Related papers: Simulation in Biology
Computer simulations have become an important tool across the biomedical sciences and beyond. For many important problems several different models or hypotheses exist and choosing which one best describes reality or observed data is not…
Biology is perhaps the most complex of the sciences, given the incredible variety of chemical species that are interconnected in spatial and temporal pathways that are daunting to understand. Their interconnections lead to emergent…
A modeling formalism is proposed for the description and study of living and life-like systems. It provides an abstract conceptual model framework for real life and evolution of biological organisms. It is proposed, that this model…
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…
Computing in the life sciences has undergone a transformative evolution, from early computational models in the 1950s to the applications of artificial intelligence (AI) and machine learning (ML) seen today. This paper highlights key…
Large language models (LLMs) are transforming cellular biology by enabling the development of "virtual cells"--computational systems that represent, predict, and reason about cellular states and behaviors. This work provides a comprehensive…
Combinatorial evolution - the creation of new things through the combination of existing things - can be a powerful way to evolve rather than design technical objects such as electronic circuits. Intriguingly, this seems to be an ongoing…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
The chapter supports educators and postgraduate students in understanding the role of simulation in software engineering research based on the authors' experience. This way, it includes a background positioning simulation-based studies in…
Solving complex real-world tasks requires cycles of actions and observations. This is particularly true in science, where tasks require many cycles of analysis, tool use, and experimentation. Language agents are promising for automating…
Speech is one of the interaction modalities that we increasingly come across in natural user interfaces. However, its use in collaborative scenarios has not yet been thoroughly investigated. In this reflection statement, we discuss the…
Currently it is widely accepted that the language of science is mathematics. This book explores an alternative idea where the future of science is based on the language of algorithms and programs. How such a language can actually be…
The computer programs most users interact with daily are driven by a graphical user interface (GUI). However, many scientific applications are used with a command line interface (CLI) for the ease of development and increased flexibility…
Information is a key concept in evolutionary biology. Information is stored in biological organism's genomes, and used to generate the organism as well as to maintain and control it. Information is also "that which evolves". When a…
Numerical simulations are ubiquitous in mathematics and computational science. Several industrial and clinical applications entail modeling complex multiphysics systems that evolve over a variety of spatial and temporal scales. This study…
This paper is a reflexion on the computability of natural language semantics. It does not contain a new model or new results in the formal semantics of natural language: it is rather a computational analysis of the logical models and…
The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an…
We provide an overview of the emergence of large language models for scientific computing applications. We highlight use cases that involve natural language processing of scientific documents and specialized languages designed to describe…
Evolutionary computation offers a variety of tools to solve complex real-world optimization problems. However, research often focuses on smaller, simplified problems and optimization algorithms that sometimes miss expectations in real-world…
We address the problem of performing semantic transformations on strings, which may represent a variety of data types (or their combination) such as a column in a relational table, time, date, currency, etc. Unlike syntactic…