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James Li
I'm the CEO and founder of the software company VisuMap Technologies Inc.
I'm the CEO and founder of the software company VisuMap Technologies Inc.
James's posts

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Deep Data Profile with VisuMap
Data profiling are normally understood as statistical methods to extract numerical features from complex systems for easy exploration. So for instance, GDP, CPI and various kind of indices are often used to profile the state of an economy. Appropriate profi...

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3D nucleotide motif map created with VisuMap, tSNE algorithm and needleman-wunsch editing distance. 

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On the shape of nucleotide motifs
Genomes of multi-cellular organism often contain short sequences with many duplicates which have been created and preserved with minor mutations during their evolutionary processes. Those nucleotide sequences, called here generically motifs , carry importan...

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VisuMap version 4.7 with Whole Genome Browser Released.
I have just released VisuMap version 4.7 on our web site . Apart from many GPU related optimizations of 3D data visualization, this release includes a heat map style data view to visualize long discrete sequences. A whole genome with billions of nucleotides...

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Visualizing Gene Sequences with complementary GMS
We now know that there are about 20 000 protein coding genes in the whole human genome. How do they relate to each other?  Is there any geometrical structure among them? What  shape do they form?  Aiming at these questions,  I'll put forward here a method t...

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Curvature as secondary profiling of GMS maps.
As a profiling method, GMS translates discrete sequences to space curves which help us to explore sequence features (treats) with help of geometrical shapes. Yet, space curves still pose a challenge for direct pattern recognition. This is especially so, whe...

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GMS for DNA profiling
In this note I am going to describe a GMS based algorithm to convert DNA sequences to geometrical shapes with visually identifiable features. I'll apply this algorithm to real genetic sequences to demonstrate its profiling capability. The  main steps of the...

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GMS with multiple scanning and aggregated affinitity
As said in the title, this note is going to put forward two variations to the GMS model. Both variations aim to create better visualization for discrete sequences. For the first variation, we have seen in a previous note that the loopy GMS can produce simpl...

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On the origin of the helix structure from the view point of GMS
Helix structure has been prevalent in biological world. It can be fund in small scale like the folding of DNA and protein sequences, and in large scale like plants. Whereas the mathematical description of the helix structure is clear; the mechanism that giv...

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