Top-K Query Processing in Edge-Labeled Graph Data

Edge-labeled graphs have proliferated rapidly over the last decade due to the increased popularity of social networks and the Semantic Web. In social networks, relationships between people are represented by edges and each edge is labeled with a semantic annotation. Hence, a huge single graph can express many different relationships between entities. The Semantic Web represents each single fragment of knowledge as a triple (subject, predicate, object), which is conceptually identical to an edge from subject to object labeled with predicates. A set of triples constitutes an edge-labeled graph on which knowledge inference is performed. Subgraph matching has been extensively used as a query language for patterns in the context of edge-labeled graphs. For example, in social networks, users can specify a subgraph matching query to find all people that have certain neighborhood relationships. Heavily used fragments of the SPARQL query language for the Semantic Web and graph queries of other graph DBMS can also be viewed as subgraph matching over large graphs. Though subgraph matching has been extensively studied as a query paradigm in the Semantic Web and in social networks, a user can get a large number of answers in response to a query. These answers can be shown to the user in accordance with an importance ranking. In this thesis proposal, we present four different scoring models along with scalable algorithms to find the top-k answers via a suite of intelligent pruning techniques. The suggested models consist of a practically important subset of the SPARQL query language augmented with some additional useful features. The first model called Substitution Importance Query (SIQ) identifies the top-k answers whose scores are calculated from matched vertices' properties in each answer in accordance with a user-specified notion of importance. The second model called Vertex Importance Query (VIQ) identifies important vertices in accordance with a user-defined scoring method that builds on top of various subgraphs articulated by the user. Approximate Importance Query (AIQ), our third model, allows partial and inexact matchings and returns top-k of them with a user-specified approximation terms and scoring functions. In the fourth model called Probabilistic Importance Query (PIQ), a query consists of several sub-blocks: one mandatory block that must be mapped and other blocks that can be opportunistically mapped. The probability is calculated from various aspects of answers such as the number of mapped blocks, vertices' properties in each block and so on and the most top-k probable answers are returned. An important distinguishing feature of our work is that we allow the user a huge amount of freedom in specifying: (i) what pattern and approximation he considers important, (ii) how to score answers - irrespective of whether they are vertices or substitution, and (iii) how to combine and aggregate scores generated by multiple patterns and/or multiple substitutions. Because so much power is given to the user, indexing is more challenging than in situations where additional restrictions are imposed on the queries the user can ask. The proposed algorithms for the first model can also be used for answering SPARQL queries with ORDER BY and LIMIT, and the method for the second model also works for SPARQL queries with GROUP BY, ORDER BY and LIMIT. We test our algorithms on multiple real-world graph databases, showing that our algorithms are far more efficient than popular triple stores.

STRUCTURE AND FUNCTION OF THE GROUP III CHAPERONINS, A UNIQUE CLADE OF PROTEIN FOLDING NANOMACHINES

The survival and descent of cells is universally dependent on maintaining their proteins in a properly folded condition. It is widely accepted that the information for the folding of the nascent polypeptide chain into a native protein is encrypted in the amino acid sequence, and the Nobel Laureate Christian Anfinsen was the first to demonstrate that a protein could spontaneously refold after complete unfolding. However, it became clear that the observed folding rates for many proteins were much slower than rates estimated in vivo. This led to the recognition of required protein-protein interactions that promote proper folding. A unique group of proteins, the molecular chaperones, are responsible for maintaining protein homeostasis during normal growth as well as stress conditions. Chaperonins (CPNs) are ubiquitous and essential chaperones. They form ATP-dependent, hollow complexes that encapsulate polypeptides in two back-to-back stacked multisubunit rings, facilitating protein folding through highly cooperative allosteric articulation. CPNs are usually classified into Group I and Group II. Here, I report the characterization of a novel CPN belonging to a third Group, recently discovered in bacteria. Group III CPNs have close phylogenetic association to the Group II CPNs found in Archaea and Eukarya, and may be a relic of the Last Common Ancestor of the CPN family. The gene encoding the Group III CPN from Carboxydothermus hydrogenoformans and Candidatus Desulforudis audaxviator was cloned in E. coli and overexpressed in order to both characterize the protein and to demonstrate its ability to function as an ATPase chaperone. The opening and closing cycle of the Chy chaperonin was examined via site-directed mutations affecting the ATP binding site at R155. To relate the mutational analysis to the structure of the CPN, the crystal structure of both the AMP-PNP (an ATP analogue) and ADP bound forms were obtained in collaboration with Sun-Shin Cha in Seoul, South Korea. The ADP and ATP binding site substitutions resulted in frozen forms of the structures in open and closed conformations. From this, mutants were designed to validate hypotheses regarding key ATP interacting sites as well as important stabilizing interactions, and to observe the physical properties of the resulting complexes by calorimetry.

JOINT ENERGY BEAMFORMING AND TIME ASSIGNMENT FOR COOPERATIVE WIRELESS POWERED NETWORKS

Wireless power transfer (WPT) and radio frequency (RF)-based energy har- vesting arouses a new wireless network paradigm termed as wireless powered com- munication network (WPCN), where some energy-constrained nodes are enabled to harvest energy from the RF signals transferred by other energy-sufficient nodes to support the communication operations in the network, which brings a promising approach for future energy-constrained wireless network design. In this paper, we focus on the optimal WPCN design. We consider a net- work composed of two communication groups, where the first group has sufficient power supply but no available bandwidth, and the second group has licensed band- width but very limited power to perform required information transmission. For such a system, we introduce the power and bandwidth cooperation between the two groups so that both group can accomplish their expected information delivering tasks. Multiple antennas are employed at the hybrid access point (H-AP) to en- hance both energy and information transfer efficiency and the cooperative relaying is employed to help the power-limited group to enhance its information transmission throughput. Compared with existing works, cooperative relaying, time assignment, power allocation, and energy beamforming are jointly designed in a single system. Firstly, we propose a cooperative transmission protocol for the considered system, where group 1 transmits some power to group 2 to help group 2 with information transmission and then group 2 gives some bandwidth to group 1 in return. Sec- ondly, to explore the information transmission performance limit of the system, we formulate two optimization problems to maximize the system weighted sum rate by jointly optimizing the time assignment, power allocation, and energy beamforming under two different power constraints, i.e., the fixed power constraint and the aver- age power constraint, respectively. In order to make the cooperation between the two groups meaningful and guarantee the quality of service (QoS) requirements of both groups, the minimal required data rates of the two groups are considered as constraints for the optimal system design. As both problems are non-convex and have no known solutions, we solve it by using proper variable substitutions and the semi-definite relaxation (SDR). We theoretically prove that our proposed solution method can guarantee to find the global optimal solution. Thirdly, consider that the WPCN has promising application potentials in future energy-constrained net- works, e.g., wireless sensor network (WSN), wireless body area network (WBAN) and Internet of Things (IoT), where the power consumption is very critical. We investigate the minimal power consumption optimal design for the considered co- operation WPCN. For this, we formulate an optimization problem to minimize the total consumed power by jointly optimizing the time assignment, power allocation, and energy beamforming under required data rate constraints. As the problem is also non-convex and has no known solutions, we solve it by using some variable substitutions and the SDR method. We also theoretically prove that our proposed solution method for the minimal power consumption design guarantees the global optimal solution. Extensive experimental results are provided to discuss the system performance behaviors, which provide some useful insights for future WPCN design. It shows that the average power constrained system achieves higher weighted sum rate than the fixed power constrained system. Besides, it also shows that in such a WPCN, relay should be placed closer to the multi-antenna H-AP to achieve higher weighted sum rate and consume lower total power.