English
Related papers

Related papers: Simple models for scaling in phylogenetic trees

200 papers

We revisit the number theoretic division model of self-organized criticality [Phys. Rev. Lett. 101, 158702 (2008)]. The model consists of a pool of $M-1$ ordered integers $\{2, 3, \cdots, M\}$, and the aim is to dynamically form a primitive…

Statistical Mechanics · Physics 2024-10-10 Rahul Chhimpa , Avinash Chand Yadav

On large scales, the Lyman-$\alpha$ forest provides insights into the expansion history of the Universe, while on small scales, it imposes strict constraints on the growth history, the nature of dark matter, and the sum of neutrino masses.…

We study the properties of random walks on complex trees. We observe that the absence of loops reflects in physical observables showing large differences with respect to their looped counterparts. First, both the vertex discovery rate and…

Statistical Mechanics · Physics 2008-10-21 Andrea Baronchelli , Michele Catanzaro , Romualdo Pastor-Satorras

Neural scaling laws are observed in a range of domains, to date with no universal understanding of why they occur. Recent theories suggest that loss power laws arise from Zipf's law, a power law observed in domains like natural language.…

Machine Learning · Computer Science 2025-10-15 Oren Neumann , Claudius Gros

Neural scaling laws aim to characterize how out-of-sample error behaves as a function of model and training dataset size. Such scaling laws guide allocation of a computational resources between model and data processing to minimize error.…

Machine Learning · Computer Science 2024-07-02 Hong Jun Jeon , Benjamin Van Roy

Hierarchies can be modeled by a set of exponential functions, from which we can derive a set of power laws indicative of scaling. The solution to a scaling relation equation is always a power law. The scaling laws are followed by many…

Physics and Society · Physics 2018-12-19 Yanguang Chen , Bin Jiang

Language models (LMs) require robust episodic grounding-the capacity to learn from and apply past experiences-to excel at physical planning tasks. Current episodic grounding approaches struggle with scalability and integration, limiting…

Computation and Language · Computer Science 2025-06-03 Chunhui Zhang , Sirui , Wang , Zhongyu Ouyang , Xiangchi Yuan , Soroush Vosoughi

Scale transformations have played an extremely successful role in studies of cosmological large-scale structure by relating the non-linear spectrum of cosmological density fluctuations to the linear primordial power at longer wavelengths.…

Astrophysics · Physics 2009-11-13 Jun Pan , Peter Coles , Istvan Szapudi

Many biological networks have been labelled scale-free as their degree distribution can be approximately described by a powerlaw distribution. While the degree distribution does not summarize all aspects of a network it has often been…

Molecular Networks · Quantitative Biology 2007-05-23 M. P. H. Stumpf , P. J. Ingram , I. Nouvel , C. Wiuf

Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…

Populations and Evolution · Quantitative Biology 2020-05-11 Mareike Fischer , Michelle Galla , Lina Herbst , Yangjing Long , Kristina Wicke

On the rooted $k$-ary tree we consider a 0-1 kinetically constrained spin model in which the occupancy variable at each node is re-sampled with rate one from the Bernoulli(p) measure iff all its children are empty. For this process the…

Probability · Mathematics 2012-11-27 Nicoletta Cancrini , Fabio Martinelli , Cyril Roberto , Cristina Toninelli

Looping, reusing a block of layers across depth, and depth growing, training shallow-to-deep models by duplicating middle layers, have both been linked to stronger reasoning, but their relationship remains unclear. We provide a mechanistic…

Computation and Language · Computer Science 2026-02-19 Ferdinand Kapl , Emmanouil Angelis , Kaitlin Maile , Johannes von Oswald , Stefan Bauer

Open string amplitudes at tree level have been studied for over fifty years, but there is no known analytic form for general $n$-point amplitudes, and their conventional representation in terms of worldsheet integrals does not make many of…

High Energy Physics - Theory · Physics 2025-04-23 Nima Arkani-Hamed , Carolina Figueiredo , Grant N. Remmen

We investigate the statistics of trees grown from some initial tree by attaching links to preexisting vertices, with attachment probabilities depending only on the valence of these vertices. We consider the asymptotic mass distribution that…

Statistical Mechanics · Physics 2007-05-23 François David , Philippe Di Francesco , Emmanuel Guitter , Thordur Jonsson

Experimental studies on the irreversible growth of field-induced chains of dipolar particles suggest an asymptotic power-law behavior of several relevant quantities. We introduce a Monte Carlo model of chain growth that explicitly…

Statistical Mechanics · Physics 2007-05-23 M. -Carmen Miguel , R. Pastor-Satorras

The body plan of the fruit fly is determined by the expression of just a handful of genes. We show that the spatial patterns of expression for several of these genes scale precisely with the size of the embryo. Concretely, discrete…

Neural scaling laws have driven significant advancements in machine learning, particularly in domains like language modeling and computer vision. However, the exploration of neural scaling laws within robotics has remained relatively…

Robotics · Computer Science 2025-01-28 Sebastian Sartor , Neil Thompson

We present a new technique for proving logarithmic upper bounds for diameters of evolving random graph models, which is based on defining a coupling between random graphs and variants of random recursive trees. The advantage of the…

Discrete Mathematics · Computer Science 2014-10-24 Abbas Mehrabian

The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…

Computational Physics · Physics 2009-11-13 Paulino R. Villas Boas , Francisco A. Rodrigues , Gonzalo Travieso , Luciano da F. Costa

In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…

Data Structures and Algorithms · Computer Science 2019-01-15 Olivier Bodini , Antoine Genitrini , Mehdi Naima