11 Friday Jan 2019
Posted in Cancer, Cancer Research, Data Mining, News
Carcinomas Miner | Find resources relevant to the types of cancers known as carcinomas (http://www.minerazzi.com/carcinomas/).
Recrawl search results and build your own curated collection of resources. Use this miner to extract valuable front/back end data from relevant sites.
You may also use its rss news channels (http://www.minerazzi.com/carcinomas/spp.php) to find news from around the Web relevant to these and other types of cancers.
20 Thursday Dec 2018
Posted in Algorithms, calculators, chemical mining, chemistry, Chemometrics, Data Mining, Programming, Software
This tool computes bond orders of diatomic species having up to 20 electrons, without using Molecular Orbital Theory! It is available at
http://www.minerazzi.com/tools/bond-order/calculator.php
We developed the tool inspired in Dr. Arijit Das set of innovative and time economic formulae for chemical education. His methodologies are suitable for computer-based learning (CBL) activities or for writing computer programs for solving chemistry problems.
In my opinion, students who know how to write programs for solving chemistry problems have an edge when taking quantitative courses like analytical chemistry, instrumental analysis, chemometrics, computational chemistry, and similar courses. I think they might be better prepared for multidisciplinary research work.
Developing this tool was really gratifying as the work inspired us to derive an algorithm for predicting number of unpaired electrons and magnetic properties of single atoms, diatomic species, and their ions. Hopefully, this algorithm will be available early next year in the form of a new chemistry calculator.
We are sincerely in debt to Dr. Arijit Das from Ramthakur College, Agartala, West Tripura, India for encouraging us to develop this tool for educators, scholars, and chemistry students.
27 Tuesday Nov 2018
Tags
binary fractals, CSS Fractal Studio, Fractal Patterns, genetic matrices, Genetic Sequences, genetics, Kronecker, Sequencing
Back in 2017, Stepanyan & Petoukhov reported that long nucleotide sequences can be modeled as binary fractals by means of Kronecker exponentiation of matrices.
https://www.mdpi.com/2078-2489/8/1/12/pdf
see also https://arxiv.org/ftp/arxiv/papers/1310/1310.8469.pdf
Abstract reads in part:
“This method uses a set of symmetries of biochemical attributes of nucleotides. It also uses the possibility of presentation of every whole set of N-mers as one of the members of a Kronecker family of genetic matrices. With this method, a long nucleotide sequence can be visually represented as an individual fractal-like mosaic or another regular mosaic of binary type.”
We added the fractal resembling the pattern of the nucleotide sequence Homo sapiens chromosome 22 genomic scaffold into our Fractal Studio tool at
http://www.minerazzi.com/tools/fractals/studio.php
Researchers can reproduce its binary mosaic, shown above, by just selecting the Homo Sapiens Mosaic option from the tool selection menu. Compare results with Figures 4 and 8 of Stepanyan & Petoukhov article. Compare also some multifractals that the tool generates with some of the genetic mosaics described in the article.
Multidisciplinary research is a beautiful thing.
18 Sunday Nov 2018
Posted in Data Mining, Mathematics, Poems
Reverend Charles Lutwidge Dodgson, better known by his pseudonym Lewis Carroll as the creator of Alice in Wonderland, proposed in 1866 a new method for computing matrix determinants called Condensation of Determinants.
An elementary proof of Dodgson’s Condensation Method is available from Main, Donor, and Harwood.
Dodgson was a real genious, although with some dark sides Wikipedia.
Anyway, hidden in his poems are some gems of linear algebra. The following lines written by Lewis Carroll read the same horizontally and vertically when cases and nonletter characters are ignored.
I often wondered when I cursed,
Often feared where I would be—
Wondered where she’d yield her love
When I yield, so will she,
I would her will be pitied!
Cursed be love! She pitied me…
See figure. That is an example of a symmetric matrix.
For Math Teachers
Here is a nice homework: Assign integer values to unique words of the poem and compute its determinant with Dodgson’s Method.
Challenge 1: Starting at the top-left corner, read matrix diagonal elements. Explain the meaning of the diagonal message in the Carroll and then in the Dodgson’s sense.
Challenge 2: There are also other hidden messages in that matrix to read. Hint: Move through rows/cols adopting a traveling pattern. Can you find them?
01 Thursday Nov 2018
This the third and last part of a tutorial series on the non-additivity of correlation coefficients.
http://www.minerazzi.com/tutorials/nonadditivity-correlations-part-3.pdf
Their bias & nature, transformations, and approximations to normality are discussed. The risks of blindly transforming scores to ranks or arbitrarily converting r-to-Z values/Z-to-r values (Fisher Transformations) are discussed. Shifted up cosine approximations to normality are also covered.
Not all researchers know that score-to-rank transformations can change the sampling distribution of a statistic (e.g. a correlation coefficient) and that Fisher transformations are sensitive to normality violations. Combining both types of transformations is a recipe for a statistical disaster.
Alas, some meta analysis and data analytic folks are guilty of that.
14 Sunday Oct 2018
Hybrid Similarity Search (HSS) Algorithm for Chemistry Searching for Fentanyl-related compounds and other drugs.
Free version: https://www.mswil.com/images/NIST/NIST17/GCMS-Hybrid-Search-AnalChem-2017.pdf
This is a news from NIST back in March (https://www.nist.gov/news-events/news/2018/03/free-software-can-help-spot-new-forms-fentanyl-and-other-illegal-drugs ) and found with the NIST RSS channel of the Chemical Substances Miner http://www.minerazzi.com/chemsubstances/spp.php
It is a nice example of Information Retrieval applied to Chemistry. They used a modified cosine similarity function. I see possible applications to topic analysis.
Original Source:
https://pubs.acs.org/doi/abs/10.1021/acs.analchem.7b03320
Anal. Chem., 2017, 89 (24), pp 13261–13268 DOI: 10.1021/acs.analchem.7b03320
Abstract:
“A mass spectral library search algorithm that identifies compounds that differ from library compounds by a single “inert” structural component is described. This algorithm, the Hybrid Similarity Search, generates a similarity score based on matching both fragment ions and neutral losses. It employs the parameter DeltaMass, defined as the mass difference between query and library compounds, to shift neutral loss peaks in the library spectrum to match corresponding neutral loss peaks in the query spectrum. When the spectra being compared differ by a single structural feature, these matching neutral loss peaks should contain that structural feature. This method extends the scope of the library to include spectra of “nearest-neighbor” compounds that differ from library compounds by a single chemical moiety. Additionally, determination of the structural origin of the shifted peaks can aid in the determination of the chemical structure and fragmentation mechanism of the query compound. A variety of examples are presented, including the identification of designer drugs and chemical derivatives not present in the library.”
09 Tuesday Oct 2018
Posted in Chemometrics, Data Mining, Mathematics, minerazzi, Statistics and Mathematics
Curating collections requires going to original sources which is gratifying.
As part of the effort of building a miner on the golden age of Statistics, I researched those from Ronald Fisher times who might still alive. I found one researcher that precisely is Fisher’s only PhD: Calyampudi Radhakrishna Rao, now 98.
I asked Dr. Rao for help in identifying important references and moments from those times. He graciously sent me his CV listing references to all of his glorious books (15), articles (477), and moments.
Even in his retirement he is still publishing:
http://www.pnas.org/content/pnas/early/2017/03/28/1702654114.full.pdf
Dr. Rao also sent me a PDF with historical photos of him with Mahalanobis, Prime Minister Nehru, Prime Minister Indira Gandhi, and others, and of many glorious moments from his career. What an honor!
His work has impacted so many fields that there are several technical terms bearing his name.
Here is an appealing quote from him:
“We study physics to solve problems in physics, chemistry to solve problems in chemistry, and botany to solve problems in botany. There are no statistical problems which we solve using statistics. We use statistics to provide a course of action with minimum risk in all areas of human endeavor under available evidence. — C. R. Rao”
06 Saturday Oct 2018
This post is part of a series on Mind Retrieval that we started long time ago back in 2010. Links to previous posts can be found here:
https://irthoughts.wordpress.com/2017/02/01/on-mind-retrieval-brain-computer-interfaces/
The Internet can be thought of as a network of nodes where each node has an assigned IP address. The Web and Deep Web are subsets of this. Traversing these nodes is done with crawlers. To retrieve the information that flows across them is what we know as information retrieval. The information might consists of data, text, sound, images. The text might convey numbers, words, phrases, topics, ideas, theses…
Now if the nodes are human brains, the information extraction from the part of the brain responsible of thoughts, emotions, senses, can be loosely termed Mind Retrieval.
So Mind Retrieval requires communications between nodes (brains). The BrainNet Project represents one step closer toward this direction. Here is an interesting link (http://info.247apk.com/brainnet-can-have-three-brains-talk-to-each-other/) where three human brains were “connected” to accomplish specific tasks.
Imagine a large scale project where the brightest minds can interact to take on bigger tasks or solve important scientific and practical problems. Imagine artificial brains (bot brains) doing the same.
When I started this series years ago, many did not believe in the idea of mind retrieval, teasing it as mere speculations.
I guess they have been retracted since then. Mind Retrieval and brain-to-brain social networks are at a corner near you, along with peripherals: browsers, reprogramming, adverts, teleports, hacks, etc.
05 Friday Oct 2018
Ronald Aylmer Fisher was considered an outsider by the statistical establishment of his time.
The links below (1-3) show his struggles & nuances with Karl Pearson, his son Egon, Bowley, their followers, and the Royal Statistical Society (RSS). His life was a story of accomplishments and noise (deceptions and nasty RSS politics). He was too ahead of his time.
That reminds me of the struggles of another maverick: Benoit Mandelbrot. Eventually and like Mandelbrot, Fisher greatness was recognized. Also like Mandelbrot, he was able to boost the signal-to-noise of his career and life.
Most statisticians consider Fisher the Father of Modern Statistics (https://en.wikipedia.org/wiki/Ronald_Fisher), even when he was not allowed to teach Statistics at the University of Cambridge (they tried to silence Fisher).
Yes, scientists too can be demeaning to other scientists, more for personal reasons than for ideas and the Scientific Method. After all, they are also mostly carbon units called “humans”.
1. Fisher in 1921 https://projecteuclid.org/download/pdfview_1/euclid.ss/1118065041
2. Fisher vs Pearson: A 1935 Exchange from Nature
http://physics.princeton.edu/~mcdonald/examples/statistics/inman_as_48_2_94.pdf
3. Fisher: The Outsider
R. A. Fisher: how an outsider revolutionized statistics
hashtag#Fisher
hashtag#Pearson
04 Thursday Oct 2018
A Goldmine for collection curators: Selected Bibliography of Statistical Literature, 1930-1957: Correlation and Regression Theory.
https://nvlpubs.nist.gov/nistpubs/jres/64B/jresv64Bn1p55_A1b.pdf
Enjoy it!
