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

In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…

Reusing ontologies in practice is still very challenging, especially when multiple ontologies are (jointly) involved. Moreover, despite recent advances, the realization of systematic ontology quality assurance remains a difficult problem.…

We propose a database model that allows users to annotate data with belief statements. Our motivation comes from scientific database applications where a community of users is working together to assemble, revise, and curate a shared data…

A pervasive problem in Data Science is that the knowledge generated by possibly expensive analytics processes is subject to decay over time, as the data used to compute it drifts, the algorithms used in the processes are improved, and the…

The explosion of the amount of data stored in cloud systems calls for more efficient paradigms for redundancy. While replication is widely used to ensure data availability, erasure correcting codes provide a much better trade-off between…

Data is replicated and stored redundantly over multiple servers for availability in distributed databases. We focus on databases with frequent reads and writes, where both read and write latencies are important. This is in contrast to…

The re-identification or de-anonymization of users from anonymized data through matching with publicly-available correlated user data has raised privacy concerns, leading to the complementary measure of obfuscation in addition to…

Effectively learning from sequential data is a longstanding goal of Artificial Intelligence, especially in the case of long sequences. From the dawn of Machine Learning, several researchers have pursued algorithms and architectures capable…

In rule-based systems, goal-oriented computations correspond naturally to the possible ways that an observation may be explained. In some applications, we need to compute explanations for a series of observations with the same domain. The…

We review a recent trend in computational systems biology which aims at using pattern recognition algorithms to infer the structure of large-scale biological networks from heterogeneous genomic data. We present several strategies that have…

As sequencing technologies become more affordable and genomic databases expand continuously, the reuse of publicly available sequencing data emerges as a powerful strategy for studying microbial pathogens. Indeed, raw sequencing reads…

Nowadays, scientific databases have become the bread-and-butter of particle physicists. These databases must be maintained and checked repeatedly to insure the accuracy of their content. The COMPETE collaboration aims at motivating data…

In biomedical applications of machine learning, relevant information often has a rich structure that is not easily encoded as real-valued predictors. Examples of such data include DNA or RNA sequences, gene sets or pathways, gene…

The re-identification or de-anonymization of users from anonymized data through matching with publicly available correlated user data has raised privacy concerns, leading to the complementary measure of obfuscation in addition to…

The rapid advance of DNA sequencing technologies has yielded databases of thousands of genomes. To search and index these databases effectively, it is important that we take advantage of the similarity between those genomes. Several authors…

With distributed computing and mobile applications becoming ever more prevalent, synchronizing diverging replicas of the same data is a common problem. Reconciliation -- bringing two replicas of the same data structure as close as possible…

We investigate a decentralised approach to committing transactions in a replicated database, under partial replication. Previous protocols either re-execute transactions entirely and/or compute a total order of transactions. In contrast,…

Recognition errors are common in human communication. Similar errors often lead to unwanted behaviour in dialogue systems or virtual assistants. In human communication, we can recover from them by repeating misrecognized words or phrases;…

The search of information in large text repositories has been plagued by the so-called document-query vocabulary gap, i.e. the semantic discordance between the contents in the stored document entities on the one hand and the human query on…

DNA as a data storage medium has several advantages, including far greater data density compared to electronic media. We propose that schemes for data storage in the DNA of living organisms may benefit from studying the reconstruction…