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Joint identifiability of ancestral sequence, phylogeny and mutation rates under ...
We consider the problem of identifying jointly the ancestral sequence, the phylogeny and the parameters in models of DNA sequence evolution with insertion and deletion (indel). Under the classical TKF91 model of sequence evoluti ... Read More >
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Inferring birth versus death dynamics for ecological interactions in stochastic ...
In this paper, we study the significance of ecological interactions and separation of birth and death dynamics in heterogeneous stochastic populations. Interactions can manifest through the birth dynamics, the death dynamics, or ... Read More >
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Reinforcement Learning for Control of Non-Markovian Cellular Population Dynamics
Many organisms and cell types, from bacteria to cancer cells, exhibit a remarkable ability to adapt to fluctuating environments. Additionally, cells can leverage memory of past environments to better survive previously-encounter ... Read More >
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Nonlinear dynamics of CAR-T cell therapy
Chimeric antigen receptor T-cell (CAR-T) therapy is considered a promising cancer treatment. The dynamic response to this therapy can be broadly divided into a short-term phase, ranging from weeks to months, and a long-term phas ... Read More >
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Chaos in opinion-driven disease dynamics
During the COVID-19 pandemic, it became evident that the effectiveness of applying intervention measures is significantly influenced by societal acceptance, which, in turn, is affected by the processes of opinion formation. This ... Read More >
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Near-ideal selection for the Standard Genetic Code
Evolutionary theorizing resembles building an aircraft while also piloting it; new results change the scaffold for older ideas, requiring revised strategy to remain airborne. A calculated kinetic pathway exists that, under expli ... Read More >
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Siamese networks for Poincaré embeddings and the reconstruction of evolutionary ...
We present a method for reconstructing evolutionary trees from high-dimensional data, with a specific application to bird song spectrograms. We address the challenge of inferring phylogenetic relationships from phenotypic traits ... Read More >
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A Review of Artificial Intelligence based Biological-Tree Construction: Prioriti ...
Biological tree analysis serves as a pivotal tool in uncovering the evolutionary and differentiation relationships among organisms, genes, and cells. Its applications span diverse fields including phylogenetics, developmental bi ... Read More >
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Adaptive efficiency of information processing in immune-pathogen co-evolution
Organisms have evolved immune systems that can counter pathogenic threats. The adaptive immune system in vertebrates consists of a diverse repertoire of immune receptors that can dynamically reorganize to specifically target the ... Read More >
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Traveling vegetation-herbivore waves can sustain ecosystems threatened by drough ...
Dryland vegetation can survive water stress by forming spatial patterns but is often subjected to herbivory as an additional stress that puts it at risk of desertification. Understanding the mutual relationships between vegetati ... Read More >