Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining

MHC (Major Histocompatibility Complex) is a key player in the immune response of an organism. It is important to be able to predict which antigenic peptides will bind to a specific MHC allele and which will not, creating possibilities for controlling immune response and for the applications of immunotherapy. However, a problem for MHC class I is the presence of bulges and loops in the peptides, changing the total length. Most machine learning methods in use today require the sequences to be of same length to successfully mine the binding motifs. We propose the use of time-based data mining methods in motif mining to be able to mine motifs position-independently. Also, the information for both binding and non-binding peptides is used on the contrary to the other methods which only rely on binding peptides. The prediction results are between 60-95% for the tested alleles

Prediction of peptides binding to MHC class I alleles by partial periodic pattern mining

MHC (Major Histocompatibility Complex) is a key player in the immune response of an organism. It is important to be able to predict which antigenic peptides will bind to a spe-cific MHC allele and which will not, creating possibilities for controlling immune response and for the applications of immunotherapy. However a problem encountered in the computational binding prediction methods for MHC class I is the presence of bulges and loops in the peptides, changing the total length. Most machine learning methods in use to-day require the sequences to be of same length to success-fully mine the binding motifs. We propose the use of time-based data mining methods in motif mining to be able to mine motifs position-independently. Also, the information for both binding and non-binding peptides are used on the contrary to the other methods which only rely on binding peptides. The prediction results are between 70-80% for the tested alleles

Near-optimal loop tiling by means of cache miss equations and genetic algorithms

The effectiveness of the memory hierarchy is critical for the performance of current processors. The performance of the memory hierarchy can be improved by means of program transformations such as loop tiling, which is a code transformation targeted to reduce capacity misses. This paper presents a novel systematic approach to perform near-optimal loop tiling based on an accurate data locality analysis (cache miss equations) and a powerful technique to search the solution space that is based on a genetic algorithm. The results show that this approach can remove practically all capacity misses for all considered benchmarks. The reduction of replacement misses results in a decrease of the miss ratio that can be as significant as a factor of 7 for the matrix multiply kernel.Peer ReviewedPostprint (published version

Periodic Pattern Mining a Algorithms and Applications

Owing to a large number of applications periodic pattern mining has been extensively studied for over a decade Periodic pattern is a pattern that repeats itself with a specific period in a give sequence Periodic patterns can be mined from datasets like biological sequences continuous and discrete time series data spatiotemporal data and social networks Periodic patterns are classified based on different criteria Periodic patterns are categorized as frequent periodic patterns and statistically significant patterns based on the frequency of occurrence Frequent periodic patterns are in turn classified as perfect and imperfect periodic patterns full and partial periodic patterns synchronous and asynchronous periodic patterns dense periodic patterns approximate periodic patterns This paper presents a survey of the state of art research on periodic pattern mining algorithms and their application areas A discussion of merits and demerits of these algorithms was given The paper also presents a brief overview of algorithms that can be applied for specific types of datasets like spatiotemporal data and social network

Cognitive networks: brains, internet, and civilizations

In this short essay, we discuss some basic features of cognitive activity at several different space-time scales: from neural networks in the brain to civilizations. One motivation for such comparative study is its heuristic value. Attempts to better understand the functioning of "wetware" involved in cognitive activities of central nervous system by comparing it with a computing device have a long tradition. We suggest that comparison with Internet might be more adequate. We briefly touch upon such subjects as encoding, compression, and Saussurean trichotomy langue/langage/parole in various environments.Comment: 16 page