Related papers: On Patterns and Re-Use in Bioinformatics Databases
Data errors are widespread in real-world databases and severely impact downstream applications, such as machine learning pipelines or business analytics reports. Causes of such errors are manifold and can arise during both the design phase…
Users issue queries to Search Engines, and try to find the desired information in the results produced. They repeat this process if their information need is not met at the first place. It is crucial to identify the important words in a…
Traditional statistical theory assumes that the analysis to be performed on a given data set is selected independently of the data themselves. This assumption breaks downs when data are re-used across analyses and the analysis to be…
Despite the large quantity of information available, thorough researches in various biological databases are still needed in order to reconstruct and understand the steps that lead to known or new phenomena. By using protein-protein…
Recently frequent and sequential pattern mining algorithms have been widely used in the field of software engineering to mine various source code or specification patterns. In practice software evolves from one version to another is needed…
Models of the dynamics of cellular interaction networks have become increasingly larger in recent years. Formal verification based on model checking provides a powerful technology to keep up with this increase in scale and complexity. The…
In Biomedical Natural Language Processing (BioNLP) tasks, such as Relation Extraction, Named Entity Recognition, and Text Classification, the scarcity of high-quality data remains a significant challenge. This limitation poisons large…
Search is a key service within constraint programming systems, and it demands the restoration of previously accessed states during the exploration of a search tree. Restoration proceeds either bottom-up within the tree to roll back…
Recursive Bayesian inference, in which posterior beliefs are updated in light of accumulating data, is a tool for implementing Bayesian models in applications with streaming and/or very large data sets. As the posterior of one iteration…
Recent studies have shown that the majority of published computational models in systems biology and physiology are not repeatable or reproducible. There are a variety of reasons for this. One of the most likely reasons is that given how…
In-database machine learning has been very popular, almost being a cliche. However, can we do it the other way around? In this work, we say "yes" by applying plain old SQL to deep learning, in a sense implementing deep learning algorithms…
We study percolation on networks, which is used as a model of the resilience of networked systems such as the Internet to attack or failure and as a simple model of the spread of disease over human contact networks. We reformulate…
Scientific progress increasingly depends on data management, particularly to clean and curate data so that it can be systematically analyzed and reused. A wealth of techniques for managing and curating data (and its provenance) have been…
We describe some recent approaches to score-based explanations for query answers in databases. The focus is on work done by the author and collaborators. Special emphasis is placed on the use of counterfactual reasoning for score…
Provenance for database queries or scientific workflows is often motivated as providing explanation, increasing understanding of the underlying data sources and processes used to compute the query, and reproducibility, the capability to…
While measurement advances now allow extensive surveys of gene activity (large numbers of genes across many samples), interpretation of these data is often confounded by noise -- expression counts can differ strongly across samples due to…
The subject of conversational mining has become of great interest recently due to the explosion of social and other online media. Supplementing this explosion of text is the advancement in pre-trained language models which have helped us to…
The gradual patterns that model the complex co-variations of attributes of the form "The more/less X, The more/less Y" play a crucial role in many real world applications where the amount of numerical data to manage is important, this is…
We consider the incidence of text "reuse" by researchers, via a systematic pairwise comparison of the text content of all articles deposited to arXiv.org from 1991--2012. We measure the global frequencies of three classes of text reuse, and…
The interest in channel models in which the data is sent as an unordered set of binary strings has increased lately, due to emerging applications in DNA storage, among others. In this paper we analyze the minimal redundancy of binary codes…