Related papers: Autoregressive Modeling of Coding Sequence Lengths…
We demonstrate a conditional autoregressive pipeline for efficient music recomposition, based on methods presented in van den Oord et al.(2017). Recomposition (Casal & Casey, 2010) focuses on reworking existing musical pieces, adhering to…
Datasets from several domains, such as life-sciences, semantic web, machine learning, natural language processing, etc. are naturally structured as acyclic graphs. These datasets, particularly those in bio-informatics and computational…
Frameshift translation is an important phenomenon that contributes to the appearance of novel Coding DNA Sequences (CDS) and functions in gene evolution, by allowing alternative amino acid translations of genes coding regions. Frameshift…
For a set of mulitple sequences, their patterns,Longest Common Subsequences (LCS) and Shortest Common Supersequences (SCS) represent different aspects of these sequences profile, and they can all be used for biological sequence comparisons…
Processes controlled by stochastic synthesis and degradation (SSD) are widespread in biology but their reaction kinetics are not well understood. Using methods borrowed from the theory of resetting processes, we determine the first-passage…
During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…
The first motivation of this paper is to study stationarity and ergodic properties for a general class of time series models defined conditional on an exogenous covariates process. The dynamic of these models is given by an autoregressive…
The random motion of molecules in living cells has consistently been reported to deviate from standard Brownian motion, a behavior coined as ``anomalous diffusion''. Fluorescence Correlation Spectroscopy (FCS) is a powerful method to…
Recursive decoding techniques are considered for Reed-Muller (RM) codes of growing length $n$ and fixed order $r.$ An algorithm is designed that has complexity of order $n\log n$ and corrects most error patterns of weight up to…
Modelling and understanding directional gene networks is a major challenge in biology as they play an important role in the architecture and function of genetic systems. Copula Directional Dependence (CDD) can measure the directed…
A new version of the partial autocorrelation plot and a new family of subset autoregressive models are introduced. A comprehensive approach to model identification, estimation and diagnostic checking is developed for these models. These…
This paper gives performance limits of the segmented compressive sampling (CS) which collects correlated samples. It is shown that the effect of correlation among samples for the segmented CS can be characterized by a penalty term in the…
Large language models~(LLMs) exhibit exceptional performance in language tasks, yet their auto-regressive inference is limited due to high computational requirements and is sub-optimal due to the exposure bias. Inspired by speculative…
Learning the dynamics of complex systems features a large number of applications in data science. Graph-based modeling and inference underpins the most prominent family of approaches to learn complex dynamics due to their ability to capture…
Statistical pattern recognition methods based on the Coherence Length Diagram (CLD) have been proposed for medical image analyses, such as quantitative characterisation of human skin textures, and for polarized light microscopy of liquid…
Recent experimental and theoretical approaches have attempted to quantify the physical organization (compaction and geometry) of the bacterial chromosome with its complement of proteins (the nucleoid). The genomic DNA exists in a complex…
Communication and coordination play a major role in the ability of bacterial cells to adapt to ever changing environments and conditions. Recent work has shown that such coordination underlies several aspects of bacterial responses…
Regenerating codes enable trading off repair bandwidth for storage in distributed storage systems (DSS). Due to their distributed nature, these systems are intrinsically susceptible to attacks, and they may also be subject to multiple…
The space time autoregressive model has been widely applied in science, in areas such as economics, public finance, political science, agricultural economics, environmental studies and transportation analyses. The classical space time…
We introduce a model for the spreading of epidemics by long-range infections and investigate the critical behaviour at the spreading transition. The model generalizes directed bond percolation and is characterized by a probability…