|
Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 46 through 60 of 94 found.
Cosmic Code
Sayama, Hiroki.
Swarm systems as a platform for open-ended evolutionary dynamics.
Philosophical Transactions A.
January,
2025.
The SUNY Binghamton director of the Center of Complex Systems (search) continues his contributions with an extensive proposal for going forward into an empowered, informed, creative futurity.
Artificial swarm systems have been extensively studied and used in computer science, robotics, engineering and other technological fields as a platform for distributed systems to achieve pre-defined objectives. In addition, heterogeneous versions can serve asl platforms for open-ended evolutionary dynamics that keep exploring diverse possibilities and generating novel outputs. In this article, I discuss my Swarm Chemistry to illustrate these beneficial characteristics including multi-scale structures and behaviours, robust self-organization, self-repair and ecological interactions of emergent patterns.
Cosmic Code
Wickelgren, Ingrid.
The Poetry Fan Who Taught an LLM to Read and Write DNA.
Quanta.
February 5,
2025.
A veteran science author and journalist (see her website) surveys the latest bioinformatic frontiers by way of a profile of Brian Hie, a lab leader at the Arc Institute (see his group page at arcinstitute.org). In a historic regard, since last year, a vibrant collaborative endeavor (see Thomas Hayes) has been facilitated by new generative, foundational and large language AI abilities which can then be tailored for genetic, protein and medical benefits. Dr. Hie notes that life’s long stochastic evolution has previously allowed harmful mutations or viruses which can just now begin to be carefully edited out.
DNA is often compared to a written language. The metaphor leaps out: Like letters of the alphabet, molecules (the nucleotide bases A, T, C and G, for adenine, thymine, cytosine and guanine) are arranged into sequences — words, paragraphs, chapters, perhaps — in every organism, from bacteria to humans. Like a language, they encode information.
The formula for Evo’s success is basic in principle. The model is large, bestowed with 7 billion variables, known in computer science as parameters, and trained on loads of data. Under that paradigm, Evo acquires an uncanny knack for divining what sequences are compatible with life and for spinning out useful variations of nature’s molecules. The affinity for scanning a sonnet or identifying structure in a well-composed English lyric is similar to wanting to develop models that make genomic or protein sequences more interpretable and reveal their hidden structure. It’s almost like literary criticism on biology sequences.
Cosmic Code > Geonativity
Zhang, Wen-Long, et al.
Self-organized critical characteristics of TeV-photons from GRB 221009A.
arXiv:2412.16052.
In December, Qufu Normal University, Chinese Academy of Sciences, Beijing, Huazhong University, Wuhan, Nanjing University and Central China Normal University astrophysicists report a sophisticated analysis to date of the presence of nature’s title phenomena even in these extreme celestial occasions.
The high-energy afterglow in GRB 221009A has been previously analyzed. In this paper, we study of the waiting time behavior of 172 TeV photons observed by LHAASO-KM2A. We found that (I) The photon distribution deviates from the exponential distribution. (II) Their behavior of these photons resembles those of a self-organized critical system, with power-law and scale-invariance features. In summary, the power-law and scale-free characteristics observed in these photons imply a self-organized critical process in the generation of TeV photons from GRB 221009A. (Excerpt)
The concept of self-organized criticality (SOC) has been widely observed in various natural systems. The primary manifestation of SOC systems is the power-law distribution of statistical parameters such as time and energy for multiple events, as well as the characteristic of scale invariance. Systems ranging from sand piles to celestial bodies such as the Earth, the Sun, black holes soft gamma-ray repeaters, and high-mass X-ray binaries, have exhibited the characteristics of self-organized critical systems. (1)
GRB 221009A was an extraordinarily bright and energetic gamma-ray burst (GRB) discovered by the Neil Gehrels Swift Observatory and the Fermi Gamma-ray Space Telescope on October 9, 2022. Despite being around 2.4 billion light-years away, it was powerful enough to affect Earth's atmosphere.
Cosmic Code > nonlinear > networks
Network Science in Medicine..
netscisociety.net.
This is a working paper posted on the home site of a new 2024 Network Science Society whose purpose is to support studies and adaptations of nature’s relational vitalities which serve to connect and flesh out all the discrete parts, molecule, cells and entities. Its president is Adilson Motter (search) with an international board that includes Albert-Laszlo Barabasi, Michelle Girvan, Thilo Gross, Filippo Radicchi and Petter Holme.
NetSci will act as a truly interdisciplinary body, aiming to bring under one umbrella a wide variety of researchers and stakeholders with direct interest in network science, from physics to computer science, biology, social sciences, economics, and so on. The main mission is to undertake the type of activities that would help the Network Science community thrive, such as organizing the yearly Network Science meeting, publishing, and working to attract fundsfunding for this effort.
Cosmic Code > nonlinear > networks
, .
Di Marco, Niccolo, et al. Decoding Musical Evolution Through Network Science. arXiv:2501.07557..
arXiv:2501.07557.
We cite this entry by Sapienza University of Rome and University of Padova scholars as a good instance in mid-decade of another nascent integral quantification and convergence between past and present so as to just now notice and hopefully hear the music of the celestial and personal spheres.
Music is deeply infused to human culture, reflecting and shaping traditions, emotions, and societal changes. In this 2025 study, we use Network Science to analyze musical complexity across six macro-genres with each composition as a weighted directed network. Our results show that Classical and Jazz versions have higher complexity and melodic diversity. A temporal analysis reveals a trend toward simplification in modern genres. Our work highlights how digital tools and streaming platforms shape musical evolution fosters new harmonies.
Cosmic Code > nonlinear > networks
Kiani, Narsis, et al, eds.
Networks of Networks in Biology: Concepts, Tools and Applications..
Cambridge: Cambridge University Press,,
2021.
Into the 2020s, this collection is indicative of a nascent phase of a convergent commonality across a wide array of living system phenomena.
Biological systems are very complex with emergent properties that cannot be explained by their individual parts. As the amount of available data grows, it becomes important to be able to analyse and integrate large data sets. This book introduces novel approaches and solutions to the Big Data problem in biomedicine, and presents new techniques in the field of graph theory. By discussing relevant problems and techniques, researchers will gain insights in the life sciences through the concept of 'network of networks'.
Cosmic Code > nonlinear > Algorithms
Kubota, Tomoyuki. et al.
Reservoir Computing Generalized.
arXiv:2412.12104..
We record this work by University of Tokyo and National Institute of Industrial Science and Technology, Japan analysts as an example whence even a domain long seen as insensate matter, can yet now be able to represent cerebral and cognitive qualities. With quantum phenomena similarly suffused with and treatable by neural nets, one is led to consider an entire atomic, cosmic and humanic existence which could as brain-like with relative sentience and knowledge.
A physical neural network (PNN) has the potential to solve machine learning tasks and learn intrinsic physical properties. Reservoir computing (RC) is an apt method to advance information processing with dynamical systems by way of PNNs. Here we propose a novel approach called generalized reservoir computing (GRC) by making conventional RC a special case. We propose a way to obtain a reliable output and show that processed inputs are retrievable and note that spatiotemporal chaos can be used to emulate complex nonlinear dynamics. Overall, our framework can build an information processing device to constructing a computational system capable of a wider variety of physical dynamics. (Excerpt)
Reservoir computing is derived from recurrent neural network theory that maps input signals into higher dimensional spaces through a fixed, non-linear system called a reservoir. After the input signal is received, a device is trained to read the state of the reservoir and map it to the desired output.
Cosmic Code > nonlinear > Rosetta Cosmos
Di Marco, Niccolo, et al.
Decoding Musical Evolution Through Network Science..
arXiv:2501.07557..
While most entries herein attest to the deep presence of complex, self-similar topologies in written prose, this entry by Sapienza University of Rome and University of Padova researchers proceeds to discern a similar intrinsic formative basis for multiplex melodious versions.
In this study, we use the latest Network Science to analyze musical complexity. Drawing on six macro-genres spanning four centuries, we represent each composition as a weighted directed network to study its structural properties. Our results show that Classical and Jazz compositions have higher complexity and melodic diversity than recently developed genres. This study highlights how digital tools and streaming platforms can shape musical evolution.
Cosmic Code > nonlinear > Rosetta Cosmos
Oliveira, Davi Alves and Hernane Borges de Barros Pereira.
Modeling texts with networks: comparing five approaches to sentence representation..
European Physical Journal B.
Vol 97/Art 77,
2024.
University of Bahia State, Brazil system linguists describe more ways that literary writings can be found to similarly exhibit and resemble nature’s complex connectivies.
Complex networks offer a powerful framework for modeling linguistic phenomena. This study compares five methods for representing sentences as networks: (1) a lines approach, where edges represent token (word) adjacency; (2) a co-occurrence view, where edges are based on tokens co-occurring at distance one or two; (3) a cliques approach, where edges connect tokens co-occurring within the same sentence; (4) a dependency-based form, where edges are defined by syntactic dependencies extracted by a parser; and (5) an IF-trimmed-subgraphs approach, where edges are determined by the Incidence-Fidelity (IF) Index. While the first four versions come from the literature, the last one is a novel proposal.
Cosmic Code > nonlinear > Common Code
Hecker, Nikolai, et al.
Enhancer-driven cell type comparison re. Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium.
Science.
February 14,
2025.
Twenty VIB Center for AI & Computational Biology. Leuven, Belgium biologists apply the latest neuroimage techniques to discern a constant recurrence of genomic sources and cerebral architectures throughout the Metazoan creatures. Once again our Earthumen acumen reveals how nature’s long developmental course reuses in kind the same patterns and processes.
Despite vast diversity in behavior and cognition, a consistent similarity in brain structures and even gene expression is being found to exist across the amniote group of reptiles, birds, and mammals. Three papers in this issue explore the development and evolution of the brain telencephalon. Rueda-Alana et al used single-cell resolution and mathematical modeling to investigate sensory circuits in chicken, gecko, and mouse. Zaremba et al generated a spatial cell atlas in chicken pallium. Hecker et al developed deep learning models to identify telencephalon cell types in chicken, human, and mouse. (Editorial)
Combinations of transcription factors govern the identity of cell types, which is reflected by genomic enhancer codes. We used deep learning to compare cell types in the telencephalon across amniotes. To this end, we resolved transcriptomics data of the chicken telencephalon. Enhancer codes of avian mesopallial neurons are most similar to those of mammalian deep-layer neurons. (Hecker Excerpt)
Cosmic Code > Genetic Info
Alvarez-Ballesteros, Yulian, et al.
Exploring the Multifractal Behavior of the Human Genome T2T-CHM13v2.0: Graphical Representations and Cytogenetics..
arXiv:2412.16705.
As whole genome sequences become completed and available, National Autonomous University of Mexico system geneticists are able to detect an intrinsic, wide spread presence of invariant, self-similar geometries in their many versions.
In this work, we applied the Chaos Game Representation (CGR) to the human genomic sequence, analyzing the entire chromosome assembly including mitochondrial DNA. Multifractal spectra were determined using two types of box-counting coverage. We also compared Binary Genomic Representation (RGB) and the Markov Chain (MC) methods which tended toward the same fractal support. Multifractal analysis highlighted quantitative differences between these representations: RGB aligned more closely with high-frequency components, while MC showed better correspondence with low frequencies. (Excerpt)
Cosmic Code > Genetic Info > DNA word
Xin, Lei, at al.
Artificial Intelligence for Central Dogma-Centric Multi-Omics.
arXiv:2412.12668.
We note this work by eleven analysts at Peking, Wuhan, Hunan, Nanjing Universities, China, University of Michigan Medical School and Harvard Medical School, (Chinese and American cooperation) because it is based on a growing appreciation of a wide array of organismic genetic-like encodings.
With the development of high-throughput sequencing platforms, many omic methods such as genomics, metabolomics, and transcriptomics are being applied to disease genetics research. However, biological data often exhibits high dimensionality and significant noise. To address this, current studies have turned to artificial intelligence for multi-omics research. This paper reviews the mathematical strategies for integrating multi-omics data, applications of AI and deep learning, foundational theories, and new technologies. We seek to provide practical guidance for computational biologists to effectively utilize AI-based multi-omics machine learning algorithms. (Excerpt)
Quickening Evolution
Bich, Leonardo.
Biological Organization.
Online: Cambridge University Press,
2024.
A Research Professor at the University of the Basque Country provides a latest (December) thorough survey of the insightful clarity and benefits that can be gained by a holistic vista which also includes the internal interactive subsystems and their own closures.
Complex living systems are made of components that tend to degrade, but nonetheless maintain themselves far from equilibrium. This requires an extraction of energy and materials from the environment in ways that allow them to keep living. The philosophical and theoretical approach discussed in this Element aims to explain these features by appealing to their biological organization. It addresses philosophic issues from origins and definitions of life to teleology and functions from a perspective focused on the whole organism, its physiology and behavior, rather than evolution. (Summary)
Quickening Evolution
Lala, Kevin, et al.
Evolution Evolving: The Developmental Origins of Adaptation and Biodiversity.
Princeton: Princeton University Press,
2024.
Five veteran authors, KL (nee Laland), Tobias Uller, Nathalie Feiner, Marcus Feldman and Scott Gilbert orient and advance a once and future proposal that life’s personal occasion and maturation, aka eco evo devo, across the extent of Metazoan animals should take the place of life’s central explanatory basis.
A new scientific view of evolution is emerging that questions and expands our understanding of how evolution works. Recent research shows that organisms differ in how effective they are at evolving because the process itself has changed over time. In this book, a group of leading biologists draw on the latest findings in evo-devo studies, as well as epigenetics, symbiosis and inheritance to examine the central role that developmental processes play.
Quickening Evolution
Sokolowski, Thomas, et al.
Deriving a genetic regulatory network from an optimization principle.
PNAS.
122/1,
2025.
Institute of Science and Technology Austria and Princeton University computational theorists including William Bialek and Gašper Tkačik post a latest, full scale representation of life’s evolution as some manner of a persistent, episodic, iterative improvement. Although at an early stage, it is far from Darwin and may presage, at last, an insightful verification of life’s actual ecosmic orthogenesis
Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. Here, we explore a detailed model of the gap gene network in the Drosophila embryo, made to maximize the information that gene expression levels provide. Our framework quantifies the tradeoffs involved in functional behavior and allows for the exploration of alternative network configurations. Our results suggest that multiple solutions to the optimization problem might exist across related organisms. (Abstract)
Previous
1
| 2
| 3
| 4
| 5
| 6
| 7
Next
|
 |