Bioinformatics

Bioinformatics
2012-02-03
Stanford

“Very similarly…”

“So this is the difference in the two algorithms.”

It’s better to be doing addition rather than multiplication of small numbers.

viterbi

epsilon

“To put it a little bit in an example, imagine…”

“Now I’m running on reserve power so that’s not zesty.”

Sorry, I didn’t understand the question.

“The definition is coming.”

“This is an easy question. Let’s see if you all are on the same page.”

“I will do this but please remind me.”

probability distribution

“It’s not a big deal, the difference.”

the markov property

“Sorry this should be pi i plus 2.”

“So good.”

“I think I did a couple of steps here, that’s why it’s a little confusing.”

“Actually, I’ll take it another way.”

“I’ll write it out, becuase if I say it it could be a little confusing.”

“This is not part of the formula.”

“Am I done? I think I’m done, right?”

“Depending on how easily you follow clunky formulas you may be a little confused now, but there is no magic to this.”

posterior decoding

“However it also has some caveats.”

“In every position we do an independent decision.”

“You might as well go for the maximum number of correctly predicted predictions.”

“These are not difficult algorithms to implement, as you can see.”

“There is a lot of art in designing it.”

“We have modeling decisions to make.”

“You can imagine a million different things you may want to model, so you have to decide how complicated you want to make the model.”

“We are going to make our modeling toolbox a little more rich, instead of the very very basic of what we have.”

“To give it memories we say every state depends on the previous two states.”

“The memory blows up exponentially.”

“Every state I blow up into a collection of states.”

“Yes, very good question. In fact I wouldn’t want to do that.”

“Oh, thank you! I confused n and k, thank you.”

“I’m not showing the self-transition because it would be too complex.”

“A Markov model is always an approximation.”

“Yeah, I was assuming you are not reading the slides.”

“This is a really cool and elegant solution.”