Computer Science

12:36 AM

anyone interested in SMT solvers? evolving & look full of potential

12

Traditionally most work with computational logic was either propositional, in which case you used a SAT (boolean satisfiability) solver, or first-order, in which case you used a first-order theorem prover. In recent years, a lot of progress has been made on SMT (satisfiability modulo theory) sol...

that [stackoverflow.se] question ought to be on Computer Science eh?

Nicholas Mancuso

6:30 AM

bloop

Juho

@NicholasMancuso Hi!

I know you at least have worked with bioinformatics. Ever stumbled upon "motif discovery"? :-)

Nicholas Mancuso

The chat lives! Sup Juho

Its been a while.

In networks... finding cliques?

Juho

haha, yes, most of the time the chat is not that active

As far as I know, motif finding has a lot of applications in bioinformatics

in something called protein-protein interaction at least

(PPI networks)

Nicholas Mancuso

Yeah PPI networks

Juho

right

Nicholas Mancuso

6:34 AM

Are you working in that area now?

Juho

the problem I am considering is the following: given a graph G, and a multiset of colors M of size k (M is known as a motif), decide if G has a connected subset of vertices whose colors agree with the motif

Not really, but we have developed a really practical and fast FPT algorithm for the above problem

I'm trying to find out more about the actual problems & datasets people use in bioinformatics

Nicholas Mancuso

Yeah I'd be the wrong person to ask regarding PPI stuff.

I'm more in pop-gen stuff now.

Juho

ah, okay

just seems to be the bio-people actual solve more complex problems than what I described

Nicholas Mancuso

Hahah yeah

Juho

that is, they want to automatically find what those "interesting" motifs are

but I might be wrong too, I only spent a few hours skimming through bioinformatics papers :-)

Nicholas Mancuso

6:37 AM

Thats the problem. You model the problem as some combinatorial problem which is NPHard, come up with some approximation or it, but the model is still far from reality.

No, that is what they want

But thats life; can't do any better yet

Juho

yeah, that's the often the case ofcourse

Nicholas Mancuso

Recomb deadline is coming up. Better hurry up and submit ;)

Juho

ah, I just recently did an 18-hour work day to finish up a conference submission too :-)

Nicholas Mancuso

Nice. Well good luck with your endeavors. I'm going to hit the hay.

Later Juho, take care.

Juho

Yup, later!

Raphael

8:28 AM

@WanderingLogic Good find, thanks! I remember something similary on Physics...

44

Q: How do I ask homework questions on Physics Stack Exchange?

What is the policy on asking homework questions on Physics Stack Exchange? What kinds of questions are considered homework questions? Are homework questions allowed? What should I include in a homework question? Why don't you provide a complete answer to homework questions?

discussion faq homework

Which has apparently been adopted from Mathematics:

105

Q: How to ask a homework question?

How to ask a homework question? Can I ask a homework question here? How do I ask a homework question on this website? What information should I include in a question about homework? Why don't you provide a complete answer to my question?

discussion faq homework

vzn

3:01 PM

Short linear motif

In molecular biology Short Linear Motifs (also known as SLiMs, Linear Motifs or minimotifs) are short stretches of protein sequence that mediate protein protein interaction. The first definition was given by Tim Hunt: “The sequences of many proteins contain short, conserved motifs that are involved in recognition and targeting activities, often separate from other functional properties of the molecule in which they occur. These motifs are linear, in the sense that three-dimensional organization is not required to bring distant segments of the molecule together to make the recognizable unit. The...

> SLiMs are usually described by regular expressions in the motif literature with the important residues defined based on a combination of experimental, structural and evolutionary evidence.

> Motif discovery tools can be split into two major categories, discovery of novel instance of known functional motifs class and discovery of functional motifs class, however, they all use a limited and overlapping set of attributes to discriminate true and false positives. The main discrimatory attributes used in motif discovery are: ...

> More recently computational methods have been developed that can identify new Short Linear Motifs de novo.[38]

is that "de novo" the same as...?

De novo protein structure prediction

In computational biology, de novo protein structure prediction refers to an algorithmic process by which protein tertiary structure is predicted from its amino acid primary sequence. The problem itself has occupied leading scientists for decades while still remaining unsolved. According to Science, the problem remains one of the top 125 outstanding issues in modern science. At present, some of the most successful methods have a reasonable probability of predicting the folds of small, single-domain proteins within 1.5 angstroms over the entire structure. De novo methods tend to require vast ...

aka protein folding problem

Wandering Logic

4:40 PM

@Raphael or @Gilles : As discussed here:

4

A: What to do about [tag:kernel] with multiple meanings

I recommend introducing the two tags os-kernel and kernel-functions, and then introducing a tag synonym kernel -> os-kernel. I do not think we need a special tag for "kernel" in the context of parametrized complexity. That's a niche topic and I don't think we need such a specialized tag. As fa...

I (1) created kernel-functions and retagged the machine learning questions to the new tag.

(2) Wrote tag wiki excerpts for kernel and kernel-functions.

@D.W.'s third suggestion is to rename kernel -> os-kernel, which I don't know how to do (other than going through and retagging all 18 questions, which will bring them all to the top of the active list.)

(And then he suggested that we make kernel an alias of os-kernel, which I can easily propose.)

Oh never mind. I'll just (a) create os-kernel and then (b) suggest the synonym, which should take care of it automatically.

Ugh. What a stupid pain.

I had to rename a couple that I had answered to os-kernel so that I would have sufficient tag score to propose a synonym.

(Which the system stil lhasn't figure out.)

Raphael

@WanderingLogic Don't worry, we can propose, approve and remove any synonym. :)

Gotta run now, but I'll check back later or tomorrow

Wandering Logic

But now there is no-one who can vote on it (except for maybe me.)

Raphael

Thanks so far!

Wandering Logic

You are very welcome.

@Raphael Ah. You can approve it without the vote.

Thank you!

Gilles

5:01 PM

@WanderingLogic don't worry about synonym votes, that's for high-traffic tags on SO

Once we have a meta consensus, moderators can implement it

@WanderingLogic renaming is a moderator-only tool

In machine learning, is “kernel function” close enough to “kernel method” that they should be tag synonyms?

Wikipedia's main article is at en.wikipedia.org/wiki/Kernel_method

Thanks for the reviews and excerpts

Wandering Logic

5:18 PM

@Gilles We only have two machine learning questions tagged kernel-function, and both are unanswered. So I don't think there's any point in making a synonym until we get a significant number of machine learning experts participating, in which case the right thing will probably happen organically.

I was "winging it" (making it up as I went along) on the tag wiki excerpt for kernel-function. I put references to the two sources I used in the tag wiki itself.

(Yes, I know that the tag wiki itself is unfindable by any mortal human. (In fact one of my sources was the Wikipedia kernel method article.))

My net experience with machine learning is ...

... um ...

I read a book about it once?

So the kernel-function tag wiki excerpt is about as authoritative as this:

Gilles

5:44 PM

@WanderingLogic that's one book more than me then

I've written many a tag wiki on a topic I knew nothing about by summarizing Wikipedia, but for easier topics

vzn

6:36 PM

Bill Watterson's Uplifting Advice To College Grads, Illustrated In 'Calvin & Hobbes' Style

Wandering Logic

7:43 PM

@vzn :)

@Gilles (and @Raphael) can you take a look at parsing vs. parsers. I think it should be parsers given our naming conventions. parsers has a tag wiki excerpt and 53 questions, parsing has no tag wiki and 46 questions (6 of which are also marked parsers). Is this one is a "no brainer" that doesn't need to go to meta?

Gilles

11:08 PM

5

Q: Are [parsing] and [parsers] synonyms?

The tags parsing and parsers are very close in meaning. Is there any difference, or should they be merged? I see maybe a very slight nuance — parsing is a bit broader in coverage of language syntax, while parsers is focused on parsing algorithms. But I'm not sure if that distinction is really me...

discussion tags tag-synonyms

Wandering Logic

11:56 PM

@Gilles Oh. Yeah. Well at least I'm consistent.

in my meandering, random kind of way.

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