The human eye can perceive a vast array of colors. Whether light or dark, the colors that our eyes can see are supposedly unlimited. However, this is not the case. In reality, every image has two aspects or descriptors to it, a reflectance and an illumination. While the reflectance essentially shows an images true color, the illumination is what causes the colors to seem different to the human eye. This effect, originally discovered by Helmholtz, is known as Color Constancy. Color Constancy ensures that the color the Human Visual System (HVS) receives is the true color of the image, regardless of illumination. As a result of this effect, in 1971, Land and McCann created the Retinex theory. Using the pixels in the image, Land tried to estimate the value of the reflectances and thus reveal the true color of the image. This theory was basically a color constancy algorithm that tried to explain why colors look different when exposed to lighting. By calculating the pixels, Land was able to depict the sameness in a gradient of colors in an image. However, the algorithm is both inefficient and complicated. Following their footsteps, many other people have tried to formulate new algorithms around the Lands original Retinex algorithm. In this paper, different methods such as least squares and discrete cosine transform are explained as well as how to enhance images using both Lands idea and histogram equalization.

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Comparing DNA or protein sequences plays an important role in the functional analysis of genomes. Despite many methods available for sequences comparison, few methods retain the information content of sequences. We propose a new approach, the Yau-Hausdorff method, which considers all translations and rotations when seeking the best match of graphical curves of DNA or protein sequences. The complexity of this method is lower than that of any other two dimensional minimum Hausdorff algorithm. The Yau-Hausdorff method can be used for measuring the similarity of DNA sequences based on two important tools: the Yau-Hausdorff distance and graphical representation of DNA sequences. The graphical representations of DNA sequences conserve all sequence information and the Yau-Hausdorff distance is mathematically proved as a true metric. Therefore, the proposed distance can preciously measure the similarity of DNA sequences. The phylogenetic analyses of DNA sequences by the Yau-Hausdorff distance show the accuracy and stability of our approach in similarity comparison of DNA or protein sequences. This study demonstrates that Yau-Hausdorff distance is a natural metric for DNA and protein sequences with high level of stability. The approach can be also applied to similarity analysis of protein sequences by graphic representations, as well as general two dimensional shape matching.

Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw biological data in a precise way. Multiple Sequence Alignment (MSA) is used frequently to analyze biological evolutions, but is very time-consuming. When the scale of data is large, alignment methods cannot finish calculation in reasonable time. Therefore, we present a new method using moments of cumulative Fourier power spectrum in clustering the DNA sequences. Each sequence is translated into a vector in Euclidean space. Distances between the vectors can reflect the relationships between sequences. The mapping between the spectra and moment vector is one-to-one, which means that no information is lost in the power spectra during the calculation. We cluster and classify several datasets including Influenza A, primates, and human rhinovirus (HRV) datasets to build up the phylogenetic trees. Results show that the new proposed cumulative Fourier power spectrum is much faster and more accurately than MSA and another alignment-free method known as k-mer. The research provides us new insights in the study of phylogeny, evolution, and efficient DNA comparison algorithms for large genomes. The computer programs of the cumulative Fourier power spectrum are available at GitHub (https://github.com/YaulabTsinghua/cumulative-Fourier-power-spectrum).

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