相关论文: Simulation in Biology
Change in language use is driven by cultural forces; it is unclear whether that extends to programming languages. They are designed to be used by humans, but interaction with computer hardware rather than a human audience may limit…
For decades, researchers have been applying computer simulation to address problems in biology. However, many of these "grand challenges" in computational biology, such as simulating how proteins fold, remained unsolved due to their great…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
The Simulation Argument has gained significant traction in the public arena. It has offered a hypothesis based on probabilistic analysis of its assumptions that we are likely to exist within a computer simulation. This has been derived from…
Bilevel optimization is defined as a mathematical program, where an optimization problem contains another optimization problem as a constraint. These problems have received significant attention from the mathematical programming community.…
Large language models (LLMs) have demonstrated an impressive ability to role-play humans and replicate complex social dynamics. While large-scale social simulations are gaining increasing attention, they still face significant challenges,…
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…
We consider a living organism as an observer of the evolution of its environment recording sensory information about the state space X of the environment in real time. Sensory information is sampled and then processed on two levels. On the…
Information access systems, such as search engines, recommender systems, and conversational assistants, have become integral to our daily lives as they help us satisfy our information needs. However, evaluating the effectiveness of these…
As software has become an integral part of scientific workflows, reproducible research practices must take it into account. In what way? Archiving source code is a necessary but insufficient condition. The ability to redeploy software…
Scientific computation is a discipline that combines numerical analysis, physical understanding, algorithm development, and structured programming. Several yottacycles per year on the world's largest computers are spent simulating problems…
Software is increasingly produced in the form of ecosystems, collections of interdependent components maintained by a distributed community. These ecosystems act as network organizations, not markets, and thus often lack actionable…
Visualization of dynamic processes in scientific high-performance computing is an immensely data intensive endeavor. Application codes have recently demonstrated scaling to full-size Exascale machines, and generating high-quality data for…
Abbreviated Abstract: The objective of Evolutionary Computation is to solve practical problems (e.g. optimization, data mining) by simulating the mechanisms of natural evolution. This thesis addresses several topics related to adaptation…
This paper introduces a procedure based on genetic programming to evolve XSLT programs (usually called stylesheets or logicsheets). XSLT is a general purpose, document-oriented functional language, generally used to transform XML documents…
We present a computational simulation of evolving entities that includes symbiosis with shifting levels of selection. Evolution by natural selection shifts from the level of the original entities to the level of the new symbiotic entity. In…
Excel is one of the most widely used productivity tools across domains, offering rich functionality but also overwhelming users with its complexity. This creates a persistent demand for tutorials to support effective usage. However, while…
Human beings possess the most sophisticated computational machinery in the known universe. We can understand language of rich descriptive power, and communicate in the same environment with astonishing clarity. Two of the many contributors…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
Language model intelligence is revolutionizing the way we program materials simulations. However, the diversity of simulation scenarios renders it challenging to precisely transform human language into a tailored simulator. Here, using…