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

Data deduplication is the task of detecting records in a database that correspond to the same real-world entity. Our goal is to develop a procedure that samples uniformly from the set of entities present in the database in the presence of…

Efficient consistency maintenance of incomplete and dynamic real-life databases is a quality label for further data analysis. In prior work, we tackled the generic problem of database updating in the presence of tuple generating constraints…

The ubiquity of computation in modern scientific research inflicts new challenges for reproducibility. While most journals now require code and data be made available, the standards for organization, annotation, and validation remain lax,…

In social networking services, users constantly change, and the network structure changes simultaneously. As the network structure changes, so does the word-of-mouth within it. To study how information transfer on the network changes with…

Information on the structure of molecules, retrieved via biochemical databases, plays a pivotal role in various disciplines, such as metabolomics, systems biology, and drug discovery. However, no such database can be complete, and the…

Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…

Current metagenomic analysis algorithms require significant computing resources, can report excessive false positives (type I errors), may miss organisms (type II errors / false negatives), or scale poorly on large datasets. This paper…

The ability to store data in the DNA of a living organism has applications in a variety of areas including synthetic biology and watermarking of patented genetically-modified organisms. Data stored in this medium is subject to errors…

Benchmark datasets play a central role in the organization of machine learning research. They coordinate researchers around shared research problems and serve as a measure of progress towards shared goals. Despite the foundational role of…

In this uncertain world, data uncertainty is inherent in many applications and its importance is growing drastically due to the rapid development of modern technologies. Nowadays, researchers have paid more attention to mine patterns in…

We present an analytical study of the quality of metadata about samples used in biomedical experiments. The metadata under analysis are stored in two well-known databases: BioSample---a repository managed by the National Center for…

Reuse of data in new contexts beyond the purposes for which it was originally collected has contributed to technological innovation and reducing the consent burden on data subjects. One of the legal mechanisms that makes such reuse possible…

Indexing massive data sets is extremely expensive for large scale problems. In many fields, huge amounts of data are currently generated, however extracting meaningful information from voluminous data sets, such as computing similarity…

As the amount of information online continues to grow, a correspondingly important opportunity is for individuals to reuse knowledge which has been summarized by others rather than starting from scratch. However, appropriate reuse requires…

From an inconsistent database non-trivial arguments may be constructed both for a proposition, and for the contrary of that proposition. Therefore, inconsistency in a logical database causes uncertainty about which conclusions to accept.…

The network paradigm is increasingly used to describe the dynamics of complex systems. Here we review the current results and propose future development areas in the assessment of perturbation waves, i.e. propagating structural changes in…

De-anonymizing user identities by matching various forms of user data available on the internet raises privacy concerns. A fundamental understanding of the privacy leakage in such scenarios requires a careful study of conditions under which…

Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range…

Paraphrasing is a useful natural language processing task that can contribute to more diverse generated or translated texts. Natural language inference (NLI) and paraphrasing share some similarities and can benefit from a joint approach. We…

The performance of replication-based distributed databases is affected due to non-uniform storage across storage nodes (also called \textit{data skew}) and reduction in the replication factor during operation, particularly due to node…