Measles is a highly contagious disease, one of the largest vaccine-preventable illnesses and leading causes of death in developing countries, claiming more than 140,000 lives each year. Measles was declared eliminated in the United States in the year 2000 due to decades of successful vaccination but it resurged in 2019 with 1,282 confirmed cases. Due to rapid spread of this disease among people in contact, rapid and automated diagnostic systems are required for early prevention. In this work, we employed transfer learning to build deep convolutional neural networks (CNNs) to distinguish measles rash from other skin conditions. Experiments with ResNet-50 model, trained on our diverse and curated skin rash image dataset, produce classification accuracy of 95.2%, sensitivity of 81.7%, and specificity of 97.1%, respectively. This indicates that our technique is effective in facilitating an accurate detection of measles to help contain outbreaks. The performance of a small CNN model MobileNet-V2 on our image data set is also discussed. Our work will facilitate healthcare professionals to effectively diagnose measles and accelerate the development of automated diagnostic tools to prevent the measles spread at various public venues.

In the product life cycle, design reuse can save cost and improve existing products conveniently in most new product development. To retrieve similar models from big database, most search algorithms convert CAD model into a shape descriptor and compute the similarity two models according to a descriptor metric. This paper proposes a new 3D shape matching approach by matching the coordinates directly. It is based on diffusion maps which integrate the rand walk and graph spectral analysis to extract shape features embedded in low dimensional spaces and then they are used to form coordinations for non-linear alignment of different models. These coordinates could capture multi-scale properties of the 3D geometric features and has shown good robustness to noise. The results also have shown better performance compared to the celebrated Eigenmap approach in the 3D model retrieval.

Gene fusions are important genomic events in human cancer because their fusion gene products can drive the development of cancer and thus are potential prognostic tools or therapeutic targets in anti-cancer treatment. Major advancements have been made in computational approaches for fusion gene discovery over the past 3 years due to improvements and widespread applications of high-throughput next generation sequencing (NGS) technologies. To identify fusions from NGS data, existing methods typically leverage the strengths of both sequencing technologies and computational strategies. In this article, we review the NGS and computational features of existing methods for fusion gene detection and suggest directions for future development.

Copy number variation (CNV) is a prevalent form of critical genetic variation that leads to an abnormal number of copies of large genomic regions in a cell. Microarray-based comparative genome hybridization (arrayCGH) or genotyping arrays have been standard technologies to detect large regions subject to copy number changes in genomes until most recently high-resolution sequence data can be analyzed by next-generation sequencing (NGS). During the last several years, NGS-based analysis has been widely applied to identify CNVs in both healthy and diseased individuals. Correspondingly, the strong demand for NGS-based CNV analyses has fuelled development of numerous computational methods and tools for CNV detection. In this article, we review the recent advances in computational methods pertaining to CNV detection using whole genome and whole exome sequencing data. Additionally, we discuss their strengths and weaknesses and suggest directions for future development.

In protein tertiary structure prediction, a crucial step is to select near-native structures from a large number of predicted structural models. Over the years, many methods have been proposed for the protein structure selection problem. Despite significant advances, the discerning power of current approaches is still unsatisfactory. In this paper, we propose a new algorithm, CC-Select, that combines consensus with clustering techniques. Given a set of predicted models, CC-Select first calculates a consensus score for each structure based on its average pair wise structural similarity to other models. Then, similar structures are grouped into clusters using multidimensional scaling and clustering algorithms. In each cluster, the one with the highest consensus score is selected as a candidate model. Using extensive benchmark sets of a large collection of predicted models, we compare CC-Select with existing state-of-the-art quality assessment methods and show significant improvement.

In protein tertiary structure prediction, a crucial step is to select near-native structures from a large number of predicted structural models. Over the years, extensive research has been conducted for the protein structure selection problem with most approaches focusing on developing more accurate energy or scoring functions. Despite significant advances in this area, the discerning power of current approaches is still unsatisfactory. In this paper, we propose a novel consensus-based algorithm for the selection of predicted protein structures. Given a set of predicted models, our method first removes redundant structures to derive a subset of reference models. Then, a structure is ranked based on its average pairwise similarity to the reference models. Using the CASP8 data set containing a large collection of predicted models for 122 targets, we compared our method with the best CASP8 quality assessment (QA) servers, which are all consensus based, and showed that our QA scores correlate better with the GDT-TSs than those of the CASP8 QA servers. We also compared our method with the state-of-the-art scoring functions and showed its improved performance for near-native model selection. The GDT-TSs of the top models picked by our method are on average more than 8 percent better than the ones selected by the best performing scoring function.

Finding the longest common subsequence (LCS) of multiple strings is an NP-hard problem, with many applications in the areas of bioinformatics and computational genomics. Although significant efforts have been made to address the problem and its special cases, the increasing complexity and size of biological data require more efficient methods applicable to an arbitrary number of strings. In this paper, we present a new algorithm for the general case of multiple LCS (or MLCS) problem, i.e., finding an LCS of any number of strings, and its parallel realization. The algorithm is based on the dominant point approach and employs a fast divide-and-conquer technique to compute the dominant points. When applied to a case of three strings, our algorithm demonstrates the same performance as the fastest existing MLCS algorithm designed for that specific case. When applied to more than three strings, our algorithm is significantly faster than the best existing sequential methods, reaching up to 2-3 orders of magnitude faster speed on large-size problems. Finally, we present an efficient parallel implementation of the algorithm. Evaluating the parallel algorithm on a benchmark set of both random and biological sequences reveals a near-linear speedup with respect to the sequential algorithm.

Finding the longest common subsequence (LCS) of multiple strings is an NP-hard problem, with many applications in the areas of bioinformatics and computational genomics. Although significant efforts have been made to address the problem and its special cases, the increasing complexity and size of biological data require more efficient methods applicable to an arbitrary number of strings. In this paper, a novel search algorithm, MLCS-A*, is presented for the general case of multiple LCS (or MLCS) problems. MLCS-A* is a variant of the A* algorithm. It maximizes a new heuristic estimate of the LCS in each search step so that the longest common subsequence can be found. As a natural extension of MLCS-A*, a fast algorithm, MLCS-APP, is also proposed to deal with large volume of biological data for which finding a LCS within reasonable time is impossible. The benchmark test shows that MLCS-APP is able to extract common subsequences close to the optimal ones and that MLCS-APP significantly outperforms existing heuristic approaches. When applied to 8 protein domain families, MLCS-APP produced more accurate results than existing multiple sequence alignment methods.

In protein tertiary structure prediction, a crucial step is to select near-native structures from a large number of predicted structural models. Over the years, extensive research has been conducted for the protein structure selection problem with most approaches focusing on developing more accurate energy or scoring functions. Despite significant advances in this area, the discerning power of current approaches is still unsatisfactory. In this paper, we propose a novel consensus-based method that outperforms state-of-the-art scoring functions. Given a set of predicted models, the method first removes redundant models to derive a subset of reference models. Then a model is ranked based on its average pairwise similarity score to the set of reference models. Using the CASP8 data set containing a large collections of predicted models for 122 targets, we compared our method with an extensive collection of state-of-the-art scoring functions and showed its superior performance. The top models selected by our method are on average more than 8% better than the ones selected by the best competing method.

Finding the multiple longest common subsequence (MLCS) is an important problem in the areas of bioinformatics and computational genomics. Approaches that are more efficient than the standard dynamic programming method have been introduced and successfully parallelized for the special cases of 2 sequences. However, the increasing complexity and size of biological data require an efficient method applicable to an arbitrary number of sequences as well as its efficient parallelization. A recently developed dominant points method for a general MLCS problem has been shown a significant performance improvement over the dynamic programming method, when number of sequences is larger than two. At the same time, the approach has revealed strong demand for its parallelization, in order to be applied to the larger families of sequences or sequences of the greater lengths. In this paper, we introduce an efficient parallel algorithm to find a MLCS for an arbitrary number of sequences, which is based on the dominant points method. When the number of processors is not greater than the size of alphabet multiplied by the number of sequences, the parallel algorithm is estimated to have the asymptotically linear speed up. We experimentally tested the algorithm using sets of randomly generated sequences over different alphabets as well as the protein sequences from a family of homologous proteins. We found that the performance of the algorithm increases with the number of input sequences and reaches a near-linear speedup for eight sequences.

In protein tertiary structure prediction, it is a crucial step to select near-native structures from a large number of candidate structural models. Despite much effort to tackle the problem of protein structure selection, the discerning power of current scoring functions is still unsatisfactory. In this paper, we developed a new clustering-based method for selecting near-native protein structures. Our method consists of three phases: filtering, clustering and cluster reduction, and centroid construction. Given a set of Cαprotein structures, we apply one or multiple existing scoring functions to filter out bad structures. Then, we group the remaining structures into clusters based on pair-wise similarity measured by RMSD. Each cluster is reduced iteratively to remove outliers and bad structures. Finally, we construct a centroid for each cluster by applying multi-dimensional scale techniques. The centroids are the final models. In experiments, we applied our method to a test set of representative proteins and obtained significant improvement over existing methods.

Wireless sensor networks have been applied to data gathering and target localization and tracking in large geograph- ical areas. In sparsely deployed sensor networks, optimal access point placement is a fundamental issue because of its marked influence on the localization accuracy and data communication rate and delay. In this paper, based on a representative sensor network system for lost hiker localization in wilderness areas, we study the problem of access point deployment in constrained environments with the goal of minimizing location uncertainty. We first identify several key problem features including the trail topology, the number of hikers, and hiker movement mode, and present theoretical analysis of the access-point placement problem for a given set of problem attributes. Then we propose algorithms to compute the location uncertainty, the optimal locations of access points and the necessary number of access points for a certain location uncertainty. The simulation results support our models.