Related papers: Multiple pattern matching: A Markov chain approach
To better understand the flows of ideas or information through social and biological systems, researchers develop maps that reveal important patterns in network flows. In practice, network flow models have implied memoryless first-order…
Fault Tree analysis is a widely used failure analysis methodology to assess a system in terms of safety or reliability in many industrial application domains. However, with Fault Tree methodology there is no possibility to express a…
Real-world networks are composed of diverse interacting and evolving entities, while most of existing researches simply characterize them as particular static networks, without consideration of the evolution trend in dynamic networks.…
Markov chain Monte Carlo (MCMC) algorithms provide a very general recipe for estimating properties of complicated distributions. While their use has become commonplace and there is a large literature on MCMC theory and practice, MCMC users…
A reaction network is a chemical system involving multiple reactions and chemical species. Stochastic models of such networks treat the system as a continuous time Markov chain on the number of molecules of each species with reactions as…
In sequence-based predictions, conventionally an input sequence is represented by a multiple sequence alignment (MSA) or a representation derived from MSA, such as a position-specific scoring matrix. Recently, inspired by the development in…
Automatic generation of sequences has been a highly explored field in the last years. In particular, natural language processing and automatic music composition have gained importance due to the recent advances in machine learning and…
Design patterns are elegant and well-tested solutions to recurrent software development problems. They are the result of software developers dealing with problems that frequently occur, solving them in the same or a slightly adapted way. A…
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…
Adaptive importance sampling is a powerful tool to sample from complicated target densities, but its success depends sensitively on the initial proposal density. An algorithm is presented to automatically perform the initialization using…
Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…
As with the development of the IT technologies, the amount of accumulated data is also increasing. Thus the role of data mining comes into picture. Association rule mining becomes one of the significant responsibilities of descriptive…
Recurrent neural networks (RNNs) provide a powerful approach in neuroscience to infer latent dynamics in neural populations and to generate hypotheses about the neural computations underlying behavior. However, past work has focused on…
We study relationships between permutation statistics and pattern-functions, counting the number of times particular patterns occur in a permutation. This allows us to write several familiar statistics as linear combinations of pattern…
The mining of graphs in terms of their local substructure is a well-established methodology to analyze networks. It was hypothesized that motifs - subgraph patterns which appear significantly more often than expected at random - play a key…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
Building upon the rule-algebraic stochastic mechanics framework, we present new results on the relationship of stochastic rewriting systems described in terms of continuous-time Markov chains, their embedded discrete-time Markov chains and…
The formal verification of large probabilistic models is important and challenging. Exploiting the concurrency that is often present is one way to address this problem. Here we study a restricted class of asynchronous distributed…
A fundamental algorithm for selecting ranks from a finite subset of an ordered set is Radix Selection. This algorithm requires the data to be given as strings of symbols over an ordered alphabet, e.g., binary expansions of real numbers. Its…
Complex networks have been characterised by their specific connectivity patterns (network motifs), but their building blocks can also be identified and described by node-motifs---a combination of local network features. One technique to…