ConSole: using modularity of contact maps to locate solenoid domains in protein structures.

BackgroundPeriodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins.ResultsConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families.ConclusionsThe ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org

Matemaattisen morfologian käyttö geometrisessa musiikinhaussa

The usual task in music information retrieval (MIR) is to find occurrences of a monophonic query pattern within a music database, which can contain both monophonic and polyphonic content. The so-called query-by-humming systems are a famous instance of content-based MIR. In such a system, the user's hummed query is converted into symbolic form to perform search operations in a similarly encoded database. The symbolic representation (e.g., textual, MIDI or vector data) is typically a quantized and simplified version of the sampled audio data, yielding to faster search algorithms and space requirements that can be met in real-life situations. In this thesis, we investigate geometric approaches to MIR. We first study some musicological properties often needed in MIR algorithms, and then give a literature review on traditional (e.g., string-matching-based) MIR algorithms and novel techniques based on geometry. We also introduce some concepts from digital image processing, namely the mathematical morphology, which we will use to develop and implement four algorithms for geometric music retrieval. The symbolic representation in the case of our algorithms is a binary 2-D image. We use various morphological pre- and post-processing operations on the query and the database images to perform template matching / pattern recognition for the images. The algorithms are basically extensions to classic image correlation and hit-or-miss transformation techniques used widely in template matching applications. They aim to be a future extension to the retrieval engine of C-BRAHMS, which is a research project of the Department of Computer Science at University of Helsinki

Generic multimodal biometric fusion

Biometric systems utilize physiological or behavioral traits to automatically identify individuals. A unimodal biometric system utilizes only one source of biometric information and suffers from a variety of problems such as noisy data, intra-class variations, restricted degrees of freedom, non-universality, spoof attacks and unacceptable error rates. Multimodal biometrics refers to a system which utilizes multiple biometric information sources and can overcome some of the limitation of unimodal system. Biometric information can be combined at 4 different levels: (i) Raw data level; (ii) Feature level; (iii) Match-score level; and (iv) Decision level. Match score fusion and decision fusion have received significant attention due to convenient information representation and raw data fusion is extremely challenging due to large diversity of representation. Feature level fusion provides a good trade-off between fusion complexity and loss of information due to subsequent processing. This work presents generic feature information fusion techniques for fusion of most of the commonly used feature representation schemes. A novel concept of Local Distance Kernels is introduced to transform the available information into an arbitrary common distance space where they can be easily fused together. Also, a new dynamic learnable noise removal scheme based on thresholding is used to remove shot noise in the distance vectors. Finally we propose the use of AdaBoost and Support Vector Machines for learning the fusion rules to obtain highly reliable final matching scores from the transformed local distance vectors. The integration of the proposed methods leads to large performance improvement over match-score or decision level fusion

Pattern Recognition

A wealth of advanced pattern recognition algorithms are emerging from the interdiscipline between technologies of effective visual features and the human-brain cognition process. Effective visual features are made possible through the rapid developments in appropriate sensor equipments, novel filter designs, and viable information processing architectures. While the understanding of human-brain cognition process broadens the way in which the computer can perform pattern recognition tasks. The present book is intended to collect representative researches around the globe focusing on low-level vision, filter design, features and image descriptors, data mining and analysis, and biologically inspired algorithms. The 27 chapters coved in this book disclose recent advances and new ideas in promoting the techniques, technology and applications of pattern recognition