相关论文: Inferring the immune response from repertoire sequ…
Biological cells sense external chemical stimuli in their environment using cell-surface receptors. To increase the sensitivity of sensing, receptors often cluster, most noticeably in bacterial chemotaxis, a paradigm for signaling and…
Recent experimental evidence suggests that acute myeloid leukemias may originate from multiple clones of malignant cells. Nevertheless it is not known how the observed clones may differ with respect to cell properties such as proliferation…
Cellular decision making is based on regulatory circuits that associate signal thresholds to specific physiological actions. This transmission of information is subjected to molecular noise what can decrease its fidelity. Here, we show…
A central mechanism in machine learning is to identify, store, and recognize patterns. How to learn, access, and retrieve such patterns is crucial in Hopfield networks and the more recent transformer architectures. We show that the…
Background: Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing steps. In addition,…
Generative diffusion models synthesize new samples by reversing a diffusive process that converts a given data set to generic noise. This is accomplished by training a neural network to match the gradient of the log of the probability…
A stochastic model for the activation of T-cells is analysed. T-cells are part of the immune system and recognize foreign antigens against a background of the body's own molecules. The model under consideration is a slight generalization of…
Relation of genome sizes to organisms complexity is still described rather equivocally. Neither the number of genes (G-value), nor the total amount of DNA (C-value) correlates consistently with phenotype complexity. Using information theory…
Targeted amplicon panels are widely used in oncology diagnostics, but providing per-gene performance guarantees for copy number variant (CNV) detection remains challenging due to amplification artifacts, process-mismatch heterogeneity, and…
Diffusion probabilistic models have been successfully used to generate data from noise. However, most diffusion models are computationally expensive and difficult to interpret with a lack of theoretical justification. Random feature models…
Quantitative analysis of the dynamics of tiny cellular and sub-cellular structures, known as particles, in time-lapse cell microscopy sequences requires the development of a reliable multi-target tracking method capable of tracking numerous…
One of the fundamental questions of cultural evolutionary research is how individual-level processes scale up to generate population-level patterns. Previous studies in music have revealed that frequency-based bias (e.g. conformity and…
We derive a novel generative model from iterative Gaussian posterior inference. By treating the generated sample as an unknown variable, we can formulate the sampling process in the language of Bayesian probability. Our model uses a…
A system is presented that segments, clusters and predicts musical audio in an unsupervised manner, adjusting the number of (timbre) clusters instantaneously to the audio input. A sequence learning algorithm adapts its structure to a…
Newberry et al. (Detecting evolutionary forces in language change, Nature 551, 2017) tackle an important but difficult problem in linguistics, the testing of selective theories of language change against a null model of drift. Having…
T cell receptor signaling must operate reliably under tight time constraints. While assuming quite different mechanisms, two prominent models of T cell receptor activation, kinetic segregation and kinetic proofreading, both introduce a…
Coevolutionary arms races form between interacting populations that constitute each other's environment and respond to mutual changes. This inherently far-from-equilibrium process finds striking manifestations in the adaptive immune system,…
The effects of demographic stochasticity in the long term behaviour of endemic infectious diseases have been considered for long as a necessary addition to an underlying deterministic theory. The latter would explain the regular behaviour…
We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is, a maximum in the regularity of the oscillations as a function of noise amplitude. The effect is manifest as a system-size effect in a…
The transduction process that occurs in the inner ear of the auditory system is a complex mechanism which requires a non-linear dynamical description. In addition to this, the stochastic phenomena that naturally arise in the inner ear…