Gene regulatory networks are networks of interactions in organisms responsible for determining the production levels of proteins and peptides. Mathematical and computational models of gene regulatory networks have been proposed, some of them rather abstract and called artificial regulatory networks. In this contribution, a spatial model for gene regulatory networks is proposed that is biologically more realistic and incorporates an artificial chemistry to realize the interaction between regulatory proteins called the transcription factors and the regulatory sites of simulated genes. The result is a system that is quite robust while able to produce complex dynamics similar to what can be observed in nature. Here an analysis of the impact of the initial states of the system on the produced dynamics is performed, showing that such models are evolvable and can be directed toward producing desired protein dynamics.
{"title":"A Spatial Artificial Chemistry Implementation of a Gene Regulatory Network Aimed at Generating Protein Concentration Dynamics","authors":"Iliya Miralavy;Wolfgang Banzhaf","doi":"10.1162/artl_a_00431","DOIUrl":"10.1162/artl_a_00431","url":null,"abstract":"Gene regulatory networks are networks of interactions in organisms responsible for determining the production levels of proteins and peptides. Mathematical and computational models of gene regulatory networks have been proposed, some of them rather abstract and called artificial regulatory networks. In this contribution, a spatial model for gene regulatory networks is proposed that is biologically more realistic and incorporates an artificial chemistry to realize the interaction between regulatory proteins called the transcription factors and the regulatory sites of simulated genes. The result is a system that is quite robust while able to produce complex dynamics similar to what can be observed in nature. Here an analysis of the impact of the initial states of the system on the produced dynamics is performed, showing that such models are evolvable and can be directed toward producing desired protein dynamics.","PeriodicalId":55574,"journal":{"name":"Artificial Life","volume":"30 1","pages":"65-90"},"PeriodicalIF":2.6,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139991959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The field of metaheuristics has a long history of finding inspiration in natural systems, starting from evolution strategies, genetic algorithms, and ant colony optimization in the second half of the 20th century. In the last decades, however, the field has experienced an explosion of metaphor-centered methods claiming to be inspired by increasingly absurd natural (and even supernatural) phenomena—several different types of birds, mammals, fish and invertebrates, soccer and volleyball, reincarnation, zombies, and gods. Although metaphors can be powerful inspiration tools, the emergence of hundreds of barely discernible algorithmic variants under different labels and nomenclatures has been counterproductive to the scientific progress of the field, as it neither improves our ability to understand and simulate biological systems nor contributes generalizable knowledge or design principles for global optimization approaches. In this article we discuss some of the possible causes of this trend, its negative consequences for the field, and some efforts aimed at moving the area of metaheuristics toward a better balance between inspiration and scientific soundness.
{"title":"Lessons from the Evolutionary Computation Bestiary","authors":"Felipe Campelo;Claus Aranha","doi":"10.1162/artl_a_00402","DOIUrl":"10.1162/artl_a_00402","url":null,"abstract":"The field of metaheuristics has a long history of finding inspiration in natural systems, starting from evolution strategies, genetic algorithms, and ant colony optimization in the second half of the 20th century. In the last decades, however, the field has experienced an explosion of metaphor-centered methods claiming to be inspired by increasingly absurd natural (and even supernatural) phenomena—several different types of birds, mammals, fish and invertebrates, soccer and volleyball, reincarnation, zombies, and gods. Although metaphors can be powerful inspiration tools, the emergence of hundreds of barely discernible algorithmic variants under different labels and nomenclatures has been counterproductive to the scientific progress of the field, as it neither improves our ability to understand and simulate biological systems nor contributes generalizable knowledge or design principles for global optimization approaches. In this article we discuss some of the possible causes of this trend, its negative consequences for the field, and some efforts aimed at moving the area of metaheuristics toward a better balance between inspiration and scientific soundness.","PeriodicalId":55574,"journal":{"name":"Artificial Life","volume":"29 4","pages":"421-432"},"PeriodicalIF":2.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9823818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The prevalence of artificial intelligence (AI) tools that filter the information given to internet users, such as recommender systems and diverse personalizers, may be creating troubling long-term side effects to the obvious short-term conveniences. Many worry that these automated influencers can subtly and unwittingly nudge individuals toward conformity, thereby (somewhat paradoxically) restricting the choices of each agent and/or the population as a whole. In its various guises, this problem has labels such as filter bubble, echo chamber, and personalization polarization. One key danger of diversity reduction is that it plays into the hands of a cadre of self-interested online actors who can leverage conformity to more easily predict and then control users’ sentiments and behaviors, often in the direction of increased conformity and even greater ease of control. This emerging positive feedback loop and the compliance that fuels it are the focal points of this article, which presents several simple, abstract, agent-based models of both peer-to-peer and AI-to-user influence. One of these AI systems functions as a collaborative filter, whereas the other represents an actor the influential power of which derives directly from its ability to predict user behavior. Many versions of the model, with assorted parameter settings, display emergent polarization or universal convergence, but collaborative filtering exerts a weaker homogenizing force than expected. In addition, the combination of basic agents and a self-interested AI predictor yields an emergent positive feedback that can drive the agent population to complete conformity.
{"title":"The Evolution of Conformity, Malleability, and Influence in Simulated Online Agents","authors":"Keith L. Downing","doi":"10.1162/artl_a_00413","DOIUrl":"10.1162/artl_a_00413","url":null,"abstract":"The prevalence of artificial intelligence (AI) tools that filter the information given to internet users, such as recommender systems and diverse personalizers, may be creating troubling long-term side effects to the obvious short-term conveniences. Many worry that these automated influencers can subtly and unwittingly nudge individuals toward conformity, thereby (somewhat paradoxically) restricting the choices of each agent and/or the population as a whole. In its various guises, this problem has labels such as filter bubble, echo chamber, and personalization polarization. One key danger of diversity reduction is that it plays into the hands of a cadre of self-interested online actors who can leverage conformity to more easily predict and then control users’ sentiments and behaviors, often in the direction of increased conformity and even greater ease of control. This emerging positive feedback loop and the compliance that fuels it are the focal points of this article, which presents several simple, abstract, agent-based models of both peer-to-peer and AI-to-user influence. One of these AI systems functions as a collaborative filter, whereas the other represents an actor the influential power of which derives directly from its ability to predict user behavior. Many versions of the model, with assorted parameter settings, display emergent polarization or universal convergence, but collaborative filtering exerts a weaker homogenizing force than expected. In addition, the combination of basic agents and a self-interested AI predictor yields an emergent positive feedback that can drive the agent population to complete conformity.","PeriodicalId":55574,"journal":{"name":"Artificial Life","volume":"29 4","pages":"394-420"},"PeriodicalIF":2.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10426976","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Collectiveness is an important property of many systems—both natural and artificial. By exploiting a large number of individuals, it is often possible to produce effects that go far beyond the capabilities of the smartest individuals or even to produce intelligent collective behavior out of not-so-intelligent individuals. Indeed, collective intelligence, namely, the capability of a group to act collectively in a seemingly intelligent way, is increasingly often a design goal of engineered computational systems—motivated by recent technoscientific trends like the Internet of Things, swarm robotics, and crowd computing, to name only a few. For several years, the collective intelligence observed in natural and artificial systems has served as a source of inspiration for engineering ideas, models, and mechanisms. Today, artificial and computational collective intelligence are recognized research topics, spanning various techniques, kinds of target systems, and application domains. However, there is still a lot of fragmentation in the research panorama of the topic within computer science, and the verticality of most communities and contributions makes it difficult to extract the core underlying ideas and frames of reference. The challenge is to identify, place in a common structure, and ultimately connect the different areas and methods addressing intelligent collectives. To address this gap, this article considers a set of broad scoping questions providing a map of collective intelligence research, mostly by the point of view of computer scientists and engineers. Accordingly, it covers preliminary notions, fundamental concepts, and the main research perspectives, identifying opportunities and challenges for researchers on artificial and computational collective intelligence engineering.
{"title":"Artificial Collective Intelligence Engineering: A Survey of Concepts and Perspectives","authors":"Roberto Casadei","doi":"10.1162/artl_a_00408","DOIUrl":"10.1162/artl_a_00408","url":null,"abstract":"Collectiveness is an important property of many systems—both natural and artificial. By exploiting a large number of individuals, it is often possible to produce effects that go far beyond the capabilities of the smartest individuals or even to produce intelligent collective behavior out of not-so-intelligent individuals. Indeed, collective intelligence, namely, the capability of a group to act collectively in a seemingly intelligent way, is increasingly often a design goal of engineered computational systems—motivated by recent technoscientific trends like the Internet of Things, swarm robotics, and crowd computing, to name only a few. For several years, the collective intelligence observed in natural and artificial systems has served as a source of inspiration for engineering ideas, models, and mechanisms. Today, artificial and computational collective intelligence are recognized research topics, spanning various techniques, kinds of target systems, and application domains. However, there is still a lot of fragmentation in the research panorama of the topic within computer science, and the verticality of most communities and contributions makes it difficult to extract the core underlying ideas and frames of reference. The challenge is to identify, place in a common structure, and ultimately connect the different areas and methods addressing intelligent collectives. To address this gap, this article considers a set of broad scoping questions providing a map of collective intelligence research, mostly by the point of view of computer scientists and engineers. Accordingly, it covers preliminary notions, fundamental concepts, and the main research perspectives, identifying opportunities and challenges for researchers on artificial and computational collective intelligence engineering.","PeriodicalId":55574,"journal":{"name":"Artificial Life","volume":"29 4","pages":"433-467"},"PeriodicalIF":2.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9823817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Editorial: A Word from the Editors","authors":"Alan Dorin;Susan Stepney","doi":"10.1162/artl_e_00422","DOIUrl":"10.1162/artl_e_00422","url":null,"abstract":"","PeriodicalId":55574,"journal":{"name":"Artificial Life","volume":"29 4","pages":"389-389"},"PeriodicalIF":2.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138447204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The main idea behind artificial intelligence was simple: what if we study living systems to develop new, practical computing systems that possess “lifelike” properties? And that’s exactly how evolutionary computing emerged. Researchers came up with ideas inspired by the principles of evolution to develop intelligent methods to tackle hard problems. The efficacy of these methods made researchers seek inspiration in living organisms and systems and extend the evolutionary concept to other nature-inspired ideas. In recent years, nature-inspired computing has exhibited an exponential increase in the number of algorithms that are presented each year. Authors claim that they are inspired by a behavior found in nature to come up with a lifelike algorithm. However, the mathematical background does not match the behavior in the majority of these cases. Thus the question is, do all nature-inspired algorithms remain lifelike? Also, are there any ideas included that contribute to computing? This study aims to (a) present some nature-inspired methods that contribute to achieving lifelike features of computing systems and (b) discuss if there is any need for new lifelike features.
{"title":"Does the Field of Nature-Inspired Computing Contribute to Achieving Lifelike Features?","authors":"Alexandros Tzanetos","doi":"10.1162/artl_a_00407","DOIUrl":"10.1162/artl_a_00407","url":null,"abstract":"The main idea behind artificial intelligence was simple: what if we study living systems to develop new, practical computing systems that possess “lifelike” properties? And that’s exactly how evolutionary computing emerged. Researchers came up with ideas inspired by the principles of evolution to develop intelligent methods to tackle hard problems. The efficacy of these methods made researchers seek inspiration in living organisms and systems and extend the evolutionary concept to other nature-inspired ideas. In recent years, nature-inspired computing has exhibited an exponential increase in the number of algorithms that are presented each year. Authors claim that they are inspired by a behavior found in nature to come up with a lifelike algorithm. However, the mathematical background does not match the behavior in the majority of these cases. Thus the question is, do all nature-inspired algorithms remain lifelike? Also, are there any ideas included that contribute to computing? This study aims to (a) present some nature-inspired methods that contribute to achieving lifelike features of computing systems and (b) discuss if there is any need for new lifelike features.","PeriodicalId":55574,"journal":{"name":"Artificial Life","volume":"29 4","pages":"487-511"},"PeriodicalIF":2.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9834236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Michael Heider;Helena Stegherr;Richard Nordsieck;Jörg Hähner
In sociotechnical settings, human operators are increasingly assisted by decision support systems. By employing such systems, important properties of sociotechnical systems, such as self-adaptation and self-optimization, are expected to improve further. To be accepted by and engage efficiently with operators, decision support systems need to be able to provide explanations regarding the reasoning behind specific decisions. In this article, we propose the use of learning classifier systems (LCSs), a family of rule-based machine learning methods, to facilitate and highlight techniques to improve transparent decision-making. Furthermore, we present a novel approach to assessing application-specific explainability needs for the design of LCS models. For this, we propose an application-independent template of seven questions. We demonstrate the approach’s use in an interview-based case study for a manufacturing scenario. We find that the answers received do yield useful insights for a well-designed LCS model and requirements for stakeholders to engage actively with an intelligent agent.
{"title":"Assessing Model Requirements for Explainable AI: A Template and Exemplary Case Study","authors":"Michael Heider;Helena Stegherr;Richard Nordsieck;Jörg Hähner","doi":"10.1162/artl_a_00414","DOIUrl":"10.1162/artl_a_00414","url":null,"abstract":"In sociotechnical settings, human operators are increasingly assisted by decision support systems. By employing such systems, important properties of sociotechnical systems, such as self-adaptation and self-optimization, are expected to improve further. To be accepted by and engage efficiently with operators, decision support systems need to be able to provide explanations regarding the reasoning behind specific decisions. In this article, we propose the use of learning classifier systems (LCSs), a family of rule-based machine learning methods, to facilitate and highlight techniques to improve transparent decision-making. Furthermore, we present a novel approach to assessing application-specific explainability needs for the design of LCS models. For this, we propose an application-independent template of seven questions. We demonstrate the approach’s use in an interview-based case study for a manufacturing scenario. We find that the answers received do yield useful insights for a well-designed LCS model and requirements for stakeholders to engage actively with an intelligent agent.","PeriodicalId":55574,"journal":{"name":"Artificial Life","volume":"29 4","pages":"468-486"},"PeriodicalIF":2.6,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=10508338","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10408327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
This article tackles the topic of the special issue “Biology in AI: New Frontiers in Hardware, Software and Wetware Modeling of Cognition” in two ways. It addresses the problem of the relevance of hardware, software, and wetware models for the scientific understanding of biological cognition, and it clarifies the contributions that synthetic biology, construed as the synthetic exploration of cognition, can offer to artificial intelligence (AI). The research work proposed in this article is based on the idea that the relevance of hardware, software, and wetware models of biological and cognitive processes—that is, the concrete contribution that these models can make to the scientific understanding of life and cognition—is still unclear, mainly because of the lack of explicit criteria to assess in what ways synthetic models can support the experimental exploration of biological and cognitive phenomena. Our article draws on elements from cybernetic and autopoietic epistemology to define a framework of reference, for the synthetic study of life and cognition, capable of generating a set of assessment criteria and a classification of forms of relevance, for synthetic models, able to overcome the sterile, traditional polarization of their evaluation between mere imitation and full reproduction of the target processes. On the basis of these tools, we tentatively map the forms of relevance characterizing wetware models of living and cognitive processes that synthetic biology can produce and outline a programmatic direction for the development of “organizationally relevant approaches” applying synthetic biology techniques to the investigative field of (embodied) AI.
{"title":"Explorative Synthetic Biology in AI: Criteria of Relevance and a Taxonomy for Synthetic Models of Living and Cognitive Processes","authors":"Luisa Damiano;Pasquale Stano","doi":"10.1162/artl_a_00411","DOIUrl":"10.1162/artl_a_00411","url":null,"abstract":"This article tackles the topic of the special issue “Biology in AI: New Frontiers in Hardware, Software and Wetware Modeling of Cognition” in two ways. It addresses the problem of the relevance of hardware, software, and wetware models for the scientific understanding of biological cognition, and it clarifies the contributions that synthetic biology, construed as the synthetic exploration of cognition, can offer to artificial intelligence (AI). The research work proposed in this article is based on the idea that the relevance of hardware, software, and wetware models of biological and cognitive processes—that is, the concrete contribution that these models can make to the scientific understanding of life and cognition—is still unclear, mainly because of the lack of explicit criteria to assess in what ways synthetic models can support the experimental exploration of biological and cognitive phenomena. Our article draws on elements from cybernetic and autopoietic epistemology to define a framework of reference, for the synthetic study of life and cognition, capable of generating a set of assessment criteria and a classification of forms of relevance, for synthetic models, able to overcome the sterile, traditional polarization of their evaluation between mere imitation and full reproduction of the target processes. On the basis of these tools, we tentatively map the forms of relevance characterizing wetware models of living and cognitive processes that synthetic biology can produce and outline a programmatic direction for the development of “organizationally relevant approaches” applying synthetic biology techniques to the investigative field of (embodied) AI.","PeriodicalId":55574,"journal":{"name":"Artificial Life","volume":"29 3","pages":"367-387"},"PeriodicalIF":2.6,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10172559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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