Combined mechanistic modeling and machine-learning approaches in systems biology - A systematic literature review

Background and objective: Mechanistic-based Model simulations (MM) are an effective approach commonly employed, for research and learning purposes, to better investigate and understand the inherent behavior of biological systems. Recent advancements in modern technologies and the large availability of omics data allowed the application of Machine Learning (ML) techniques to different research fields, including systems biology. However, the availability of information regarding the analyzed biological context, sufficient experimental data, as well as the degree of computational complexity, represent some of the issues that both MMs and ML techniques could present individually. For this reason, recently, several studies suggest overcoming or significantly reducing these drawbacks by combining the above-mentioned two methods. In the wake of the growing interest in this hybrid analysis approach, with the present review, we want to systematically investigate the studies available in the scientific literature in which both MMs and ML have been combined to explain biological processes at genomics, proteomics, and metabolomics levels, or the behavior of entire cellular populations. Methods: Elsevier Scopus®, Clarivate Web of Science™ and National Library of Medicine PubMed® databases were enquired using the queries reported in Table 1, resulting in 350 scientific articles. Results: Only 14 of the 350 documents returned by the comprehensive search conducted on the three major online databases met our search criteria, i.e. present a hybrid approach consisting of the synergistic combination of MMs and ML to treat a particular aspect of systems biology. Conclusions: Despite the recent interest in this methodology, from a careful analysis of the selected papers, it emerged how examples of integration between MMs and ML are already present in systems biology, highlighting the great potential of this hybrid approach to both at micro and macro biological scales

Aspects of algorithms and dynamics of cellular paradigms

Els paradigmes cel·lulars, com les xarxes neuronals cel·lulars (CNN, en anglès) i els autòmats cel·lulars (CA, en anglès), són una eina excel·lent de càlcul, al ser equivalents a una màquina universal de Turing. La introducció de la màquina universal CNN (CNN-UM, en anglès) ha permès desenvolupar hardware, el nucli computacional del qual funciona segons la filosofia cel·lular; aquest hardware ha trobat aplicació en diversos camps al llarg de la darrera dècada. Malgrat això, encara hi ha moltes preguntes a obertes sobre com definir els algoritmes d'una CNN-UM i com estudiar la dinàmica dels autòmats cel·lulars. En aquesta tesis es tracten els dos problemes: primer, es demostra que es possible acotar l'espai dels algoritmes per a la CNN-UM i explorar-lo gràcies a les tècniques genètiques; i segon, s'expliquen els fonaments de l'estudi dels CA per mitjà de la dinàmica no lineal (segons la definició de Chua) i s'il·lustra com aquesta tècnica ha permès trobar resultats innovadors.Los paradigmas celulares, como las redes neuronales celulares (CNN, eninglés) y los autómatas celulares (CA, en inglés), son una excelenteherramienta de cálculo, al ser equivalentes a una maquina universal deTuring. La introducción de la maquina universal CNN (CNN-UM, eninglés) ha permitido desarrollar hardware cuyo núcleo computacionalfunciona según la filosofía celular; dicho hardware ha encontradoaplicación en varios campos a lo largo de la ultima década. Sinembargo, hay aun muchas preguntas abiertas sobre como definir losalgoritmos de una CNN-UM y como estudiar la dinámica de los autómatascelular. En esta tesis se tratan ambos problemas: primero se demuestraque es posible acotar el espacio de los algoritmos para la CNN-UM yexplorarlo gracias a técnicas genéticas; segundo, se explican losfundamentos del estudio de los CA por medio de la dinámica no lineal(según la definición de Chua) y se ilustra como esta técnica hapermitido encontrar resultados novedosos.Cellular paradigms, like Cellular Neural Networks (CNNs) and Cellular Automata (CA) are an excellent tool to perform computation, since they are equivalent to a Universal Turing machine. The introduction of the Cellular Neural Network - Universal Machine (CNN-UM) allowed us to develop hardware whose computational core works according to the principles of cellular paradigms; such a hardware has found application in a number of fields throughout the last decade. Nevertheless, there are still many open questions about how to define algorithms for a CNN-UM, and how to study the dynamics of Cellular Automata. In this dissertation both problems are tackled: first, we prove that it is possible to bound the space of all algorithms of CNN-UM and explore it through genetic techniques; second, we explain the fundamentals of the nonlinear perspective of CA (according to Chua's definition), and we illustrate how this technique has allowed us to find novel results

A Survey on Reservoir Computing and its Interdisciplinary Applications Beyond Traditional Machine Learning

Reservoir computing (RC), first applied to temporal signal processing, is a recurrent neural network in which neurons are randomly connected. Once initialized, the connection strengths remain unchanged. Such a simple structure turns RC into a non-linear dynamical system that maps low-dimensional inputs into a high-dimensional space. The model's rich dynamics, linear separability, and memory capacity then enable a simple linear readout to generate adequate responses for various applications. RC spans areas far beyond machine learning, since it has been shown that the complex dynamics can be realized in various physical hardware implementations and biological devices. This yields greater flexibility and shorter computation time. Moreover, the neuronal responses triggered by the model's dynamics shed light on understanding brain mechanisms that also exploit similar dynamical processes. While the literature on RC is vast and fragmented, here we conduct a unified review of RC's recent developments from machine learning to physics, biology, and neuroscience. We first review the early RC models, and then survey the state-of-the-art models and their applications. We further introduce studies on modeling the brain's mechanisms by RC. Finally, we offer new perspectives on RC development, including reservoir design, coding frameworks unification, physical RC implementations, and interaction between RC, cognitive neuroscience and evolution.Comment: 51 pages, 19 figures, IEEE Acces

Analog Photonics Computing for Information Processing, Inference and Optimisation

This review presents an overview of the current state-of-the-art in photonics computing, which leverages photons, photons coupled with matter, and optics-related technologies for effective and efficient computational purposes. It covers the history and development of photonics computing and modern analogue computing platforms and architectures, focusing on optimization tasks and neural network implementations. The authors examine special-purpose optimizers, mathematical descriptions of photonics optimizers, and their various interconnections. Disparate applications are discussed, including direct encoding, logistics, finance, phase retrieval, machine learning, neural networks, probabilistic graphical models, and image processing, among many others. The main directions of technological advancement and associated challenges in photonics computing are explored, along with an assessment of its efficiency. Finally, the paper discusses prospects and the field of optical quantum computing, providing insights into the potential applications of this technology.Comment: Invited submission by Journal of Advanced Quantum Technologies; accepted version 5/06/202

Second Generation General System Theory: Perspectives in Philosophy and Approaches in Complex Systems

Following the classical work of Norbert Wiener, Ross Ashby, Ludwig von Bertalanffy and many others, the concept of System has been elaborated in different disciplinary fields, allowing interdisciplinary approaches in areas such as Physics, Biology, Chemistry, Cognitive Science, Economics, Engineering, Social Sciences, Mathematics, Medicine, Artificial Intelligence, and Philosophy. The new challenge of Complexity and Emergence has made the concept of System even more relevant to the study of problems with high contextuality. This Special Issue focuses on the nature of new problems arising from the study and modelling of complexity, their eventual common aspects, properties and approaches—already partially considered by different disciplines—as well as focusing on new, possibly unitary, theoretical frameworks. This Special Issue aims to introduce fresh impetus into systems research when the possible detection and correction of mistakes require the development of new knowledge. This book contains contributions presenting new approaches and results, problems and proposals. The context is an interdisciplinary framework dealing, in order, with electronic engineering problems; the problem of the observer; transdisciplinarity; problems of organised complexity; theoretical incompleteness; design of digital systems in a user-centred way; reaction networks as a framework for systems modelling; emergence of a stable system in reaction networks; emergence at the fundamental systems level; behavioural realization of memoryless functions