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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…

Biological Physics · Physics 2009-10-30 Edoardo Milotti , Alessio Del Fabbro , Roberto Chignola

As deep learning systems are scaled up to many billions of parameters, relating their internal structure to external behaviors becomes very challenging. Although daunting, this problem is not new: Neuroscientists and cognitive scientists…

We harness the power of Bayesian emulation techniques, designed to aid the analysis of complex computer models, to examine the structure of complex Bayesian analyses themselves. These techniques facilitate robust Bayesian analyses and/or…

Methodology · Statistics 2017-03-06 Ian Vernon , John Paul Gosling

Many biological and physical systems exhibit behaviour at multiple spatial, temporal or population scales. Multiscale processes provide challenges when they are to be simulated using numerical techniques. While coarser methods such as…

Quantitative Methods · Quantitative Biology 2018-02-12 Cameron A. Smith , Christian A. Yates

Inspired by biological swarms, robotic swarms are envisioned to solve real-world problems that are difficult for individual agents. Biological swarms can achieve collective intelligence based on local interactions and simple rules; however,…

Robotics · Computer Science 2017-09-21 Qiyang Li , Xintong Du , Yizhou Huang , Quinlan Sykora , Angela P. Schoellig

We have designed a machine that becomes increasingly better at behaving in underspecified circumstances, in a goal-directed way, on the job, by modeling itself and its environment as experience accumulates. Based on principles of…

Computational experiments have emerged as a valuable method for studying complex systems, involving the algorithmization of counterfactuals. However, accurately representing real social systems in Agent-based Modeling (ABM) is challenging…

Artificial Intelligence · Computer Science 2024-02-02 Qun Ma , Xiao Xue , Deyu Zhou , Xiangning Yu , Donghua Liu , Xuwen Zhang , Zihan Zhao , Yifan Shen , Peilin Ji , Juanjuan Li , Gang Wang , Wanpeng Ma

Model-based process simulation can be used to derive designs and operating conditions of chemical processes that optimally balance multiple objectives, such as quality, costs, or environmental impacts. This work focuses on identifying…

One major criticism of deep learning centers around the biological implausibility of the credit assignment schema used for learning -- backpropagation of errors. This implausibility translates into practical limitations, spanning scientific…

Neural and Evolutionary Computing · Computer Science 2024-03-29 Alexander Ororbia , Ankur Mali , Adam Kohan , Beren Millidge , Tommaso Salvatori

Machine learning techniques are now routinely encountered in research laboratories across the globe. Impressive progress has been made through ML and AI techniques with regards to large data set processing. This progress has increased the…

Machine Learning · Computer Science 2026-02-27 Ilya Balabin , Thomas M. Kaiser

The diffusion-driven Turing instability is a potential mechanism for spatial pattern formation in numerous biological and chemical systems. However, engineering these patterns and demonstrating that they are produced by this mechanism is…

Biological Physics · Physics 2025-12-02 Antonio Matas-Gil , Robert G. Endres

Various research initiatives try to utilize the operational principles of organisms and brains to develop alternative, biologically inspired computing paradigms and artificial cognitive systems. This paper reviews key features of the…

Adaptation and Self-Organizing Systems · Physics 2012-01-25 Andreas Schierwagen

Autonomous scientific research, capable of independently conducting complex experiments and serving non-specialists, represents a long-held aspiration. Achieving it requires a fundamental paradigm shift driven by artificial intelligence…

Artificial Intelligence · Computer Science 2025-07-04 Mingyu Wu , Zhaoguo Wang , Jiabin Wang , Zhiyuan Dong , Jingkai Yang , Qingting Li , Tianyu Huang , Lei Zhao , Mingqiang Li , Fei Wang , Chunhai Fan , Haibo Chen

The rapid evolution of artificial intelligence has led to expectations of transformative impact on science, yet current systems remain fundamentally limited in enabling genuine scientific discovery. This perspective contends that progress…

Artificial Intelligence · Computer Science 2025-12-16 Karthik Duraisamy

Robustness of spatial pattern against perturbations is an indispensable property of developmental processes for organisms, which need to adapt to changing environments. Although specific mechanisms for this robustness have been extensively…

Adaptation and Self-Organizing Systems · Physics 2017-04-05 Tetsuhiro S. Hatakeyama , Kunihiko Kaneko

Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…

Molecular Networks · Quantitative Biology 2022-05-16 William Poole , Thomas Ouldridge , Manoj Gopalkrishnan , Erik Winfree

Reasoning about hypotheses and updating knowledge through empirical observations are central to scientific discovery. In this work, we applied logic-based machine learning methods to drive biological discovery by guiding experimentation.…

Molecular Networks · Quantitative Biology 2025-06-09 Lun Ai , Stephen H. Muggleton , Shi-Shun Liang , Geoff S. Baldwin

According to cognitive psychology and related disciplines, the development of complex problem-solving behaviour in biological agents depends on hierarchical cognitive mechanisms. Hierarchical reinforcement learning is a promising…

Artificial Intelligence · Computer Science 2022-08-19 Manfred Eppe , Christian Gumbsch , Matthias Kerzel , Phuong D. H. Nguyen , Martin V. Butz , Stefan Wermter

The difficulty of simulating quantum systems, well-known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on…

Artificial intelligence (AI), and especially its sub-field of Machine Learning (ML), are impacting the daily lives of everyone with their ubiquitous applications. In recent years, AI researchers and practitioners have introduced principles…

Machine Learning · Computer Science 2024-10-30 Firas Bayram , Bestoun S. Ahmed