相关论文: Causality, Information and Biological Computation:…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
Independent computational reproducibility of scientific results is rapidly becoming of pivotal importance in scientific progress as computation itself plays a more and more central role in so many branches of science. Historically,…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
Social evolutionary theory seeks to explain increases in the scale and complexity of human societies, from origins to present. Over the course of the twentieth century, social evolutionary theory largely fell out of favor as a way of…
The term artificial implies an inherent dichotomy from the natural or organic. However, AI, as we know it, is a product of organic ingenuity: designed, implemented, and iteratively improved by human cognition. The very principles that…
Advances in biology have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. Theoretical biology used to primarily provide a basis to rationally examine the frameworks…
Computational methods are the most effective tools we have besides scientific experiments to explore the properties of complex biological systems. Progress is slowing because digital silicon computers have reached their limits in terms of…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…
The design of new devices and experiments in science and engineering has historically relied on the intuitions of human experts. This credo, however, has changed. In many disciplines, computer-inspired design processes, also known as…
We present multiscale models of cancer tumor invasion with components at the molecular, cellular, and tissue levels. We provide biological justifications for the model components, present computational results from the model, and discuss…
A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a…
To better understand the deep significance of our best physical theories it could be interesting to compare our Universe with its models. It may happen that the differences between the model and reality can be made indistinguishable, to the…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
The study of the fundamental limits of information systems is a central theme in information theory. Both the traditional analytical approach and the recently proposed computational approach have significant limitations, where the former is…
Composition is a powerful principle for systems biology, focused on the interfaces, interconnections, and orchestration of distributed processes to enable integrative multiscale simulations. Whereas traditional models focus on the structure…
This paper presents the principal challenges and opportunities associated with computational biomechanics research. The underlying cognitive control involved in the process of human motion is inherently complex, dynamic, multidimensional,…
Most work on computational complexity is concerned with time. However this course will try to show that program-size complexity, which measures algorithmic information, is of much greater philosophical significance. I'll discuss how one can…
Bio-digital systems that merge microbial life with technology promise new modes of computation, combining biological adaptability with digital precision. Yet realizing this potential symbiotically -- where biological and digital agents…