{"title":"COVID-19 epidemic: From data to mathematical models","authors":"François Hamel","doi":"10.1016/j.plrev.2024.11.011","DOIUrl":"10.1016/j.plrev.2024.11.011","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 404-406"},"PeriodicalIF":13.7,"publicationDate":"2024-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142680482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Kinematic coding: Measuring information in naturalistic behaviour","authors":"Cristina Becchio , Kiri Pullar , Eugenio Scaliti , Stefano Panzeri","doi":"10.1016/j.plrev.2024.11.009","DOIUrl":"10.1016/j.plrev.2024.11.009","url":null,"abstract":"<div><div>Recent years have seen an explosion of interest in naturalistic behaviour and in machine learning tools for automatically tracking it. However, questions about what to measure, how to measure it, and how to relate naturalistic behaviour to neural activity and cognitive processes remain unresolved. In this Perspective, we propose a general experimental and computational framework – kinematic coding – for measuring how information about cognitive states is encoded in structured patterns of behaviour and how this information is read out by others during social interactions. This framework enables the design of new experiments and the generation of testable hypotheses that link behaviour, cognition, and neural activity at the single-trial level. Researchers can employ this framework to identify single-subject, single-trial encoding and readout computations and address meaningful questions about how information encoded in bodily motion is transmitted and communicated.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 442-458"},"PeriodicalIF":13.7,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142702597","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Andrew Morozov , Ulrike Feudel , Alan Hastings , Karen C. Abbott , Kim Cuddington , Christopher M. Heggerud , Sergei Petrovskii
{"title":"Long-living transients in ecological models: Recent progress, new challenges, and open questions","authors":"Andrew Morozov , Ulrike Feudel , Alan Hastings , Karen C. Abbott , Kim Cuddington , Christopher M. Heggerud , Sergei Petrovskii","doi":"10.1016/j.plrev.2024.11.004","DOIUrl":"10.1016/j.plrev.2024.11.004","url":null,"abstract":"<div><div>Traditionally, mathematical models in ecology placed an emphasis on asymptotic, long-term dynamics. However, a large number of recent studies highlighted the importance of transient dynamics in ecological and eco-evolutionary systems, in particular ‘long transients’ that can last for hundreds of generations or even longer. Many models as well as empirical studies indicated that a system can function for a long time in a certain state or regime (a ‘metastable regime’) but later exhibits an abrupt transition to another regime not preceded by any parameter change (or following the change that occurred long before the transition). This scenario where tipping occurs without any apparent source of a regime shift is also referred to as ‘metastability’. Despite considerable evidence of the presence of long transients in real-world systems as well as models, until recently research into long-living transients in ecology has remained in its infancy, largely lacking systematisation. Within the past decade, however, substantial progress has been made in creating a unifying theory of long transients in deterministic as well as stochastic systems. This has considerably accelerated further studies on long transients, in particular on those characterised by more complicated patterns and/or underlying mechanisms. The main goal of this review is to provide an overview of recent research on long transients and related regime shifts in models of ecological dynamics. We pay special attention to the role of environmental stochasticity, the effect of multiple timescales (slow-fast systems), transient spatial patterns, and relation between transients and spatial synchronisation. We also discuss current challenges and open questions in understanding transients with applications to ecosystems dynamics.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 423-441"},"PeriodicalIF":13.7,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142702598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Persons and their affective experiences. Comment on “The affective grounds of the mind. The affective pertinentization (APER) model” by salvatore et al.","authors":"Tania Zittoun","doi":"10.1016/j.plrev.2024.11.005","DOIUrl":"10.1016/j.plrev.2024.11.005","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 399-401"},"PeriodicalIF":13.7,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Affect and human functioning: Comment on the affective grounds of the mind: The Affective Pertinientization (APER) model by S. Salvatore, A. Palmieri, R. De Luca Picione, V. Bochnicchio, M. Reho, M. Rita Serio, G. Salvatore","authors":"Stephen Soldz","doi":"10.1016/j.plrev.2024.11.006","DOIUrl":"10.1016/j.plrev.2024.11.006","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 402-403"},"PeriodicalIF":13.7,"publicationDate":"2024-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142638184","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The circuit of cognition: Operational closure and the interpenetration of views. Comment on “The affective grounds of the mind. The affective pertinentization (APER) model” by Salvatore et al.","authors":"Gordon Sammut, Rebekah Mifsud, Noellie Brockdorff","doi":"10.1016/j.plrev.2024.11.003","DOIUrl":"10.1016/j.plrev.2024.11.003","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 397-398"},"PeriodicalIF":13.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"What are the psychic forces present within a psychopathological state? Comment on “Nature heals: An informational entropy account of self-organization and change in field psychotherapy” by Pietro Sarasso, Wolfgang Tschacher, Felix Schoeller, Gianni Francesetti, Jan Roubal, Michela Gecele, Katiuscia Sacco, Irene Ronga","authors":"G. de Felice","doi":"10.1016/j.plrev.2024.11.001","DOIUrl":"10.1016/j.plrev.2024.11.001","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 395-396"},"PeriodicalIF":13.7,"publicationDate":"2024-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611543","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Affective dynamics in unionization and solidarity: Comment on “The affective grounds of the mind. The Affective Pertinentization (APER) model” by Salvatore et al.","authors":"Kevin R. Carriere , Michael Richardson","doi":"10.1016/j.plrev.2024.11.002","DOIUrl":"10.1016/j.plrev.2024.11.002","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 392-394"},"PeriodicalIF":13.7,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142611521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"A theory of affect for social intervention? Comment on “The Affective Grounds of the Mind: The Affective Pertinentization (APER) Model” by Sergio Salvatore, Arianna Palmieri, Raffaele De Luca Picione, Vincenzo Bochicchio, Matteo Reho, Maria Rita Serio, Giampaolo Salvatore","authors":"T. Mannarini","doi":"10.1016/j.plrev.2024.10.014","DOIUrl":"10.1016/j.plrev.2024.10.014","url":null,"abstract":"","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 390-391"},"PeriodicalIF":13.7,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142585477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yikang Lu , Alberto Aleta , Chunpeng Du , Lei Shi , Yamir Moreno
{"title":"LLMs and generative agent-based models for complex systems research","authors":"Yikang Lu , Alberto Aleta , Chunpeng Du , Lei Shi , Yamir Moreno","doi":"10.1016/j.plrev.2024.10.013","DOIUrl":"10.1016/j.plrev.2024.10.013","url":null,"abstract":"<div><div>The advent of Large Language Models (LLMs) offers to transform research across natural and social sciences, offering new paradigms for understanding complex systems. In particular, Generative Agent-Based Models (GABMs), which integrate LLMs to simulate human behavior, have attracted increasing public attention due to their potential to model complex interactions in a wide range of artificial environments. This paper briefly reviews the disruptive role LLMs are playing in fields such as network science, evolutionary game theory, social dynamics, and epidemic modeling. We assess recent advancements, including the use of LLMs for predicting social behavior, enhancing cooperation in game theory, and modeling disease propagation. The findings demonstrate that LLMs can reproduce human-like behaviors, such as fairness, cooperation, and social norm adherence, while also introducing unique advantages such as cost efficiency, scalability, and ethical simplification. However, the results reveal inconsistencies in their behavior tied to prompt sensitivity, hallucinations and even the model characteristics, pointing to challenges in controlling these AI-driven agents. Despite their potential, the effective integration of LLMs into decision-making processes —whether in government, societal, or individual contexts— requires addressing biases, prompt design challenges, and understanding the dynamics of human-machine interactions. Future research must refine these models, standardize methodologies, and explore the emergence of new cooperative behaviors as LLMs increasingly interact with humans and each other, potentially transforming how decisions are made across various systems.</div></div>","PeriodicalId":403,"journal":{"name":"Physics of Life Reviews","volume":"51 ","pages":"Pages 283-293"},"PeriodicalIF":13.7,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142560696","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}