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A Colour Rendering Index for Dichromats

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2017-10
Abstract: 

We propose a method of evaluating the colour rendering quality of light sources tailored to dichromatic vision. To the best of our knowledge, the proposed color rendering index (CRI) is the first such index to be specifically designed for dichromats. Previous CRIs have been defined only for trichromats and they generally rely on measuring ΔE colour differences in a standardized uniform colour space such as CAM02-UCS. Since these spaces are defined only for trichromatic colour vision these methods do not generalize to the case of dichromatic colour vision. The proposed dichromat CRI is based on the metamer mismatch index, which applies to both the trichromatic and dichromatic cases.

Document type: 
Conference presentation
File(s): 

Colorizing Color Images

Author: 
Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2018-02
Abstract: 

This paper describes a method of improving the quality of the color in color images by colorizing them. In particular, color quality may suffer from improper white balance and other factors such as inadequate camera characterization. Colorization generally refers to the problem of turning a luminance image into a realistic looking color image and impressive results have been reported in the computer vision literature. Based on the assumption that if colorization can successfully predict colors from luminance data alone then it should certainly be able to predict colors from color data, the proposed method employs colorization to ‘color’ color images. Tests show that the proposed method quite effectively removes color casts—including spatially varying color casts—created by changes in the illumination. The colorization method itself is based on training a deep neural network to learn the connection between the colors in an improperly balanced image and those in a properly balanced one. Unlike many traditional white-balance methods, the proposed method is image-inimage- out and does not explicitly estimate the chromaticity of the illumination nor apply a von-Kries-type adaptation step. The colorization method is also spatially varying and so handles spatially varying illumination conditions without further modification.

Document type: 
Conference presentation
File(s): 

HUE: The Hourly Usage of Energy Dataset for Buildings in British Columbia

Author: 
Peer reviewed: 
No, item is not peer reviewed.
Date created: 
2018-09-03
Abstract: 

The HUE dataset contains donated data from residential customers of BCHydro, a provincial power utility. There are currently twenty-two houses contain within the dataset with most houses having three years of consumption history. Data is downloaded from BCHydro’s customer web porthole by each customer how donated the data. The porthole only allows customers to download a maximum of three years worth of data. Only BCHydro customers were asked to donate to keep the data quality consistent. Weather data from the nearest weather station is also included.

Document type: 
Technical Report
File(s): 

DIDA: Distributed Indexing Dispatched Alignment

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2015
Abstract: 

One essential application in bioinformatics that is affected by the high-throughput sequencing data deluge is the sequence alignment problem, where nucleotide or amino acid sequences are queried against targets to find regions of close similarity. When queries are too many and/or targets are too large, the alignment process becomes computationally challenging. This is usually addressed by preprocessing techniques, where the queries and/or targets are indexed for easy access while searching for matches. When the target is static, such as in an established reference genome, the cost of indexing is amortized by reusing the generated index. However, when the targets are non-static, such as contigs in the intermediate steps of a de novo assembly process, a new index must be computed for each run. To address such scalability problems, we present DIDA, a novel framework that distributes the indexing and alignment tasks into smaller subtasks over a cluster of compute nodes. It provides a workflow beyond the common practice of embarrassingly parallel implementations. DIDA is a cost-effective, scalable and modular framework for the sequence alignment problem in terms of memory usage and runtime. It can be employed in large-scale alignments to draft genomes and intermediate stages of de novo assembly runs. The DIDA source code, sample files and user manual are available through http://www.bcgsc.ca/platform/bioinfo/software/dida. The software is released under the British Columbia Cancer Agency License (BCCA), and is free for academic use.

Document type: 
Article
File(s): 

Robustness of Massively Parallel Sequencing Platforms

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2015
Abstract: 

The improvements in high throughput sequencing technologies (HTS) made clinical sequencing projects such as ClinSeq and Genomics England feasible. Although there are significant improvements in accuracy and reproducibility of HTS based analyses, the usability of these types of data for diagnostic and prognostic applications necessitates a near perfect data generation. To assess the usability of a widely used HTS platform for accurate and reproducible clinical applications in terms of robustness, we generated whole genome shotgun (WGS) sequence data from the genomes of two human individuals in two different genome sequencing centers. After analyzing the data to characterize SNPs and indels using the same tools (BWA, SAMtools, and GATK), we observed significant number of discrepancies in the call sets. As expected, the most of the disagreements between the call sets were found within genomic regions containing common repeats and segmental duplications, albeit only a small fraction of the discordant variants were within the exons and other functionally relevant regions such as promoters. We conclude that although HTS platforms are sufficiently powerful for providing data for first-pass clinical tests, the variant predictions still need to be confirmed using orthogonal methods before using in clinical applications.

Document type: 
Article
File(s): 

Rethinking Colour Constancy

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2015
Abstract: 

Colour constancy needs to be reconsidered in light of the limits imposed by metamer mismatching. Metamer mismatching refers to the fact that two objects reflecting metameric light under one illumination may reflect non-metameric light under a second; so two objects appearing as having the same colour under one illuminant can appear as having different colours under a second. Yet since Helmholtz, object colour has generally been believed to remain relatively constant. The deviations from colour constancy registered in experiments are usually thought to be small enough that they do not contradict the notion of colour constancy. However, it is important to determine how the deviations from colour constancy relate to the limits metamer mismatching imposes on constancy. Hence, we calculated metamer mismatching’s effect for the 20 Munsell papers and 8 pairs of illuminants employed in the colour constancy study by Logvinenko and Tokunaga and found it to be so extensive that the two notions—metamer mismatching and colour constancy—must be mutually exclusive. In particular, the notion of colour constancy leads to some paradoxical phenomena such as the possibility of 20 objects having the same colour under chromatic light dispersing into a hue circle of colours under neutral light. Thus, colour constancy refers to a phenomenon, which because of metamer mismatching, simply cannot exist. Moreover, it obscures the really important visual phenomenon; namely, the alteration of object colours induced by illumination change. We show that colour is not an independent, intrinsic attribute of an object, but rather an attribute of an object/light pair, and then define a concept of material colour in terms of equivalence classes of such object/light pairs. We suggest that studying the shift in material colour under a change in illuminant will be more fruitful than pursuing colour constancy’s false premise that colour is an intrinsic attribute of an object.

Document type: 
Article
File(s): 

Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014
Abstract: 

Background

Increasing genetic and phenotypic differences found among natural isolates of C. elegans have encouraged researchers to explore the natural variation of this nematode species.

Results

Here we report on the identification of genomic differences between the reference strain N2 and the Hawaiian strain CB4856, one of the most genetically distant strains from N2. To identify both small- and large-scale genomic variations (GVs), we have sequenced the CB4856 genome using both Roche 454 (~400 bps single reads) and Illumina GA DNA sequencing methods (101 bps paired-end reads). Compared to previously described variants (available in WormBase), our effort uncovered twice as many single nucleotide variants (SNVs) and increased the number of small InDels almost 20-fold. Moreover, we identified and validated large insertions, most of which range from 150 bps to 1.2 kb in length in the CB4856 strain. Identified GVs had a widespread impact on protein-coding sequences, including 585 single-copy genes that have associated severe phenotypes of reduced viability in RNAi and genetics studies. Sixty of these genes are homologs of human genes associated with diseases. Furthermore, our work confirms previously identified GVs associated with differences in behavioural and biological traits between the N2 and CB4856 strains.

Conclusions

The identified GVs provide a rich resource for future studies that aim to explain the genetic basis for other trait differences between the N2 and CB4856 strains.

Document type: 
Article
File(s): 

Ribofsm: Frequent Subgraph Mining For the Discovery of RNA Structures and Interactions

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014
Abstract: 

Frequent subgraph mining is a useful method for extracting meaningful patterns from a set of graphs or a single large graph. Here, the graph represents all possible RNA structures and interactions. Patterns that are significantly more frequent in this graph over a random graph are extracted. We hypothesize that these patterns are most likely to represent biological mechanisms. The graph representation used is a directed dual graph, extended to handle intermolecular interactions. The graph is sampled for subgraphs, which are labeled using a canonical labeling method and counted. The resulting patterns are compared to those created from a randomized dataset and scored. The algorithm was applied to the mitochondrial genome of the kinetoplastid species Trypanosoma brucei, which has a unique RNA editing mechanism. The most significant patterns contain two stem-loops, indicative of gRNA, and represent interactions of these structures with target mRNA.

Document type: 
Article
File(s): 

Creating Groups with Similar Expected Behavioural Response in Randomized Controlled Trials: A Fuzzy Cognitive Map Approach

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014
Abstract: 

Background

Controlling bias is key to successful randomized controlled trials for behaviour change. Bias can be generated at multiple points during a study, for example, when participants are allocated to different groups. Several methods of allocations exist to randomly distribute participants over the groups such that their prognostic factors (e.g., socio-demographic variables) are similar, in an effort to keep participants’ outcomes comparable at baseline. Since it is challenging to create such groups when all prognostic factors are taken together, these factors are often balanced in isolation or only the ones deemed most relevant are balanced. However, the complex interactions among prognostic factors may lead to a poor estimate of behaviour, causing unbalanced groups at baseline, which may introduce accidental bias.

Methods

We present a novel computational approach for allocating participants to different groups. Our approach automatically uses participants’ experiences to model (the interactions among) their prognostic factors and infer how their behaviour is expected to change under a given intervention. Participants are then allocated based on their inferred behaviour rather than on selected prognostic factors.

Results

In order to assess the potential of our approach, we collected two datasets regarding the behaviour of participants (n = 430 and n = 187). The potential of the approach on larger sample sizes was examined using synthetic data. All three datasets highlighted that our approach could lead to groups with similar expected behavioural changes.

Conclusions

The computational approach proposed here can complement existing statistical approaches when behaviours involve numerous complex relationships, and quantitative data is not readily available to model these relationships. The software implementing our approach and commonly used alternatives is provided at no charge to assist practitioners in the design of their own studies and to compare participants' allocations.

Document type: 
Article
File(s): 

Whole Genome Sequencing of Turkish Genomes Reveals Functional Private Alleles and Impact of Genetic Interactions with Europe, Asia and Africa

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2014
Abstract: 

Background

Turkey is a crossroads of major population movements throughout history and has been a hotspot of cultural interactions. Several studies have investigated the complex population history of Turkey through a limited set of genetic markers. However, to date, there have been no studies to assess the genetic variation at the whole genome level using whole genome sequencing. Here, we present whole genome sequences of 16 Turkish individuals resequenced at high coverage (32 × -48×).

Results

We show that the genetic variation of the contemporary Turkish population clusters with South European populations, as expected, but also shows signatures of relatively recent contribution from ancestral East Asian populations. In addition, we document a significant enrichment of non-synonymous private alleles, consistent with recent observations in European populations. A number of variants associated with skin color and total cholesterol levels show frequency differentiation between the Turkish populations and European populations. Furthermore, we have analyzed the 17q21.31 inversion polymorphism region (MAPT locus) and found increased allele frequency of 31.25% for H1/H2 inversion polymorphism when compared to European populations that show about 25% of allele frequency.

Conclusion

This study provides the first map of common genetic variation from 16 western Asian individuals and thus helps fill an important geographical gap in analyzing natural human variation and human migration. Our data will help develop population-specific experimental designs for studies investigating disease associations and demographic history in Turkey.

Document type: 
Article
File(s):