Search PubMed⌕ Search

Biomedical subjects

F Ercal

Publications and source records attributed to F Ercal.

2 recordsLinked to original sources
PubMed2004

Parallel hash-based EST clustering algorithm for gene sequencing.

EST clustering is a simple, yet effective method to discover all the genes present in a variety of species. Although using ESTs is a cost-effective approach in gene discovery, the amount of data, and hence the computational resources required, make it a very challenging problem. Time and storage requirements for EST clustering problems are prohibitively expensive. Existing tools have quadratic time complexity resulting from all against all sequence comparisons. With the rapid growth of EST data we need better and faster clustering tools. In this paper, we present HECT (Hash based EST Clustering Tool), a novel time- and memory-efficient algorithm for EST clustering. We report that HECT can cluster a 10,000 Human EST dataset (which is also used in benchmarking d2_cluster), in 207 minutes on a 1 GHz Pentium III processor which is 36 times faster than the original d2_cluster algorithm. A parallel version of HECT (PECT) is also developed and used to cluster 269,035 soybean EST sequences on IA-32 Linux cluster at National Center for Supercomputing Applications at UIUC. The parallel algorithm exhibited excellent speedup over its sequential counterpart and its memory requirements are almost negligible making it suitable to run virtually on any data size. The performance of the proposed clustering algorithms is compared against other known clustering techniques and results are reported in the paper.

Algorithms↗
PubMed1994

Neural network diagnosis of malignant melanoma from color images.

Malignant melanoma is the deadliest form of all skin cancers. Approximately 32,000 new cases of malignant melanoma were diagnosed in 1991 in the United States, with approximately 80% of patients expected to survive five years [1]. Fortunately, if detected early, even malignant melanoma may be treated successfully. Thus, in recent years, there has been rising interest in the automated detection and diagnosis of skin cancer, particularly malignant melanoma [2]. In this paper, we present a novel neural network approach for the automated separation of melanoma from three benign categories of tumors which exhibit melanoma-like characteristics. Our approach uses discriminant features, based on tumor shape and relative tumor color, that are supplied to an artificial neural network for classification of tumor images as malignant or benign. With this approach, for reasonably balanced training/testing sets, we are able to obtain above 80% correct classification of the malignant and benign tumors on real skin tumor images.

Adolescent↗