The all-pairs suffix-prefix matching problem is a basic problem in string processing. It has an application in the de novo genome assembly task, which is one of the major bioinformatics problems. Due to the large size of the input data, it is crucial to use fast and space efficient solutions. In this paper, we present a space-economical solution to this problem using the generalized Sadakane compressed suffix tree. Furthermore, we present a parallel algorithm to provide more speed for shared memory computers. Our sequential and parallel algorithms are optimized by exploiting features of the

This paper presents improved automatic moving target detection and tracking framework that is suitable for UAV imagery. The framework is comprised of motion compensation phase to detect moving targets from a moving camera, target state estimation with Kalman filter, and overlap-rate-based data association. Finally, P-N learning is used to maintain target appearance by utilizing novel structural constraints to select positive and negative samples, where data association decisions are used as positive (P) constraints. After learning target appearance, a cascaded classifier is employed to detect

Background: Given a set of DNA sequences s1,..., st, the (l, d) motif problem is to find an l-length motif sequence M, not necessary existing in any of the input sequences, such that for each sequence si, 1 ≤ i ≤ t, there is at least one subsequence differing with at most d mismatches from M. Many exact algorithms have been developed to solve the motif finding problem in the last three decades. However, the problem is still challenging and its solution is limited to small values of l and d. Results: In this paper we present a new efficient method to improve the performance of the exact

In this work, a novel active shape model (ASM) paradigm is proposed to segment the right ventricle (RV) in cardiac magnetic resonance image sequences. The proposed paradigm includes modifications to two fundamental steps in the ASM algorithm. The first modification includes employing the 2D-Principal Component Analysis (PCA) to capture the inter-profile relations among shape’s neighboring landmarks and then model the inter-profile variations between the training set. The second modification is based on using a multi-stage searching algorithm to find the best profile match based on the best

EGEPT (Middle East GenBank Post) is a database that monitors submissions to the GenBank nucleotide database from Middle East countries. The data in EGEPT is browsable by country, institute, author, organism, and related publications. Statistics about the dataset is provided and charts that compare the Middle East countries to each other are automatically generated. EGEPT revealed that Qatar, Egypt, Oman, Tunisia, and Morocco are leading in terms of sequence submissions and related publications. However, the total submissions of all Arab countries is greatly lagging behind other Middle East

Optic Disc (OD) localization is an important pre-processing step that significantly simplifies subsequent segmentation of the OD and other retinal structures. Current OD localization techniques suffer from impractically-high computation times (few minutes/image). In this work, we present an ultrafast technique that requiresless than a second to localize the OD. The technique is based on reducing the dimensionality of the search space by projecting the 2D image feature space onto two orthogonal (x- and y-) axes. This results in two 1D signals that can be used to determine the x- and y-

Recent findings suggest an implication of the gut microbiome in Parkinson’s disease (PD) patients. PD onset and progression has also been linked with various environmental factors such as physical activity, exposure to pesticides, head injury, nicotine, and dietary factors. In this study, we used a mouse model, overexpressing the complete human SNCA gene (SNCA-TG mice) modeling familial and sporadic forms of PD to study whether environmental conditions such as standard vs. enriched environment changes the gut microbiome and influences disease progression. We performed 16S rRNA DNA sequencing

Research addressing Sentiment Analysis has witnessed great attention over the last decade especially after the huge increase in social media networks usage. Social networks like Facebook and Twitter generate an incredible amount of data on a daily basis, containing posts that discuss all kinds of different topics ranging from sports and products to politics and current events. Since data generated within these mediums is created by users from all over the world, it is multilingual in nature. Arabic is one of the important languages recently targeted by many sentiment analysis efforts. However

Named Entity Recognition (NER) is an important task in many natural language processing applications. There are several studies that have focused on NER for the English language. However, there are some limitations when applying the current methodologies directly on the Arabic language text. Recent studies have shown the effectiveness of pooled contextual embedding representations and significant improvements in English NER tasks. This work investigates the performance of pooled contextual embeddings and bidirectional encoder representations from Transformers (BERT) model when used for NER on

In this paper, we investigate the problem of recognizing entities which are targeted by text sentiment in Arabic tweets. To do so, we train a bidirectional LSTM deep neural network with conditional random fields as a classification layer on top of the network to discover the features of this specific set of entities and extract them from Arabic tweets. We’ve evaluated the network performance against a baseline method which makes use of a regular named entity recognizer and a sentiment analyzer. The deep neural network has shown a noticeable advantage in extracting sentiment target entities