Related papers: SBtab - Conventions for structured data tables in …

Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage of these frameworks is that they do not require precise…

Structured (tabular) data in the preclinical and clinical domains contains valuable information about individuals and an efficient table-to-text summarization system can drastically reduce manual efforts to condense this data into reports.…

Computational models are invaluable in capturing the complexities of real-world biological processes. Yet, the selection of appropriate algorithms for inference tasks, especially when dealing with real-world observational data, remains a…

Clinical information extraction, which involves structuring clinical concepts from unstructured medical text, remains a challenging problem that could benefit from the inclusion of tabular background information available in electronic…

There is a wide range of available biological databases developed by bioinformatics experts, employing different methods to extract biological data. In this paper, we investigate and evaluate the performance of some of these methods in…

Motivation: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard…

Data collection is often difficult in critical fields such as medicine, physics, and chemistry. As a result, classification methods usually perform poorly with these small datasets, leading to weak predictive performance. Increasing the…

Entity linking is an important step towards constructing knowledge graphs that facilitate advanced question answering over scientific documents, including the retrieval of relevant information included in tables within these documents. This…

Health informatics can inform decisions that practitioners, patients, policymakers, and researchers need to make about health and disease. Health informatics is built upon patient health data leading to the need to codify patient health…

Unstructured enterprise data such as reports, manuals and guidelines often contain tables. The traditional way of integrating data from these tables is through a two-step process of table detection/extraction and mapping the table layouts…

We highlight the role of Data Science in Biomedicine. Our manuscript goes from the general to the particular, presenting a global definition of Data Science and showing the trend for this discipline together with the terms of cloud…

The scientific literature is growing exponentially, and professionals are no more able to cope with the current amount of publications. Text mining provided in the past methods to retrieve and extract information from text; however, most of…

Recent years showed a strong increase in biomedical sciences and an inherent increase in publication volume. Extraction of specific information from these sources requires highly sophisticated text mining and information extraction tools.…

The importance of stochasticity within biological systems has been shown repeatedly during the last years and has raised the need for efficient stochastic tools. We present SABRE, a tool for stochastic analysis of biochemical reaction…

Large language models (LLMs) are becoming attractive as few-shot reasoners to solve Natural Language (NL)-related tasks. However, the understanding of their capability to process structured data like tables remains an under-explored area.…

One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…

All aspects of our society, including the life sciences, need a mechanism for people working within them to represent the concepts they employ to carry out their research. For the information systems being designed and developed to support…

The output structure of database-like tables, consisting of values structured in horizontal rows and vertical columns identifiable by name, can cover a wide range of NLP tasks. Following this constatation, we propose a framework for…

Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…

Knowledge graphs, collectively as a knowledge network, have become critical tools for knowledge discovery in computable and explainable knowledge systems. Due to the semantic and structural complexities of biomedical data, these knowledge…