Related papers: A context dependent pair hidden Markov model for s…
Denoising Diffusion Probabilistic Models (DDPMs) represent a contemporary class of generative models with exceptional qualities in both synthesis and maximizing the data likelihood. These models work by traversing a forward Markov Chain…
We study a variable length Markov chain model associated with a group of stationary processes that share the same context tree but each process has potentially different conditional probabilities. We propose a new model selection and…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Standard practice in Hidden Markov Model (HMM) selection favors the candidate with the highest full-sequence likelihood, although this is equivalent to making a decision based on a single realization. We introduce a \emph{fragment-based}…
Pairwise Choice Markov Chains (PCMC) have been recently introduced to overcome limitations of choice models based on traditional axioms unable to express empirical observations from modern behavior economics like context effects occurring…
The number of academic papers being published is increasing exponentially in recent years, and recommending adequate citations to assist researchers in writing papers is a non-trivial task. Conventional approaches may not be optimal, as the…
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…
We consider the problem of breakpoint detection in a regression modeling framework. To that end, we introduce a novel method, the max-EM algorithm which combines a constrained Hidden Markov Model with the Classification-EM (CEM) algorithm.…
The paper studies an improved estimate for the rate of convergence for nonlinear homogeneous discrete-time Markov chains. These processes are nonlinear in terms of the distribution law. Hence, the transition kernels are dependent on the…
Modeling the time evolution of discrete sets of items (e.g., genetic mutations) is a fundamental problem in many biomedical applications. We approach this problem through the lens of continuous-time Markov chains, and show that the…
In a real life process evolving over time, the relationship between its relevant variables may change. Therefore, it is advantageous to have different inference models for each state of the process. Asymmetric hidden Markov models fulfil…
Recently, significant improvements have been achieved in various natural language processing tasks using neural sequence-to-sequence models. While aiming for the best generation quality is important, ultimately it is also necessary to…
We consider deep multivariate models for heterogeneous collections of random variables. In the context of computer vision, such collections may e.g. consist of images, segmentations, image attributes, and latent variables. When developing…
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,…
One reason why classical phylogenetic reconstruction methods fail to correctly infer the underlying topology is because they assume oversimplified models. In this paper we propose a topology reconstruction method consistent with the most…
We propose a new neurally-inspired model that can learn to encode the global relationship context of visual events across time and space and to use the contextual information to modulate the analysis by synthesis process in a predictive…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…
Studying the neurological, genetic and evolutionary basis of human vocal communication mechanisms using animal vocalization models is an important field of neuroscience. The data sets typically comprise structured sequences of syllables or…
Token representation strategies within large-scale neural architectures often rely on contextually refined embeddings, yet conventional approaches seldom encode structured relationships explicitly within token interactions. Self-attention…