Related papers: On Patterns and Re-Use in Bioinformatics Databases

Ancestral sequence reconstruction is a key task in computational biology. It consists in inferring a molecular sequence at an ancestral species of a known phylogeny, given descendant sequences at the tip of the tree. In addition to its many…

Achieving complete reproducibility in science, particularly in research fields such as biodiversity, is challenging due to analytical choices, bias and interpretation. Here, we examine examples of reproducibility in biological systematics,…

The paradigm of large language models in natural language processing (NLP) has also shown promise in modeling biological languages, including proteins, RNA, and DNA. Both the auto-regressive generation paradigm and evaluation metrics have…

High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…

Consider the case where a programmer has written some part of a program, but has left part of the program (such as a method or a function body) incomplete. The goal is to use the context surrounding the missing code to automatically 'figure…

Relational databases play a central role in many information systems. Their schema contains structural (e.g. tables and columns) and behavioral (e.g. stored procedures or views) entity descriptions. Then, just like for ``normal'' software,…

Recently, different works proposed a new way to mine patterns in databases with pathological size. For example, experiments in genome biology usually provide databases with thousands of attributes (genes) but only tens of objects…

The analysis of intermittent data is improved. The standard method of recovering the history of a particle cascade is proved in general not to reproduce the structure of the true cascade. The recovering corrections to the standard method…

DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…

We describe and analyze different approaches to represent ordinal patterns. All of these can be found in the literature. The most important representations (plus sub-classes) are compared in terms of their applicability from different…

Software engineering is not an empirically based discipline. Consequently, many of its practices are based on little more than a generally agreed feeling that something may be true. Part of the problem is that it is both relatively young…

Ensuring consistency between research papers and their corresponding software code implementations is a fundamental prerequisite for guaranteeing the reproducibility of scientific findings and the reliability of software systems. However,…

Good database design is crucial to obtain a sound, consistent database, and - in turn - good database design methodologies are the best way to achieve the right design. These methodologies are taught to most Computer Science undergraduates,…

Consistent answers to a query from a possibly inconsistent database are answers that are simultaneously retrieved from every possible repair of the database. Repairs are consistent instances that minimally differ from the original…

Software reuse is a subfield of software engineering that is used to adopt the existing software for similar purposes. Reuse Metrics determine the extent to which an existing software component is reused in new software with an objective to…

Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…

The general trace reconstruction problem seeks to recover an original sequence from its noisy copies independently corrupted by deletions, insertions, and substitutions. This problem arises in applications such as DNA data storage, a…

Data compression plays an important role to deal with high volumes of DNA sequences in the field of Bioinformatics. Again data compression techniques directly affect the alignment of DNA sequences. So the time needed to decompress a…

We posit that striving for distributed systems that provide "single system image" semantics is fundamentally flawed and at odds with how systems operate in the physical world. We realize the database as an optimization of this system: a…