiscale simulation platform for morphogenesis and biological active matter. Morphogenesis and biological active matter represent keystone problems in biology with additional, far-reaching implications…
Data processing pipelines need to be executed at scales ranging from small runs up through large production data release runs resulting in millions of data products. As part of the Rubin Observatory's pipeline execution system, BPS is the…
For a software system, its architecture is typically defined as the fundamental organization of the system incorporated by its components, their relationships to one another and their environment, and the principles governing their design.…
This paper introduces Bifr\"ost, a novel 3D-aware framework that is built upon diffusion models to perform instruction-based image composition. Previous methods concentrate on image compositing at the 2D level, which fall short in handling…
A general and basic model of primordial evolution--a soup of reacting finitary and discrete processes--is employed to identify and analyze fundamental mechanisms that generate and maintain complex structures in prebiotic systems. The…
This volume contains the accepted papers at the third Workshop on Membrane Computing and Biologically Inspired Process Calculi, held in Bologna on 5th September 2009. The papers are devoted to both membrane computing and biologically…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer…