Related papers: Autoregressive Modeling of Coding Sequence Lengths…
Large language and music models are increasingly used for constrained generation: rhyming lines, fixed meter, inpainting or infilling, positional endings, and other global form requirements. These systems often perform strikingly well, but…
We introduce a simple and extendable coevolution model for the analysis of longitudinal network and nodal attribute data. The model features parameters that describe three phenomena: homophily, contagion and autocorrelation of the network…
We introduce and theoretically investigate a minimal particle-based model for a new class of active matter where particles exhibit directional, volume-conserving division in confinement while interacting sterically, mimicking cells in early…
Neural autoregressive sequence models smear the probability among many possible sequences including degenerate ones, such as empty or repetitive sequences. In this work, we tackle one specific case where the model assigns a high probability…
This paper revisits the ordered statistics decoding (OSD). It provides a comprehensive analysis of the OSD algorithm by characterizing the statistical properties, evolution and the distribution of the Hamming distance and weighted Hamming…
My analysis uses methods developed for data mining microarray experiments, adapted for ageing research. Methods bridge knowledge of statistical mechanics with data mining methods developed in statistical mathematics. Analyses can reveal how…
We revisit recent methods that employ graph neural networks for decoding error correcting codes and employ messages that are computed in an autoregressive manner. The outgoing messages of the variable nodes are conditioned not only on the…
Controlled branching processes are stochastic growth population models in which the number of individuals with reproductive capacity in each generation is controlled by a random control function. The purpose of this work is to examine the…
Designing mechanical linkages to achieve target end-effector trajectories presents a fundamental challenge due to the intricate coupling between continuous node placements, discrete topological configurations, and nonlinear kinematic…
Approximate Bayesian computation (ABC) has gained popularity in recent years owing to its easy implementation, nice interpretation and good performance. Its advantages are more visible when one encounters complex models where maximum…
Quasi-complementary sequence sets (QCSSs) have attracted sustained research interests for simultaneously supporting more active users in multi-carrier code-division multiple-access (MC-CDMA) systems compared to complete complementary codes…
Automatic cell tracking in dense environments is plagued by inaccurate correspondences and misidentification of parent-offspring relationships. In this paper, we introduce a novel cell tracking algorithm named DenseTrack, which integrates…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
The anaerobic bacterium \textit{Geobacter sulfurreducens} produces extracellular, electronically conductive cytochrome polymer wires that are conductive over micron length scales. Structure models from cryo-electron microscopy data show…
In the application of autoregressive models the order of the model is often estimated using either a sequence of likelihood ratio tests, a likelihood based information criterion, or a residual based test. The properties of such procedures…
A new approach to describing correlation properties of complex dynamic systems with long-range memory based on a concept of additive Markov chains (Phys. Rev. E 68, 061107 (2003)) is developed. An equation connecting a memory function of…
In many real-world scenarios, it is crucial to be able to reliably and efficiently reason under uncertainty while capturing complex relationships in data. Probabilistic circuits (PCs), a prominent family of tractable probabilistic models,…
The ability to learn and respond to recurrent events depends on the capacity to remember transient biological signals received in the past. Moreover, it may be desirable to remember or ignore these transient signals conditioned upon other…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Despite the significance of the high flexibility exhibited by short DNAs, there remains an incomplete understanding of their anomalous persistence length. In this study, we propose a novel approach wherein each fundamental characteristic of…