Chromosome classification using dynamic time warping

Robust Identification System for Spanish Sign Language Based on Three-Dimensional Frame Information

Nowadays, according to the World Health Organization (WHO), of the world's population suffers from a hearing disorder that makes oral communication with other people challenging. At the same time, in an era of technological evolution and digitization, designing tools that could help these people to communicate daily is the base of much scientific research such as that discussed herein. This article describes one of the techniques designed to transcribe Spanish Sign Language (SSL). A Leap Motion volumetric sensor has been used in this research due to its capacity to recognize hand movements in 3 dimensions. In order to carry out this research project, an impaired hearing subject has collaborated in the recording of 176 dynamic words. Finally, for the development of the research, Dynamic Time Warping (DTW) has been used to compare the samples and predict the input with an accuracy of 95.17%.

Machine Learning Classifiers Evaluation for Automatic Karyogram Generation from G-Banded Metaphase Images

This work proposes the evaluation of a set of algorithms of machine learning and the selection of the most appropriate one for the classification of segmented chromosomes images acquired using the Giemsa staining technique (G-banding). The evaluation and selection of the best classification algorithms was carried out over a dataset of 119 Q-banding chromosomes images, and the obtained results were then applied to a dataset of 24 G-band chromosomes images, manually classified by an expert of the Laboratory of Cytogenetic of the Children’s Hospital of Tamaulipas. The results of evaluation of 51 classifiers yielded that the best classification accuracy for the selected features was obtained by a backpropagation neural network. One of the main contributions of this study is the proposal of a two-stage classification scheme based on the best classifier found by the initial evaluation. In stage 1, chromosome images are classified into three major groups. In stage 2, the output of phase 1 is used as the input of a multiclass classifier. Using this scheme, 82% of the IGB bank samples and 88% of the samples of a bank of images obtained with a Q-band available in the literature consisting of 119 chromosome studies were successfully classified. The proposed work is a part of an desktop application that allows cytogeneticist to automatically generate cytogenetic reports.

Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

BACKGROUND

In short-read DNA sequencing experiments, the read coverage is a key parameter to successfully assemble the reads and reconstruct the sequence of the input DNA. When coverage is very low, the original sequence reconstruction from the reads can be difficult because of the occurrence of uncovered gaps. Reference guided assembly can then improve these assemblies. However, when the available reference is phylogenetically distant from the sequencing reads, the mapping rate of the reads can be extremely low. Some recent improvements in read mapping approaches aim at modifying the reference according to the reads dynamically. Such approaches can significantly improve the alignment rate of the reads onto distant references but the processing of insertions and deletions remains challenging.

RESULTS

Here, we introduce a new algorithm to update the reference sequence according to previously aligned reads. Substitutions, insertions and deletions are performed in the reference sequence dynamically. We evaluate this approach to assemble a western-grey kangaroo mitochondrial amplicon. Our results show that more reads can be aligned and that this method produces assemblies of length comparable to the truth while limiting error rate when classic approaches fail to recover the correct length. Finally, we discuss how the core algorithm of this method could be improved and combined with other approaches to analyse larger genomic sequences.

CONCLUSIONS

We introduced an algorithm to perform dynamic alignment of reads on a distant reference. We showed that such approach can improve the reconstruction of an amplicon compared to classically used bioinformatic pipelines. Although not portable to genomic scale in the current form, we suggested several improvements to be investigated to make this method more flexible and allow dynamic alignment to be used for large genome assemblies.

Image processing in biodosimetry: A proposal of a generic free software platform

The scoring of chromosome aberrations is the most reliable biological method for evaluating individual exposure to ionizing radiation. However, microscopic analyses of chromosome human metaphases, generally employed to identify aberrations mainly dicentrics (chromosome with two centromeres), is a laborious task. This method is time consuming and its application in biological dosimetry would be almost impossible in case of a large scale radiation incidents. In this project, a generic software was enhanced for automatic chromosome image processing from a framework originally developed for the Framework V project Simbio, of the European Union for applications in the area of source localization from electroencephalographic signals. The platforms capability is demonstrated by a study comparing automatic segmentation strategies of chromosomes from microscopic images.

LocateMe

Fine-grained localization is extremely important to accurately locate a user indoors. Although innovative solutions have already been proposed, there is no solution that is universally accepted, easily implemented, user centric, and, most importantly, works in the absence of GSM coverage or WiFi availability. The advent of sensor rich smartphones has paved a way to develop a solution that can cater to these requirements.

By employing a smartphone's built-in magnetic field sensor, magnetic signatures were collected inside buildings. These signatures displayed a uniqueness in their patterns due to the presence of different kinds of pillars, doors, elevators, etc., that consist of ferromagnetic materials like steel or iron. We theoretically analyze the cause of this uniqueness and then present an indoor localization solution by classifying signatures based on their patterns. However, to account for user walking speed variations so as to provide an application usable to a variety of users, we follow a dynamic time-warping-based approach that is known to work on similar signals irrespective of their variations in the time axis.

Our approach resulted in localization distances of approximately 2m--6m with accuracies between 80--100% implying that it is sufficient to walk short distances across hallways to be located by the smartphone. The implementation of the application on different smartphones yielded response times of less than five secs, thereby validating the feasibility of our approach and making it a viable solution.

Classification of genomic signals using dynamic time warping

BACKGROUND

Classification methods of DNA most commonly use comparison of the differences in DNA symbolic records, which requires the global multiple sequence alignment. This solution is often inappropriate, causing a number of imprecisions and requires additional user intervention for exact alignment of the similar segments. The similar segments in DNA represented as a signal are characterized by a similar shape of the curve. The DNA alignment in genomic signals may adjust whole sections not only individual symbols. The dynamic time warping (DTW) is suitable for this purpose and can replace the multiple alignment of symbolic sequences in applications, such as phylogenetic analysis.

METHODS

The proposed method is composed of three main parts. The first part represent conversion of symbolic representation of DNA sequences in the form of a string of A,C,G,T symbols to signal representation in the form of cumulated phase of complex components defined for each symbol. Next part represents signals size adjustment realized by standard signal preprocessing methods: median filtration, detrendization and resampling. The final part necessary for genomic signals comparison is position and length alignment of genomic signals by dynamic time warping (DTW).

RESULTS

The application of the DTW on set of genomic signals was evaluated in dendrogram construction using cluster analysis. The resulting tree was compared with a classical phylogenetic tree reconstructed using multiple alignment. The classification of genomic signals using the DTW is evolutionary closer to phylogeny of organisms. This method is more resistant to errors in the sequences and less dependent on the number of input sequences.

CONCLUSIONS

Classification of genomic signals using dynamic time warping is an adequate variant to phylogenetic analysis using the symbolic DNA sequences alignment; in addition, it is robust, quick and more precise technique.

AN AUTOMATIC ALGORITHM FOR IDENTIFICATION AND STRAIGHTENING IMAGES OF CURVED HUMAN CHROMOSOMES

Karyotyping is a standard method for presenting the complete set of the pictures of human chromosomes in a table-like format. It is usually used by a cytogenetic expert to predict the common genetic abnormalities. Producing a Karyotype from microscopic images of human chromosomes is a tedious and time-consuming task, so an automatic Karyotyping system would help the cytogenetic expert in his/her routine work. Automatic Karyotyping algorithms usually suffer the non-rigid nature of the chromosomes, which makes them to have unpredictable shapes and sizes in the images. One such problem that usually needs the operator's interaction is the existence of curved chromosomes within the images. In this paper, an effective algorithm for identification and straightening of curved human chromosomes is presented. This will extend the domain of application of the most of the previously reported algorithms to the curved chromosomes. The proposed algorithm is applied to single chromosomes that are initially modified by means of a Median filter. The medial axis (MA) of the filtered image is then extracted using a thinning procedure, which is carried out on the binary version of the image. By comparing the Euclidean distance of the endpoints and the length of the MA, a curved chromosome is identified. For chromosome straightening, the initially extracted medial axis is then modified by extending it in both ends considering the slope of the MA. Next, the original input image is intensity sampled over many closely located perpendicular lines to the MA along the chromosome which are then mapped into a matrix (as rows) producing a vertically oriented straight chromosome. For evaluation, the algorithm is applied to 54 selected highly curved chromosomes obtained at the pro-metaphase stage, which were provided by the Cytogenetic Laboratory of Cancer Institute, Imam Hospital, Tehran, Iran. The density profile and the centromeric index of the chromosomes which are among the most important and commonly used features for chromosome identification are calculated by the expert both before and after the straightening procedure. The mean squared error and the variance of the difference between the two are then obtained and compared. The results show a good agreement between the two, hence the effectiveness of the proposed method. The proposed algorithm therefore extends the domain of application of the previously reported algorithms to the highly curved chromosomes.

A modular framework for the automatic classification of chromosomes in Q-band images

The manual analysis of the karyogram is a complex and time-consuming operation, as it requires meticulous attention to details and well-trained personnel. Routine Q-band laboratory images show chromosomes that are randomly rotated, blurred or corrupted by overlapping and dye stains. We address here the problem of robust automatic classification, which is still an open issue. The proposed method starts with an improved estimation of the chromosome medial axis, along which an established set of features is then extracted. The following novel polarization stage estimates the chromosome orientation and makes this feature set independent on the reading direction along the axis. Feature rescaling and normalizing techniques take full advantage of the results of the polarization step, reducing the intra-class and increasing the inter-class variances. After a standard neural network based classification, a novel class reassignment algorithm is employed to maximize the probability of correct classification, by exploiting the constrained composition of the human karyotype. An average 94% of correct classification was achieved by the proposed method on 5474 chromosomes, whose images were acquired during laboratory routine and comprise karyotypes belonging to slightly different prometaphase stages. In order to provide the scientific community with a public dataset, all the data we used are publicly available for download.

Automatic classification of chromosomes in Q-band images

The manual analysis of the karyogram is a complex, wearing and time-consuming operation. It requires a very meticulous attention to details and calls for well-trained personnel. Even though existing commercial software packages provide a reasonable support to cytogenetists, they very often require human intervention to correct challenging situations. We developed a robust automatic classification system conceived to cope with routine images in which chromosomes are randomly rotated, possibly blurred or also corrupted by overlapping or by dye stains. It consists in a sequence of modules comprising robust feature extraction based on medial axis, chromosome polarization, feature pre-processing, and Neural Network classification followed by a class reassigning algorithm.We show the effectiveness of the proposed method on data comprising karyotypes belonging to slightly different stage of the prometaphase. This dataset contains 119 karyotypes (5474 chromosomes), 70 of which were used for training and validation and 49 for the final testing. In this latter set of images, the system achieved a classification accuracy, as compared to manual ground truth, of 95.6%.