Related papers: New Sequence Alignment Algorithm using AI Rules an…
We propose a new alignment-free algorithm by constructing a compact vector representation on $\mathbb{R}^{24}$ of a DNA sequence of arbitrary length. Each component of this vector is obtained from a representative sequence, the elements of…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
This paper proposes an algorithm for alignment-free sequence comparison using Logical Match. Here, we compute the score using fuzzy membership values which generate automatically from the number of matches and mismatches. We demonstrate the…
DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base…
As AI adoption expands across human society, the problem of aligning AI models to match human preferences remains a grand challenge. Currently, the AI alignment field is deeply divided between behavioral and representational approaches,…
Pyrosequencing is among the emerging sequencing techniques, capable of generating upto 100,000 overlapping reads in a single run. This technique is much faster and cheaper than the existing state of the art sequencing technique such as…
Network alignment (NA) is the task of finding the correspondence of nodes between two networks based on the network structure and node attributes. Our study is motivated by the fact that, since most of existing NA methods have attempted to…
Network alignment, the process of finding correspondences between nodes in different graphs, has many scientific and industrial applications. Existing unsupervised network alignment methods find suboptimal alignments that break up node…
Finding a globally optimal Bayesian Network using exhaustive search is a problem with super-exponential complexity, which severely restricts the number of variables that it can work for. We implement a dynamic programming based algorithm…
Epigenetics encompasses mechanisms that can alter the expression of genes without changing the underlying genetic sequence. The epigenetic regulation of gene expression is initiated and sustained by several mechanisms such as DNA…
With recent high-throughput technology we can synthesize large heterogeneous collections of DNA structures, and also read them all out precisely in a single procedure. Can we use these tools, not only to do things faster, but also to devise…
Sequence comparison is a widely used computational technique in modern molecular biology. In spite of the frequent use of sequence comparisons the important problem of assigning statistical significance to a given degree of similarity is…
The composition of training data mixtures is critical for effectively training large language models (LLMs), as it directly impacts their performance on downstream tasks. Our goal is to identify an optimal data mixture to specialize an LLM…
With current hardware and software, a standard computer can now hold in RAM an index for approximate pattern matching on about half a dozen human genomes. Sequencing technologies have improved so quickly, however, that scientists will soon…
Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…
The many successes of deep neural networks (DNNs) over the past decade have largely been driven by computational scale rather than insights from biological intelligence. Here, we explore if these trends have also carried concomitant…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
Sequence alignment forms an important backbone in many sequencing applications. A commonly used strategy for sequence alignment is an approximate string matching with a two-dimensional dynamic programming approach. Although some prior work…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
The breakthrough in Deep Learning neural networks has transformed the use of AI and machine learning technologies for the analysis of very large experimental datasets. These datasets are typically generated by large-scale experimental…