Related papers: Pyro-Align: Sample-Align based Multiple Alignment …
We consider the classical exact multiple string matching problem. Our solution is based on $q$-grams combined with pattern superimposition, bit-parallelism and alphabet size reduction. We discuss the pros and cons of the various…
Multi-image alignment, bringing a group of images into common register, is an ubiquitous problem and the first step of many applications in a wide variety of domains. As a result, a great amount of effort is being invested in developing…
We outline a procedure for jointly sampling substitution matrices and multiple sequence alignments, according to an approximate posterior distribution, using an MCMC-based algorithm. This procedure provides an efficient and simple method by…
Multidimensional separations data have the capacity to reveal detailed information about complex biological samples. However, data analysis has been an ongoing challenge in the area since the peaks that represent chemical factors may drift…
Pyrosequencing is emerging as one of the important next-generation sequencing technologies. We derive the statistical distributions of this technique in terms of nucleotide probabilities of the target sequences. We give exact distributions…
This article introduces the idea that probabilistic reasoning (PR) may be understood as "information compression by multiple alignment, unification and search" (ICMAUS). In this context, multiple alignment has a meaning which is similar to…
The hierarchical distribution matching (Hi-DM) approach for probabilistic shaping is described. The potential of Hi-DM in terms of trade-off between performance,complexity, and memory is illustrated through three case studies.
Probabilistic programming languages (PPLs) are a popular tool for high-level modelling across many fields. They provide a range of algorithms for probabilistic inference, which analyse models by learning their parameters from a dataset or…
We propose a modified MSA algorithm on quantum annealers with applications in areas of bioinformatics and genetic sequencing. To understand the human genome, researchers compare extensive sets of these genetic sequences -- or their protein…
Hinging on ideas from physical-layer network coding, some promising proposals of coded random access systems seek to improve system performance (while preserving low complexity) by means of packet repetitions and decoding of linear…
Word alignments identify translational correspondences between words in a parallel sentence pair and is used, for instance, to learn bilingual dictionaries, to train statistical machine translation systems , or to perform quality…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
System modeling is a classical approach to ensure their reliability since it is suitable both for a formal verification and for software testing techniques. In the context of model-based testing an approach combining random testing and…
Projection algorithms are well known for their simplicity and flexibility in solving feasibility problems. They are particularly important in practice due to minimal requirements for software implementation and maintenance. In this work, we…
Large language models (LLMs) alignment aims to ensure that the behavior of LLMs meets human preferences. While collecting data from multiple fine-grained, aspect-specific preferences becomes more and more feasible, existing alignment…
The article proposes a heuristic approximation approach to the bin packing problem under multiple objectives. In addition to the traditional objective of minimizing the number of bins, the heterogeneousness of the elements in each bin is…
Background: Computational analysis of next-generation sequencing data is outpaced by data generation in many cases. In one such case, paired-end reads can be produced from the Illumina sequencing method faster than they can be overlapped by…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
Copy mechanisms are employed in sequence to sequence models (seq2seq) to generate reproductions of words from the input to the output. These frameworks, operating at the lexical type level, fail to provide an explicit alignment that records…
We present a new multi-layer peeling technique to cluster points in a metric space. A well-known non-parametric objective is to embed the metric space into a simpler structured metric space such as a line (i.e., Linear Arrangement) or a…