Atalay Mert İleri

Aryan Singh Dalal, Yinglun Zhang, Duru Doğan et al.

The focus on "food as medicine" is gaining traction in the field of health and several studies conducted in the past few years discussed this aspect of food in the literature. However, very little research has been done on representing the relationship between food and health in a standardized, machine-readable format using a semantic web that can help us leverage this knowledge effectively. To address this gap, this study aims to create a knowledge graph to link food and health through the knowledge graph's ability to combine information from various platforms focusing on flavonoid contents of food found in the USDA databases and cancer connections found in the literature. We looked closely at these relationships using KNARM methodology and represented them in machine-operable format. The proposed knowledge graph serves as an example for researchers, enabling them to explore the complex interplay between dietary choices and disease management. Future work for this study involves expanding the scope of the knowledge graph by capturing nuances, adding more related data, and performing inferences on the acquired knowledge to uncover hidden relationships.

Atalay Mert Ileri, Nalen Rangarajan, Jack Cannell et al.

Over the past two decades, the Web Ontology Language (OWL) has been instrumental in advancing the development of ontologies and knowledge graphs, providing a structured framework that enhances the semantic integration of data. However, the reliability of deductive reasoning within these systems remains challenging, as evidenced by inconsistencies among popular reasoners in recent competitions. This evidence underscores the limitations of current testing-based methodologies, particularly in high-stakes domains such as healthcare. To mitigate these issues, in this paper, we have developed VEL, a formally verified EL++ reasoner equipped with machine-checkable correctness proofs that ensure the validity of outputs across all possible inputs. This formalization, based on the algorithm of Baader et al., has been transformed into executable OCaml code using the Coq proof assistant's extraction capabilities. Our formalization revealed several errors in the original completeness proofs, which led to changes to the algorithm to ensure its completeness. Our work demonstrates the necessity of mechanization of reasoning algorithms to ensure their correctness at theoretical and implementation levels.

Atalay M. Ileri, Halil I. Ozercan, Alper Gundogdu et al.

Rate of growth of the amount of data generated using the high throughput sequencing (HTS) platforms now exceeds the growth stipulated by Moore's Law. The HTS data is expected to surpass those of other "big data" domains such as astronomy, before the year 2025. In addition to sequencing genomes for research purposes, genome and exome sequencing in clinical settings will be a routine part of health care. The analysis of such large amounts of data, however, is not without computational challenges. This burden is even more increased due to the periodic updates to reference genomes, which typically require re-analysis of existing data. Here we propose Coin-Application Mediator Interface (Coinami) to distribute the workload for mapping reads to reference genomes using a volunteer grid computer approach similar to Berkeley Open Infrastructure for Network Computing (BOINC). However, since HTS read mapping requires substantial computational resources and fast analysis turnout is desired, Coinami uses the HTS read mapping as proof-of-work to generate valid blocks to main its own cryptocurrency system, which may help motivate volunteers to dedicate more resources. The Coinami protocol includes mechanisms to ensure that jobs performed by volunteers are correct, and provides genomic data privacy. The prototype implementation of Coinami is available at http://coinami.github.io/.