Legand L. Burge

Performance Analysis of Homing Pigeon based Delay Tolerant Networks

This paper presents and analyzes a new type of delay tolerant network where each node owns a dedicated messenger (called a pigeon). The only form of inter-node communication is for a pigeon to periodically carry a batch of messages originated at the home node, deliver them to the corresponding destination nodes and return home. Clearly, given message expiration times, some messages may not reach their destinations by the deadline. Through theoretical analysis and simulations, we study the relationship between the arrival rate (at the home node), batch size, expiration time and delivery ratio (the percentage of messages reaching destinations before they expire) of messages. The simplistic assumptions we make render the problem tractable, and help us gather experience in this topic.

A ubiquitous stable storage for mobile computing devices

Mobile computing devices have become increasingly prevalent as professionals discover the benefits of having their electronic work/data available at all times. Although mobile computing offers these benefits, there are still risks in terms of data reliability and dependability in the event of a device related failure. Often, failure of mobile computing devices occurs before backup and synchronization of mobile data. In this research, we propose an infrastructure of ubiquitous stable storage for mobile computing devices. Our framework is based on wireless Jini technology.

An advanced assessment tool and process

In this paper we describe a tool developed as part of the assessment process used at our university. The tool allows the automatic determination of the degree to which individual students meet the learning objectives that indicate how well students meet both course objectives and program directives. We also describe a portion of our assessment process that helps us perform the difficult step of closing the loop to make sure that the results of our data analysis are used to insure continuous program improvement.

PROTEIN FOLD CLASSIFICATION WITH GENETIC ALGORITHMS AND FEATURE SELECTION

Protein fold classification is a key step to predicting protein tertiary structures. This paper proposes a novel approach based on genetic algorithms and feature selection to classifying protein folds. Our dataset is divided into a training dataset and a test dataset. Each individual for the genetic algorithms represents a selection function of the feature vectors of the training dataset. A support vector machine is applied to each individual to evaluate the fitness value (fold classification rate) of each individual. The aim of the genetic algorithms is to search for the best individual that produces the highest fold classification rate. The best individual is then applied to the feature vectors of the test dataset and a support vector machine is built to classify protein folds based on selected features. Our experimental results on Ding and Dubchaks benchmark dataset of 27-class folds show that our approach achieves an accuracy of 71.28%, which outperforms current state-of-the-art protein fold predictors.

Can students reengineer

A recent paper by David Lechner stated that for many long-lived systems, it is more efficient to reengineer portions of systems than to continually repair them. That paper made an implicit assumption about the ability of software engineers to determine precisely which software should be reengineered. We report the results of a study that addresses the readiness of graduates, who will soon be beginning software engineers, to make such an assessment, based on comprehension of reusable vs. reengineered software. We address this comprehension in the context of software engineering education.

Rapid and accurate generation of peptide sequence tags with a graph search approach

Protein peptide identification from a tandem mass spectrum (MS/MS) is a challenging task. Previous approaches for peptide identification with database search are time consuming due to huge search space. De novo sequencing approaches which derive a peptide sequence directly from a MS/MS spectrum usually are of high complexities and the accuracies of the approaches highly depend on the quality of the spectra. In this paper, we developed an accurate and efficient algorithm for peptide identification. Our work consisted of the following steps. Firstly, we found a pair of complementary mass peaks that are b-ion and y-ion, respectively. We then used the two mass peaks as two tree nodes and extend the trees such that in the end the nodes of the trees are elements of a b-ion set and a yion set, respectively. Secondly, we applied breadth first search to the trees to generate peptide sequence tags. Finally, we designed a weight function to evaluate the reliabilities of the tags and rank the tags. Our experiment on 2620 experimental MS/MS spectra with one PTM showed that our algorithm achieved better accuracy than other approaches with higher efficiency.

Peptide Sequence Tag-Based Blind Identification-based SVM Model

Identifying the ion types for a mass spectrum is essential for interpreting the spectrum and deriving its peptide sequence. In this paper, we proposed a novel method for identifying ion types and deriving matched peptide sequences for tandem mass spectra. We first divided our dataset into a training set and a testing set and then preprocessed the data using a Support Vector Machine and a 5-fold cross validation based dual denoting model. Then we constructed a syntax tree and generated a rule set to match the mass values from experimental mass spectra with the mass spectral values from corresponding theoretical mass spectra. Finally we applied the proposed algorithm to a tandem mass spectral dataset consisting of 2656 spectra from yeast. Compared with other methods, the experimental results showed that the proposed method can effectively filter noise and successfully derive peptide sequences.

A Heuristic Algorithm for Finding the Longest Pathways in a Biochemical Network

Finding the longest cycle is a novel concept in biochemical feedback loop analysis in systems biology. Biochemical networks are often represented as directed graphs in which vertices represent chemical compounds and edges represent chemical reactions between compounds. Therefore, a biochemical longest feedback loop can be formulated as the longest cycle in a directed graph. Because finding the longest cycle in a directed graph is NP-hard, in this paper, we proposed an intelligent heuristic algorithm to find the longest cycle in a directed graph. We tested the algorithm on both randomly generated complex networks and real biochemical networks extracted from the KEGG database. The results showed that our algorithm is able to find more than 70% of the real longest cycles in the 200 randomly generated complex networks and also can find the feedback loop in the longest pathway. Compared with the traditional breadth first search pathway finding algorithm, the search efficiency of the proposed algorithm has been improved dramatically. Among the feedbacks found from the KEGG database using the proposed algorithm, the longest feedback includes 8 compounds, 9 reactions, and 6 pathways across different modules.

Multicast Using Static Trees

IP multicast has been known to have deployment difficulties. Among many contributing factors, the model per se is probably one of the most critical. Overlay multicast does not solve all the problems either. We therefore proposed a new multicast architecture named MUST, inspired by previous efforts. In essence, the architecture uses an overlay network to interconnect statically configured IP multicast trees to create the data paths for improvised multicast groups. While being incrementally deployed, it can evolve towards higher efficiency. In this paper, we described the model in detail, theoretically estimated its cost, and compared the cost with that of overlay multicast.

Comparative Analysis of Email Filtering Technologies

Different filtering technologies are currently in use with varying results. This paper reviews and compares a number of them by focusing on the expectation of their users and their actual capabilities