Documents

This workflow is part of the EJP RD case study on CAKUT published here: Bayjanov, J.R., Doornbos, C., Ozisik, O. et al. Integrative analysis of multi-omics data reveals importance of collagen and the PI3K AKT signalling pathway in CAKUT. Sci Rep 14, 20731 (2024). https://doi.org/10.1038/s41598-024-71721-8

Beyond Topology: Deterministic and Order-Preserving Graph Visualization with the Keçeci Layout

Mehmet Keçeci1 1ORCID : https://orcid.org/0000-0001-9937-9839, İstanbul, Türkiye

Received: 03.07.2025

Özet/Abstract:

The visualization of scientific data is a fundamental step in uncovering hidden patterns and relationships within complex systems. While conventional force-directed graph layout algorithms (e.g., spring layout) are effective at displaying the general topology and clustering tendencies of ...

Hilbert spaces provide the fundamental mathematical framework for describing quantum mechanical systems. Their structure, characterized by an inner product and completeness, allows for the representation of quantum states as vectors and physical observables as self-adjoint operators. Key quantum phenomena such as superposition and entanglement find natural expression within this formalism. Superposition, where a quantum system can exist in multiple states simultaneously, is represented by linear ...

Protein domains can be viewed as building blocks, essential for understanding structure-function relationships in proteins. However, each domain database classifies protein domains using its own methodology. Thus, in many cases, boundaries between different domains or families differ from one domain database to the other, raising the question of domain definition and enumeration. The answer to this question cannot be found in a single database. Rather, expert integration and curation of various ...

This study extends the domain of Keçeci Numbers, a unique class of sequences generated by a distinctive algorithm, beyond standard number systems into advanced mathematical structures such as neutrosophic and hyperreal numbers. Keçeci Numbers are sequences produced via a recursive algorithm based on a starting value and an incremental scalar, governed by rules of divisibility and primality. The primary objective of this paper is to investigate the behaviour of this deterministic algorithm within ...

Bu çalışma, harmonik serilerin hesaplanmasında geleneksel saf Python tabanlı bir yaklaşım ile modern JAX kütüphanesine dayalı bir yaklaşımın performans, ölçeklenebilirlik ve verimlilik açısından karşılaştırılmasını sunmaktadır. Harmonik seri ve matematiksel analizde önemli bir yere sahip olan ıraksak bir seridir. Hesaplamalı matematikte bu tür serilerin etkin bir şekilde değerlendirilmesi, özellikle büyük veri ve yüksek hassasiyet gerektiren uygulamalarda kritik öneme sahiptir. Geleneksel saf ...

Keçeci Deterministic Zigzag Layout (Keçeci Zigzag Layout Algorithm, Keçeci Layout) is a deterministic node layout algorithm designed for graph visualization in Python. Its primary purpose is to position the nodes of a graph in a predefined, sequential, and repeatable manner. The algorithm processes nodes sequentially, placing them along a user-defined primary axis (e.g., top-down or left-to-right) while applying an offset on the secondary axis in a zigzag pattern. This zigzag pattern helps prevent ...