Related papers: On Patterns and Re-Use in Bioinformatics Databases
A constant influx of new data poses a challenge in keeping the annotation in biological databases current. Most biological databases contain significant quantities of textual annotation, which often contains the richest source of knowledge.…
Databases covering all individuals of a population are increasingly used for research and decision-making. The massive size of such databases is often mistaken as a guarantee for valid inferences. However, population data have…
Motivation: Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires…
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many…
Recent large language models have been trained on vast datasets, but also often on repeated data, either intentionally for the purpose of upweighting higher quality data, or unintentionally because data deduplication is not perfect and the…
Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big…
Long-term data-driven studies have become indispensable in many areas of science. Often, the data formats, structures and semantics of data change over time, the data sets evolve. Therefore, studies over several decades in particular have…
Natural language user interfaces to database systems have been studied for several decades now. They have mainly focused on parsing and interpreting natural language queries to generate them in a formal database language. We envision the…
Ascertaining the feasibility of independent falsification or repetition of published results is vital to the scientific process, and replication or reproduction experiments are routinely performed in many disciplines. Unfortunately, such…
Recent trends in information management involve the periodic transcription of data onto secondary devices in a networked environment, and the proper scheduling of these transcriptions is critical for efficient data management. To assist in…
Deep learning has recently become very popular on account of its incredible success in many complex data-driven applications, such as image classification and speech recognition. The database community has worked on data-driven applications…
DNA is emerging as an increasingly attractive medium for data storage due to a number of important and unique advantages it offers, most notably the unprecedented durability and density. While the technology is evolving rapidly, the…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
Analytic queries enable sophisticated large-scale data analysis within many commercial, scientific and medical domains today. Data skew is a ubiquitous feature of these real-world domains. In a retail database, some products are typically…
Due to the rapid development of science and technology, the importance of imprecise, noisy, and uncertain data is increasing at an exponential rate. Thus, mining patterns in uncertain databases have drawn the attention of researchers.…
Many database columns contain string or numerical data that conforms to a pattern, such as phone numbers, dates, addresses, product identifiers, and employee ids. These patterns are useful in a number of data processing applications,…
Science is a social process with far-reaching impact on our modern society. In the recent years, for the first time we are able to scientifically study the science itself. This is enabled by massive amounts of data on scientific…
As text and code resources have expanded, large-scale pre-trained models have shown promising capabilities in code generation tasks, typically employing supervised fine-tuning with problem statement-program pairs. However, increasing model…
Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common…
Lexical resources are crucial for cross-linguistic analysis and can provide new insights into computational models for natural language learning. Here, we present an advanced database for comparative studies of words with multiple meanings,…