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At least 19 recordsLinked to original sources

arXiv2026

FeynTune: Large Language Models for High-Energy Theory

We present specialized Large Language Models for theoretical High-Energy Physics, obtained as 20 fine-tuned variants of the 8-billion parameter Llama-3.1 model. Each variant was trained on arXiv abstracts (through August 2024) from different combinations of hep-th, hep-ph and gr-qc. For a comparative study, we also trained models on datasets that contained abstracts from disparate fields such as the q-bio and cs categories. All models were fine-tuned using two distinct Low-Rank Adaptation fine-tuning approaches and varying dataset sizes, and outperformed the base model on hep-th abstract completion tasks. We compare performance against leading commercial LLMs (ChatGPT, Claude, Gemini, DeepSeek) and derive insights for further developing specialized language models for High-Energy Theoretical Physics.

cs.CL↗

arXiv1994

On Modelling Life

We present a theoretical as well as experimental investigation of a population of self-replicating segments of code subject to random mutation and survival of the fittest. Under the assumption that such a system constitutes a minimal system with characteristics of life, we obtain a number of statements on the evolution of complexity and the trade-off between entropy and information.

adap-org↗

arXiv1994

Evolutionary Learning in the 2D Artificial Life System "Avida"

We present a new tierra-inspired artificial life system with local interactions and two-dimensional geometry, based on an update mechanism akin to that of 2D cellular automata. We find that the spatial geometry is conducive to the development of diversity and thus improves adaptive capabilities. We also demonstrate the adaptive strength of the system by breeding cells with simple computational abilities, and study the dependence of this adaptability on mutation rate and population size.

adap-org↗

arXiv1995

A Theory of Differentiation with Dynamic Clustering

A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled chemical networks and division process lead to the following scenario of the differentiation: Up to some numbers of cells, divisions bring about almost identical cells with synchronized metabolic oscillations. As the number is increased the oscillations lose the synchrony, leading to groups of cells with different phases of oscillations. At later stage this differentiation is fixed in time, and cells spilt into groups with different chemical constituents spontaneously, which are transmitted to daughter cells by cell divisions. Hierarchical differentiation, origin of stem cells, and anomalous differentiation by transplantations are also discussed with relevance to real biological experimental results. (Keywords: differentiation, metabolic network, cell division, clustering, open chaos)

adap-org↗

arXiv1995

Self-Organization in Models of Populations with Two-Parent Reproduction on a Rugged Fitness Landscape

The two-parent reproduction model of Derrida and Peliti is simulated on a rugged fitness landscape. Fixed fitness values for each possible genotype are assigned randomly, with all fit individuals having the same probability of reproduction. The previously observed transition to a self-organized state of the population with less recombinational load, implies an abrupt change of genetic overlap distributions, showing up characteristics of a phase transition. A crossover variant of the model has a smoother transition to the adapted regime, with a residual collective adaptation for small values of the threshold in fitness. When a geographical constraint (shortest possible distance) on pairwise reproduction in a population arranged one-dimensionally is imposed, a poised state results, suggestive of self-organized criticality.

adap-org↗

arXiv1996

Isologous Diversification: A Theory of Cell Differentiation

Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of the interaction-based dynamical systems model, the following scenario of the cell differentiation is proposed. (1) Up to some threshold number, divisions bring about almost identical cells with synchronized biochemical oscillations. (2)As the number is increased the oscillations lose the synchrony, leading to groups of cells with different phases of oscillations. (3)Amplitudes of oscillation and averaged chemical compositions start to differ by groups of cells. The differentiated behavior of states is transmitted to daughter cells. (4)Recursivity is formed so that the daughter cells keep the identical chemical character. This ``memory" is made possible through the transfer of initial conditions. (5) Successive differentiation proceeds. Mechanism of tumor cell formation, origin of stem cells, anomalous differentiation by transplantations, apoptosis and other features of cell differentiation process are also discussed, with some novel predictions. (Keywords: differentiation, chemical network, cell division, clustering, open chaos)

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arXiv1997

A condition for the genotype-phenotype mapping: Causality

The appropriate choice of the genotype-phenotype mapping in combination with the mutation operator is important for a successful evolutionary search process. We suggest a measure to quantify the quality of this combination by addressing the question whether the relation among distances is carried over from one space to the other. Search processes which do not destroy the neighbourhood structure are termed strongly causal. We apply the proposed measure to parameter and structure optimisation problems in order to assess the combination (mapping, mutation operator) and at the same time to be able to propose improved settings.

adap-org↗

arXiv1997

Sentient Networks

In this paper we consider the question whether a distributed network of sensors and data processors can form "perceptions" based on the sensory data. Because sensory data can have exponentially many explanations, the use of a central data processor to analyze the outputs from a large ensemble of sensors will in general introduce unacceptable latencies for responding to dangerous situations. A better idea is to use a distributed "Helmholtz machine" architecture in which the collective state of the network as a whole provides an explanation for the sensory data.

adap-org↗

arXiv1997

Effects of neutral selection on the evolution of molecular species

We introduce a new model of evolution on a fitness landscape possessing a tunable degree of neutrality. The model allows us to study the general properties of molecular species undergoing neutral evolution. We find that a number of phenomena seen in RNA sequence-structure maps are present also in our general model. Examples are the occurrence of "common" structures which occupy a fraction of the genotype space which tends to unity as the length of the genotype increases, and the formation of percolating neutral networks which cover the genotype space in such a way that a member of such a network can be found within a small radius of any point in the space. We also describe a number of new phenomena which appear to be general properties of neutrally evolving systems. In particular, we show that the maximum fitness attained during the adaptive walk of a population evolving on such a fitness landscape increases with increasing degree of neutrality, and is directly related to the fitness of the most fit percolating network.

adap-org↗

arXiv1998

Modelling coevolution in multispecies communities

We introduce the Webworld model, which links together the ecological modelling of food web structure with the evolutionary modelling of speciation and extinction events. The model describes dynamics of ecological communities on an evolutionary timescale. Species are defined as sets of characteristic features, and these features are used to determine interaction scores between species. A simple rule is used to transfer resources from the external environment through the food web to each of the species, and to determine mean population sizes. A time step in the model represents a speciation event. A new species is added with features similar to those of one of the existing species and a new food web structure is then calculated. The new species may (i) add stably to the web, (ii) become extinct immediately because it is poorly adapted, or (iii) cause one or more other species to become extinct due to competition for resources. We measure various properties of the model webs and compare these with data on real food webs. These properties include the proportions of basal, intermediate and top species, the number of links per species and the number of trophic levels. We also study the evolutionary dynamics of the model ecosystem by following the fluctuations in the total number of species in the web. Extinction avalanches occur when novel organisms arise which are significantly better adapted than existing ones. We discuss these results in relation to the observed extinction events in the fossil record, and to the theory of self-organized criticality.

adap-org↗

arXiv1998

Emergence of Rules in Cell Society: Differentiation, Hierarchy, and Stability

A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the isologous diversification. Following features of the differentiation are obtained: (1)Hierarchical differentiation from a ``stem'' cell to other cell types, with the emergence of the interaction-dependent rules for differentiation; (2)Global stability of an ensemble of cells consisting of several cell types, that is sustained by the emergent, autonomous control on the rate of differentiation; (3)Existence of several cell colonies with different cell-type distributions. The results provide a novel viewpoint on the origin of complex cell society, while relevance to some biological problems, especially to the hemopoietic system, is also discussed.

adap-org↗

arXiv1998

Distributed Self-regulation Induced by Negative Feedbacks in Ecological and Economic Systems

We consider an ecological system governed by Lotka-Volterra dynamics and an example of an economic system as a mesomarket with perfect competition. We propose a mechanism for cooperative self-regulation that enables the system under consideration to respond properly to changes in the environment. This mechanism is based on (1) active individual behavior of the system elements at each hierarchical level and (2) self-processing of information caused by the hierarchical organization. It is shown how the proposed mechanism suppresses nonlocal interaction of elements belonging to a particular level as mediated by higher levels.

adap-org↗

arXiv2001

Cumulant Dynamics of a Population under Multiplicative Selection, Mutation and Drift

We revisit the classical population genetics model of a population evolving under multiplicative selection, mutation and drift. The number of beneficial alleles in a multi-locus system can be considered a trait under exponential selection. Equations of motion are derived for the cumulants of the trait distribution in the diffusion limit and under the assumption of linkage equilibrium. Because of the additive nature of cumulants, this reduces to the problem of determining equations of motion for the expected allele distribution cumulants at each locus. The cumulant equations form an infinite dimensional linear system and in an authored appendix Adam Prugel-Bennett provides a closed form expression for these equations. We derive approximate solutions which are shown to describe the dynamics well for a broad range of parameters. In particular, we introduce two approximate analytical solutions: (1) Perturbation theory is used to solve the dynamics for weak selection and arbitrary mutation rate. The resulting expansion for the system's eigenvalues reduces to the known diffusion theory results for the limiting cases with either mutation or selection absent. (2) For low mutation rates we observe a separation of time-scales between the slowest mode and the rest which allows us to develop an approximate analytical solution for the dominant slow mode. The solution is consistent with the perturbation theory result and provides a good approximation for much stronger selection intensities.

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arXiv1999

Scaling in a Multispecies Network Model Ecosystem

A new model ecosystem consisting of many interacting species is introduced. The species are connected through a random matrix with a given connectivity. It is shown that the system is organized close to a boundary of marginal stability in such a way that fluctuations follow power law distributions both in species abundance and their lifetimes for some slow-driving (immigration) regime. The connectivity and the number of species are linked through a scaling relation which is the one observed in real ecosystems. These results suggest that the basic macroscopic features of real, species-rich ecologies might be linked with a critical state. A natural link between lognormal and power law distributions of species abundances is suggested.

adap-org↗

arXiv1999

Phase Transition in Random Networks with Multiple States

The critical boundaries separating ordered from chaotic behavior in randomly wired S-state networks are calculated. These networks are a natural generalization of random Boolean nets and are proposed as on extended approach to genetic regulatory systems, sets of cells in different states or collectives of agents engaged into a set of S possible tasks. A order parameter for the transition is computed and analysed. The relevance of these networks to biology, their relationships with standard cellular automata and possible extensions are outlined.

adap-org↗

arXiv1999

Models of Extinction: A Review

We review recent work aimed at modeling species extinction over geological time. We discuss a number of models which, rather than dealing with the direct causes of particular extinction events, attempt to predict overall statistical trends, such as the relative frequencies of large and small extinctions, or the distribution of the lifetimes of species, genera or higher taxa. We also describe the available fossil and other data, and compare the trends visible in these data with the predictions of the models.

adap-org↗

arXiv1999

Analysis of the optimality principles responsible for vascular network architectonics

The equivalence of two optimality principles leading to Murray's law has been discussed. The first approach is based on minimization of biological work needed for maintaining the blood flow through the vessels at required level. The second one is the principle of minimal drag and lumen volume. Characteristic features of these principles are considered. An alternative approach leading to Murray's law has been proposed. For that we model the microcirculatory bed in terms of delivering vascular network with symmetrical bifurcation nodes, embedded uniformly into the cellular tissue. It was shown that Murray's law can be regarded as a direct consequence of the organism capacity for controlling the blood flow redistribution over the microcirculatory beds.

adap-org↗

arXiv1997

Strange Attractor in Immunology of Tumor Growth

The time delayed cytotoxic T-lymphocyte response on the tumor growth has been developed on the basis of discrete approximation (2-dimensional map). The growth kinetic has been described by logistic law with growth rate being the bifurcation parameter. Increase in the growth rate results in instability of the tumor state and causes period-doubling bifurcations in the immune+tumor system. For larger values of tumor growth rate a strange attractor has been observed. The model proposed is able to describe the metastable-state production when time series data of the immune state and the number of tumor cells are irregular and unpredictable. This metastatic disease may be caused not by exterior (medical) factors, but interior density dependent ones.

chao-dyn↗