Browsing by Author "Akkaya, Ali"

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A Computational Drug Repositioning Effort using Patients' Reviews Dataset
(Institute of Electrical and Electronics Engineers Inc., 2023) Akkaya, Ali; Bakal, Gokhan; 0000-0003-2897-3894; AGÜ, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü; Akkaya, Ali; Bakal, Gokhan
The drug discovery process is one of the core motivations in both medical and, specifically, pharmaceutical disciplines. Due to the nature of the process, it requires an excessive amount of time, clinical experiments, and budget to cover each discovery phase. In this sense, computational drug discovery efforts can shorten the discovery process by providing plausible candidates since many of the attempts fail for several reasons, such as a lack of participants, financial problems, or ineffective results. In this study, the goal is to identify plausible candidate drugs for diseases. To do that, we utilize a personal experience of drugs dataset generated by patients. Beyond the user-generated comments, the users also give a rate between 1 and 10. Since we want to ensure the dataset quality, we first performed sentiment analysis experiments to prove that the reviews/comments are consistent with the given rating score. Then, only the review pairs having an effectiveness rate of 6 or more are selected as pre-filtered drug-disease pairs. We also build a knowledge graph using treatment-related biomedical relations using predications from Semantic Medline Database to identify drug similarities utilizing the Simrank similarity algorithm. As a result, we reported a list of plausible drugs as repurposing/repositioning candidates for further experiments.
Understanding Communication via Diffusion: Simulation Design and Intricacies
(SPRINGER INTERNATIONAL PUBLISHING AGGEWERBESTRASSE 11, CHAM, CH-6330, SWITZERLAND, 2017) Acar, Bilal; Akkaya, Ali; Genc, Gaye; Yilmaz, H. Birkan; Kuran, M. Sukru; Tugcu, Tuna; AGÜ, Mühendislik Fakültesi, Elektrik - Elektronik Mühendisliği Bölümü; Yılmaz, Bülent
Understanding Communication via Diffusion (CvD) is key to molecular communications research since it dominates the movement at the nano-scale. The researcher needs to properly understand the random diffusion of the molecules for the analysis of a molecular communication system. This chapter aims explaining the dynamics of diffusion from a communication engineer's perspective as well as providing useful hints for an effective simulation design by discussing some key intricacies. The chapter starts with a brief survey of simulators for molecular communications, followed by the basics of the simulation of Brownian motion and CvD. Several intricacies are addressed to help the researcher in simulation design, such as the number of replications required in terms of movement and bit sequence. We utilize this information further by discussing the design of more complex CvD systems such as tunnel-based approach that utilizes destroyer molecules and distributed simulator design based on HLA. Introduction of more complex CvD systems provides significant improvements in data rate and communications in general, bridging the gap between human-scale and nano-scale systems and enabling nanonetworking as a viable technology.