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773
help-10
d0ef48004630404188fa0844059ae384
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Arthek
02/19/2022 11:36:46
**Background of this problem :** I want to use machine learning on a set of data. The scale mentioned above is the IDP-hydropathy scale of amino acids (AA), or simply put : their affinity with water (see pic above) I have an alignment of proteins, and at each position on this alignment, i captured the different amin...
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idioticbaka1824
02/19/2022 13:32:14
I might be misunderstanding your question. A variable that captures the change of hydropathy from the old AA to the new AA could simply be the difference of their hydropathy values, right?
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Arthek
02/19/2022 13:51:47
Yes, but i have the impression i would miss some information Like : ** Case 1 : ** oldAA score = -2 newAA score = 3 Then difference = 5 **Case 2 :** oldAA score = 1 newAA score = 6 difference = 5 the difference is the same in both case But in case 1 the newAA changes the direction of hydropathy, it goes from hydroph...
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idioticbaka1824
02/19/2022 13:52:14
Ah, OK, so you want to capture sign changes
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Arthek
02/19/2022 13:52:32
Yes exactly
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Arthek
02/19/2022 13:52:59
and maybe the "neutral" (close to 0) ? but thats maybe too much to ask xD
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idioticbaka1824
02/19/2022 13:54:11
This is a crude example: the difference if there's no sign change, but double the difference if there's a sign change? Something like that?
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Arthek
02/19/2022 13:56:06
Actually yes maybe that could work, i was actually trying to work my mind around this I don't want to involve too much arbitrary values like saying x2 when opposite sign
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help-10
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Arthek
02/19/2022 13:56:20
but i guess thats the easiest way to do it
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idioticbaka1824
02/19/2022 13:56:49
Yeah, I don't like it either
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idioticbaka1824
02/19/2022 13:57:04
How important is the flip, as compared to the absolute difference?
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idioticbaka1824
02/19/2022 13:57:15
Also what do you mean by this?
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Arthek
02/19/2022 13:57:56
This is hard to tell, i supposed it depends on where the amino acid is located
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Arthek
02/19/2022 13:59:01
the protein is located in the membrane so part of it is hydrophobic, while some are hydrophilic
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Arthek
02/19/2022 13:59:48
an hydrophobic amino acid in the external part of the membrane might have more impact
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Arthek
02/19/2022 14:00:19
neutral is close to 0, it doesnt have much relation with water
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idioticbaka1824
02/19/2022 14:00:42
On second thought, taking all of this into account might make the model a bit too complicated :sadcat:
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idioticbaka1824
02/19/2022 14:01:05
Like maybe stick with a simplistic idea first and see how the results are, and refine it as you go on
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Arthek
02/19/2022 14:03:45
i tried, i'm at the stage where i try to improve the model 😄 And the hydropathy of amino acid is known to be important for the structure of the protein, especially for proteins located in the membrane, that's why i want to make use of this feature
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idioticbaka1824
02/19/2022 14:04:25
Aha I see that's cool
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Arthek
02/19/2022 14:04:57
Similar to this problem, i used the volume
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Arthek
02/19/2022 14:05:01
but the volume was different
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idioticbaka1824
02/19/2022 14:06:22
Okay so let's say the old and new values are x and y. We want a function that increases with their difference, but is weighted higher if they are of different signs, ie in quadrants 2 and 4. How about a 2d sigmoid kind of thing to accomplish this?
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Arthek
02/19/2022 14:08:04
i'm afraid you're mentioning things out of my scope of knowledge haha Let me google that one second (thanks for the help btw! )
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Arthek
02/19/2022 14:10:18
ok, so i should create a function that transform my data through a sigmoid function ?
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idioticbaka1824
02/19/2022 14:11:25
|x-y|.(1 - 1/(1+e^-x)). (1/(1+e^-y))
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idioticbaka1824
02/19/2022 14:11:34
Oh heck one sec
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idioticbaka1824
02/19/2022 14:11:55
Try plotting that
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Arthek
02/19/2022 14:17:14
Plotting ? you have a specific tool for that? with which data? Sorry im a bit confused
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idioticbaka1824
02/19/2022 14:25:15
Sorry, gimme a couple minutes
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Arthek
02/19/2022 14:43:41
im a big noob in maths so bare with me, i just copied your formula but i have no idea what it does lol It seems something might be wrong though I don't know if it's what you suggested me to do, but i did that :
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Arthek
02/19/2022 14:43:51
https://cdn.discordapp.c…9_a_20.42.28.png
Capture_decran_2022-02-19_a_20.42.28.png
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idioticbaka1824
02/19/2022 14:51:22
Yo I am so sorry that was a fool's errand I had no idea what I was doing
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idioticbaka1824
02/19/2022 14:51:26
please forget about it
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Arthek
02/19/2022 14:52:16
Ok np 😄
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idioticbaka1824
02/19/2022 14:58:49
Okay, so what I'm suggesting, after more experimentation, is that for the difference, instead of using |x-y|, you could use |x-y|\*((1-1/(1+exp(-2x)))\*(1/(1+exp(-2y)))+(1-1/(1+exp(-2y)))\*(1/(1+exp(-2x))))
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idioticbaka1824
02/19/2022 14:59:16
The '2' inside the exp represents how strongly you want the flips to matter
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idioticbaka1824
02/19/2022 14:59:23
you could make it more or less
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Arthek
02/19/2022 15:06:07
ok thx im gonna try plotting that 😄
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idioticbaka1824
02/19/2022 15:06:26
https://c3d.libretexts.org/CalcPlot3D/index.html
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idioticbaka1824
02/19/2022 15:06:55
basically it takes the absolute difference and boosts its importance if the two numbers have different signs
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idioticbaka1824
02/19/2022 15:07:22
which would help if paying attention to hydrophobic to hydrophilic changes
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Arthek
02/19/2022 15:13:38
Alright! thanks!
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Arthek
02/19/2022 15:14:13
How did you come up with that formula ? 😄
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idioticbaka1824
02/19/2022 15:15:13
uhh... trial and error, let's say 😅
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S0n⁷
02/19/2022 15:27:59
sorry for interrupt
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S0n⁷
02/19/2022 15:28:15
but when can i ask my quesiton?
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Arthek
02/19/2022 15:28:32
?
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Arthek
02/19/2022 15:29:08
About my current problem ? go ahead 😄 Or do you mean a new question for your own math problem ?
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S0n⁷
02/19/2022 15:29:19
sec ome
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S0n⁷
02/19/2022 15:29:30
one*
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d0ef48004630404188fa0844059ae384
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Arthek
02/19/2022 15:29:54
check the "available" channels section to ask a new question
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Arthek
02/19/2022 15:31:34
it looks beautiful but i got no idea how that works haha I recognize some logistic function ( i just googled them) Im gonna test in the machine learning model later after diner, see if it improves it, thanks a lot for your help, will keep you in touch
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idioticbaka1824
02/19/2022 15:32:43
I think the two features can basically be built with the same idea, only difference is y=old AA or y=mean of AA, yeah?
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Arthek
02/19/2022 15:32:57
right
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Arthek
02/19/2022 15:33:13
but there's also the standard deviation giving a good info on the spread of data
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Arthek
02/19/2022 15:33:34
the more spread = the less conserved = the less impact of a mutation
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idioticbaka1824
02/19/2022 15:34:06
wait, wouldn't more spread mean the mutation is more impactful?
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Arthek
02/19/2022 15:34:15
no
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idioticbaka1824
02/19/2022 15:34:17
like it can do more stuf.. idk..
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Arthek
02/19/2022 15:34:40
no it's like the evolution kept things really specific for important things
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idioticbaka1824
02/19/2022 15:35:11
oh i think i see what you mean
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Arthek
02/19/2022 15:35:14
if one amino acid is hydrophobic and among all related proteins it is also hydrophobic, that means this amino acid has a specific role and must remain hydrophobic
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idioticbaka1824
02/19/2022 15:35:29
makes sense
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idioticbaka1824
02/19/2022 15:36:02
so basically, if the variance is more, the "difference" is less?
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Arthek
02/19/2022 15:36:53
thats why if the mean is hydrophobic++ or hydrophilic++ and has a really low standard deviation, there's a high chance that a mutation changing the hydro score will have a bad impact so we want to capture that
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Arthek
02/19/2022 15:37:02
yes 🙂
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idioticbaka1824
02/19/2022 15:38:13
this is some big brain logic here
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idioticbaka1824
02/19/2022 15:41:12
hm okay then. Let x=newAA, y=mean of old AA, s=stdev or variance of the old AAs. Then you could just use the formula from earlier, but throw in an additional factor of 3*(1-1/(1+exp(-2s) ))
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idioticbaka1824
02/19/2022 15:41:26
the 3 and 2 are just parameters you can adjust to your liking
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Arthek
02/19/2022 15:43:39
Sounds good yes :) thank you i will test that
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idioticbaka1824
02/19/2022 15:43:59
cool then! i hope it works
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Nonna
02/19/2022 19:56:33
How many complex roots does a polynomial of degree 2.5 (or more generally a polynomial of non-integer degree) have? (Sorry for the bad english)
1
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ae20229f065f4ec3bcf220ee65f310b6
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Shuri2060
02/19/2022 19:57:53
A polynomial has non-negative integer degree by definition.
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ae20229f065f4ec3bcf220ee65f310b6
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Nonna
02/19/2022 19:58:07
Oh
1
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Nonna
02/19/2022 19:58:11
I didn't knew it
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Shuri2060
02/19/2022 19:58:24
$z^{2.5} = a$
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null
774
help-10
ae20229f065f4ec3bcf220ee65f310b6
510,789,298,321,096,700
TeXit
02/19/2022 19:58:31
**Shuri2060**
https://cdn.discordapp.c…119171756033.png
321445119171756033.png
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1
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null
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774
help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 19:58:32
Are you referring to this?
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740,938,819,125,248,100
idioticbaka1824
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idioticbaka1824
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help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 19:58:37
Or something more general?
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376,014,466,585,722,900
Arthek
5238
Arthek
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774
help-10
ae20229f065f4ec3bcf220ee65f310b6
573,905,759,134,548,000
Nonna
02/19/2022 19:58:49
Yeah, something like that
1
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376,014,466,585,722,900
Arthek
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Arthek
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774
help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 19:58:54
Well this should have 5 roots
0
1
null
null
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774
help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 19:59:33
I will ignore the modulus
0
1
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help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 20:00:05
$$e^{i \frac{a}{b}\theta} = e^{i(\phi + 2n\pi)}$$
0
1
null
null
null
null
null
774
help-10
ae20229f065f4ec3bcf220ee65f310b6
510,789,298,321,096,700
TeXit
02/19/2022 20:00:27
**Shuri2060**
https://cdn.discordapp.c…119171756033.png
321445119171756033.png
0
1
null
null
null
null
null
774
help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 20:00:37
We perhaps have something like this?
0
1
null
null
null
null
null
774
help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 20:00:50
You exponentiate both sides by b/a
0
1
null
null
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null
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774
help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 20:01:16
This should result in `a` roots mod 2pi
0
1
null
null
null
null
null
774
help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 20:01:38
If you don't have a rational power... I'm not so sure.
0
1
null
null
null
null
null
774
help-10
ae20229f065f4ec3bcf220ee65f310b6
321,445,119,171,756,000
Shuri2060
02/19/2022 20:01:46
It feels like you have infinite roots.
0
1
null
null
null
null
null
774
help-10
ae20229f065f4ec3bcf220ee65f310b6
573,905,759,134,548,000
Nonna
02/19/2022 20:02:22
Thanks a lot, I really mean it
1
0
null
null
null
null
null
774
help-10
ae20229f065f4ec3bcf220ee65f310b6
573,905,759,134,548,000
Nonna
02/19/2022 20:02:23
exactly what I needed
1
0
null
null
null
null
null
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help-10
ae20229f065f4ec3bcf220ee65f310b6
573,905,759,134,548,000
Nonna
02/19/2022 20:02:41
.close
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510,789,298,321,096,700
TeXit
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TeXit
true
775
help-10
ae7b0ed6a95d412abd80453d61c57bdb
469,258,940,455,321,600
H1tle7
02/19/2022 20:19:27
Hey @MetalNinja27 Can you help me with my homework plz
1
0
null
null
null
null
null
775
help-10
ae7b0ed6a95d412abd80453d61c57bdb
200,013,547,491,688,450
a disappointing son
02/19/2022 20:20:53
:flonshed:
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help-10
ae7b0ed6a95d412abd80453d61c57bdb
186,109,587,366,215,680
Omegabet_
02/19/2022 20:22:05
#❓how-to-get-help
0
1
null
null
null
null
null
775
help-10
ae7b0ed6a95d412abd80453d61c57bdb
929,724,109,011,681,300
RDT
02/19/2022 20:23:49
#❓how-to-get-help
0
1
null
null
null
null
null
775
help-10
ae7b0ed6a95d412abd80453d61c57bdb
229,743,249,877,762,050
MetalNinja27
02/19/2022 20:36:39
uh
0
1
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775
help-10
ae7b0ed6a95d412abd80453d61c57bdb
229,743,249,877,762,050
MetalNinja27
02/19/2022 20:36:40
.close
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help-10
f10d9bff875c417c8c372e50de3576d5
216,996,711,413,973,000
momo
02/19/2022 20:48:37
can someone help me out with this problem
1
0
null
null
null
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null