Related papers: Finite Width Model Sequence Comparison
In genomics, pattern matching against a sequence of nucleotides plays a pivotal role for DNA sequence alignment and comparing genomes. This helps tackling some diseases, such as cancer in humans. The complexity of searching biological…
Measuring the distance between data points is fundamental to many statistical techniques, such as dimension reduction or clustering algorithms. However, improvements in data collection technologies has led to a growing versatility of…
A new numerical characterization of symbolic sequences is proposed. The partition of sequence based on Ke and Tong algorithm is a starting point. Algorithm decomposes original sequence into set of distinct subsequences - a patterns. The set…
Sequential modelling entails making sense of sequential data, which naturally occurs in a wide array of domains. One example is systems that interact with users, log user actions and behaviour, and make recommendations of items of potential…
Understanding the structure and dynamics of biological networks is one of the important challenges in system biology. In addition, increasing amount of experimental data in biological networks necessitate the use of efficient methods to…
The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
Conformance checking encompasses a body of process mining techniques which aim to find and describe the differences between a process model capturing the expected process behavior and a corresponding event log recording the observed…
Conformance checking is a set of process mining functions that compare process instances with a given process model. It identifies deviations between the process instances' actual behaviour ("as-is") and its modelled behaviour ("to-be").…
This paper investigates the length problem in sequence-level relative reinforcement learning. We observe that, although existing methods partially alleviate length-related phenomena, a more fundamental issue remains insufficiently…
The Longest Common Subsequence (LCS) problem is a fundamental problem of sequence comparison. A natural approximation to this problem is a model in which every pairs of letters of two ``sequences'' are matched independently of the other…
Linearizability has become the key correctness criterion for concurrent data structures, ensuring that histories of the concurrent object under consideration are consistent, where consistency is judged with respect to a sequential history…
Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex…
The identification of anomalies in temporal data is a core component of numerous research areas such as intrusion detection, fault prevention, genomics and fraud detection. This article provides an experimental comparison of the novelty…
This talk will review a little over a decade's research on applying certain stochastic models to biological sequence analysis. The models themselves have a longer history, going back over 30 years, although many novel variants have arisen…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
Finding the longest common subsequence in $k$-length substrings (LCS$k$) is a recently proposed problem motivated by computational biology. This is a generalization of the well-known LCS problem in which matching symbols from two sequences…
Biomolecular structure comparison not only reveals evolutionary relationships, but also sheds light on biological functional properties. However, traditional definitions of structure or sequence similarity always involve superposition or…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Using a time series model to mimic an observed time series has a long history. However, with regard to this objective, conventional estimation methods for discrete-time dynamical models are frequently found to be wanting. In fact, they are…