De Novo Assembly of Nucleotide Sequences in a Compressed Feature Space

Sequencing technologies allow for an in-depth analysis of biological species but the size of the generated datasets introduce a number of analytical challenges. Recently, we demonstrated the application of numerical sequence representations and data transformations for the alignment of short reads to a reference genome. Here, we expand out approach for de novo assembly of short reads. Our results demonstrate that highly compressed data can encapsulate the signal suffi- ciently to accurately assemble reads to big contigs or complete genomes

Content-Based Video Retrieval in Historical Collections of the German Broadcasting Archive

The German Broadcasting Archive (DRA) maintains the cultural heritage of radio and television broadcasts of the former German Democratic Republic (GDR). The uniqueness and importance of the video material stimulates a large scientific interest in the video content. In this paper, we present an automatic video analysis and retrieval system for searching in historical collections of GDR television recordings. It consists of video analysis algorithms for shot boundary detection, concept classification, person recognition, text recognition and similarity search. The performance of the system is evaluated from a technical and an archival perspective on 2,500 hours of GDR television recordings.Comment: TPDL 2016, Hannover, Germany. Final version is available at Springer via DO

K-nearest Neighbor Search by Random Projection Forests

K-nearest neighbor (kNN) search has wide applications in many areas, including data mining, machine learning, statistics and many applied domains. Inspired by the success of ensemble methods and the flexibility of tree-based methodology, we propose random projection forests (rpForests), for kNN search. rpForests finds kNNs by aggregating results from an ensemble of random projection trees with each constructed recursively through a series of carefully chosen random projections. rpForests achieves a remarkable accuracy in terms of fast decay in the missing rate of kNNs and that of discrepancy in the kNN distances. rpForests has a very low computational complexity. The ensemble nature of rpForests makes it easily run in parallel on multicore or clustered computers; the running time is expected to be nearly inversely proportional to the number of cores or machines. We give theoretical insights by showing the exponential decay of the probability that neighboring points would be separated by ensemble random projection trees when the ensemble size increases. Our theory can be used to refine the choice of random projections in the growth of trees, and experiments show that the effect is remarkable.Comment: 15 pages, 4 figures, 2018 IEEE Big Data Conferenc

An unbalanced approach to metric space searching

Proximity queries (the searching problem generalized beyond exact match) is mostly modeled as metric space. A metric space consists of a collection of objects and a distance function defined among them. The goal is to preprocess the data set (a slow procedure) to quickly answer proximity queries. This problem have received a lot of attention recently, specially in the pattern recognition community. The Excluded Middle Vantage Point Forest (VP–forest) is a data structure designed to search in high dimensional vector spaces. A VP–forest is built as a collection of balanced Vantage Point Trees (VP–trees). In this work we propose a novel two-fold approach for searching. Firstly we extend the VP– forest to search in metric spaces, and more importantly we test a counterintuitive modification to the VP–tree, namely to unbalance it. In exact searching an unbalanced data structure perform poorly, and most of the algorithmic effort is directed to obtain a balanced data structure. The unbalancing approach is motivated by a recent data structure (the List of Clusters ) specialized in high dimensional metric space searches, which is an extremely unbalanced data structure (a linked list) outperforming other approaches.Eje: AlgoritmosRed de Universidades con Carreras en Informática (RedUNCI

Boosting Nearest Neighbor Classifiers for Multiclass Recognition

This paper introduces an algorithm that uses boosting to learn a distance measure for multiclass k-nearest neighbor classification. Given a family of distance measures as input, AdaBoost is used to learn a weighted distance measure, that is a linear combination of the input measures. The proposed method can be seen both as a novel way to learn a distance measure from data, and as a novel way to apply boosting to multiclass recognition problems, that does not require output codes. In our approach, multiclass recognition of objects is reduced into a single binary recognition task, defined on triples of objects. Preliminary experiments with eight UCI datasets yield no clear winner among our method, boosting using output codes, and k-nn classification using an unoptimized distance measure. Our algorithm did achieve lower error rates in some of the datasets, which indicates that, in some domains, it may lead to better results than existing methods