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Conceptual modeling is an important part of information systems development and use that involves identifying and representing relevant aspects of reality. Although the past decades have experienced continuous digitalization of services and…
Bionic vision is a rapidly advancing field aimed at developing visual neuroprostheses ('bionic eyes') to restore useful vision to people who are blind. However, a major outstanding challenge is predicting what people 'see' when they use…
In digital pathology, the spatial context of cells is important for cell classification, cancer diagnosis and prognosis. To model such complex cell context, however, is challenging. Cells form different mixtures, lineages, clusters and…
Artificial intelligence has demonstrated immense potential in scientific research. Within molecular science, it is revolutionizing the traditional computer-aided paradigm, ushering in a new era of deep learning. With recent progress in…
In this study, we present the Physical-Bio Translator, an agent-based simulation model designed to simulate cellular responses following irradiation. This simulation framework is based on a novel cell-state transition model that accurately…
Bioinformatics has witnessed a paradigm shift with the increasing integration of artificial intelligence (AI), particularly through the adoption of foundation models (FMs). These AI techniques have rapidly advanced, addressing historical…
Cells exhibit a wide variety of different shapes. This diversity poses a challenge for computational approaches that attempt to shed light on the role cell geometry plays in regulating cell physiology and behavior. The simulation platform…
Foundation models, first introduced in 2021, refer to large-scale pretrained models (e.g., large language models (LLMs) and vision-language models (VLMs)) that learn from extensive unlabeled datasets through unsupervised methods, enabling…
Data-driven dynamic models of cell biology can be used to predict cell response to unseen perturbations. Recent work (CellBox) had demonstrated the derivation of interpretable models with explicit interaction terms, in which the parameters…
Multiscale models allow for the treatment of complex phenomena involving different scales, such as remodeling and growth of tissues, muscular activation, and cardiac electrophysiology. Numerous numerical approaches have been developed to…
Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in…
We present models for automotive software that capture quantitative and qualitative aspects of software systems and the underlying hardware architecture. In particular, we consider different levels of computing power. These range from…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Molecular dynamics simulations have the potential to provide atomic-level detail and insight to important questions in chemical physics that cannot be observed in typical experiments. However, simply generating a long trajectory is…
The development of Internet wide resources for general purpose parallel computing poses the challenging task of matching computation and communication complexity. A number of parallel computing models exist that address this for traditional…
Both conceptual modeling and machine learning have long been recognized as important areas of research. With the increasing emphasis on digitizing and processing large amounts of data for business and other applications, it would be helpful…
Central to the digital transformation of the process industry are Digital Twins (DTs), virtual replicas of physical manufacturing systems that combine sensor data with sophisticated data-based or physics-based models, or a combination…
Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical…
The field of computational modeling of the brain is advancing so rapidly that now it is possible to model large scale networks representing different brain regions with a high level of biological detail in terms of numbers and synapses. For…
A key challenge in modern computing is to develop systems that address complex, dynamic problems in a scalable and efficient way, because the increasing complexity of software makes designing and maintaining efficient and flexible systems…