Related papers: Time series model based on global structure of com…

Time-series data exists in every corner of real-world systems and services, ranging from satellites in the sky to wearable devices on human bodies. Learning representations by extracting and inferring valuable information from these time…

We propose a compartmental model for a disease with temporary immunity and secondary infections. From our assumptions on the parameters involved in the model, the system naturally evolves in three time scales. We characterize the equilibria…

We study a minimal model for genome evolution whose elementary processes are single site mutation, duplication and deletion of sequence regions and insertion of random segments. These processes are found to generate long-range correlations…

We outline the global control architecture of genomes. A theory of genomic control information is presented. The concept of a developmental control network called a cene (for control gene) is introduced. We distinguish parts-genes from…

Based on the law of mass action (and its microscopic foundation) and mass conservation, we present here a method to derive consistent dynamic models for the time evolution of systems with an arbitrary number of species. Equations are…

In this article, we review the different models and methods to understand and estimate correlated evolution within the same genome, individual or species. We describe correlated evolution among traits, among genetic components and finally…

We propose general conditions for the emergence of Turing patterns in a domain that changes size through homogeneous growth/shrinkage based on the qualitative changes of a potential function. For this part of the work, we consider the most…

We introduce a generalized promotion time cure model motivated by a new biological consideration. The new approach is flexible to model heterogeneous survival data, in particular for addressing intra-sample heterogeneity. We also indicate…

DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…

Language models for biological and chemical sequences enable crucial applications such as drug discovery, protein engineering, and precision medicine. Currently, these language models are predominantly based on Transformer architectures.…

Time series data are often obtained only within a limited time range due to interruptions during observation process. To classify such partial time series, we need to account for 1) the variable-length data drawn from 2) different…

In this paper, I introduce a Sequence-based Multiscale Model (SeqMM) for the biomolecular data analysis. With the combination of spectral graph method, I reveal the essential difference between the global scale models and local scale ones…

The emergence and development of cancer is a consequence of the accumulation over time of genomic mutations involving a specific set of genes, which provides the cancer clones with a functional selective advantage. In this work, we model…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

De novo assembly is the process of reconstructing the genome sequence of an organism from sequencing reads. Genome sequences are essential to biology, and assembly has been a central problem in bioinformatics for four decades. Until…

We study the use of a time series encoder to learn representations that are useful on data set types with which it has not been trained on. The encoder is formed of a convolutional neural network whose temporal output is summarized by a…

Turing patterns play a fundamental role in morphogenesis and population dynamics, encoding key information about the underlying biological mechanisms. Yet, traditional inverse problems have largely relied on non-biological data such as…

Statistical analysis of distributions of occurrence frequencies of short words in 108 microbial complete genomes reveals the existence of a set of universal "root-sequence lengths" shared by all microbial genomes. These lengths and their…

Time series classification is a field which has drawn much attention over the past decade. A new approach for classification of time series uses classification trees based on shapelets. A shapelet is a subsequence extracted from one of the…

Models of contagion arise broadly both in the biological and social sciences, with applications ranging from the transmission of infectious diseases to the diffusion of innovations and the spread of cultural fads. In this Letter, we…