<div dir="ltr">
<p style="margin:0px;text-indent:0px"><span style="font-family:"ubuntu";font-size:12pt">Dear Henrique,</span></p>
<p style="margin:0px;text-indent:0px;font-family:"ubuntu";font-size:12pt"><br></p>
<p style="margin:0px;text-indent:0px"><span style="font-family:"ubuntu";font-size:12pt">I agree with Robert on the use of a supervised algorithm and I would also suggest you to try a semisupervised one if you have trouble in labeling your data. </span></p>
<p style="margin:0px;text-indent:0px;font-family:"ubuntu";font-size:12pt"><br></p>
<p style="margin:0px;text-indent:0px"><span style="font-family:"ubuntu";font-size:12pt">Moreover, as a chemist I think that the input you are thinking to use is not the in the best form for machine learning because you are trying to predict coupling J(AB) but in the future space you have only coordinates (XYZ). What I suggest is to generate the pair of atoms externally and then use a matrix of the form (Mx3), where M are the pairs of atoms you want to predict your J and 3 are the features of the two atoms (distance, angle, unpaired electrons). For a supervised approach you will need a training set where the J is know so your training data will be of the form Mx4 and the fourth feature will be the J you know.</span></p>
<p style="margin:0px;text-indent:0px"><span style="font-family:"ubuntu";font-size:12pt">Hope that this is clear, if not I will be happy to help more</span></p>
<p style="margin:0px;text-indent:0px;font-family:"ubuntu";font-size:12pt"><br></p>
<p style="margin:0px;text-indent:0px"><span style="font-family:"ubuntu";font-size:12pt">Sincerely</span></p>
<p style="margin:0px;text-indent:0px"><span style="font-family:"ubuntu";font-size:12pt">Tommaso</span></p></div><div class="gmail_extra"><br><div class="gmail_quote">2017-03-27 13:46 GMT-04:00 Henrique C. S. Junior <span dir="ltr"><<a href="mailto:henriquecsj@gmail.com" target="_blank">henriquecsj@gmail.com</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_default" style="font-family:monospace,monospace">Dear Robert, thank you. Yes, I'd like to talk about some specifics on the project.</div><div class="gmail_default" style="font-family:monospace,monospace">Thank you again.</div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Mar 27, 2017 at 2:25 PM, Robert Slater <span dir="ltr"><<a href="mailto:rdslater@gmail.com" target="_blank">rdslater@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">You definitely can use some of the tools in sci-kit learn for supervised machine learning. The real trick will be how well your training system is representative of your future predictions. All of the various regression algorithms would be of some value and you make even consider an ensemble to help generalize. There will be some important questions to answer--what kind of loss function do you want to look at? I assumed regression (continuous response) but it could also classify--paramagnetic, diamagnetic, ferromagnetic, etc...<div><br></div><div>Another task to think about might be dimension reduction.</div><div>There is no guarantee you will get fantastic results--every problem is unique and much will depend on exactly what you want out of the solution--it may be that we get '10%' accuracy at best--for some systems that is quite good, others it is horrible.<br></div><div><br></div><div>If you'd like to talk specifics, feel free to contact me at this email. I have a background in magnetism (PhD in magnetic multilayers--i was physics, but as you are probably aware chemisty and physics blend in this area) and have a fairly good knowledge of sci-kit learn and machine learning. </div><div><br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote"><div><div class="m_6033336047822367828h5">On Mon, Mar 27, 2017 at 10:50 AM, Henrique C. S. Junior <span dir="ltr"><<a href="mailto:henriquecsj@gmail.com" target="_blank">henriquecsj@gmail.com</a>></span> wrote:<br></div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="m_6033336047822367828h5"><div dir="ltr"><div class="gmail_default" style="font-family:monospace,monospace"><p style="margin:0cm 0cm 12pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><span style="color:rgb(36,39,41)" lang="EN-US">I'm a chemist with some rudimentary programming skills (getting started with python) and in the middle of the year I'll be starting a Ph.D. project that uses computers to describe magnetism in molecular systems.<span></span></span></p>
<p style="margin:0cm 0cm 12pt;background-image:initial;background-position:initial;background-size:initial;background-repeat:initial;background-origin:initial;background-clip:initial"><span style="color:rgb(36,39,41)" lang="EN-US">Most of the time I get my results after several simulations and experiments, so, I know that one of the hardest tasks in molecular magnetism is to predict the nature of magnetic interactions. That's why I'll try to tackle this problem with Machine Learning (because such interactions are dependent, basically, of distances, angles and number of unpaired electrons). The idea is to feed the computer with a large training set (with number of unpaired electrons, XYZ coordinates of each molecule and experimental magnetic couplings) and see if it can predict the magnetic couplings (J(AB)) of new systems:<span></span></span></p></div><div><div class="gmail_default" style="font-family:monospace,monospace">(see example in the attached image)</div><div class="gmail_default" style="font-family:monospace,monospace"><br></div><div class="gmail_default" style="font-family:monospace,monospace">Can Scikit-Learn handle the task, knowing that the matrix used to represent atomic coordinates will probably have a different number of atoms (because some molecules have more atoms than others)? Or is this a job better suited for another software/approach? </div><span class="m_6033336047822367828m_-1717598575983325084HOEnZb"><font color="#888888"><br></font></span></div><span class="m_6033336047822367828m_-1717598575983325084HOEnZb"><font color="#888888"><div><br></div>-- <br><div class="m_6033336047822367828m_-1717598575983325084m_-4201444065020757644gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><span style="color:rgb(139,139,139)"><font face="monospace, monospace"><b><font color="#808080">Henrique C. S. Junior</font></b><br>Industrial Chemist - UFRRJ</font></span></div><div dir="ltr"><span style="color:rgb(139,139,139)"><font face="monospace, monospace">M. Sc. Inorganic Chemistry - UFRRJ<br>Data Processing Center - PMP</font><br></span></div></div><div><span style="color:rgb(139,139,139)"><font face="monospace, monospace">Visite o <a href="http://mundoquimico.com.br" target="_blank">Mundo Químico</a></font></span></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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