Scientific Computing Laboratory
Overview
The Scientific Computing Laboratory (SCL) is one of the eight research laboratories under the Department of Computer Science, University of the Philippines Diliman, which is founded in 2009, and interested in the construction of mathematical models and numerical techniques for optimization, configuration and design of complex systems to better understand scientific, social scientific and engineering problems.
Currently, it has five regular members, actively participating in five special interest groups on modeling various complex systems, such as biological, physical and social systems, among others. It is currently headed by Dr. Adrian Roy L. Valdez, PhD.
In response to the broad multidisciplinary nature of the problems that the laboratory is interested in, SCL is actively consulting and collaborating with local academic and governmental institutions, and partnering with foreign universities and research institutes to create a more comprehensive and sound solution to emerging problems.
Furthermore, another effort of the laboratory is to create an active community of practice in scientific computing, which stimulates the culture of research discourse inside and outside the university.
Research Interests
The faculty members of SCL have a strong focus on mathematical and computational modeling, with applications in systems biology, transportation engineering, finance and spatiotemporal ecological dynamics, among others.
They are actively participating in five special interest groups under SCL, namely:
● Computational Systems Biology and Bioinformatics Group: This is a special research interest group under SCL that aims to understand the properties and behavior of complex biological systems, in terms of its individual (molecular) components and how they interact at different levels of the organization. Specifically, we are interested in the study of efficient extraction, storage, analysis and integration of important biological information from these systems through utilization of different computational approaches, such as modeling, data mining, machine learning and visualization, to give meaningful insights from these biological data, and for us to provide answers to pressing problems in computational systems biology.
● Data Analytics Group: The group is interested in the development and application of novel computational techniques to simultaneously study the persistence of patterns over time and illuminate any unusual patterns. Specifically, the groups aim to study continuous and discrete changes of spatial and non-spatial properties of spatio-temporal objects and the influence of collocated neighboring spatio-temporal objects on one another.
● Intelligent Transportation Systems Group: This is one of the research interest groups in SCL which is working on different approaches and trends in transport and traffic research and technology, aiming to solve escalating problems of congestions, pollution, transport efficiency, safety and security of passengers and goods.
● Mathematical and Computational Finance Group: This is one of the research interest groups under SCL that focuses on the quantitative modeling of financial markets and mathematical tools and theories, such as probability, statistics, partial differential equations, optimization and simulation. By applying these methods to economics questions, the risks and opportunities presented by securities, companies, currencies or competition can be more easily assessed.
● Mathematical Informatics Group: This is a special research interest group under SCL that is concerned with mathematical models for life sciences, from cell biology and neuroscience to medical science and social interaction. Our interdisciplinary research covers computation (machine learning), science (mathematical biology) and engineering (signal processing).
Lab Members
Laboratory Head: Adrian Roy L. Valdez, Ph.D.
Regular Members:
Jaymar B. Soriano, D.Sc.
Ivan Carlo Balingit
Research and Development Projects
The laboratory is currently involved in the following research and development projects:
Cyber-Physical Transportation Systems (CPTS)
Project Leader: Dr. Adrian Roy L. Valdez, PhD
(in cooperation with Intelligent Transportation Systems Laboratory, UP National Center for Transportation Studies, and funded by DOST-Philippine Council for Industry, Energy and Emerging Technologies Research and Development)
This project tries to design an intelligent land vehicle control system with advanced computing and sensing capabilities to improve safety and throughput to meet increasing transportation demands. The SCL team is working under the Software Development and R&D components of the project, where they calibrate models of macroscopic traffic demand and traffic intersection optimization.
Maritime Transportation Information Systems (MARIS)
Project Leader: Dr. John Justine S. Villar, PhD
(in cooperation with Intelligent Transportation Systems Laboratory, UP National Center for Transportation Studies and Maritime Industry Authority (MARINA), and funded by DOST-Philippine Council for Industry, Energy and Emerging Technologies Research and Development)
This project addresses the areas of intelligent transport systems for maritime industry in the Philippines through the development and deployment of software and analysis tools needed for a prototype forecasting system. In particular, the project targets the operation of the software components by developing and designing modular offline mechanisms for an effective Route Capacity Measurement System.
Construction and Analysis of Potential Energy Hypersurfaces for Protein Structure Prediction through Quantum Chemical Calculations
John Justine Villar, PhD in collaboration with David Setiadi, PhD (University of Toronto, Canada), Anita Rágyanszki, PhD (University of York, Canada), Amador Muriel, Ph.D. (The City University of New York, USA) and Imre Csizmadia, PhD (University of Miskolc, Hungary)
This study aims to construct precise potential energy surfaces (PES) of different amino acids through ab initio calculations to provide insights on the potential energy hypersurface given an amino acid sequence. We intend to compare our findings to results from well-known force fields, among others. Furthermore, the relationship between polypeptide PES and amino acid PES are also explored.
Understanding seizure progression in epilepsy and the feasibility of thermal neuromodulation using computational brain models
Jaymar Soriano in collaboration with Mathematical Informatics Laboratory at Nara Institute of Science and Technology in Japan.
This study aims to construct precise potential energy surfaces (PES) of different amino acids through ab initio calculations to provide insight
Selected Publications
J. Soriano, T. Kubo, and K. Ikeda
Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference (Vol. 2020, pp. 2532-2535).
Welfare maximization under a three-choice minority game model for energy demand allocation
Catalina A. Montes, Adrian Roy L. Valdez.
International Journal of Smart Grid and Clean Energy 9(1), 2020. 212-217.
John Justine Villar, Patrick Vincent Lubenia, Eduardo Mendoza, Carlene P. C. Pilar-Arceo.
Philippine Journal of Science 148(3), 2019. 523-533.
Single Rail Train Dispatch Time Optimization Under Static Demand and Fixed Train Capacity
Virgilio Ma. Ramos, Jebus Edrei Taguiam, John Justine Villar and Adrian Roy Valdez
Proceedings of 13th International Conference of the Eastern Asia Society for Transportation Studies, Colombo, Sri Lanka, September 9-12, 2019
Sequential Intermediate Destination Approach to Route Choice Set Generation
Anjilo Carigma, Mel Francis Eden, John Justine Villar and Adrian Roy Valdez
Proceedings of 13th International Conference of the Eastern Asia Society for Transportation Studies, Colombo, Sri Lanka, September 9-12, 2019
Discrete Optimization for Path Generation Using Parallel Computing
Anjilo Carigma, Mel Francis Eden, John Justine Villar and Adrian Roy Valdez
Proceedings of 13th International Conference of the Eastern Asia Society for Transportation Studies, Colombo, Sri Lanka, September 9-12, 2019
A three-choice minority game model with homogeneous agent preferences for resource allocation
Catalina A. Montes, Adrian Roy L. Valdez.
Procedia Computer Science 140, 2018. 56-63.
Formation of Acetamide in Interstellar Medium
Lois Foo, Attila Surányi, Andrea Guljas, Milán Szőri, John Justine Villar, Béla Viskolcz, Imre G.Csizmadia, Anita Rágyanszki, Béla Fiser.
Molecular Astrophysics 13, 2018. 1-5.
John Justine Villar, Logine Negm, Anita Rágyanszki, David Setiadi, Adrian Roy Valdez, Béla Viskolcz and Imre G. Csizmadia.
Canadian Journal of Chemistry 96(10), 2018. 912-921.
Contact us
Location: Rm 315, UP Alumni Engineers Centennial Hall, Velasquez St., University of the Philippines,
Diliman, Quezon City 1101 Philippines
Website: scl.dcs.upd.edu.ph
Email: scl.upd*at*up.edu.ph