Gilchan Park
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View article: Pathway-based analyses of gene expression profiles at low doses of ionizing radiation
Pathway-based analyses of gene expression profiles at low doses of ionizing radiation Open
Radiation exposure poses a significant threat to human health. Emerging research indicates that even low-dose radiation once believed to be safe, may have harmful effects. This perception has spurred a growing interest in investigating the…
View article: Density estimation via measure transport: Outlook for applications in the biological sciences
Density estimation via measure transport: Outlook for applications in the biological sciences Open
One among several advantages of measure transport methods is that they allow or a unified framework for processing and analysis of data distributed according to a wide class of probability measures. Within this context, we present results …
View article: Density Estimation via Measure Transport: Outlook for Applications in the Biological Sciences
Density Estimation via Measure Transport: Outlook for Applications in the Biological Sciences Open
One among several advantages of measure transport methods is that they allow for a unified framework for processing and analysis of data distributed according to a wide class of probability measures. Within this context, we present results…
View article: Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge
Comparative Performance Evaluation of Large Language Models for Extracting Molecular Interactions and Pathway Knowledge Open
Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…
View article: Data and code example for the article: "Massively parallel hybrid quantum-classical machine learning for kernelized time-series classification"
Data and code example for the article: "Massively parallel hybrid quantum-classical machine learning for kernelized time-series classification" Open
Data needed to reproduce the figures of https://arxiv.org/abs/2305.05881 and a simple code example of a quantum-convex-classical neural network used to train a sine versus cosine classification problem.
View article: Data and code example for the article: "Massively parallel hybrid quantum-classical machine learning for kernelized time-series classification"
Data and code example for the article: "Massively parallel hybrid quantum-classical machine learning for kernelized time-series classification" Open
Data needed to reproduce the figures of https://arxiv.org/abs/2305.05881 and a simple code example of a quantum-convex-classical neural network used to train a sine versus cosine classification problem.
View article: Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response
Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response Open
There are various sources of ionizing radiation exposure, where medical exposure for radiation therapy or diagnosis is the most common human-made source. Understanding how gene expression is modulated after ionizing radiation exposure and …
View article: Automated Extraction of Molecular Interactions and Pathway Knowledge using Large Language Model, Galactica: Opportunities and Challenges
Automated Extraction of Molecular Interactions and Pathway Knowledge using Large Language Model, Galactica: Opportunities and Challenges Open
Gilchan Park, Byung-Jun Yoon, Xihaier Luo, Vanessa Lpez-Marrero, Patrick Johnstone, Shinjae Yoo, Francis Alexander. The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks. 2023.
View article: Extracting Protein-Protein Interactions (PPIs) from Biomedical Literature using Attention-based Relational Context Information
Extracting Protein-Protein Interactions (PPIs) from Biomedical Literature using Attention-based Relational Context Information Open
Because protein-protein interactions (PPIs) are crucial to understand living\nsystems, harvesting these data is essential to probe disease development and\ndiscern gene/protein functions and biological processes. Some curated datasets\ncon…
View article: Figure Descriptive Text Extraction using Ontological Representation
Figure Descriptive Text Extraction using Ontological Representation Open
Experimental research publications provide figure form resources including graphs, charts, and any type of images to effectively support and convey methods and results. To describe figures, authors add captions, which are often incomplete,…
View article: Quantum multi-programming for Grover's search
Quantum multi-programming for Grover's search Open
Quantum multi-programming is a method utilizing contemporary noisy intermediate-scale quantum computers by executing multiple quantum circuits concurrently. Despite early research on it, the research remains on quantum gates or small-size …
View article: Towards Text-based Phishing Detection
Towards Text-based Phishing Detection Open
This paper reports on an experiment into text-based phishing detection using readily available resources and without the use of semantics. The developed algorithm is a modified version of previously published work that works with the same …
View article: Advances in scientific literature mining for interpreting materials characterization
Advances in scientific literature mining for interpreting materials characterization Open
Using synchrotron light sources, such as the National Synchrotron Light Source II at Brookhaven National Laboratory, scientists in fields as diverse as physics, biology, and materials science, identify the atomic structure, chemical compos…
View article: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 Open
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of t…
View article: Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 Open
We present a supercomputer-driven pipeline for in-silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. We also describe preliminary results obtained for 23 systems involving eight protein targets of t…
View article: Figure Descriptive Text Extraction Using Ontological Representation
Figure Descriptive Text Extraction Using Ontological Representation Open
Experimental research publications provide figure form re-sources including graphs, charts, and any type of images to effectively support and convey methods and results. To de-scribe figures, authors add captions, which are often incomplet…
View article: Figure Descriptive Text Extraction Using Ontological Representation
Figure Descriptive Text Extraction Using Ontological Representation Open
Experimental research publications provide figure form re-sources including graphs, charts, and any type of images to effectively support and convey methods and results. To de-scribe figures, authors add captions, which are often incomplet…
View article: Scientific Literature Mining for Experiment Information in Materials Design
Scientific Literature Mining for Experiment Information in Materials Design Open
Scientific literature is a plethora of documents written in natural language, where the agglomeration of well-cogitated knowledge is inextricably intertwined. The large-scale knowledge source might have the great potential to derive valuab…
View article: Using Syntactic Features for Phishing Detection
Using Syntactic Features for Phishing Detection Open
This paper reports on the comparison of the subject and object of verbs in their usage between phishing emails and legitimate emails. The purpose of this research is to explore whether the syntactic structures and subjects and objects of v…