Related papers: On Patterns and Re-Use in Bioinformatics Databases
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Interpretability is often pointed out as a key requirement for trustworthy machine learning. However, learning and releasing models that are inherently interpretable leaks information regarding the underlying training data. As such…
The improved method of intermittent data analysis is proposed. It exploits, in addition to the standard density moments, the information on the bin-bin correlations, observed in the data and expressed in terms of the density correlators.…
With the advent of the Internet and Internet-connected devices, modern business applications can experience rapid increases as well as variability in transactional workloads. Database replication has been employed to scale performance and…
The issue of internal fragmentation in data structures is a fundamental challenge in database design. A seminal result of Yao in this field shows that evenly splitting the leaves of a B-tree against a workload of uniformly random insertions…
Databases are widespread, yet extracting relevant data can be difficult. Without substantial domain knowledge, multivariate search queries often return sparse or uninformative results. This paper introduces an approach for searching…
Computer simulations of complex population genetic models are an essential tool for making sense of the large-scale datasets of multiple genome sequences from a single species that are becoming increasingly available. A widely used approach…
Citation analysis is one of the most frequently used methods in research evaluation. We are seeing significant growth in citation analysis through bibliometric metadata, primarily due to the availability of citation databases such as the…
Cloud computing has recently emerged as a key technology to provide individuals and companies with access to remote computing and storage infrastructures. In order to achieve highly-available yet high-performing services, cloud data stores…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
Several tasks in information retrieval (IR) rely on assumptions regarding the distribution of some property (such as term frequency) in the data being processed. This thesis argues that such distributional assumptions can lead to incorrect…
A self-replicating system where the elements belonging to a solution category can replicate themselves by copying their own informations, is considered. The information carried by each element is defined by an element of all the n multiple…
In this review paper, we delve into the nascent field of molecular data storage, focusing on system implementations and code constructions. We start by providing an overview of basic concepts in synthetic and computational biology.…
Software technology based on reuse is identified as a process of designing software for the reuse purpose. The software reuse is a process in which the existing software is used to build new software. A metric is a quantitative indicator of…
An applied problem facing all areas of data science is harmonizing data sources. Joining data from multiple origins with unmapped and only partially overlapping features is a prerequisite to developing and testing robust, generalizable…
A longstanding challenge for the Machine Learning community is the one of developing models that are capable of processing and learning from very long sequences of data. The outstanding results of Transformers-based networks (e.g., Large…
Language models have emerged as powerful predictors of the viability of biological sequences. During training these models learn the rules of the grammar obeyed by sequences of amino acids or nucleotides. Once trained, these models can take…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…
Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this…
In the past, the semantic issues raised by the non-monotonic nature of aggregates often prevented their use in the recursive statements of logic programs and deductive databases. However, the recently introduced notion of Pre-mappability…