John Paul C. Vergara

Sorting by Short Swaps

A short swap is an operation on a permutation that switches two elements that have at most one element between them. This paper investigates the problem of finding a minimum-length sorting sequence of short swaps for a given permutation. A polynomial-time 2-approximation algorithm for this problem is presented, and bounds for the short-swap diameter (the length of the longest minimum sorting sequence among all permutations of a given length) are also obtained.

Sorting by bounded block-moves

Given a permutation π, a block-move is an operation that switches two adjacent blocks of elements in π. The problem of finding the minimum number of block-moves required to sort π has applications in computational biology, particularly in the study of genome rearrangements. This paper investigates variants of the problem where bounds are imposed on the lengths of the blocks moved. Algorithms and reduction results are presented for these variants.

Edge-Packing in Planar Graphs

Abstract. Maximum G Edge-Packing (EPackG ) is the problem of finding the maximum number of edge-disjoint isomorphic copies of a fixed guest graph G in a host graph H . This paper investigates the computational complexity of edge-packing for planar guests and planar hosts. Edge-packing is solvable in polynomial time when both G and H are trees. Edge-packing is solvable in linear time when H is outerplanar and G is either a 3-cycle or a k -star (a graph isomorphic to K1,k ). Edge-packing is NP-complete when H is planar and G is either a cycle or a tree with

Edge-packing planar graphs by cyclic graphs

\geq 3

eHealth TABLET: A Developing Country Perspective in Managing the Development and Deployment of a Mobile - Cloud Electronic Medical Record for Local Government Units

edges. A strategy for developing polynomial-time approximation algorithms for planar hosts is exemplified by a linear-time approximation algorithm that finds a k -star edge-packing of size at least half the optimal.

MINING POSETS FROM LINEAR ORDERS

Maximum G Edge-Packing is the problem of finding the maximum number of edge-disjoint isomorphic copies of a fixed guest graph G in a host graph H. This paper considers the cases where G and H are planar and G is cyclic. Recent work on the general problem is surveyed, inadequacies and limitations in these results are identified, and NP-completeness proofs for key cases are presented.

Extracting temporal signatures for comprehending systems biology models

In January 2013, the eHealth TABLET (Technology Assisted Boards for Local government unit Efficiency and Transparency) project began with a two-fold objective of: 1) creating a tablet based system that will integrate existing health information systems to address the national objective of a unified health information management system by 2015 and 2) to create a transparency layer at the local government units such that communication lines between municipal health officers and the mayor are monitored. Bottom up approach was used to ensure that all features requested by multi-stakeholders are included in the design of the system. The end product was a mobile - web based system with the mobile application having three main components: the electronic medical record (EMR) application which comprises of the patient record and diagnosis module, the requests/approval application, and the dashboard application for data visualization. Responding to the needs of intended users, the web based application provides the following features: web auxiallry entry, aggregated disease report application and usage monitoring. Regular usage monitoring increased usage over time. For ICT development projects in public health, iteratve involvement of multi-stakeholders is necessary to ensure higher acceptance and adoption. From a design perspective, technologies should be designed to be interoperable such that interfacing with existing systems will be seamless.

Algorithms for Feature Selection in Rank-Order Spaces

There has been much research on the combinatorial problem of generating the linear extensions of a given poset. This paper focuses on the reverse of that problem, where the input is a set of linear orders, and the goal is to construct a poset or set of posets that generates the input. Such a problem finds applications in computational neuroscience, systems biology, paleontology, and physical plant engineering. In this paper, two algorithms are presented for efficiently finding a single poset, if, such a poset exists whose linear extensions are exactly the same as the input set of linear orders. The variation of the problem where a minimum set of posets that cover the input is also explored. This variation is shown to be polynomially solvable for one class of simple posets (kite(2) posets) but NP-complete for a related class (hammock(2,2,2) posets).

Some experiments on the sorting by reversals problem

Systems biology has made massive strides in recent years, with capabilities to model complex systems including cell division, stress response, energy metabolism, and signaling pathways. Concomitant with their improved modeling capabilities, however, such biochemical network models have also become notoriously complex for humans to comprehend. We propose network comprehension as a key problem for the KDD community, where the goal is to create explainable representations of complex biological networks. We formulate this problem as one of extracting temporal signatures from multi-variate time series data, where the signatures are composed of ordinal comparisons between time series components. We show how such signatures can be inferred by formulating the data mining problem as one of feature selection in rank-order space. We propose five new feature selection strategies for rank-order space and assess their selective superiorities. Experimental results on budding yeast cell cycle models demonstrate compelling results comparable to human interpretations of the cell cycle.