Entity linking is a process of connecting mentions of entities in a document to corresponding entries in a knowledge base. Traditional models for entity linking often require specific fine-tuning to work with knowledge bases other than those they were originally pretrained on, which limits their flexibility and scalability. Building on the concept of entity profile generation, we propose a novel approach that enables entity linking across various knowledge bases without the need for such fine-tuning. Our pipeline leverages a fine-tuned Large Language Model, a generic embedding model, and a vector store to achieve high precision on the TweekiGold and Reuters-128 datasets. Additionally, it demonstrates strong retrieval rates across the TweekiGold , Reuters-128 , and ISTEX-1000 Wikidata entity linking datasets. We also illustrate the applicability of our method to other knowledge bases, using the Agrovoc knowledge base as an example. This solution offers a more versatile and scalable approach to entity linking.

Graphlet Degree Distribution Agreement (GDDA) is a comparison metric created for graphlets. Unfortunately, it has been reported and confirmed that it has an issue with the stability of result values in low-density graphs. Recently, graphlets have been modified for comparison of Petri net-based models of biological systems. It is crucial to find out if those problems reaper in the case of the modified graphlets, establish a scale of the instability impact on the GDDA value, and find out if it is a common problem for models of biological systems represented by Petri nets. Our results confirmed that the GDDA metric when used for the new graphlets is also unstable for part of the searched density spectrum. Because of that, some biological networks represented by Petri nets are vulnerable to this problem. While instability occurs in the Petri net environment, its characteristics have changed. The scale of an instability impact on the GDDA value is around half of its original size. The localization of vulnerable density areas is different from that in the case of undirected Protein-Protein Interaction (PPI) models. In contrast to the latter, the existence of a high stability area for very sparse models has been observed.

MOTIVATION: The first and necessary step in systems approach to study biological phenomena is building a formal model. One of the possibilities is to construct a model based on Petri nets. They have an intuitive graphical representation on one hand, and on the other, can be analyzed using formal mathematical methods. Finding homologies or conserved processes playing important roles in various biological systems can be done by comparing models. The ones expressed as Petri nets are especially well-suited for such a comparison, but there is a lack of software tools for this task. RESULTS: To resolve this problem, a new analytical tool has been implemented in Holmes application and described in this article. It offers four different comparison methods, i.e. the ones based on t-invariants, decomposition, graphlets and branching vertices. AVAILABILITY AND IMPLEMENTATION: Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Essential hypertension is the world’s most prevalent cardiovascular disorder, however, its etiology remains poorly understood, making it difficult to study. The evidence suggests that inflammation can lead to the development of hypertension and that oxidative stress and endothelial dysfunction are involved in the inflammatory cascade. In this work, to investigate the influence of these factors on the essential hypertension development, a stochastic Petri net model has been built and then analyzed. To obtain appropriate initial marking and kinetic rate constants for the model, a simple heuristic has been developed. The application of this variant of Petri nets allowed for taking into account some important dependencies present in the modeled system what would be impossible in the case of qualitative models. This has enabled for an in-depth analysis of the studied phenomenon and a validation of biological conclusions previously obtained on the basis of a qualitative model.

SUMMARY: Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers a tool for such a task. Since the rapid development of computer science, a variety of tools for Petri nets emerged, offering various analytical algorithms. From this follows a problem of using different programs to analyse a single model. Many file formats and different representations of results make the analysis much harder. Especially for larger nets the ability to visualize the results in a proper form provides a huge help in the understanding of their significance. We present a new tool for Petri nets development and analysis called Holmes. Our program contains algorithms for model analysis based on different types of Petri nets, e.g. invariant generator, Maximum Common Transitions (MCT) sets and cluster modules, simulation algorithms or knockout analysis tools. A very important feature is the ability to visualize the results of almost all analytical modules. The integration of such modules into one graphical environment allows a researcher to fully devote his or her time to the model building and analysis. AVAILABILITY AND IMPLEMENTATION: Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html. CONTACT: [email protected].

Abstract Motivation: A new heuristic algorithm for solving DNA sequencing by hybridization problem with positive and negative errors. Results: A heuristic algorithm providing better solutions than algorithms known from the literature based on tabu search method. Contact: [email protected] * To whom correspondence should be addressed.

Abstract Motivation: A formulation of a new problem of the restriction map construction based on a simplified digestion experiment and a development of an algorithm for solving both ideal and noisy data cases of the introduced problem. Results: A simplified partial digest problem and a branch and cut algorithm for finding the solution of the problem. Contact: [email protected] * To whom correspondence should be addressed. † Fellowship holder of the Foundation for Polish Sciences.