Dear All, Thank you all very much for your feedback! Actually, the number of collisions didn't decrease when I increased the bit length, though increasing radius to 3 did help a bit. Overall, it is good to know that great results are not to be expected. Best wishes, Michal
On Wed, 10 Oct 2018 at 13:31, Chris Earnshaw <cgearns...@gmail.com> wrote: > Hi > > It sounds to me like you're already getting better results than you could > reasonably expect. > > Prediction of melting point is a phenomenally difficult thing to do; > you're trying to find the temperature at which a (generally undefined) > solid crystalline phase is in equilibrium with a (probably even less > defined) liquid phase. You also need to consider that the crystalline form > of your solid phase is not necessarily truly constant - what polymorph is > involved? Melting points of alternative polymorphs can be radically > different and this is one of the real bugbears of pharmaceutical and > agrochemical development. If you haven't found the most stable form early > in the development process there can be very nasty surprises downstream. > > Expecting to handle all these challenges with a descriptor as simple as a > molecular fingerprint - regardless of bit-length, collisions etc. is > probably over optimistic... > > Regards, > Chris Earnshaw > > On Wed, 10 Oct 2018 at 13:16, Michal Krompiec <michal.kromp...@gmail.com> > wrote: > >> Hi Thomas, >> Radius 2, 2048 bits, 5200 data points. >> >> On Wed, 10 Oct 2018 at 13:13, Thomas Evangelidis <teva...@gmail.com> >> wrote: >> >>> What's your bitvector length and radius? How many training samples do >>> you have? >>> >>> On Wed, 10 Oct 2018 at 13:51, Michal Krompiec <michal.kromp...@gmail.com> >>> wrote: >>> >>>> Hi all, >>>> I have a slightly off-topic question. I'm trying to train a neural >>>> network on a dataset of small molecules and their melting points. I did get >>>> a not-so-bad accuracy with Morgan fingerprints, but I've realised that >>>> regardless of FP radius and bitvector length, several dozen molecules have >>>> the same fingerprints but wildly different melting points. I am pretty sure >>>> this is a "solved problem" so I don't want to reinvent the wheel. What is >>>> the recommended/usual way of dealing with this? >>>> Thanks, >>>> Michal >>>> >>>> >>>> _______________________________________________ >>>> Rdkit-discuss mailing list >>>> Rdkit-discuss@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>>> >>> >>> >>> -- >>> >>> ====================================================================== >>> >>> Dr Thomas Evangelidis >>> >>> Research Scientist >>> >>> IOCB - Institute of Organic Chemistry and Biochemistry of the Czech >>> Academy of Sciences <https://www.uochb.cz/web/structure/31.html?lang=en> >>> Prague, Czech Republic >>> & >>> CEITEC - Central European Institute of Technology >>> <https://www.ceitec.eu/> >>> Brno, Czech Republic >>> >>> email: teva...@gmail.com >>> >>> website: https://sites.google.com/site/thomasevangelidishomepage/ >>> >>> >>> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
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