Publications by authors named "Harun Pirim"

Article Synopsis
  • The study investigates how machine learning, particularly traditional methods and graph neural networks (GNNs), can be used to predict diseases by analyzing complex protein-protein interactions (PPIs).
  • PPIs are challenging to analyze due to their complexity and variability, making traditional computational methods less effective.
  • Machine learning and GNNs are shown to be more effective in detecting complex patterns and achieving better accuracy in predictions across networks of different sizes, with an emphasis on the importance of network features.
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Systems Thinking (ST) has become essential for practitioners and experts when dealing with turbulent and complex environments. Twitter medium harbors social capital including systems thinkers, however there are limited studies available in the extant literature that investigate how experts' systems thinking skills, if possible at all, can be revealed within Twitter analysis. This study aims to reveal systems thinking levels of experts from their Twitter accounts represented as a network.

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The increasing availability of high temporal resolution neuroimaging data has increased the efforts to understand the dynamics of neural functions. Until recently, there are few studies on generative models supporting classification and prediction of neural systems compared to the description of the architecture. However, the requirement of collapsing data spatially and temporally in the state-of-the art methods to analyze functional magnetic resonance imaging (fMRI), electroencephalogram (EEG) and magnetoencephalography (MEG) data cause loss of important information.

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Persistent homology, a topological data analysis (TDA) method, is applied to microarray data sets. Although there are a few papers referring to TDA methods in microarray analysis, the usage of persistent homology in the comparison of several weighted gene coexpression networks (WGCN) was not employed before to the very best of our knowledge. We calculate the persistent homology of weighted networks constructed from 38 Arabidopsis microarray data sets to test the relevance and the success of this approach in distinguishing the stress factors.

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To address important challenges in bioinformatics, high throughput data technologies are needed to interpret biological data efficiently and reliably. Clustering is widely used as a first step to interpreting high dimensional biological data, such as the gene expression data measured by microarrays. A good clustering algorithm should be efficient, reliable, and effective, as demonstrated by its capability of determining biologically relevant clusters.

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High throughput biological data need to be processed, analyzed, and interpreted to address problems in life sciences. Bioinformatics, computational biology, and systems biology deal with biological problems using computational methods. Clustering is one of the methods used to gain insight into biological processes, particularly at the genomics level.

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