Related papers: Performance Evaluation of Structured and Semi-Stru…
Web archives are a valuable resource for researchers of various disciplines. However, to use them as a scholarly source, researchers require a tool that provides efficient access to Web archive data for extraction and derivation of smaller…
We describe the current state and future plans for a set of tools for scientific data management (SDM) designed to support scientific transparency and reproducible research. SDM has been in active use at our MRI Center for more than two…
A Natural Language Interface (NLI) facilitates users to pose queries to retrieve information from a database without using any artificial language such as the Structured Query Language (SQL). Several applications in various domains…
Open source bioinformatics tools running under MS Windows are rare to find, and those running under Windows HPC cluster are almost non-existing. This is despite the fact that the Windows is the most popular operating system used among life…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
This short paper gives an introduction to a research project to analyze how digital documents are structured and described. Using a phenomenological approach, this research will reveal common patterns that are used in data, independent from…
Research is a tertiary priority in the EHR, where the priorities are patient care and billing. Because of this, the data is not standardized or formatted in a manner easily adapted to machine learning approaches. Data may be missing for a…
Retrieval systems are increasingly used in biomedical and clinical natural language processing applications, yet practical guidance for researchers building such systems is limited. In this work, we provide such guidance through an…
In recent years, the management and processing of data streams has become a topic of active research in several fields of computer science such as, distributed systems, database systems, and data mining. A data stream can be thought of as a…
The web contains countless semi-structured websites, which can be a rich source of information for populating knowledge bases. Existing methods for extracting relations from the DOM trees of semi-structured webpages can achieve high…
Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we…
As the quantity of data being depositing into biological databases continues to increase, it becomes ever more vital to develop methods that enable us to understand this data and ensure that the knowledge is correct. It is widely-held that…
The explosion of scientific literature has made the efficient and accurate extraction of structured data a critical component for advancing scientific knowledge and supporting evidence-based decision-making. However, existing tools often…
In the current context of Big Data, a multitude of new NoSQL solutions for storing, managing, and extracting information and patterns from semi-structured data have been proposed and implemented. These solutions were developed to relieve…
Querying both structured and unstructured data has become a new paradigm in data analytics and recommendation. With unstructured data, such as text and videos, are converted to high-dimensional vectors and queried with approximate nearest…
Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require…
Requirements identification in textual documents or extraction is a tedious and error prone task that many researchers suggest automating. We manually annotated the PURE dataset and thus created a new one containing both requirements and…
This article introduces the Data Retrieval Web Engine (also referred to as doctor web), a flexible and modular tool for extracting structured data from web pages using a simple query language. We discuss the engineering challenges addressed…
Answering science questions posed in natural language is an important AI challenge. Answering such questions often requires non-trivial inference and knowledge that goes beyond factoid retrieval. Yet, most systems for this task are based on…
Understanding the connections between unstructured text and semi-structured table is an important yet neglected problem in natural language processing. In this work, we focus on content-based table retrieval. Given a query, the task is to…