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Increasingly, keyword, natural language and NoSQL queries are being used for information retrieval from traditional as well as non-traditional databases such as web, document, image, GIS, legal, and health databases. While their popularity…
Motivation: DNA data is transcribed into single-stranded RNA, which folds into specific molecular structures. In this paper we pose the question to what extent sequence- and structure-information correlate. We view this correlation as…
Crystal structure prediction is a long-standing challenge in materials science, with most data-driven methods developed for inorganic systems. This leaves an important gap for organic crystals, which are central to pharmaceuticals,…
The extraction of structured knowledge from scientific literature remains a major bottleneck in nutraceutical research, particularly when identifying microbial strains involved in compound biosynthesis. This study presents a domain-adapted…
We introduce a general abstract framework for database repairs, where the repair notions are defined using formal logic. We distinguish between integrity constraints and so-called query constraints. The former are used to model consistency…
The predictive ability of database classifiers constructed with a network of interacting chemical oscillators is studied. Databases considered here are composed of records, where each record contains a number of parameters (predictors)…
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…
Since the advent of various pre-trained large language models, extracting structured knowledge from scientific text has experienced a revolutionary change compared with traditional machine learning or natural language processing techniques.…
In this paper we present SynKB, an open-source, automatically extracted knowledge base of chemical synthesis protocols. Similar to proprietary chemistry databases such as Reaxsys, SynKB allows chemists to retrieve structured knowledge about…
BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these…
With the advancement of high-throughput biotechnologies, we increasingly accumulate biomedical data about diseases, especially cancer. There is a need for computational models and methods to sift through, integrate, and extract new…
One of the most challenging and recurring problems when modelling plasmas is the lack of data on key atomic and molecular reactions that drive plasma processes. Even when there are data for some reactions, complete and validated datasets of…
Disordered proteins play essential roles in myriad cellular processes, yet their structural characterization remains a major challenge due to their dynamic and heterogeneous nature. We here present a community-driven initiative to address…
Modern business applications and scientific databases call for inherently dynamic data storage environments. Such environments are characterized by two challenging features: (a) they have little idle system time to devote on physical…
Schema linking is a critical bottleneck in applying existing Text-to-SQL models to real-world, large-scale, multi-database environments. Through error analysis, we identify two major challenges in schema linking: (1) Database Retrieval:…
This paper concerns the paraconsistent logic LPQ$^{\supset,\mathsf{F}}$ and an application of it in the area of relational database theory. The notions of a relational database, a query applicable to a relational database, and a consistent…
Understanding the structure of a protein complex is crucial indetermining its function. However, retrieving accurate 3D structures from microscopy images is highly challenging, particularly as many imaging modalities are two-dimensional.…
We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely available at…
Biological databases can be analysed as a complex network which may reveal some its underlying biological mechanisms. Frequently, such databases are identified as scale-free networks or as hierarchical networks depending on connectivity…
Dynamical systems in biology are complex, and one often does not have comprehensive knowledge about the interactions involved. Chemical reaction network (CRN) inference aims to identify, from observing species concentrations over time, the…