Biomedical subjects

Jerry Sun

Publications and source records attributed to Jerry Sun.

4 recordsLinked to original sources

PubMed2005

Ontology-based structured cosine similarity in document summarization: with applications to mobile audio-based knowledge management.

Development of algorithms for automated text categorization in massive text document sets is an important research area of data mining and knowledge discovery. Most of the text-clustering methods were grounded in the term-based measurement of distance or similarity, ignoring the structure of the documents. In this paper, we present a novel method named structured cosine similarity (SCS) that furnishes document clustering with a new way of modeling on document summarization, considering the structure of the documents so as to improve the performance of document clustering in terms of quality, stability, and efficiency. This study was motivated by the problem of clustering speech documents (of no rich document features) attained from the wireless experience oral sharing conducted by mobile workforce of enterprises, fulfilling audio-based knowledge management. In other words, this problem aims to facilitate knowledge acquisition and sharing by speech. The evaluations also show fairly promising results on our method of structured cosine similarity.

Algorithms↗

PubMed2003

Towards the development of computational tools for evaluating phylogenetic network reconstruction methods.

We report on a suite of algorithms and techniques that together provide a simulation flow for studying the topological accuracy of methods for reconstructing phylogenetic networks. We implemented those algorithms and techniques and used three phylogenetic reconstruction methods for a case study of our tools. We present the results of our experimental studies in analyzing the relative performance of these methods. Our results indicate that our simulator and our proposed measure of accuracy, the latter an extension of the widely used Robinson-Foulds measure, offer a robust platform for the evaluation of network reconstruction algorithms.

Algorithms↗

PubMed2002

The accuracy of fast phylogenetic methods for large datasets.

Whole-genome phylogenetic studies require various sources of phylogenetic signals to produce an accurate picture of the evolutionary history of a group of genomes. In particular, sequence-based reconstruction will play an important role, especially in resolving more recent events. But using sequences at the level of whole genomes means working with very large amounts of data--large numbers of sequences--as well as large phylogenetic distances, so that reconstruction methods must be both fast and robust as well as accurate. We study the accuracy, convergence rate, and speed of several fast reconstruction methods: neighbor-joining, Weighbor (a weighted version of neighbor-joining), greedy parsimony, and a new phylogenetic reconstruction method based on disk-covering and parsimony search (DCM-NJ + MP). Our study uses extensive simulations based on random birth-death trees, with controlled deviations from ultrametricity. We find that Weighbor, thanks to its sophisticated handling of probabilities, outperforms other methods for short sequences, while our new method is the best choice for sequence lengths above 100. For very large sequence lengths, all four methods have similar accuracy, so that the speed of neighbor-joining and greedy parsimony makes them the two methods of choice.

Amino Acid Sequence↗

PubMedDate not supplied

Phylogenetic networks: modeling, reconstructibility, and accuracy.

Phylogenetic networks model the evolutionary history of sets of organisms when events such as hybrid speciation and horizontal gene transfer occur. In spite of their widely acknowledged importance in evolutionary biology, phylogenetic networks have so far been studied mostly for specific data sets. We present a general definition of phylogenetic networks in terms of directed acyclic graphs (DAGs) and a set of conditions. Further, we distinguish between model networks and reconstructible ones and characterize the effect of extinction and taxon sampling on the reconstructibility of the network. Simulation studies are a standard technique for assessing the performance of phylogenetic methods. A main step in such studies entails quantifying the topological error between the model and inferred phylogenies. While many measures of tree topological accuracy have been proposed, none exist for phylogenetic networks. Previously, we proposed the first such measure, which applied only to a restricted class of networks. In this paper, we extend that measure to apply to all networks, and prove that it is a metric on the space of phylogenetic networks. Our results allow for the systematic study of existing network methods, and for the design of new accurate ones.

Algorithms↗